position; //用来记录内部节点所有后代的叶节点代表的后缀的起始位置，如果是叶节点就只有一个整数值，就是它代表的后缀的起始位置
- public int label;//记录叶节点代表的后缀的起始位置，内部结点可能也有值，要通过chars的最后是否是$来判断
- public Node(char[] chars) {
- this.chars = chars;
- //position = new ArrayList();
- }
-
- @Override
- public String toString() {
- //return "Node [chars=" + String.valueOf(chars) + "]"+"position:"+String.valueOf(position);
- return "Node [chars=" + String.valueOf(chars) + "]";
- }
-
- public void print(String prefix) {
- System.out.print(String.valueOf(chars));
- if(chars[chars.length-1]=='$'){
- System.out.print(label);
- }
- if (null != this.suffixNode) {
- System.out.println("--" + String.valueOf(this.suffixNode.chars));
- } else {
- System.out.println();
- }
- Node child = this.child;
- while (null != child) {
- System.out.print(prefix + "|——");
- child.print(prefix + prefix);
- child = child.brother;
- }
- }
- }
-
- /**
- *
- * 活动点(active point)，一个三元组：(active_node,active_edge,active_length)
- * 活动边的父亲是point,儿子是index；活动点应该是point,提取存储的字符串要从儿子index的chars中找(0,length)
- *
- */
- private class ActivePoint {
- public Node point;
- public Node index;
- public int length;
-
- public ActivePoint(Node point, Node index, int length) {
- this.point = point;
- this.index = index;
- this.length = length;
- }
-
- @Override
- public String toString() {
- return "ActivePoint [point=" + point + ", index=" + index + ", length=" + length + "]";
- }
- }
- /**
- * 对String格式化,删除非法字符(只保留agctn,其余字符全部替换成n),全部转换成小写,u全部换成t
- * @param s
- * @return
- */
- private static String format(String s){
- s=s.toLowerCase();
- s=s.replace('u', 't');
- StringBuffer sb = new StringBuffer(s);
-
- for(int i=0;i0){
- s=String.valueOf(start.chars)+s;
- start=start.father;
- }
- s=String.valueOf(start.chars)+s;
- return s;
- }
-
-
- public static void main(String[] args) {
-
- SuffixTree suffixTree = new SuffixTree();
- //String s1 ="ACACCGATGAGTCTGTCACGCGATAGCATGACGCTGCACCCTATGCTCGATAGCATTGCGAC";
- //String s1 ="ACACCGATGAGTCTGTCACGCGATAGCATGAC";
- //String s1 ="ACCACAACACCACAACACCACCACAACACCACCAACCACCT";
- String s1 ="ACTDGDG";
- //String s1="GGGAGCCATGCATT";
- s1 = format(s1)+"$";
- suffixTree.build(s1);
- //suffixTree.print();
-
- //System.out.println(String.valueOf(centerstar.root.child));
-
- //System.out.println(String.valueOf(centerstar.root.child.chars));
-
- /*Node start=centerstar.root.child.brother.child.child.child;
- Integer[] startpos= (Integer[]) getNodeAllLeafSonLabel(start).toArray(new Integer[getNodeAllLeafSonLabel(start).size()]);
- System.out.println(Arrays.toString(startpos));
- System.out.println(getNodeString(start));*/
-
- //System.out.println(centerstar.select("CACAAC"));
- String word = "AGTDGDG";
- word = word.toLowerCase();
- System.out.println(Arrays.toString(suffixTree.selectPrefixForAlignment(word, 0)));
-
- AlignSubstring alignSubstring = new AlignSubstring(suffixTree, word);
- System.out.println(Arrays.toString(suffixTree.selectPrefixForAlignment(word, 0)));
- int[][] findCommonSubstrings = alignSubstring.findCommonSubstrings();
-
- System.out.println("OK!");
- }
-}
diff --git a/maven-src/target/classes/java/jaligner/Alignment.java b/maven-src/target/classes/java/jaligner/Alignment.java
deleted file mode 100644
index 7592331..0000000
--- a/maven-src/target/classes/java/jaligner/Alignment.java
+++ /dev/null
@@ -1,442 +0,0 @@
-/*
- * $Id: Alignment.java,v 1.19 2005/04/02 17:10:27 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner;
-
-import jaligner.matrix.Matrix;
-import jaligner.util.Commons;
-
-import java.text.DecimalFormat;
-
-/**
- * Holds the output of a pairwise sequences alignment.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class Alignment {
-
- /**
- * Gap character
- */
- public static final char GAP = '-';
-
- /**
- * Default name for sequence #1
- */
- private static final String DEFAULT_SEQUENCE1_NAME = "jaligner_1";
-
- /**
- * Default name for sequence #2
- */
- private static final String DEFAULT_SEQUENCE2_NAME = "jaligner_2";
-
- /**
- * Scoring matrix
- */
- private Matrix matrix;
-
- /**
- * Gap open cost
- */
- private float open;
-
- /**
- * Gap extend cost
- */
- private float extend;
-
- /**
- * Alignment score
- */
- private float score;
-
- /**
- * Aligned sequence #1
- */
- private char[] sequence1;
-
- /**
- * Name of sequence #1
- */
- private String name1;
-
- /**
- * Alignment start location in sequence #1
- */
- private int start1;
-
- /**
- * Aligned sequence #2
- */
- private char[] sequence2;
-
- /**
- * Name of sequence #2
- */
- private String name2;
-
- /**
- * Alignment start location in sequence #2
- */
- private int start2;
-
- /**
- * Markup line
- */
- private char[] markupLine;
-
- /**
- * Count of identical locations
- */
- private int identity;
-
- /**
- * Count of similar locations
- */
- private int similarity;
-
- /**
- * Count of gap locations
- */
- private int gaps;
-
- /**
- * Constructor for Alignment
- */
-
- public Alignment() {
- super();
- }
-
- /**
- * @return Returns the extend.
- */
- public float getExtend() {
- return extend;
- }
-
- /**
- * @param extend
- * The extend to set.
- */
- public void setExtend(float extend) {
- this.extend = extend;
- }
-
- /**
- * @return Returns the matrix.
- */
- public Matrix getMatrix() {
- return matrix;
- }
-
- /**
- * @param matrix
- * The matrix to set.
- */
- public void setMatrix(Matrix matrix) {
- this.matrix = matrix;
- }
-
- /**
- * @return Returns the name1.
- */
- public String getName1() {
- return name1 == null || name1.length() == 0 ? DEFAULT_SEQUENCE1_NAME
- : name1;
- }
-
- /**
- * @param name1
- * The name1 to set.
- */
- public void setName1(String name1) {
- this.name1 = name1;
- }
-
- /**
- * @return Returns the name2.
- */
- public String getName2() {
- return name2 == null || name2.length() == 0 ? DEFAULT_SEQUENCE2_NAME
- : name2;
- }
-
- /**
- * @param name2
- * The name2 to set.
- */
- public void setName2(String name2) {
- this.name2 = name2;
- }
-
- /**
- * @return Returns the open.
- */
- public float getOpen() {
- return open;
- }
-
- /**
- * @param open
- * The open to set.
- */
- public void setOpen(float open) {
- this.open = open;
- }
-
- /**
- * @return Returns the score.
- */
- public float getScore() {
- return score;
- }
-
- /**
- * @param score
- * The score to set.
- */
- public void setScore(float score) {
- this.score = score;
- }
-
- /**
- * @return Returns the sequence1.
- */
- public char[] getSequence1() {
- return sequence1;
- }
-
- /**
- * @param sequence1
- * The sequence1 to set.
- */
- public void setSequence1(char[] sequence1) {
- this.sequence1 = sequence1;
- }
-
- /**
- * @return Returns the sequence2.
- */
- public char[] getSequence2() {
- return sequence2;
- }
-
- /**
- * @param sequence2
- * The sequence2 to set.
- */
- public void setSequence2(char[] sequence2) {
- this.sequence2 = sequence2;
- }
-
- /**
- * @return Returns the start1.
- */
- public int getStart1() {
- return start1;
- }
-
- /**
- * @param start1
- * The start1 to set.
- */
- public void setStart1(int start1) {
- this.start1 = start1;
- }
-
- /**
- * @return Returns the start2.
- */
- public int getStart2() {
- return start2;
- }
-
- /**
- * @param start2
- * The start2 to set.
- */
- public void setStart2(int start2) {
- this.start2 = start2;
- }
-
- /**
- * @return Returns the gaps.
- */
- public int getGaps() {
- return gaps;
- }
-
- /**
- * @param gaps
- * The gaps to set.
- */
- public void setGaps(int gaps) {
- this.gaps = gaps;
- }
-
- /**
- * @return Returns the identity.
- */
- public int getIdentity() {
- return identity;
- }
-
- /**
- * @param identity
- * The identity to set.
- */
- public void setIdentity(int identity) {
- this.identity = identity;
- }
-
- /**
- * @return Returns the markupLine.
- */
- public char[] getMarkupLine() {
- return markupLine;
- }
-
- /**
- * @param markupLine
- * The markupLine to set.
- */
- public void setMarkupLine(char[] markupLine) {
- this.markupLine = markupLine;
- }
-
- /**
- * @return Returns the similarity.
- */
- public int getSimilarity() {
- return similarity;
- }
-
- /**
- * @param similarity
- * The similarity to set.
- */
- public void setSimilarity(int similarity) {
- this.similarity = similarity;
- }
-
- /**
- * Returns a summary for alignment
- *
- * @return alignment summary
- */
- public String getSummary() {
- StringBuffer buffer = new StringBuffer();
- DecimalFormat f1 = new DecimalFormat("0.00");
- DecimalFormat f2 = new DecimalFormat("0.00%");
-
- int length = getSequence1().length;
-
- buffer.append("Sequence #1: " + getName1());
- buffer.append(Commons.getLineSeparator());
- buffer.append("Sequence #2: " + getName2());
- buffer.append(Commons.getLineSeparator());
- buffer.append("Length #1: " + sequence1.length);
- buffer.append(Commons.getLineSeparator());
- buffer.append("Length #2: " + sequence2.length);
- buffer.append(Commons.getLineSeparator());
- buffer.append("Matrix: "
- + (matrix.getId() == null ? "" : matrix.getId()));
- buffer.append(Commons.getLineSeparator());
- buffer.append("Gap open: " + open);
- buffer.append(Commons.getLineSeparator());
- buffer.append("Gap extend: " + extend);
- buffer.append(Commons.getLineSeparator());
- buffer.append("Length: " + length);
- buffer.append(Commons.getLineSeparator());
- buffer.append("Identity: " + identity + "/" + length + " ("
- + f2.format(identity / (float) length) + ")");
- buffer.append(Commons.getLineSeparator());
- buffer.append("Similarity: " + similarity + "/" + length + " ("
- + f2.format(similarity / (float) length) + ")");
- buffer.append(Commons.getLineSeparator());
- buffer.append("Gaps: " + gaps + "/" + length + " ("
- + f2.format(gaps / (float) length) + ")");
- buffer.append(Commons.getLineSeparator());
- buffer.append("Score: " + f1.format(score));
- buffer.append(Commons.getLineSeparator());
-
- return buffer.toString();
- }
-
- /**
- * Calculate the score of the alignment, not using the score field (the
- * function only uses sequence1, sequence2, matrix and gap penalties). (By:
- * Bram Minnaert)
- *
- * @return the calculated score
- */
- public float calculateScore() {
- float calcScore = 0; // the calculated score
- boolean previous1wasGap = false; // in the previous step there was a gap
- // in the first sequence
- boolean previous2wasGap = false; // in the previous step there was a gap
- // in the second sequence
- char c1, c2; // the next character
- for (int i = 0, n = sequence1.length; i < n; i++) {
- c1 = sequence1[i];
- c2 = sequence2[i];
- // the next character in the first sequence is a gap
- if (c1 == GAP) {
- if (previous1wasGap) {
- calcScore -= extend;
- } else {
- calcScore -= open;
- }
- previous1wasGap = true;
- previous2wasGap = false;
- }
- // the next character in the second sequence is a gap
- else if (c2 == GAP) {
- if (previous2wasGap) {
- calcScore -= extend;
- } else {
- calcScore -= open;
- }
- previous1wasGap = false;
- previous2wasGap = true;
- }
- // the next characters in boths sequences are not gaps
- else {
- calcScore += matrix.getScore(c1, c2);
- previous1wasGap = false;
- previous2wasGap = false;
- }
- }
- return calcScore;
- }
-
- /**
- * Check if the calculated score matches the field score.
- *
- * @return true if equal, else false. (By: Bram Minnaert)
- */
- public boolean checkScore() {
- if (calculateScore() == score) {
- return true;
- } else {
- return false;
- }
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/Cell.java b/maven-src/target/classes/java/jaligner/Cell.java
deleted file mode 100644
index e452403..0000000
--- a/maven-src/target/classes/java/jaligner/Cell.java
+++ /dev/null
@@ -1,98 +0,0 @@
-/*
- * $Id: Cell.java,v 1.5 2004/11/30 05:10:29 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner;
-
-/**
- * A cell in a similarity matrix, to hold row, column and score.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class Cell {
- /**
- * Row of the cell
- */
- private int row;
- /**
- * Column of the cell
- */
- private int col;
- /**
- * Alignment score at this cell
- */
- private float score;
-
- /**
- * Constructor
- */
- public Cell() {
- super();
- this.row = 0;
- this.col = 0;
- this.score = Float.NEGATIVE_INFINITY;
- }
- /**
- * @return Returns the col.
- */
- public int getCol() {
- return this.col;
- }
- /**
- * @param col The col to set.
- */
- public void setCol(int col) {
- this.col = col;
- }
- /**
- * @return Returns the row.
- */
- public int getRow() {
- return this.row;
- }
- /**
- * @param row The row to set.
- */
- public void setRow(int row) {
- this.row = row;
- }
- /**
- * @return Returns the score.
- */
- public float getScore() {
- return this.score;
- }
- /**
- * @param score The score to set.
- */
- public void setScore(float score) {
- this.score = score;
- }
-
- /**
- * Sets the row, column and score of the cell.
- * @param row The row to set.
- * @param col The col to set.
- * @param score The score to set.
- */
- public void set(int row, int col, float score) {
- this.row = row;
- this.col = col;
- this.score = score;
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/Directions.java b/maven-src/target/classes/java/jaligner/Directions.java
deleted file mode 100644
index f876864..0000000
--- a/maven-src/target/classes/java/jaligner/Directions.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * $Id: Directions.java,v 1.10 2004/11/30 05:10:29 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner;
-
-/**
- * Traceback directions.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public abstract class Directions {
- /**
- * Traceback direction stop
- */
- public static final byte STOP = 0;
- /**
- * Traceback direction left
- */
- public static final byte LEFT = 1;
- /**
- * Traceback direction diagonal
- */
- public static final byte DIAGONAL = 2;
- /**
- * Traceback direction up
- */
- public static final byte UP = 3;
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/Markups.java b/maven-src/target/classes/java/jaligner/Markups.java
deleted file mode 100644
index 4b3b342..0000000
--- a/maven-src/target/classes/java/jaligner/Markups.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * $Id: Markups.java,v 1.2 2004/11/30 05:10:29 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner;
-
-/**
- * Markups line characters.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public abstract class Markups {
- /**
- * Markup line identity character
- */
- public static final char IDENTITY = '|';
-
- /**
- * Markup line similarity character
- */
- public static final char SIMILARITY = ':';
-
- /**
- * Markup line gap character
- */
- public static final char GAP = ' ';
-
- /**
- * Markup line mismatch character
- */
- public static final char MISMATCH = '.';
-}
diff --git a/maven-src/target/classes/java/jaligner/Sequence.java b/maven-src/target/classes/java/jaligner/Sequence.java
deleted file mode 100644
index c01498a..0000000
--- a/maven-src/target/classes/java/jaligner/Sequence.java
+++ /dev/null
@@ -1,195 +0,0 @@
-/*
- * $Id: Sequence.java,v 1.12 2005/04/14 14:44:45 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner;
-
-import java.io.Serializable;
-
-/**
- * A basic (nucleic or smithwaterman) sequence. It's a wrapper to {@link String}.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class Sequence implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 3256721801357898297L;
-
- /**
- * Sequence type nucleic.
- */
- public static final int NUCLEIC = 0;
-
- /**
- * Sequence type smithwaterman.
- */
- public static final int PROTEIN = 1;
-
- /**
- * Sequence
- */
- private String sequence;
-
- /**
- * Sequence id.
- */
- private String id = null;
-
- /**
- * Sequence description.
- */
- private String description = null;
-
- /**
- * Sequence type.
- */
- private int type = PROTEIN;
-
- /**
- * Constructor
- */
- public Sequence( ) {
- super();
- }
-
- /**
- * Constructor
- * @param sequence
- */
- public Sequence(String sequence) {
- super();
- this.sequence = sequence;
- }
-
-
- /**
- * Constructor
- * @param sequence
- * @param id
- * @param description
- * @param type
- */
- public Sequence(String sequence, String id, String description, int type) {
- super();
- this.sequence = sequence;
- this.id = id;
- this.description = description;
- this.type = type;
- }
-
- /**
- * Returns the sequence string
- * @return Returns the sequence
- */
- public String getSequence() {
- return sequence;
- }
-
- /**
- * Sets the sequence string
- * @param sequence The sequence to set
- */
- public void setSequence(String sequence) {
- this.sequence = sequence;
- }
-
- /**
- * Returns the sequence id
- * @return Returns the id
- */
- public String getId() {
- return id;
- }
-
- /**
- * Sets the sequence id
- * @param id The id to set
- */
- public void setId(String id) {
- this.id = id;
- }
-
- /**
- * Returns the sequence description
- * @return Returns the description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * Sets the sequence description
- * @param description The description to set
- */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /**
- * Returns the sequence type (nucleic or smithwaterman)
- * @return Returns the type
- */
- public int getType() {
- return type;
- }
-
- /**
- * Sets the sequence type (nucleic or smithwaterman)
- * @param type The type to set
- */
- public void setType(int type) {
- this.type = type;
- }
-
- /**
- * Returns the length of the sequence
- * @return sequence length
- */
- public int length( ) {
- return this.sequence.length();
- }
-
- /**
- * Returns a subsequence
- * @param index start index
- * @param length length of subsequence
- * @return subsequence
- */
- public String subsequence(int index, int length) {
- return this.sequence.substring(index, index + length);
- }
-
- /**
- * Returns the acid at specific location in the sequence
- * @param index
- * @return acid at index
- */
- public char acidAt(int index) {
- return this.sequence.charAt(index);
- }
-
- /**
- * Returns the sequence as an array of characters.
- * @return array of chars.
- */
- public char[] toArray( ) {
- return this.sequence.toCharArray();
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/SmithWatermanGotoh.java b/maven-src/target/classes/java/jaligner/SmithWatermanGotoh.java
deleted file mode 100644
index 9728bbd..0000000
--- a/maven-src/target/classes/java/jaligner/SmithWatermanGotoh.java
+++ /dev/null
@@ -1,358 +0,0 @@
-/*
- * $Id: SmithWatermanGotoh.java,v 1.18 2005/04/03 19:38:21 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner;
-
-import jaligner.matrix.Matrix;
-
-import java.util.logging.Logger;
-
-/**
- * An implementation of the Smith-Waterman algorithm with Gotoh's improvement
- * for biological local pairwise sequence alignment.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class SmithWatermanGotoh {
- /**
- * Hidden constructor
- */
- private SmithWatermanGotoh() {
- super();
- }
-
- /**
- * Logger
- */
- private static final Logger logger = Logger
- .getLogger(SmithWatermanGotoh.class.getName());
-
- /**
- * Aligns two sequences by Smith-Waterman algorithm
- *
- * @param s1
- * sequene #1 ({@link Sequence})
- * @param s2
- * sequene #2 ({@link Sequence})
- * @param matrix
- * scoring matrix ({@link Matrix})
- * @param o
- * open gap penalty
- * @param e
- * extend gap penalty
- * @return alignment object contains the two aligned sequences, the
- * alignment score and alignment statistics
- * @see Sequence
- * @see Matrix
- */
- public static Alignment align(Sequence s1, Sequence s2, Matrix matrix,
- float o, float e) {
- //logger.info("Started...");
- long start = System.currentTimeMillis();
- float[][] scores = matrix.getScores();
-
- SmithWatermanGotoh sw = new SmithWatermanGotoh();
-
- int m = s1.length() + 1;
- int n = s2.length() + 1;
-
- byte[] pointers = new byte[m * n];
-
- // Initializes the boundaries of the traceback matrix to STOP.
- for (int i = 0, k = 0; i < m; i++, k += n) {
- pointers[k] = Directions.STOP;
- }
- for (int j = 1; j < n; j++) {
- pointers[j] = Directions.STOP;
- }
-
- short[] sizesOfVerticalGaps = new short[m * n];
- short[] sizesOfHorizontalGaps = new short[m * n];
- for (int i = 0, k = 0; i < m; i++, k += n) {
- for (int j = 0; j < n; j++) {
- sizesOfVerticalGaps[k + j] = sizesOfHorizontalGaps[k + j] = 1;
- }
- }
-
- Cell cell = sw.construct(s1, s2, scores, o, e, pointers,
- sizesOfVerticalGaps, sizesOfHorizontalGaps);
- Alignment alignment = sw.traceback(s1, s2, matrix, pointers, cell,
- sizesOfVerticalGaps, sizesOfHorizontalGaps);
- alignment.setName1(s1.getId());
- alignment.setName2(s2.getId());
- alignment.setMatrix(matrix);
- alignment.setOpen(o);
- alignment.setExtend(e);
- //logger.info("Finished in " + (System.currentTimeMillis() - start)
- // + " milliseconds");
- return alignment;
- }
-
- /**
- * Constructs directions matrix for the traceback
- *
- * @param s1
- * sequence #1
- * @param s2
- * sequence #2
- * @param matrix
- * scoring matrix
- * @param o
- * open gap penalty
- * @param e
- * extend gap penalty
- * @return The cell where the traceback starts.
- */
- private Cell construct(Sequence s1, Sequence s2, float[][] matrix, float o,
- float e, byte[] pointers, short[] sizesOfVerticalGaps,
- short[] sizesOfHorizontalGaps) {
- //logger.info("Started...");
- long start = System.currentTimeMillis();
-
- char[] a1 = s1.toArray();
- char[] a2 = s2.toArray();
-
- int m = s1.length() + 1;
- int n = s2.length() + 1;
-
- float f; // score of alignment x1...xi to y1...yi if xi aligns to yi
- float[] g = new float[n]; // score if xi aligns to a gap after yi
- float h; // score if yi aligns to a gap after xi
- float[] v = new float[n]; // best score of alignment x1...xi to y1...yi
- float vDiagonal;
-
- g[0] = Float.NEGATIVE_INFINITY;
- h = Float.NEGATIVE_INFINITY;
- v[0] = 0;
-
- for (int j = 1; j < n; j++) {
- g[j] = Float.NEGATIVE_INFINITY;
- v[j] = 0;
- }
-
- float similarityScore, g1, g2, h1, h2;
-
- Cell cell = new Cell();
-
- for (int i = 1, k = n; i < m; i++, k += n) {
- h = Float.NEGATIVE_INFINITY;
- vDiagonal = v[0];
- for (int j = 1, l = k + 1; j < n; j++, l++) {
- similarityScore = matrix[a1[i - 1]][a2[j - 1]];
-
- // Fill the matrices
- f = vDiagonal + similarityScore;
-
- g1 = g[j] - e;
- g2 = v[j] - o;
- if (g1 > g2) {
- g[j] = g1;
- sizesOfVerticalGaps[l] = (short) (sizesOfVerticalGaps[l - n] + 1);
- } else {
- g[j] = g2;
- }
-
- h1 = h - e;
- h2 = v[j - 1] - o;
- if (h1 > h2) {
- h = h1;
- sizesOfHorizontalGaps[l] = (short) (sizesOfHorizontalGaps[l - 1] + 1);
- } else {
- h = h2;
- }
-
- vDiagonal = v[j];
- v[j] = maximum(f, g[j], h, 0);
-
- // Determine the traceback direction
- if (v[j] == 0) {
- pointers[l] = Directions.STOP;
- } else if (v[j] == f) {
- pointers[l] = Directions.DIAGONAL;
- } else if (v[j] == g[j]) {
- pointers[l] = Directions.UP;
- } else {
- pointers[l] = Directions.LEFT;
- }
-
- // Set the traceback start at the current cell i, j and score
- if (v[j] > cell.getScore()) {
- cell.set(i, j, v[j]);
- }
- }
- }
- /*logger.info("Finished in " + (System.currentTimeMillis() - start)
- + " milliseconds");*/
- return cell;
- }
-
- /**
- * Returns the alignment of two sequences based on the passed array of
- * pointers
- *
- * @param s1
- * sequence #1
- * @param s2
- * sequence #2
- * @param m
- * scoring matrix
- * @param cell
- * The cell where the traceback starts.
- * @return {@link Alignment}with the two aligned sequences and alignment
- * score.
- * @see Cell
- * @see Alignment
- */
- private Alignment traceback(Sequence s1, Sequence s2, Matrix m,
- byte[] pointers, Cell cell, short[] sizesOfVerticalGaps,
- short[] sizesOfHorizontalGaps) {
- //logger.info("Started...");
- long start = System.currentTimeMillis();
-
- char[] a1 = s1.toArray();
- char[] a2 = s2.toArray();
-
- float[][] scores = m.getScores();
-
- int n = s2.length() + 1;
-
- Alignment alignment = new Alignment();
- alignment.setScore(cell.getScore());
-
- int maxlen = s1.length() + s2.length(); // maximum length after the
- // aligned sequences
-
- char[] reversed1 = new char[maxlen]; // reversed sequence #1
- char[] reversed2 = new char[maxlen]; // reversed sequence #2
- char[] reversed3 = new char[maxlen]; // reversed markup
-
- int len1 = 0; // length of sequence #1 after alignment
- int len2 = 0; // length of sequence #2 after alignment
- int len3 = 0; // length of the markup line
-
- int identity = 0; // count of identitcal pairs
- int similarity = 0; // count of similar pairs
- int gaps = 0; // count of gaps
-
- char c1, c2;
-
- int i = cell.getRow(); // traceback start row
- int j = cell.getCol(); // traceback start col
- int k = i * n;
-
- boolean stillGoing = true; // traceback flag: true -> continue & false
- // -> stop
-
- while (stillGoing) {
- switch (pointers[k + j]) {
- case Directions.UP:
- for (int l = 0, len = sizesOfVerticalGaps[k + j]; l < len; l++) {
- reversed1[len1++] = a1[--i];
- reversed2[len2++] = Alignment.GAP;
- reversed3[len3++] = Markups.GAP;
- k -= n;
- gaps++;
- }
- break;
- case Directions.DIAGONAL:
- c1 = a1[--i];
- c2 = a2[--j];
- k -= n;
- reversed1[len1++] = c1;
- reversed2[len2++] = c2;
- if (c1 == c2) {
- reversed3[len3++] = Markups.IDENTITY;
- identity++;
- similarity++;
- } else if (scores[c1][c2] > 0) {
- reversed3[len3++] = Markups.SIMILARITY;
- similarity++;
- } else {
- reversed3[len3++] = Markups.MISMATCH;
- }
- break;
- case Directions.LEFT:
- for (int l = 0, len = sizesOfHorizontalGaps[k + j]; l < len; l++) {
- reversed1[len1++] = Alignment.GAP;
- reversed2[len2++] = a2[--j];
- reversed3[len3++] = Markups.GAP;
- gaps++;
- }
- break;
- case Directions.STOP:
- stillGoing = false;
- }
- }
-
- alignment.setSequence1(reverse(reversed1, len1));
- alignment.setStart1(i);
- alignment.setSequence2(reverse(reversed2, len2));
- alignment.setStart2(j);
- alignment.setMarkupLine(reverse(reversed3, len3));
- alignment.setIdentity(identity);
- alignment.setGaps(gaps);
- alignment.setSimilarity(similarity);
-
- /*logger.info("Finished in " + (System.currentTimeMillis() - start)
- + " milliseconds");*/
- return alignment;
- }
-
- /**
- * Returns the maximum of 4 float numbers.
- *
- * @param a
- * float #1
- * @param b
- * float #2
- * @param c
- * float #3
- * @param d
- * float #4
- * @return The maximum of a, b, c and d.
- */
- private static float maximum(float a, float b, float c, float d) {
- if (a > b) {
- if (a > c) {
- return a > d ? a : d;
- } else {
- return c > d ? c : d;
- }
- } else if (b > c) {
- return b > d ? b : d;
- } else {
- return c > d ? c : d;
- }
- }
-
- /**
- * Reverses an array of chars
- *
- * @param a
- * @param len
- * @return the input array of char reserved
- */
- private static char[] reverse(char[] a, int len) {
- char[] b = new char[len];
- for (int i = len - 1, j = 0; i >= 0; i--, j++) {
- b[j] = a[i];
- }
- return b;
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/example/Example.java b/maven-src/target/classes/java/jaligner/example/Example.java
deleted file mode 100644
index 9ac0a4e..0000000
--- a/maven-src/target/classes/java/jaligner/example/Example.java
+++ /dev/null
@@ -1,119 +0,0 @@
-/*
- * $Id: Example.java,v 1.3 2005/04/03 19:38:21 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.example;
-
-import jaligner.Alignment;
-import jaligner.Sequence;
-import jaligner.SmithWatermanGotoh;
-import jaligner.formats.Pair;
-import jaligner.matrix.MatrixLoader;
-import jaligner.util.SequenceParser;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-/**
- * Example of using JAligner API to align P53 human aganist
- * P53 mouse using Smith-Waterman-Gotoh algorithm.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class Example {
-
- /**
- *
- */
- private static final String SAMPLE_SEQUENCE_P35_HUMAN = "jaligner/example/sequences/p53_human.fasta";
-
- /**
- *
- */
- private static final String SAMPLE_SEQUENCE_P35_MOUSE = "jaligner/example/sequences/p53_mouse.fasta";
-
- /**
- * Logger
- */
- private static final Logger logger = Logger.getLogger(Example.class.getName());
-
- /**
- *
- * @param args
- */
- public static void main(String[] args) {
- try {
- logger.info("Running example...");
- String st1 = "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPRVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACAGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD";
- String st2 = "MTAMEESQSDISLELPLSQETFSGLWKLLPPEDILPSPHCMDDLLLPQDVEEFFEGPSEALRVSGAPAAQDPVTETPGPAAPAPATPWPLSSFVPSQKTYQGNYGFHLGFLQSGTAKSVMCTYSPPLNKLFCQLAKTCPVQLWVSATPPAGSRVRAMAIYKKSQHMTEVVRRCPHHERCSDGDGLAPPQHLIRVEGNLYPEYLEDRQTFRHSVVVPYEPPEAGSEYTTIHYKYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENFRKKEVLCPELPPGSAKRALPTCTSASPPQKKKPLDGEYFTLKIRGRKRFEMFRELNEALELKDAHATEESGDSRAHSSYLKTKKGQSTSRHKKTMVKKVGPDSD";
-
- /*Sequence s1 = SequenceParser.parse(loadP53Human());
- Sequence s2 = SequenceParser.parse(loadP53Mouse());*/
- Sequence s1 = SequenceParser.parse(st1);
- Sequence s2 = SequenceParser.parse(st2);
-
- Alignment alignment = SmithWatermanGotoh.align(s1, s2, MatrixLoader.load("BLOSUM62"), 10f, 0.5f);
-
- System.out.println ( alignment.getSummary() );
- System.out.println ( new Pair().format(alignment) );
- System.out.println("----------------------------");
- System.out.println ( alignment.getSequence1() );
- System.out.println ( alignment.getSequence2() );
-
- logger.info("Finished running example");
- } catch (Exception e) {
- logger.log(Level.SEVERE, "Failed running example: " + e.getMessage(), e);
- }
- }
-
- /**
- *
- * @param path location of the sequence
- * @return sequence string
- * @throws IOException
- */
- private static String loadSampleSequence(String path) throws IOException {
- InputStream inputStream = Example.class.getClassLoader().getResourceAsStream(path);
- StringBuffer buffer = new StringBuffer();
- int ch;
- while ((ch = inputStream.read()) != -1) {
- buffer.append((char)ch);
- }
- return buffer.toString();
- }
-
- /**
- *
- * @return sequence string
- * @throws IOException
- */
- public static String loadP53Human( ) throws IOException {
- return loadSampleSequence(SAMPLE_SEQUENCE_P35_HUMAN);
- }
-
- /**
- *
- * @return sequence string
- * @throws IOException
- */
- public static String loadP53Mouse( ) throws IOException {
- return loadSampleSequence(SAMPLE_SEQUENCE_P35_MOUSE);
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/example/package.html b/maven-src/target/classes/java/jaligner/example/package.html
deleted file mode 100644
index c42043b..0000000
--- a/maven-src/target/classes/java/jaligner/example/package.html
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
-
-
-Example for using API of JAligner to perform pairwise sequence alignment.
-@author Ahmed Moustafa (ahmed@users.sf.net)
-
-
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/example/sequences/p53_human.fasta b/maven-src/target/classes/java/jaligner/example/sequences/p53_human.fasta
deleted file mode 100644
index 1591a95..0000000
--- a/maven-src/target/classes/java/jaligner/example/sequences/p53_human.fasta
+++ /dev/null
@@ -1,7 +0,0 @@
->p53_human
-MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAA
-PRVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKT
-CPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRN
-TFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACAGR
-DRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALEL
-KDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/example/sequences/p53_mouse.fasta b/maven-src/target/classes/java/jaligner/example/sequences/p53_mouse.fasta
deleted file mode 100644
index 4bb7ffb..0000000
--- a/maven-src/target/classes/java/jaligner/example/sequences/p53_mouse.fasta
+++ /dev/null
@@ -1,10 +0,0 @@
->p53_mouse
-MTAMEESQSDISLELPLSQETFSGLWKLLPPEDILPSPHCMDDLLLPQDVEEFFEGPSEA
-LRVSGAPAAQDPVTETPGPAAPAPATPWPLSSFVPSQKTYQGNYGFHLGFLQSGTAKSVM
-CTYSPPLNKLFCQLAKTCPVQLWVSATPPAGSRVRAMAIYKKSQHMTEVVRRCPHHERCS
-DGDGLAPPQHLIRVEGNLYPEYLEDRQTFRHSVVVPYEPPEAGSEYTTIHYKYMCNSSCM
-GGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENFRKKEVLCPELPPGS
-AKRALPTCTSASPPQKKKPLDGEYFTLKIRGRKRFEMFRELNEALELKDAHATEESGDSR
-AHSSYLKTKKGQSTSRHKKTMVKKVGPDSD
-
-
diff --git a/maven-src/target/classes/java/jaligner/formats/CLUSTAL.java b/maven-src/target/classes/java/jaligner/formats/CLUSTAL.java
deleted file mode 100644
index 5630321..0000000
--- a/maven-src/target/classes/java/jaligner/formats/CLUSTAL.java
+++ /dev/null
@@ -1,121 +0,0 @@
-/*
- * $Id: CLUSTAL.java,v 1.15 2004/11/30 05:10:29 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.formats;
-
-import jaligner.Alignment;
-
-/**
- * CLUSTAL format.
- * Example:
- *
- *
- * CLUSTAL_FORMAT W(1.60) multiple sequence alignment
- *
- *
- * JC2395 NVSDVNLNK---YIWRTAEKMK---ICDAKKFARQHKIPESKIDEIEHNSPQDAAE----
- * KPEL_DROME MAIRLLPLPVRAQLCAHLDAL-----DVWQQLATAVKLYPDQVEQISSQKQRGRS-----
- * FASA_MOUSE NASNLSLSK---YIPRIAEDMT---IQEAKKFARENNIKEGKIDEIMHDSIQDTAE----
- *
- *
- * JC2395 -------------------------QKIQLLQCWYQSHGKT--GACQALIQGLRKANRCD
- * KPEL_DROME -------------------------ASNEFLNIWGGQYN----HTVQTLFALFKKLKLHN
- * FASA_MOUSE -------------------------QKVQLLLCWYQSHGKS--DAYQDLIKGLKKAECRR
- *
- *
- * JC2395 IAEEIQAM
- * KPEL_DROME AMRLIKDY
- * FASA_MOUSE TLDKFQDM
- *
- *
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class CLUSTAL extends Format {
-
- /**
- * Name width
- */
- private static final int NAME_WIDTH = 36;
-
- /**
- * Sequence width
- */
- private static final int SEQUENCE_WIDTH = 50;
-
- /**
- * CLUSTAL header
- */
- private static final String HEADER = "CLUSTAL_FORMAT W(1.60) multiple sequence alignment\n\n";
-
- /**
- * Constructor
- */
- public CLUSTAL() {
- super( );
- setId("CLUSTAL");
- }
-
- /**
- * Returns CLUSTAL format
- * @param names array of the names of the sequences.
- * @param sequences array of the sequences
- */
- public String format(String[] names, String[] sequences) {
- StringBuffer buffer = new StringBuffer (HEADER);
- int maxSequenceLength = 0;
- for (int i = 0; i < sequences.length; i++) {
- if (sequences[i].length() > maxSequenceLength) {
- maxSequenceLength = sequences[i].length();
- }
- }
-
- for (int i = 0; i * SEQUENCE_WIDTH < maxSequenceLength; i++) {
-
- for (int j = 0; j < sequences.length; j++) {
- buffer.append( NAME_WIDTH <= names[j].length() ? names[j].substring(0, NAME_WIDTH - 1) : names[j] );
- for (int k = names[j].length(); k < NAME_WIDTH; k++) {
- buffer.append(" ");
- }
- if (names[j].length() >= NAME_WIDTH) {
- buffer.append(" ");
- }
- buffer.append(sequences[j].substring(i * SEQUENCE_WIDTH, ((i + 1) * SEQUENCE_WIDTH) < sequences[j].length() ? (i + 1) * SEQUENCE_WIDTH: sequences[j].length()));
- if (j < sequences.length) {
- buffer.append("\n");
- }
- }
- if ((i + 1) * SEQUENCE_WIDTH < maxSequenceLength) {
- buffer.append("\n\n");
- }
- }
- return buffer.toString();
- }
-
- /**
- * Returns CLUSTAL format of the alignment
- * @param alignment ({@link Alignment})
- * @return CLUSTAL format of the alignment
- */
- public String format (Alignment alignment) {
- String[] sequences = {new String(alignment.getSequence1()), new String(alignment.getSequence2())};
- String[] names = {alignment.getName1(), alignment.getName2()};
- return format (names, sequences);
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/formats/FASTA.java b/maven-src/target/classes/java/jaligner/formats/FASTA.java
deleted file mode 100644
index 2a3b3f3..0000000
--- a/maven-src/target/classes/java/jaligner/formats/FASTA.java
+++ /dev/null
@@ -1,79 +0,0 @@
-/*
- * $Id: FASTA.java,v 1.19 2004/11/30 05:10:29 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.formats;
-
-import jaligner.Alignment;
-import jaligner.Sequence;
-
-/**
- * FASTA format.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class FASTA extends Format {
-
- /**
- * Number of characters per line
- */
- private static final int LINE_WIDTH = 60;
-
- /**
- * Constructor for FASTA.
- */
- public FASTA() {
- super( );
- setId("FASTA");
- }
-
- /**
- * Returns the name, description and sequence combined in one string.
- * The length of each line in the sequence is FASTA.LINE_LENGTH
- *
- * @return String
- */
- public String format (Sequence sequence) {
- StringBuffer buffer = new StringBuffer (">");
- buffer.append(sequence.getId() == null ? "" : sequence.getId());
- buffer.append("\n");
- for (int i = 0, n = sequence.length(); i * LINE_WIDTH < n; i++) {
- for (int j = i * LINE_WIDTH, m = (i + 1) * LINE_WIDTH < n ? (i + 1) * LINE_WIDTH: n; j < m; j++) {
- buffer.append(sequence.subsequence(j, 1));
- }
- buffer.append("\n");
- }
- return buffer.toString( );
- }
-
- /**
- *
- * @param alignment
- * @return FASTA format of the input alignment
- */
- public String format (Alignment alignment) {
- StringBuffer buffer = new StringBuffer();
- StringBuffer s1 = new StringBuffer();
- StringBuffer s2 = new StringBuffer();
- s1.append(alignment.getSequence1());
- s2.append(alignment.getSequence2());
- buffer.append(format(new Sequence(s1.toString(), alignment.getName1(), "", Sequence.PROTEIN)));
- buffer.append(format(new Sequence(s2.toString(), alignment.getName2(), "", Sequence.PROTEIN)));
- return buffer.toString();
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/formats/Format.java b/maven-src/target/classes/java/jaligner/formats/Format.java
deleted file mode 100644
index f59cdae..0000000
--- a/maven-src/target/classes/java/jaligner/formats/Format.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- * $Id: Format.java,v 1.4 2004/11/30 05:10:29 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.formats;
-
-import jaligner.Alignment;
-
-/**
- * Abstract format
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public abstract class Format {
-
- /**
- * Format id
- */
- private String id = null;
-
- /**
- * Formats alignment
- * @param alignment
- * @return formatted alignment
- * @see Alignment
- */
- public abstract String format(Alignment alignment);
-
- /**
- * Sets format id
- * @param id to set
- */
- public void setId (String id) {
- this.id = id;
- }
-
- /**
- * Returns format id
- * @return id
- */
- public String getId ( ) {
- return this.id == null ? this.getClass().getName() : this.id;
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/formats/FormatFactory.java b/maven-src/target/classes/java/jaligner/formats/FormatFactory.java
deleted file mode 100644
index ba884de..0000000
--- a/maven-src/target/classes/java/jaligner/formats/FormatFactory.java
+++ /dev/null
@@ -1,84 +0,0 @@
-/*
- * $Id: FormatFactory.java,v 1.7 2004/11/30 05:10:29 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.formats;
-
-import java.util.Collection;
-import java.util.HashMap;
-
-/**
- * Formats factory.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class FormatFactory {
- /**
- * Instance of {@link FormatFactory}
- */
- private static FormatFactory instance = null;
-
- /**
- * {@link HashMap} of {@link Format}
- */
- private HashMap formats = new HashMap();
-
- /**
- * Hidden constructor
- *
- */
- private FormatFactory ( ) {
- super();
- }
-
- /**
- * Returns an instance for {@link FormatFactory}.
- * @return {@link FormatFactory}
- */
- public static FormatFactory getInstance() {
- if (instance == null) {
- instance = new FormatFactory();
- }
- return instance;
- }
-
- /**
- * Registers format.
- * @param format instance of format
- */
- public void registerFormat(Format format) {
- formats.put(format.getId(), format);
- }
-
- /**
- * Returns an instance of {@link Format}.
- * @param id format id
- * @return {@link Format} or null if id not found
- */
- public Format getFormat(String id) {
- return (Format) formats.get(id);
- }
-
- /**
- * Returns a list of registered formats
- * @return {@link Collection}
- */
- public Collection getFormats( ) {
- return formats.keySet();
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/formats/Pair.java b/maven-src/target/classes/java/jaligner/formats/Pair.java
deleted file mode 100644
index cf707bb..0000000
--- a/maven-src/target/classes/java/jaligner/formats/Pair.java
+++ /dev/null
@@ -1,191 +0,0 @@
-/*
- * $Id: Pair.java,v 1.18 2004/11/30 05:10:29 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.formats;
-
-import jaligner.Alignment;
-import jaligner.util.Commons;
-
-/**
- * Pair format.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class Pair extends Format {
-
- /**
- * Name width
- */
- private static final int NAME_WIDTH = 13;
-
- /**
- * Position width
- */
- private static final int POSITION_WIDTH = 6;
-
- /**
- * Sequence width
- */
- private static final int SEQUENCE_WIDTH = 50;
-
- /**
- * Space
- */
- private static final String BLANK = " ";
-
- /**
- * Constructor
- *
- */
- public Pair( ) {
- super();
- setId("Pair");
- }
-
- /**
- * Formats an alignment object to the Pair_FORMAT format
- * @param alignment alignment object to be formated
- * @return string of the alignment pair-formatted
- */
- public String format(Alignment alignment) {
- char[] sequence1 = alignment.getSequence1();
- char[] sequence2 = alignment.getSequence2();
- char[] markup = alignment.getMarkupLine();
-
- int length = sequence1.length > sequence2.length ? sequence2.length : sequence1.length;
-
- String name1 = adjustName(alignment.getName1());
- String name2 = adjustName(alignment.getName2());
-
- StringBuffer buffer = new StringBuffer ( );
-
- StringBuffer preMarkup = new StringBuffer ( );
- for (int j = 0; j < NAME_WIDTH + 1 + POSITION_WIDTH + 1; j++) {
- preMarkup.append(BLANK);
- }
-
- int oldPosition1, position1 = 1 + alignment.getStart1();
- int oldPosition2, position2 = 1 + alignment.getStart2();
-
- char[] subsequence1;
- char[] subsequence2;
- char[] submarkup;
- int line;
-
- char c1, c2;
-
- for (int i = 0; i * SEQUENCE_WIDTH < length; i++) {
-
- oldPosition1 = position1;
- oldPosition2 = position2;
-
- line = ((i + 1) * SEQUENCE_WIDTH) < length ? (i + 1) * SEQUENCE_WIDTH: length;
-
- subsequence1 = new char[line - i * SEQUENCE_WIDTH];
- subsequence2 = new char[line - i * SEQUENCE_WIDTH];
- submarkup = new char[line - i * SEQUENCE_WIDTH];
-
- for (int j = i * SEQUENCE_WIDTH, k = 0; j < line; j++, k++) {
- subsequence1[k] = sequence1[j];
- subsequence2[k] = sequence2[j];
- submarkup[k] = markup[j];
- c1 = subsequence1[k];
- c2 = subsequence2[k];
- if (c1 == c2) {
- position1++;
- position2++;
- } else if (c1 == Alignment.GAP) {
- position2++;
- } else if (c2 == Alignment.GAP) {
- position1++;
- } else {
- position1++;
- position2++;
- }
- }
-
- buffer.append(name1);
- buffer.append(BLANK);
- buffer.append(adjustPosition(new Integer(oldPosition1).toString()));
- buffer.append(BLANK);
- buffer.append(subsequence1);
- buffer.append(BLANK);
- buffer.append(adjustPosition(new Integer(position1 - 1).toString()));
- buffer.append(Commons.getLineSeparator());
-
- buffer.append(preMarkup);
- buffer.append(submarkup);
- buffer.append(Commons.getLineSeparator());
-
- buffer.append(name2);
- buffer.append(BLANK);
- buffer.append(adjustPosition(new Integer(oldPosition2).toString()));
- buffer.append(BLANK);
- buffer.append(subsequence2);
- buffer.append(BLANK);
- buffer.append(adjustPosition(new Integer(position2 - 1).toString()));
- buffer.append(Commons.getLineSeparator());
-
- buffer.append(Commons.getLineSeparator());
- }
- return buffer.toString();
- }
-
- /**
- *
- * @param name name to adjusted
- * @return adjusted name
- */
- private String adjustName(String name) {
- StringBuffer buffer = new StringBuffer ( );
-
- if (name.length() > NAME_WIDTH) {
- buffer.append(name.substring(0, NAME_WIDTH));
- } else {
- buffer.append(name);
- for (int j = buffer.length(); j < NAME_WIDTH; j++) {
- buffer.append (BLANK);
- }
- }
- return buffer.toString();
- }
-
- /**
- *
- * @param position
- * @return string
- */
- private String adjustPosition(String position) {
- StringBuffer buffer1 = new StringBuffer( );
- StringBuffer buffer2 = new StringBuffer( );
-
- if (position.length() > POSITION_WIDTH) {
- buffer1.append(position.substring(position.length() - POSITION_WIDTH, position.length()));
- } else {
- buffer1.append(position);
- }
-
- for (int j = 0, n = POSITION_WIDTH - buffer1.length(); j < n; j++) {
- buffer2.append(BLANK);
- }
-
- buffer2.append(buffer1.toString());
- return buffer2.toString();
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/formats/package.html b/maven-src/target/classes/java/jaligner/formats/package.html
deleted file mode 100644
index 5b3633b..0000000
--- a/maven-src/target/classes/java/jaligner/formats/package.html
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
-
-
-Group of formats for output alignments.
-@author Ahmed Moustafa (ahmed@users.sf.net)
-
-
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/matrix/MatricesCompartor.java b/maven-src/target/classes/java/jaligner/matrix/MatricesCompartor.java
deleted file mode 100644
index 6aedcdd..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/MatricesCompartor.java
+++ /dev/null
@@ -1,68 +0,0 @@
-/*
- * $Id: MatricesCompartor.java,v 1.1 2005/01/11 16:48:25 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.matrix;
-
-import java.util.Comparator;
-
-/**
- * Comparator to sort the scoring matrices by their names.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class MatricesCompartor implements Comparator {
-
- /* (non-Javadoc)
- * @see java.util.Comparator#compare(java.lang.Object, java.lang.Object)
- */
- public int compare(Object o1, Object o2) {
- String s1 = (String) o1;
- String s2 = (String) o2;
-
- int index1 = firstDigitIndex(s1);
- int index2 = firstDigitIndex(s2);
-
- if (index1 == -1 || index2 == -1) {
- return s1.compareToIgnoreCase(s2);
- } else {
- String s3 = s1.substring(0, index1);
- String s4 = s2.substring(0, index2);
- if (s3.equalsIgnoreCase(s4)) {
- return new Integer(s1.substring(index1)).compareTo(new Integer(s2.substring(index2)));
- } else {
- return s1.compareToIgnoreCase(s2);
- }
- }
- }
-
- /**
- * Returns the index of the first digit in a String.
- * If there are no digits, returns -1.
- * @param s String to be searched for the digits in
- * @return int
- */
- private int firstDigitIndex (String s) {
- for (int i = 0; i < s.length(); i++) {
- if (s.charAt(i) >= '0' && s.charAt(i) <= '9') {
- return i;
- }
- }
- return -1;
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/matrix/Matrix.java b/maven-src/target/classes/java/jaligner/matrix/Matrix.java
deleted file mode 100644
index 79ae0e3..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/Matrix.java
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- * $Id: Matrix.java,v 1.2 2005/04/14 14:44:42 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.matrix;
-
-import java.io.Serializable;
-
-/**
- * Scoring matrix.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class Matrix implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 3833742170619524400L;
-
- /**
- * Matrix id (or name)
- */
- private String id = null;
-
- /**
- * Scores
- */
- private float[][] scores = null;
-
- public Matrix(String id, float[][] scores) {
- this.id = id;
- this.scores = scores;
- }
-
- /**
- * @return Returns the id.
- */
- public String getId() {
- return this.id;
- }
-
- /**
- * @return Returns the scores.
- */
- public float[][] getScores() {
- return this.scores;
- }
-
- /**
- *
- * @param a
- * @param b
- * @return score
- */
- public float getScore(char a, char b) {
- return this.scores[a][b];
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/matrix/MatrixLoader.java b/maven-src/target/classes/java/jaligner/matrix/MatrixLoader.java
deleted file mode 100644
index 2ba5039..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/MatrixLoader.java
+++ /dev/null
@@ -1,220 +0,0 @@
-/*
- * $Id: MatrixLoader.java,v 1.2 2005/01/25 11:54:30 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.matrix;
-
-import jaligner.ui.filechooser.NamedInputStream;
-import jaligner.util.Commons;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.JarURLConnection;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.StringTokenizer;
-import java.util.jar.JarEntry;
-import java.util.jar.JarFile;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-/**
- * Scoring matrices loader from a jar file or a file system.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class MatrixLoader {
- /**
- * The starter character of a comment line.
- */
- private static final char COMMENT_STARTER = '#';
-
- /**
- * The size of the scoring matrix. It is the number of the characters in the ASCII table.
- * It is more than the 20 amino acids just to save the processing time of the mapping.
- */
- private static final int SIZE = 127;
-
- /**
- * The path to the matrices within the package.
- */
- //private static final String MATRICES_HOME = "jaligner/matrix/matrices/";
- private static final String MATRICES_HOME = "";
- /**
- * Logger
- */
- private static final Logger logger = Logger.getLogger(MatrixLoader.class.getName());
-
- /**
- * Loads scoring matrix from Jar file or file system.
- * @param matrix to load
- * @return loaded matrix
- * @throws MatrixLoaderException
- * @see Matrix
- */
- public static Matrix load (String matrix) throws MatrixLoaderException {
- InputStream is = null;
-
- if (new StringTokenizer(matrix, Commons.getFileSeparator()).countTokens() == 1) {
- // Matrix does not include the path
- // Load the matrix from matrices.jar
- is = MatrixLoader.class.getClassLoader().getResourceAsStream(MATRICES_HOME + matrix);
- } else {
- // Matrix includes the path information
- // Load the matrix from the file system
- try {
- is = new FileInputStream(matrix);
- } catch (Exception e) {
- String message = "Failed opening input stream: " + e.getMessage();
- //logger.log(Level.SEVERE, message, e);
- throw new MatrixLoaderException (message);
- }
- }
-
- return load(new NamedInputStream(matrix, is));
- }
-
- /**
- * Loads scoring matrix from {@link InputStream}
- * @param nis named input stream
- * @return loaded matrix
- * @throws MatrixLoaderException
- * @see Matrix
- * @see NamedInputStream
- */
- public static Matrix load (NamedInputStream nis) throws MatrixLoaderException {
- //logger.info("Loading scoring matrix...");
- char[] acids = new char[SIZE];
-
- // Initialize the acids array to null values (ascii = 0)
- for (int i = 0; i < SIZE; i++) {
- acids[i] = 0;
- }
-
- float[][] scores = new float[SIZE][SIZE];
-
- BufferedReader reader = new BufferedReader(new InputStreamReader(nis.getInputStream()));
-
- String line;
-
- try {
- // Skip the comment lines
- while ((line = reader.readLine()) != null && line.trim().charAt(0) == COMMENT_STARTER);
- } catch (Exception e) {
- String message = "Failed reading from input stream: " + e.getMessage();
- //logger.log(Level.SEVERE, message, e);
- throw new MatrixLoaderException (message);
- }
-
- // Read the headers line (the letters of the acids)
- StringTokenizer tokenizer;
- tokenizer = new StringTokenizer ( line.trim( ) );
- for (int j = 0; tokenizer.hasMoreTokens(); j++) {
- acids[j] = tokenizer.nextToken().charAt(0);
- }
-
- try {
- // Read the scores
- while ((line = reader.readLine()) != null) {
- tokenizer = new StringTokenizer ( line.trim( ) );
- char acid = tokenizer.nextToken().charAt(0);
- for (int i = 0; i < SIZE; i++) {
- if (acids[i] != 0) {
- scores[acid][acids[i]] = Float.parseFloat(tokenizer.nextToken());
- }
- }
- }
- } catch (Exception e) {
- String message = "Failed reading from input stream: " + e.getMessage();
- //logger.log(Level.SEVERE, message, e);
- throw new MatrixLoaderException (message);
- }
- //logger.info("Finished loading scoring matrix");
- return new Matrix(nis.getName(), scores);
- }
-
- /**
- * Returns a list of the scoring matrices in the matrices home directory
- * @param sort flag to sort the list or not
- * @return sorted array of scoring matrices
- * @throws MatrixLoaderException
- */
- public static Collection list (boolean sort ) throws MatrixLoaderException {
- //logger.info("Loading list of scoring matrices...");
- ArrayList matrices = new ArrayList();
- URL url = MatrixLoader.class.getClassLoader().getResource(MATRICES_HOME);
- if (url.getFile().toString().indexOf("!") != -1) {
- // Load from Jar
- JarURLConnection connection = null;
- JarFile jar = null;
- try {
- connection = (JarURLConnection) url.openConnection();
- jar = connection.getJarFile();
- } catch (Exception e) {
- String message = "Failed opening a connection to jar: " + e.getMessage();
- //logger.log(Level.SEVERE, message, e);
- throw new MatrixLoaderException (message);
- }
- Enumeration entries = jar.entries();
- JarEntry entry;
- String entryName;
- int length = MATRICES_HOME.length();
- while (entries.hasMoreElements()) {
- entry = (JarEntry) entries.nextElement();
- if (!entry.isDirectory()) {
- entryName = entry.getName();
- if (entryName.startsWith(MATRICES_HOME)) {
- matrices.add(entryName.substring(length));
- }
- }
- }
- } else {
- // Load from file system
- String home = url.getFile( );
- File dir = new File (home);
- String files[] = dir.list( );
- File file;
- for (int i = 0, n = files.length; i < n; i++) {
- file = new File (home + files[i]);
- if (file.isFile() && file.canRead()) {
- matrices.add(file.getName());
- }
- }
- }
- if (sort) {
- Collections.sort(matrices, new MatricesCompartor());
- }
- //logger.info("Finished loading list of scoring matrices");
- return matrices;
- }
-
- /**
- * Returns a list of the scoring matrices in the matrices home directory
- * @return sorted array of scoring matrices
- * @throws MatrixLoaderException
- */
- public static Collection list ( ) throws MatrixLoaderException {
- return list(false);
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/matrix/MatrixLoaderException.java b/maven-src/target/classes/java/jaligner/matrix/MatrixLoaderException.java
deleted file mode 100644
index a62783b..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/MatrixLoaderException.java
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * @author Ahmed Moustafa (ahmed at users.sourceforge.net)
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.matrix;
-
-/**
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class MatrixLoaderException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 3906364935142586680L;
-
- /**
- * @param message
- */
- public MatrixLoaderException(String message) {
- super(message);
- }
-}
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM100 b/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM100
deleted file mode 100644
index 46e9e85..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM100
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum100_3.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 100
-# Entropy = 1.4516, Expected = -1.0948
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 8 -3 -4 -5 -2 -2 -3 -1 -4 -4 -4 -2 -3 -5 -2 1 -1 -6 -5 -2 -4 -2 -2 -10
-R -3 10 -2 -5 -8 0 -2 -6 -1 -7 -6 3 -4 -6 -5 -3 -3 -7 -5 -6 -4 -1 -3 -10
-N -4 -2 11 1 -5 -1 -2 -2 0 -7 -7 -1 -5 -7 -5 0 -1 -8 -5 -7 5 -2 -3 -10
-D -5 -5 1 10 -8 -2 2 -4 -3 -8 -8 -3 -8 -8 -5 -2 -4 -10 -7 -8 6 0 -4 -10
-C -2 -8 -5 -8 14 -7 -9 -7 -8 -3 -5 -8 -4 -4 -8 -3 -3 -7 -6 -3 -7 -8 -5 -10
-Q -2 0 -1 -2 -7 11 2 -5 1 -6 -5 2 -2 -6 -4 -2 -3 -5 -4 -5 -2 5 -2 -10
-E -3 -2 -2 2 -9 2 10 -6 -2 -7 -7 0 -5 -8 -4 -2 -3 -8 -7 -5 0 7 -3 -10
-G -1 -6 -2 -4 -7 -5 -6 9 -6 -9 -8 -5 -7 -8 -6 -2 -5 -7 -8 -8 -3 -5 -4 -10
-H -4 -1 0 -3 -8 1 -2 -6 13 -7 -6 -3 -5 -4 -5 -3 -4 -5 1 -7 -2 -1 -4 -10
-I -4 -7 -7 -8 -3 -6 -7 -9 -7 8 2 -6 1 -2 -7 -5 -3 -6 -4 4 -8 -7 -3 -10
-L -4 -6 -7 -8 -5 -5 -7 -8 -6 2 8 -6 3 0 -7 -6 -4 -5 -4 0 -8 -6 -3 -10
-K -2 3 -1 -3 -8 2 0 -5 -3 -6 -6 10 -4 -6 -3 -2 -3 -8 -5 -5 -2 0 -3 -10
-M -3 -4 -5 -8 -4 -2 -5 -7 -5 1 3 -4 12 -1 -5 -4 -2 -4 -5 0 -7 -4 -3 -10
-F -5 -6 -7 -8 -4 -6 -8 -8 -4 -2 0 -6 -1 11 -7 -5 -5 0 4 -3 -7 -7 -4 -10
-P -2 -5 -5 -5 -8 -4 -4 -6 -5 -7 -7 -3 -5 -7 12 -3 -4 -8 -7 -6 -5 -4 -4 -10
-S 1 -3 0 -2 -3 -2 -2 -2 -3 -5 -6 -2 -4 -5 -3 9 2 -7 -5 -4 -1 -2 -2 -10
-T -1 -3 -1 -4 -3 -3 -3 -5 -4 -3 -4 -3 -2 -5 -4 2 9 -7 -5 -1 -2 -3 -2 -10
-W -6 -7 -8 -10 -7 -5 -8 -7 -5 -6 -5 -8 -4 0 -8 -7 -7 17 2 -5 -9 -7 -6 -10
-Y -5 -5 -5 -7 -6 -4 -7 -8 1 -4 -4 -5 -5 4 -7 -5 -5 2 12 -5 -6 -6 -4 -10
-V -2 -6 -7 -8 -3 -5 -5 -8 -7 4 0 -5 0 -3 -6 -4 -1 -5 -5 8 -7 -5 -3 -10
-B -4 -4 5 6 -7 -2 0 -3 -2 -8 -8 -2 -7 -7 -5 -1 -2 -9 -6 -7 6 0 -4 -10
-Z -2 -1 -2 0 -8 5 7 -5 -1 -7 -6 0 -4 -7 -4 -2 -3 -7 -6 -5 0 6 -2 -10
-X -2 -3 -3 -4 -5 -2 -3 -4 -4 -3 -3 -3 -3 -4 -4 -2 -2 -6 -4 -3 -4 -2 -3 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM30 b/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM30
deleted file mode 100644
index 81ebd98..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM30
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum30.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/5 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 30
-# Entropy = 0.1424, Expected = -0.1074
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 4 -1 0 0 -3 1 0 0 -2 0 -1 0 1 -2 -1 1 1 -5 -4 1 0 0 0 -7
-R -1 8 -2 -1 -2 3 -1 -2 -1 -3 -2 1 0 -1 -1 -1 -3 0 0 -1 -2 0 -1 -7
-N 0 -2 8 1 -1 -1 -1 0 -1 0 -2 0 0 -1 -3 0 1 -7 -4 -2 4 -1 0 -7
-D 0 -1 1 9 -3 -1 1 -1 -2 -4 -1 0 -3 -5 -1 0 -1 -4 -1 -2 5 0 -1 -7
-C -3 -2 -1 -3 17 -2 1 -4 -5 -2 0 -3 -2 -3 -3 -2 -2 -2 -6 -2 -2 0 -2 -7
-Q 1 3 -1 -1 -2 8 2 -2 0 -2 -2 0 -1 -3 0 -1 0 -1 -1 -3 -1 4 0 -7
-E 0 -1 -1 1 1 2 6 -2 0 -3 -1 2 -1 -4 1 0 -2 -1 -2 -3 0 5 -1 -7
-G 0 -2 0 -1 -4 -2 -2 8 -3 -1 -2 -1 -2 -3 -1 0 -2 1 -3 -3 0 -2 -1 -7
-H -2 -1 -1 -2 -5 0 0 -3 14 -2 -1 -2 2 -3 1 -1 -2 -5 0 -3 -2 0 -1 -7
-I 0 -3 0 -4 -2 -2 -3 -1 -2 6 2 -2 1 0 -3 -1 0 -3 -1 4 -2 -3 0 -7
-L -1 -2 -2 -1 0 -2 -1 -2 -1 2 4 -2 2 2 -3 -2 0 -2 3 1 -1 -1 0 -7
-K 0 1 0 0 -3 0 2 -1 -2 -2 -2 4 2 -1 1 0 -1 -2 -1 -2 0 1 0 -7
-M 1 0 0 -3 -2 -1 -1 -2 2 1 2 2 6 -2 -4 -2 0 -3 -1 0 -2 -1 0 -7
-F -2 -1 -1 -5 -3 -3 -4 -3 -3 0 2 -1 -2 10 -4 -1 -2 1 3 1 -3 -4 -1 -7
-P -1 -1 -3 -1 -3 0 1 -1 1 -3 -3 1 -4 -4 11 -1 0 -3 -2 -4 -2 0 -1 -7
-S 1 -1 0 0 -2 -1 0 0 -1 -1 -2 0 -2 -1 -1 4 2 -3 -2 -1 0 -1 0 -7
-T 1 -3 1 -1 -2 0 -2 -2 -2 0 0 -1 0 -2 0 2 5 -5 -1 1 0 -1 0 -7
-W -5 0 -7 -4 -2 -1 -1 1 -5 -3 -2 -2 -3 1 -3 -3 -5 20 5 -3 -5 -1 -2 -7
-Y -4 0 -4 -1 -6 -1 -2 -3 0 -1 3 -1 -1 3 -2 -2 -1 5 9 1 -3 -2 -1 -7
-V 1 -1 -2 -2 -2 -3 -3 -3 -3 4 1 -2 0 1 -4 -1 1 -3 1 5 -2 -3 0 -7
-B 0 -2 4 5 -2 -1 0 0 -2 -2 -1 0 -2 -3 -2 0 0 -5 -3 -2 5 0 -1 -7
-Z 0 0 -1 0 0 4 5 -2 0 -3 -1 1 -1 -4 0 -1 -1 -1 -2 -3 0 4 0 -7
-X 0 -1 0 -1 -2 0 -1 -1 -1 0 0 0 0 -1 -1 0 0 -2 -1 0 -1 0 -1 -7
-* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM35 b/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM35
deleted file mode 100644
index a6d99f5..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM35
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum35.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/4 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 35
-# Entropy = 0.2111, Expected = -0.1550
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -1 -1 -1 -2 0 -1 0 -2 -1 -2 0 0 -2 -2 1 0 -2 -1 0 -1 -1 0 -5
-R -1 8 -1 -1 -3 2 -1 -2 -1 -3 -2 2 0 -1 -2 -1 -2 0 0 -1 -1 0 -1 -5
-N -1 -1 7 1 -1 1 -1 1 1 -1 -2 0 -1 -1 -2 0 0 -2 -2 -2 4 0 0 -5
-D -1 -1 1 8 -3 -1 2 -2 0 -3 -2 -1 -3 -3 -1 -1 -1 -3 -2 -2 5 1 -1 -5
-C -2 -3 -1 -3 15 -3 -1 -3 -4 -4 -2 -2 -4 -4 -4 -3 -1 -5 -5 -2 -2 -2 -2 -5
-Q 0 2 1 -1 -3 7 2 -2 -1 -2 -2 0 -1 -4 0 0 0 -1 0 -3 0 4 -1 -5
-E -1 -1 -1 2 -1 2 6 -2 -1 -3 -1 1 -2 -3 0 0 -1 -1 -1 -2 0 5 -1 -5
-G 0 -2 1 -2 -3 -2 -2 7 -2 -3 -3 -1 -1 -3 -2 1 -2 -1 -2 -3 0 -2 -1 -5
-H -2 -1 1 0 -4 -1 -1 -2 12 -3 -2 -2 1 -3 -1 -1 -2 -4 0 -4 0 -1 -1 -5
-I -1 -3 -1 -3 -4 -2 -3 -3 -3 5 2 -2 1 1 -1 -2 -1 -1 0 4 -2 -3 0 -5
-L -2 -2 -2 -2 -2 -2 -1 -3 -2 2 5 -2 3 2 -3 -2 0 0 0 2 -2 -2 0 -5
-K 0 2 0 -1 -2 0 1 -1 -2 -2 -2 5 0 -1 0 0 0 0 -1 -2 0 1 0 -5
-M 0 0 -1 -3 -4 -1 -2 -1 1 1 3 0 6 0 -3 -1 0 1 0 1 -2 -2 0 -5
-F -2 -1 -1 -3 -4 -4 -3 -3 -3 1 2 -1 0 8 -4 -1 -1 1 3 1 -2 -3 -1 -5
-P -2 -2 -2 -1 -4 0 0 -2 -1 -1 -3 0 -3 -4 10 -2 0 -4 -3 -3 -1 0 -1 -5
-S 1 -1 0 -1 -3 0 0 1 -1 -2 -2 0 -1 -1 -2 4 2 -2 -1 -1 0 0 0 -5
-T 0 -2 0 -1 -1 0 -1 -2 -2 -1 0 0 0 -1 0 2 5 -2 -2 1 -1 -1 0 -5
-W -2 0 -2 -3 -5 -1 -1 -1 -4 -1 0 0 1 1 -4 -2 -2 16 3 -2 -3 -1 -1 -5
-Y -1 0 -2 -2 -5 0 -1 -2 0 0 0 -1 0 3 -3 -1 -2 3 8 0 -2 -1 -1 -5
-V 0 -1 -2 -2 -2 -3 -2 -3 -4 4 2 -2 1 1 -3 -1 1 -2 0 5 -2 -2 0 -5
-B -1 -1 4 5 -2 0 0 0 0 -2 -2 0 -2 -2 -1 0 -1 -3 -2 -2 5 0 -1 -5
-Z -1 0 0 1 -2 4 5 -2 -1 -3 -2 1 -2 -3 0 0 -1 -1 -1 -2 0 4 0 -5
-X 0 -1 0 -1 -2 -1 -1 -1 -1 0 0 0 0 -1 -1 0 0 -1 -1 0 -1 0 -1 -5
-* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM40 b/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM40
deleted file mode 100644
index 1a4baa2..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM40
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum40.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/4 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 40
-# Entropy = 0.2851, Expected = -0.2090
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -2 -1 -1 -2 0 -1 1 -2 -1 -2 -1 -1 -3 -2 1 0 -3 -2 0 -1 -1 0 -6
-R -2 9 0 -1 -3 2 -1 -3 0 -3 -2 3 -1 -2 -3 -1 -2 -2 -1 -2 -1 0 -1 -6
-N -1 0 8 2 -2 1 -1 0 1 -2 -3 0 -2 -3 -2 1 0 -4 -2 -3 4 0 -1 -6
-D -1 -1 2 9 -2 -1 2 -2 0 -4 -3 0 -3 -4 -2 0 -1 -5 -3 -3 6 1 -1 -6
-C -2 -3 -2 -2 16 -4 -2 -3 -4 -4 -2 -3 -3 -2 -5 -1 -1 -6 -4 -2 -2 -3 -2 -6
-Q 0 2 1 -1 -4 8 2 -2 0 -3 -2 1 -1 -4 -2 1 -1 -1 -1 -3 0 4 -1 -6
-E -1 -1 -1 2 -2 2 7 -3 0 -4 -2 1 -2 -3 0 0 -1 -2 -2 -3 1 5 -1 -6
-G 1 -3 0 -2 -3 -2 -3 8 -2 -4 -4 -2 -2 -3 -1 0 -2 -2 -3 -4 -1 -2 -1 -6
-H -2 0 1 0 -4 0 0 -2 13 -3 -2 -1 1 -2 -2 -1 -2 -5 2 -4 0 0 -1 -6
-I -1 -3 -2 -4 -4 -3 -4 -4 -3 6 2 -3 1 1 -2 -2 -1 -3 0 4 -3 -4 -1 -6
-L -2 -2 -3 -3 -2 -2 -2 -4 -2 2 6 -2 3 2 -4 -3 -1 -1 0 2 -3 -2 -1 -6
-K -1 3 0 0 -3 1 1 -2 -1 -3 -2 6 -1 -3 -1 0 0 -2 -1 -2 0 1 -1 -6
-M -1 -1 -2 -3 -3 -1 -2 -2 1 1 3 -1 7 0 -2 -2 -1 -2 1 1 -3 -2 0 -6
-F -3 -2 -3 -4 -2 -4 -3 -3 -2 1 2 -3 0 9 -4 -2 -1 1 4 0 -3 -4 -1 -6
-P -2 -3 -2 -2 -5 -2 0 -1 -2 -2 -4 -1 -2 -4 11 -1 0 -4 -3 -3 -2 -1 -2 -6
-S 1 -1 1 0 -1 1 0 0 -1 -2 -3 0 -2 -2 -1 5 2 -5 -2 -1 0 0 0 -6
-T 0 -2 0 -1 -1 -1 -1 -2 -2 -1 -1 0 -1 -1 0 2 6 -4 -1 1 0 -1 0 -6
-W -3 -2 -4 -5 -6 -1 -2 -2 -5 -3 -1 -2 -2 1 -4 -5 -4 19 3 -3 -4 -2 -2 -6
-Y -2 -1 -2 -3 -4 -1 -2 -3 2 0 0 -1 1 4 -3 -2 -1 3 9 -1 -3 -2 -1 -6
-V 0 -2 -3 -3 -2 -3 -3 -4 -4 4 2 -2 1 0 -3 -1 1 -3 -1 5 -3 -3 -1 -6
-B -1 -1 4 6 -2 0 1 -1 0 -3 -3 0 -3 -3 -2 0 0 -4 -3 -3 5 2 -1 -6
-Z -1 0 0 1 -3 4 5 -2 0 -4 -2 1 -2 -4 -1 0 -1 -2 -2 -3 2 5 -1 -6
-X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 0 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -6
-* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM45 b/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM45
deleted file mode 100644
index 18c3323..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM45
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum45.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 45
-# Entropy = 0.3795, Expected = -0.2789
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -2 -2 0 -1 -1 0 -5
-R -2 7 0 -1 -3 1 0 -2 0 -3 -2 3 -1 -2 -2 -1 -1 -2 -1 -2 -1 0 -1 -5
-N -1 0 6 2 -2 0 0 0 1 -2 -3 0 -2 -2 -2 1 0 -4 -2 -3 4 0 -1 -5
-D -2 -1 2 7 -3 0 2 -1 0 -4 -3 0 -3 -4 -1 0 -1 -4 -2 -3 5 1 -1 -5
-C -1 -3 -2 -3 12 -3 -3 -3 -3 -3 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -2 -3 -2 -5
-Q -1 1 0 0 -3 6 2 -2 1 -2 -2 1 0 -4 -1 0 -1 -2 -1 -3 0 4 -1 -5
-E -1 0 0 2 -3 2 6 -2 0 -3 -2 1 -2 -3 0 0 -1 -3 -2 -3 1 4 -1 -5
-G 0 -2 0 -1 -3 -2 -2 7 -2 -4 -3 -2 -2 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -5
-H -2 0 1 0 -3 1 0 -2 10 -3 -2 -1 0 -2 -2 -1 -2 -3 2 -3 0 0 -1 -5
-I -1 -3 -2 -4 -3 -2 -3 -4 -3 5 2 -3 2 0 -2 -2 -1 -2 0 3 -3 -3 -1 -5
-L -1 -2 -3 -3 -2 -2 -2 -3 -2 2 5 -3 2 1 -3 -3 -1 -2 0 1 -3 -2 -1 -5
-K -1 3 0 0 -3 1 1 -2 -1 -3 -3 5 -1 -3 -1 -1 -1 -2 -1 -2 0 1 -1 -5
-M -1 -1 -2 -3 -2 0 -2 -2 0 2 2 -1 6 0 -2 -2 -1 -2 0 1 -2 -1 -1 -5
-F -2 -2 -2 -4 -2 -4 -3 -3 -2 0 1 -3 0 8 -3 -2 -1 1 3 0 -3 -3 -1 -5
-P -1 -2 -2 -1 -4 -1 0 -2 -2 -2 -3 -1 -2 -3 9 -1 -1 -3 -3 -3 -2 -1 -1 -5
-S 1 -1 1 0 -1 0 0 0 -1 -2 -3 -1 -2 -2 -1 4 2 -4 -2 -1 0 0 0 -5
-T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1 2 5 -3 -1 0 0 -1 0 -5
-W -2 -2 -4 -4 -5 -2 -3 -2 -3 -2 -2 -2 -2 1 -3 -4 -3 15 3 -3 -4 -2 -2 -5
-Y -2 -1 -2 -2 -3 -1 -2 -3 2 0 0 -1 0 3 -3 -2 -1 3 8 -1 -2 -2 -1 -5
-V 0 -2 -3 -3 -1 -3 -3 -3 -3 3 1 -2 1 0 -3 -1 0 -3 -1 5 -3 -3 -1 -5
-B -1 -1 4 5 -2 0 1 -1 0 -3 -3 0 -2 -3 -2 0 0 -4 -2 -3 4 2 -1 -5
-Z -1 0 0 1 -3 4 4 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -3 2 4 -1 -5
-X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 0 -2 -1 -1 -1 -1 -1 -5
-* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM50 b/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM50
deleted file mode 100644
index 3f62e3c..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM50
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum50.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 50
-# Entropy = 0.4808, Expected = -0.3573
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -1 -1 -5
-R -2 7 -1 -2 -4 1 0 -3 0 -4 -3 3 -2 -3 -3 -1 -1 -3 -1 -3 -1 0 -1 -5
-N -1 -1 7 2 -2 0 0 0 1 -3 -4 0 -2 -4 -2 1 0 -4 -2 -3 4 0 -1 -5
-D -2 -2 2 8 -4 0 2 -1 -1 -4 -4 -1 -4 -5 -1 0 -1 -5 -3 -4 5 1 -1 -5
-C -1 -4 -2 -4 13 -3 -3 -3 -3 -2 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -3 -3 -2 -5
-Q -1 1 0 0 -3 7 2 -2 1 -3 -2 2 0 -4 -1 0 -1 -1 -1 -3 0 4 -1 -5
-E -1 0 0 2 -3 2 6 -3 0 -4 -3 1 -2 -3 -1 -1 -1 -3 -2 -3 1 5 -1 -5
-G 0 -3 0 -1 -3 -2 -3 8 -2 -4 -4 -2 -3 -4 -2 0 -2 -3 -3 -4 -1 -2 -2 -5
-H -2 0 1 -1 -3 1 0 -2 10 -4 -3 0 -1 -1 -2 -1 -2 -3 2 -4 0 0 -1 -5
-I -1 -4 -3 -4 -2 -3 -4 -4 -4 5 2 -3 2 0 -3 -3 -1 -3 -1 4 -4 -3 -1 -5
-L -2 -3 -4 -4 -2 -2 -3 -4 -3 2 5 -3 3 1 -4 -3 -1 -2 -1 1 -4 -3 -1 -5
-K -1 3 0 -1 -3 2 1 -2 0 -3 -3 6 -2 -4 -1 0 -1 -3 -2 -3 0 1 -1 -5
-M -1 -2 -2 -4 -2 0 -2 -3 -1 2 3 -2 7 0 -3 -2 -1 -1 0 1 -3 -1 -1 -5
-F -3 -3 -4 -5 -2 -4 -3 -4 -1 0 1 -4 0 8 -4 -3 -2 1 4 -1 -4 -4 -2 -5
-P -1 -3 -2 -1 -4 -1 -1 -2 -2 -3 -4 -1 -3 -4 10 -1 -1 -4 -3 -3 -2 -1 -2 -5
-S 1 -1 1 0 -1 0 -1 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 0 -1 -5
-T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 2 5 -3 -2 0 0 -1 0 -5
-W -3 -3 -4 -5 -5 -1 -3 -3 -3 -3 -2 -3 -1 1 -4 -4 -3 15 2 -3 -5 -2 -3 -5
-Y -2 -1 -2 -3 -3 -1 -2 -3 2 -1 -1 -2 0 4 -3 -2 -2 2 8 -1 -3 -2 -1 -5
-V 0 -3 -3 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -3 -1 5 -4 -3 -1 -5
-B -2 -1 4 5 -3 0 1 -1 0 -4 -4 0 -3 -4 -2 0 0 -5 -3 -4 5 2 -1 -5
-Z -1 0 0 1 -3 4 5 -2 0 -3 -3 1 -1 -4 -1 0 -1 -2 -2 -3 2 5 -1 -5
-X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 0 -3 -1 -1 -1 -1 -1 -5
-* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM55 b/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM55
deleted file mode 100644
index c0cf3ff..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM55
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum55.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 55
-# Entropy = 0.5637, Expected = -0.4179
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -2 -2 -2 0 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 2 0 -4 -2 0 -2 -1 -1 -5
-R -2 8 -1 -2 -4 1 0 -3 0 -4 -3 3 -2 -3 -3 -1 -1 -3 -2 -3 -1 0 -1 -5
-N -2 -1 8 2 -3 0 0 0 1 -4 -4 0 -3 -4 -2 1 0 -5 -2 -4 4 0 -1 -5
-D -2 -2 2 8 -4 0 2 -2 -1 -4 -5 -1 -4 -5 -2 0 -1 -5 -3 -4 5 1 -2 -5
-C 0 -4 -3 -4 13 -4 -4 -3 -4 -2 -2 -4 -2 -3 -3 -1 -1 -4 -3 -1 -4 -4 -2 -5
-Q -1 1 0 0 -4 7 2 -2 1 -4 -3 2 0 -4 -1 0 -1 -2 -1 -3 0 4 -1 -5
-E -1 0 0 2 -4 2 7 -3 -1 -4 -4 1 -3 -4 -1 0 -1 -3 -2 -3 1 5 -1 -5
-G 0 -3 0 -2 -3 -2 -3 8 -2 -5 -5 -2 -3 -4 -3 0 -2 -3 -4 -4 -1 -3 -2 -5
-H -2 0 1 -1 -4 1 -1 -2 11 -4 -3 0 -2 -1 -3 -1 -2 -3 2 -4 0 0 -1 -5
-I -2 -4 -4 -4 -2 -4 -4 -5 -4 6 2 -4 2 0 -3 -3 -1 -3 -1 4 -4 -4 -1 -5
-L -2 -3 -4 -5 -2 -3 -4 -5 -3 2 6 -3 3 1 -4 -3 -2 -3 -1 1 -4 -3 -1 -5
-K -1 3 0 -1 -4 2 1 -2 0 -4 -3 6 -2 -4 -1 0 -1 -4 -2 -3 0 1 -1 -5
-M -1 -2 -3 -4 -2 0 -3 -3 -2 2 3 -2 8 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5
-F -3 -3 -4 -5 -3 -4 -4 -4 -1 0 1 -4 0 9 -5 -3 -3 2 4 -1 -5 -4 -2 -5
-P -1 -3 -2 -2 -3 -1 -1 -3 -3 -3 -4 -1 -3 -5 10 -1 -1 -5 -4 -3 -2 -1 -2 -5
-S 2 -1 1 0 -1 0 0 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 0 -1 -5
-T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -3 -1 2 6 -3 -2 0 -1 -1 -1 -5
-W -4 -3 -5 -5 -4 -2 -3 -3 -3 -3 -3 -4 -2 2 -5 -4 -3 15 3 -4 -5 -3 -3 -5
-Y -2 -2 -2 -3 -3 -1 -2 -4 2 -1 -1 -2 -1 4 -4 -2 -2 3 9 -2 -3 -2 -1 -5
-V 0 -3 -4 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -4 -2 5 -4 -3 -1 -5
-B -2 -1 4 5 -4 0 1 -1 0 -4 -4 0 -3 -5 -2 0 -1 -5 -3 -4 5 2 -1 -5
-Z -1 0 0 1 -4 4 5 -3 0 -4 -3 1 -2 -4 -1 0 -1 -3 -2 -3 2 5 -1 -5
-X -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -3 -1 -1 -1 -1 -1 -5
-* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM60 b/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM60
deleted file mode 100644
index 4fd1943..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM60
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum60.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 60
-# Entropy = 0.6603, Expected = -0.4917
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 4 -1 -1 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4
-R -1 5 0 -1 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -2 -1 0 -1 -4
-N -1 0 6 1 -2 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4
-D -2 -1 1 6 -3 0 2 -1 -1 -3 -3 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4
-C 0 -3 -2 -3 9 -3 -3 -2 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4
-Q -1 1 0 0 -3 5 2 -2 1 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4
-E -1 0 0 2 -3 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
-G 0 -2 0 -1 -2 -2 -2 6 -2 -3 -4 -1 -2 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4
-H -2 0 1 -1 -3 1 0 -2 7 -3 -3 -1 -1 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4
-I -1 -3 -3 -3 -1 -3 -3 -3 -3 4 2 -3 1 0 -3 -2 -1 -2 -1 3 -3 -3 -1 -4
-L -1 -2 -3 -3 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -4
-K -1 2 0 -1 -3 1 1 -1 -1 -3 -2 4 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4
-M -1 -1 -2 -3 -1 0 -2 -2 -1 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4
-F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4
-P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4
-S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4
-T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 4 -2 -2 0 0 -1 0 -4
-W -3 -3 -4 -4 -2 -2 -3 -2 -2 -2 -2 -3 -1 1 -4 -3 -2 10 2 -3 -4 -2 -2 -4
-Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 6 -1 -2 -2 -1 -4
-V 0 -2 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4
-B -2 -1 3 4 -3 0 1 -1 0 -3 -3 0 -3 -3 -2 0 0 -4 -2 -3 4 1 -1 -4
-Z -1 0 0 1 -3 3 4 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -2 1 3 -1 -4
-X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4
-* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM62 b/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM62
deleted file mode 100644
index 205f139..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM62
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum62.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 62
-# Entropy = 0.6979, Expected = -0.5209
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4
-R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4
-N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4
-D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4
-C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4
-Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4
-E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
-G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4
-H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4
-I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4
-L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4
-K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4
-M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4
-F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4
-P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4
-S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4
-T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4
-W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4
-Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4
-V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4
-B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4
-Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
-X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4
-* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM65 b/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM65
deleted file mode 100644
index 1eacd14..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM65
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum65.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 65
-# Entropy = 0.7576, Expected = -0.5675
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -2 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -5
-R -1 6 0 -2 -4 1 0 -2 0 -3 -2 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5
-N -2 0 6 1 -3 0 0 -1 1 -3 -4 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -5
-D -2 -2 1 6 -4 0 2 -1 -1 -3 -4 -1 -3 -4 -2 0 -1 -5 -3 -3 4 1 -1 -5
-C 0 -4 -3 -4 9 -3 -4 -3 -3 -1 -1 -3 -2 -2 -3 -1 -1 -2 -2 -1 -3 -4 -2 -5
-Q -1 1 0 0 -3 6 2 -2 1 -3 -2 1 0 -3 -1 0 -1 -2 -2 -2 0 3 -1 -5
-E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -3 1 4 -1 -5
-G 0 -2 -1 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -3 -3 -3 -1 -2 -2 -5
-H -2 0 1 -1 -3 1 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -5
-I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -2 -1 3 -3 -3 -1 -5
-L -2 -2 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 1 -4 -3 -1 -5
-K -1 2 0 -1 -3 1 1 -2 -1 -3 -3 5 -2 -3 -1 0 -1 -3 -2 -2 0 1 -1 -5
-M -1 -2 -2 -3 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5
-F -2 -3 -3 -4 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -2 -5
-P -1 -2 -2 -2 -3 -1 -1 -2 -2 -3 -3 -1 -3 -4 8 -1 -1 -4 -3 -2 -2 -1 -2 -5
-S 1 -1 1 0 -1 0 0 0 -1 -2 -3 0 -2 -2 -1 4 1 -3 -2 -2 0 0 -1 -5
-T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5
-W -3 -3 -4 -5 -2 -2 -3 -3 -2 -2 -2 -3 -2 1 -4 -3 -3 10 2 -3 -4 -3 -2 -5
-Y -2 -2 -2 -3 -2 -2 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -5
-V 0 -3 -3 -3 -1 -2 -3 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -5
-B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -5
-Z -1 0 0 1 -4 3 4 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -5
-X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -5
-* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM70 b/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM70
deleted file mode 100644
index 3e4093f..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM70
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum70.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 70
-# Entropy = 0.8391, Expected = -0.6313
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 4 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -5
-R -2 6 -1 -2 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5
-N -2 -1 6 1 -3 0 0 -1 0 -4 -4 0 -2 -3 -2 0 0 -4 -2 -3 3 0 -1 -5
-D -2 -2 1 6 -4 -1 1 -2 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -4 -4 4 1 -2 -5
-C -1 -4 -3 -4 9 -3 -4 -3 -4 -1 -2 -4 -2 -2 -3 -1 -1 -3 -3 -1 -4 -4 -2 -5
-Q -1 1 0 -1 -3 6 2 -2 1 -3 -2 1 0 -3 -2 0 -1 -2 -2 -2 0 3 -1 -5
-E -1 0 0 1 -4 2 5 -2 0 -4 -3 1 -2 -4 -1 0 -1 -4 -3 -3 1 4 -1 -5
-G 0 -3 -1 -2 -3 -2 -2 6 -2 -4 -4 -2 -3 -4 -3 -1 -2 -3 -4 -4 -1 -2 -2 -5
-H -2 0 0 -1 -4 1 0 -2 8 -4 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 -1 0 -1 -5
-I -2 -3 -4 -4 -1 -3 -4 -4 -4 4 2 -3 1 0 -3 -3 -1 -3 -1 3 -4 -3 -1 -5
-L -2 -3 -4 -4 -2 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -2 -2 -1 1 -4 -3 -1 -5
-K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -3 -1 0 -1 -3 -2 -3 -1 1 -1 -5
-M -1 -2 -2 -3 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5
-F -2 -3 -3 -4 -2 -3 -4 -4 -1 0 0 -3 0 6 -4 -3 -2 1 3 -1 -4 -4 -2 -5
-P -1 -2 -2 -2 -3 -2 -1 -3 -2 -3 -3 -1 -3 -4 8 -1 -1 -4 -3 -3 -2 -1 -2 -5
-S 1 -1 0 0 -1 0 0 -1 -1 -3 -3 0 -2 -3 -1 4 1 -3 -2 -2 0 0 -1 -5
-T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5
-W -3 -3 -4 -5 -3 -2 -4 -3 -2 -3 -2 -3 -2 1 -4 -3 -3 11 2 -3 -4 -3 -3 -5
-Y -2 -2 -2 -4 -3 -2 -3 -4 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -2 -3 -2 -2 -5
-V 0 -3 -3 -4 -1 -2 -3 -4 -3 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -3 -3 -1 -5
-B -2 -1 3 4 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -4 -3 -3 4 0 -1 -5
-Z -1 0 0 1 -4 3 4 -2 0 -3 -3 1 -2 -4 -1 0 -1 -3 -2 -3 0 4 -1 -5
-X -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -3 -2 -1 -1 -1 -1 -5
-* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM75 b/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM75
deleted file mode 100644
index 98964be..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM75
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum75.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 75
-# Entropy = 0.9077, Expected = -0.6845
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 4 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -1 -1 -5
-R -2 6 -1 -2 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5
-N -2 -1 6 1 -3 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -4 -3 -3 3 0 -1 -5
-D -2 -2 1 6 -4 -1 1 -2 -1 -4 -4 -1 -4 -4 -2 -1 -1 -5 -4 -4 4 1 -2 -5
-C -1 -4 -3 -4 9 -3 -5 -3 -4 -1 -2 -4 -2 -2 -4 -1 -1 -3 -3 -1 -4 -4 -2 -5
-Q -1 1 0 -1 -3 6 2 -2 1 -3 -3 1 0 -4 -2 0 -1 -2 -2 -2 0 3 -1 -5
-E -1 0 -1 1 -5 2 5 -3 0 -4 -4 1 -2 -4 -1 0 -1 -4 -3 -3 1 4 -1 -5
-G 0 -3 -1 -2 -3 -2 -3 6 -2 -5 -4 -2 -3 -4 -3 -1 -2 -3 -4 -4 -1 -2 -2 -5
-H -2 0 0 -1 -4 1 0 -2 8 -4 -3 -1 -2 -2 -2 -1 -2 -2 2 -4 -1 0 -1 -5
-I -2 -3 -4 -4 -1 -3 -4 -5 -4 4 1 -3 1 0 -3 -3 -1 -3 -2 3 -4 -4 -2 -5
-L -2 -3 -4 -4 -2 -3 -4 -4 -3 1 4 -3 2 0 -3 -3 -2 -2 -1 1 -4 -3 -1 -5
-K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -4 -1 0 -1 -4 -2 -3 -1 1 -1 -5
-M -1 -2 -3 -4 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -2 1 -3 -2 -1 -5
-F -3 -3 -4 -4 -2 -4 -4 -4 -2 0 0 -4 0 6 -4 -3 -2 1 3 -1 -4 -4 -2 -5
-P -1 -2 -3 -2 -4 -2 -1 -3 -2 -3 -3 -1 -3 -4 8 -1 -1 -5 -4 -3 -2 -2 -2 -5
-S 1 -1 0 -1 -1 0 0 -1 -1 -3 -3 0 -2 -3 -1 5 1 -3 -2 -2 0 0 -1 -5
-T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5
-W -3 -3 -4 -5 -3 -2 -4 -3 -2 -3 -2 -4 -2 1 -5 -3 -3 11 2 -3 -5 -3 -3 -5
-Y -2 -2 -3 -4 -3 -2 -3 -4 2 -2 -1 -2 -2 3 -4 -2 -2 2 7 -2 -3 -3 -2 -5
-V 0 -3 -3 -4 -1 -2 -3 -4 -4 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -4 -3 -1 -5
-B -2 -1 3 4 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -3 -4 4 0 -2 -5
-Z -1 0 0 1 -4 3 4 -2 0 -4 -3 1 -2 -4 -2 0 -1 -3 -3 -3 0 4 -1 -5
-X -1 -1 -1 -2 -2 -1 -1 -2 -1 -2 -1 -1 -1 -2 -2 -1 -1 -3 -2 -1 -2 -1 -1 -5
-* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM80 b/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM80
deleted file mode 100644
index 78172a3..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM80
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum80_3.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 80
-# Entropy = 0.9868, Expected = -0.7442
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 7 -3 -3 -3 -1 -2 -2 0 -3 -3 -3 -1 -2 -4 -1 2 0 -5 -4 -1 -3 -2 -1 -8
-R -3 9 -1 -3 -6 1 -1 -4 0 -5 -4 3 -3 -5 -3 -2 -2 -5 -4 -4 -2 0 -2 -8
-N -3 -1 9 2 -5 0 -1 -1 1 -6 -6 0 -4 -6 -4 1 0 -7 -4 -5 5 -1 -2 -8
-D -3 -3 2 10 -7 -1 2 -3 -2 -7 -7 -2 -6 -6 -3 -1 -2 -8 -6 -6 6 1 -3 -8
-C -1 -6 -5 -7 13 -5 -7 -6 -7 -2 -3 -6 -3 -4 -6 -2 -2 -5 -5 -2 -6 -7 -4 -8
-Q -2 1 0 -1 -5 9 3 -4 1 -5 -4 2 -1 -5 -3 -1 -1 -4 -3 -4 -1 5 -2 -8
-E -2 -1 -1 2 -7 3 8 -4 0 -6 -6 1 -4 -6 -2 -1 -2 -6 -5 -4 1 6 -2 -8
-G 0 -4 -1 -3 -6 -4 -4 9 -4 -7 -7 -3 -5 -6 -5 -1 -3 -6 -6 -6 -2 -4 -3 -8
-H -3 0 1 -2 -7 1 0 -4 12 -6 -5 -1 -4 -2 -4 -2 -3 -4 3 -5 -1 0 -2 -8
-I -3 -5 -6 -7 -2 -5 -6 -7 -6 7 2 -5 2 -1 -5 -4 -2 -5 -3 4 -6 -6 -2 -8
-L -3 -4 -6 -7 -3 -4 -6 -7 -5 2 6 -4 3 0 -5 -4 -3 -4 -2 1 -7 -5 -2 -8
-K -1 3 0 -2 -6 2 1 -3 -1 -5 -4 8 -3 -5 -2 -1 -1 -6 -4 -4 -1 1 -2 -8
-M -2 -3 -4 -6 -3 -1 -4 -5 -4 2 3 -3 9 0 -4 -3 -1 -3 -3 1 -5 -3 -2 -8
-F -4 -5 -6 -6 -4 -5 -6 -6 -2 -1 0 -5 0 10 -6 -4 -4 0 4 -2 -6 -6 -3 -8
-P -1 -3 -4 -3 -6 -3 -2 -5 -4 -5 -5 -2 -4 -6 12 -2 -3 -7 -6 -4 -4 -2 -3 -8
-S 2 -2 1 -1 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2 7 2 -6 -3 -3 0 -1 -1 -8
-T 0 -2 0 -2 -2 -1 -2 -3 -3 -2 -3 -1 -1 -4 -3 2 8 -5 -3 0 -1 -2 -1 -8
-W -5 -5 -7 -8 -5 -4 -6 -6 -4 -5 -4 -6 -3 0 -7 -6 -5 16 3 -5 -8 -5 -5 -8
-Y -4 -4 -4 -6 -5 -3 -5 -6 3 -3 -2 -4 -3 4 -6 -3 -3 3 11 -3 -5 -4 -3 -8
-V -1 -4 -5 -6 -2 -4 -4 -6 -5 4 1 -4 1 -2 -4 -3 0 -5 -3 7 -6 -4 -2 -8
-B -3 -2 5 6 -6 -1 1 -2 -1 -6 -7 -1 -5 -6 -4 0 -1 -8 -5 -6 6 0 -3 -8
-Z -2 0 -1 1 -7 5 6 -4 0 -6 -5 1 -3 -6 -2 -1 -2 -5 -4 -4 0 6 -1 -8
-X -1 -2 -2 -3 -4 -2 -2 -3 -2 -2 -2 -2 -2 -3 -3 -1 -1 -5 -3 -2 -3 -1 -2 -8
-* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM85 b/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM85
deleted file mode 100644
index cb47fd2..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM85
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum85.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 85
-# Entropy = 1.0805, Expected = -0.8153
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -2 -3 -1 1 0 -3 -3 -1 -2 -1 -1 -6
-R -2 6 -1 -2 -4 1 -1 -3 0 -4 -3 2 -2 -4 -2 -1 -2 -4 -3 -3 -2 0 -2 -6
-N -2 -1 7 1 -4 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -5 -3 -4 4 -1 -2 -6
-D -2 -2 1 7 -5 -1 1 -2 -2 -5 -5 -1 -4 -4 -2 -1 -2 -6 -4 -4 4 1 -2 -6
-C -1 -4 -4 -5 9 -4 -5 -4 -5 -2 -2 -4 -2 -3 -4 -2 -2 -4 -3 -1 -4 -5 -3 -6
-Q -1 1 0 -1 -4 6 2 -3 1 -4 -3 1 0 -4 -2 -1 -1 -3 -2 -3 -1 4 -1 -6
-E -1 -1 -1 1 -5 2 6 -3 -1 -4 -4 0 -3 -4 -2 -1 -1 -4 -4 -3 0 4 -1 -6
-G 0 -3 -1 -2 -4 -3 -3 6 -3 -5 -5 -2 -4 -4 -3 -1 -2 -4 -5 -4 -1 -3 -2 -6
-H -2 0 0 -2 -5 1 -1 -3 8 -4 -3 -1 -3 -2 -3 -1 -2 -3 2 -4 -1 0 -2 -6
-I -2 -4 -4 -5 -2 -4 -4 -5 -4 5 1 -3 1 -1 -4 -3 -1 -3 -2 3 -5 -4 -2 -6
-L -2 -3 -4 -5 -2 -3 -4 -5 -3 1 4 -3 2 0 -4 -3 -2 -3 -2 0 -5 -4 -2 -6
-K -1 2 0 -1 -4 1 0 -2 -1 -3 -3 6 -2 -4 -2 -1 -1 -5 -3 -3 -1 1 -1 -6
-M -2 -2 -3 -4 -2 0 -3 -4 -3 1 2 -2 7 -1 -3 -2 -1 -2 -2 0 -4 -2 -1 -6
-F -3 -4 -4 -4 -3 -4 -4 -4 -2 -1 0 -4 -1 7 -4 -3 -3 0 3 -1 -4 -4 -2 -6
-P -1 -2 -3 -2 -4 -2 -2 -3 -3 -4 -4 -2 -3 -4 8 -1 -2 -5 -4 -3 -3 -2 -2 -6
-S 1 -1 0 -1 -2 -1 -1 -1 -1 -3 -3 -1 -2 -3 -1 5 1 -4 -2 -2 0 -1 -1 -6
-T 0 -2 0 -2 -2 -1 -1 -2 -2 -1 -2 -1 -1 -3 -2 1 5 -4 -2 0 -1 -1 -1 -6
-W -3 -4 -5 -6 -4 -3 -4 -4 -3 -3 -3 -5 -2 0 -5 -4 -4 11 2 -3 -5 -4 -3 -6
-Y -3 -3 -3 -4 -3 -2 -4 -5 2 -2 -2 -3 -2 3 -4 -2 -2 2 7 -2 -4 -3 -2 -6
-V -1 -3 -4 -4 -1 -3 -3 -4 -4 3 0 -3 0 -1 -3 -2 0 -3 -2 5 -4 -3 -1 -6
-B -2 -2 4 4 -4 -1 0 -1 -1 -5 -5 -1 -4 -4 -3 0 -1 -5 -4 -4 4 0 -2 -6
-Z -1 0 -1 1 -5 4 4 -3 0 -4 -4 1 -2 -4 -2 -1 -1 -4 -3 -3 0 4 -1 -6
-X -1 -2 -2 -2 -3 -1 -1 -2 -2 -2 -2 -1 -1 -2 -2 -1 -1 -3 -2 -1 -2 -1 -2 -6
-* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM90 b/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM90
deleted file mode 100644
index 71441b5..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUM90
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum90.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 90
-# Entropy = 1.1806, Expected = -0.8887
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -2 -2 -3 -1 -1 -1 0 -2 -2 -2 -1 -2 -3 -1 1 0 -4 -3 -1 -2 -1 -1 -6
-R -2 6 -1 -3 -5 1 -1 -3 0 -4 -3 2 -2 -4 -3 -1 -2 -4 -3 -3 -2 0 -2 -6
-N -2 -1 7 1 -4 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -5 -3 -4 4 -1 -2 -6
-D -3 -3 1 7 -5 -1 1 -2 -2 -5 -5 -1 -4 -5 -3 -1 -2 -6 -4 -5 4 0 -2 -6
-C -1 -5 -4 -5 9 -4 -6 -4 -5 -2 -2 -4 -2 -3 -4 -2 -2 -4 -4 -2 -4 -5 -3 -6
-Q -1 1 0 -1 -4 7 2 -3 1 -4 -3 1 0 -4 -2 -1 -1 -3 -3 -3 -1 4 -1 -6
-E -1 -1 -1 1 -6 2 6 -3 -1 -4 -4 0 -3 -5 -2 -1 -1 -5 -4 -3 0 4 -2 -6
-G 0 -3 -1 -2 -4 -3 -3 6 -3 -5 -5 -2 -4 -5 -3 -1 -3 -4 -5 -5 -2 -3 -2 -6
-H -2 0 0 -2 -5 1 -1 -3 8 -4 -4 -1 -3 -2 -3 -2 -2 -3 1 -4 -1 0 -2 -6
-I -2 -4 -4 -5 -2 -4 -4 -5 -4 5 1 -4 1 -1 -4 -3 -1 -4 -2 3 -5 -4 -2 -6
-L -2 -3 -4 -5 -2 -3 -4 -5 -4 1 5 -3 2 0 -4 -3 -2 -3 -2 0 -5 -4 -2 -6
-K -1 2 0 -1 -4 1 0 -2 -1 -4 -3 6 -2 -4 -2 -1 -1 -5 -3 -3 -1 1 -1 -6
-M -2 -2 -3 -4 -2 0 -3 -4 -3 1 2 -2 7 -1 -3 -2 -1 -2 -2 0 -4 -2 -1 -6
-F -3 -4 -4 -5 -3 -4 -5 -5 -2 -1 0 -4 -1 7 -4 -3 -3 0 3 -2 -4 -4 -2 -6
-P -1 -3 -3 -3 -4 -2 -2 -3 -3 -4 -4 -2 -3 -4 8 -2 -2 -5 -4 -3 -3 -2 -2 -6
-S 1 -1 0 -1 -2 -1 -1 -1 -2 -3 -3 -1 -2 -3 -2 5 1 -4 -3 -2 0 -1 -1 -6
-T 0 -2 0 -2 -2 -1 -1 -3 -2 -1 -2 -1 -1 -3 -2 1 6 -4 -2 -1 -1 -1 -1 -6
-W -4 -4 -5 -6 -4 -3 -5 -4 -3 -4 -3 -5 -2 0 -5 -4 -4 11 2 -3 -6 -4 -3 -6
-Y -3 -3 -3 -4 -4 -3 -4 -5 1 -2 -2 -3 -2 3 -4 -3 -2 2 8 -3 -4 -3 -2 -6
-V -1 -3 -4 -5 -2 -3 -3 -5 -4 3 0 -3 0 -2 -3 -2 -1 -3 -3 5 -4 -3 -2 -6
-B -2 -2 4 4 -4 -1 0 -2 -1 -5 -5 -1 -4 -4 -3 0 -1 -6 -4 -4 4 0 -2 -6
-Z -1 0 -1 0 -5 4 4 -3 0 -4 -4 1 -2 -4 -2 -1 -1 -4 -3 -3 0 4 -1 -6
-X -1 -2 -2 -2 -3 -1 -2 -2 -2 -2 -2 -1 -1 -2 -2 -1 -1 -3 -2 -2 -2 -1 -2 -6
-* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUMN b/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUMN
deleted file mode 100644
index df064c8..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/BLOSUMN
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosumn.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= -2
-# Entropy = 1.5172, Expected = -1.1484
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 6 -2 -2 -3 -2 -1 -2 -1 -3 -3 -3 -2 -2 -4 -1 1 -1 -4 -4 -1 -3 -2 -1 -7
-R -2 7 -1 -3 -6 0 -2 -4 -1 -5 -4 2 -3 -4 -3 -2 -2 -5 -4 -4 -2 -1 -2 -7
-N -2 -1 7 1 -4 -1 -1 -2 0 -5 -5 -1 -4 -5 -4 0 -1 -6 -4 -4 4 -1 -2 -7
-D -3 -3 1 7 -6 -2 1 -3 -2 -6 -6 -2 -5 -5 -3 -2 -2 -7 -5 -5 4 0 -3 -7
-C -2 -6 -4 -6 9 -5 -7 -5 -6 -2 -3 -5 -3 -3 -5 -2 -2 -5 -4 -2 -5 -6 -4 -7
-Q -1 0 -1 -2 -5 7 1 -4 0 -4 -3 1 -1 -4 -2 -1 -2 -4 -3 -4 -1 4 -2 -7
-E -2 -2 -1 1 -7 1 6 -4 -1 -5 -5 0 -4 -5 -3 -1 -2 -5 -4 -4 0 5 -2 -7
-G -1 -4 -2 -3 -5 -4 -4 6 -4 -6 -6 -3 -5 -5 -4 -1 -3 -5 -6 -5 -2 -4 -3 -7
-H -3 -1 0 -2 -6 0 -1 -4 9 -5 -4 -2 -3 -3 -4 -2 -3 -4 1 -5 -1 -1 -3 -7
-I -3 -5 -5 -6 -2 -4 -5 -6 -5 6 1 -4 1 -1 -5 -4 -2 -4 -3 2 -5 -5 -2 -7
-L -3 -4 -5 -6 -3 -3 -5 -6 -4 1 5 -4 2 0 -5 -4 -3 -4 -3 0 -5 -4 -2 -7
-K -2 2 -1 -2 -5 1 0 -3 -2 -4 -4 6 -2 -4 -2 -1 -2 -6 -4 -4 -1 0 -2 -7
-M -2 -3 -4 -5 -3 -1 -4 -5 -3 1 2 -2 8 -1 -4 -3 -2 -2 -3 0 -5 -3 -2 -7
-F -4 -4 -5 -5 -3 -4 -5 -5 -3 -1 0 -4 -1 7 -5 -4 -3 0 3 -2 -5 -5 -3 -7
-P -1 -3 -4 -3 -5 -2 -3 -4 -4 -5 -5 -2 -4 -5 8 -2 -3 -5 -5 -4 -4 -3 -3 -7
-S 1 -2 0 -2 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2 6 1 -4 -3 -3 -1 -1 -1 -7
-T -1 -2 -1 -2 -2 -2 -2 -3 -3 -2 -3 -2 -2 -3 -3 1 6 -5 -3 -1 -2 -2 -1 -7
-W -4 -5 -6 -7 -5 -4 -5 -5 -4 -4 -4 -6 -2 0 -5 -4 -5 11 1 -3 -6 -4 -4 -7
-Y -4 -4 -4 -5 -4 -3 -4 -6 1 -3 -3 -4 -3 3 -5 -3 -3 1 8 -3 -4 -4 -3 -7
-V -1 -4 -4 -5 -2 -4 -4 -5 -5 2 0 -4 0 -2 -4 -3 -1 -3 -3 5 -5 -4 -2 -7
-B -3 -2 4 4 -5 -1 0 -2 -1 -5 -5 -1 -5 -5 -4 -1 -2 -6 -4 -5 4 1 -2 -7
-Z -2 -1 -1 0 -6 4 5 -4 -1 -5 -4 0 -3 -5 -3 -1 -2 -4 -4 -4 1 4 -2 -7
-X -1 -2 -2 -3 -4 -2 -2 -3 -3 -2 -2 -2 -2 -3 -3 -1 -1 -4 -3 -2 -2 -2 -2 -7
-* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/DAYHOFF b/maven-src/target/classes/java/jaligner/matrix/matrices/DAYHOFF
deleted file mode 100644
index e287ed0..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/DAYHOFF
+++ /dev/null
@@ -1,32 +0,0 @@
-#Date: Wed, 18 Sep 91 17:36:51 EDT
-#From: altschul@ray.nlm.nih.gov (Stephen Altschul)
-#To: gish@ray.nlm.nih.gov
-#Subject: Vanilla-flavored PAM-250
-#
-# substitution scores for B, Z, X, and * were obtained with "pam" version 1.0.5
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -4 1 1 1 -6 -3 0 0 0 0 -8
-R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -8
-N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
-D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 -8
-C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 0 -2 -4 -5 -3 -8
-Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -8
-E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 -1 0 0 -7 -4 -2 3 3 -1 -8
-G 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 -1 1 0 -7 -5 -1 0 0 -1 -8
-H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -8
-I -1 -2 -2 -2 -2 -2 -2 -3 -2 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -8
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -3 -3 -1 -8
-K -1 3 1 0 -5 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 0 -1 -8
-M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -2 -1 -4 -2 2 -2 -2 -1 -8
-F -4 -4 -4 -6 -4 -5 -5 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -4 -5 -2 -8
-P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8
-S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -2 -3 -1 0 0 0 -8
-T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8
-W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 -4 -8
-Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -8
-V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 -8
-B 0 -1 2 3 -4 1 3 0 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 -1 -8
-Z 0 0 1 3 -5 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 -8
-X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 -8
-* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/EDNAFULL b/maven-src/target/classes/java/jaligner/matrix/matrices/EDNAFULL
deleted file mode 100644
index bfec6d9..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/EDNAFULL
+++ /dev/null
@@ -1,25 +0,0 @@
-#
-# This matrix was created by Todd Lowe 12/10/92
-#
-# Uses ambiguous nucleotide codes, probabilities rounded to
-# nearest integer
-#
-# Lowest score = -4, Highest score = 5
-#
- A T G C S W R Y K M B V H D N U
-A 5 -4 -4 -4 -4 1 1 -4 -4 1 -4 -1 -1 -1 -2 -4
-T -4 5 -4 -4 -4 1 -4 1 1 -4 -1 -4 -1 -1 -2 5
-G -4 -4 5 -4 1 -4 1 -4 1 -4 -1 -1 -4 -1 -2 -4
-C -4 -4 -4 5 1 -4 -4 1 -4 1 -1 -1 -1 -4 -2 -4
-S -4 -4 1 1 -1 -4 -2 -2 -2 -2 -1 -1 -3 -3 -1 -4
-W 1 1 -4 -4 -4 -1 -2 -2 -2 -2 -3 -3 -1 -1 -1 1
-R 1 -4 1 -4 -2 -2 -1 -4 -2 -2 -3 -1 -3 -1 -1 -4
-Y -4 1 -4 1 -2 -2 -4 -1 -2 -2 -1 -3 -1 -3 -1 1
-K -4 1 1 -4 -2 -2 -2 -2 -1 -4 -1 -3 -3 -1 -1 1
-M 1 -4 -4 1 -2 -2 -2 -2 -4 -1 -3 -1 -1 -3 -1 -4
-B -4 -1 -1 -1 -1 -3 -3 -1 -1 -3 -1 -2 -2 -2 -1 -1
-V -1 -4 -1 -1 -1 -3 -1 -3 -3 -1 -2 -1 -2 -2 -1 -4
-H -1 -1 -4 -1 -3 -1 -3 -1 -3 -1 -2 -2 -1 -2 -1 -1
-D -1 -1 -1 -4 -3 -1 -1 -3 -1 -3 -2 -2 -2 -1 -1 -1
-N -2 -2 -2 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2
-U -4 5 -4 -4 -4 1 -4 1 1 -4 -1 -4 -1 -1 -2 5
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/GONNET b/maven-src/target/classes/java/jaligner/matrix/matrices/GONNET
deleted file mode 100644
index d7bd4f4..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/GONNET
+++ /dev/null
@@ -1,26 +0,0 @@
-# PAM 250 matrix recommended by Gonnet, Cohen & Benner
-# Science June 5, 1992.
-# Values rounded to nearest integer
- C S T P A G N D E Q H R K M I L V F Y W X *
-C 12 0 0 -3 0 -2 -2 -3 -3 -2 -1 -2 -3 -1 -1 -2 0 -1 0 -1 -3 -8
-S 0 2 2 0 1 0 1 0 0 0 0 0 0 -1 -2 -2 -1 -3 -2 -3 0 -8
-T 0 2 2 0 1 -1 0 0 0 0 0 0 0 -1 -1 -1 0 -2 -2 -4 0 -8
-P -3 0 0 8 0 -2 -1 -1 0 0 -1 -1 -1 -2 -3 -2 -2 -4 -3 -5 -1 -8
-A 0 1 1 0 2 0 0 0 0 0 -1 -1 0 -1 -1 -1 0 -2 -2 -4 0 -8
-G -2 0 -1 -2 0 7 0 0 -1 -1 -1 -1 -1 -4 -4 -4 -3 -5 -4 -4 -1 -8
-N -2 1 0 -1 0 0 4 2 1 1 1 0 1 -2 -3 -3 -2 -3 -1 -4 0 -8
-D -3 0 0 -1 0 0 2 5 3 1 0 0 0 -3 -4 -4 -3 -4 -3 -5 -1 -8
-E -3 0 0 0 0 -1 1 3 4 2 0 0 1 -2 -3 -3 -2 -4 -3 -4 -1 -8
-Q -2 0 0 0 0 -1 1 1 2 3 1 2 2 -1 -2 -2 -2 -3 -2 -3 -1 -8
-H -1 0 0 -1 -1 -1 1 0 0 1 6 1 1 -1 -2 -2 -2 0 2 -1 -1 -8
-R -2 0 0 -1 -1 -1 0 0 0 2 1 5 3 -2 -2 -2 -2 -3 -2 -2 -1 -8
-K -3 0 0 -1 0 -1 1 0 1 2 1 3 3 -1 -2 -2 -2 -3 -2 -4 -1 -8
-M -1 -1 -1 -2 -1 -4 -2 -3 -2 -1 -1 -2 -1 4 2 3 2 2 0 -1 -1 -8
-I -1 -2 -1 -3 -1 -4 -3 -4 -3 -2 -2 -2 -2 2 4 3 3 1 -1 -2 -1 -8
-L -2 -2 -1 -2 -1 -4 -3 -4 -3 -2 -2 -2 -2 3 3 4 2 2 0 -1 -1 -8
-V 0 -1 0 -2 0 -3 -2 -3 -2 -2 -2 -2 -2 2 3 2 3 0 -1 -3 -1 -8
-F -1 -3 -2 -4 -2 -5 -3 -4 -4 -3 0 -3 -3 2 1 2 0 7 5 4 -2 -8
-Y 0 -2 -2 -3 -2 -4 -1 -3 -3 -2 2 -2 -2 0 -1 0 -1 5 8 4 -2 -8
-W -1 -3 -4 -5 -4 -4 -4 -5 -4 -3 -1 -2 -4 -1 -2 -1 -3 4 4 14 -4 -8
-X -3 0 0 -1 0 -1 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 -2 -4 -1 -8
-* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/IDENTITY b/maven-src/target/classes/java/jaligner/matrix/matrices/IDENTITY
deleted file mode 100644
index 63913d5..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/IDENTITY
+++ /dev/null
@@ -1,25 +0,0 @@
- A R N B D C Q Z E G H I L K M F P S T W Y V X *
-A 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-R -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-N -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-B -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-D -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-C -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-Q -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-Z -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-E -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-G -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-H -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-I -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-L -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-K -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-M -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-F -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-P -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-S -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000
-T -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000
-W -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000
-Y -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000
-V -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000
-X -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 0 -10000
-* -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 0
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/MATCH b/maven-src/target/classes/java/jaligner/matrix/matrices/MATCH
deleted file mode 100644
index cda9e49..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/MATCH
+++ /dev/null
@@ -1,25 +0,0 @@
- A R N B D C Q Z E G H I L K M F P S T W Y V X *
-A 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-R -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-N -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-B -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-D -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-C -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-Q -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-Z -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-E -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-G -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-H -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-I -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-L -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-K -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-M -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-F -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1
-P -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1
-S -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1
-T -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1
-W -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1
-Y -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1
-V -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1
-X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 -1
-* -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM10 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM10
deleted file mode 100644
index c164b06..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM10
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 10 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -8.27, Entropy = 3.43 bits
-#
-# Lowest score = -23, Highest score = 13
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 7 -10 -7 -6 -10 -7 -5 -4 -11 -8 -9 -10 -8 -12 -4 -3 -3 -20 -11 -5 -6 -6 -6 -23
-R -10 9 -9 -17 -11 -4 -15 -13 -4 -8 -12 -2 -7 -12 -7 -6 -10 -5 -14 -11 -11 -7 -9 -23
-N -7 -9 9 -1 -17 -7 -5 -6 -2 -8 -10 -4 -15 -12 -9 -2 -5 -11 -7 -12 7 -6 -6 -23
-D -6 -17 -1 8 -21 -6 0 -6 -7 -11 -19 -8 -17 -21 -12 -7 -8 -21 -17 -11 7 -1 -9 -23
-C -10 -11 -17 -21 10 -20 -20 -13 -10 -9 -21 -20 -20 -19 -11 -6 -11 -22 -7 -9 -18 -20 -13 -23
-Q -7 -4 -7 -6 -20 9 -1 -10 -2 -11 -8 -6 -7 -19 -6 -8 -9 -19 -18 -10 -6 7 -8 -23
-E -5 -15 -5 0 -20 -1 8 -7 -9 -8 -13 -7 -10 -20 -9 -7 -9 -23 -11 -10 -1 7 -8 -23
-G -4 -13 -6 -6 -13 -10 -7 7 -13 -17 -14 -10 -12 -12 -10 -4 -10 -21 -20 -9 -6 -8 -8 -23
-H -11 -4 -2 -7 -10 -2 -9 -13 10 -13 -9 -10 -17 -9 -7 -9 -11 -10 -6 -9 -4 -4 -8 -23
-I -8 -8 -8 -11 -9 -11 -8 -17 -13 9 -4 -9 -3 -5 -12 -10 -5 -20 -9 -1 -9 -9 -8 -23
-L -9 -12 -10 -19 -21 -8 -13 -14 -9 -4 7 -11 -2 -5 -10 -12 -10 -9 -10 -5 -12 -10 -9 -23
-K -10 -2 -4 -8 -20 -6 -7 -10 -10 -9 -11 7 -4 -20 -10 -7 -6 -18 -12 -13 -5 -6 -8 -23
-M -8 -7 -15 -17 -20 -7 -10 -12 -17 -3 -2 -4 12 -7 -11 -8 -7 -19 -17 -4 -16 -8 -9 -23
-F -12 -12 -12 -21 -19 -19 -20 -12 -9 -5 -5 -20 -7 9 -13 -9 -12 -7 -1 -12 -14 -20 -12 -23
-P -4 -7 -9 -12 -11 -6 -9 -10 -7 -12 -10 -10 -11 -13 8 -4 -7 -20 -20 -9 -10 -7 -8 -23
-S -3 -6 -2 -7 -6 -8 -7 -4 -9 -10 -12 -7 -8 -9 -4 7 -2 -8 -10 -10 -4 -8 -6 -23
-T -3 -10 -5 -8 -11 -9 -9 -10 -11 -5 -10 -6 -7 -12 -7 -2 8 -19 -9 -6 -6 -9 -7 -23
-W -20 -5 -11 -21 -22 -19 -23 -21 -10 -20 -9 -18 -19 -7 -20 -8 -19 13 -8 -22 -13 -21 -16 -23
-Y -11 -14 -7 -17 -7 -18 -11 -20 -6 -9 -10 -12 -17 -1 -20 -10 -9 -8 10 -10 -9 -13 -11 -23
-V -5 -11 -12 -11 -9 -10 -10 -9 -9 -1 -5 -13 -4 -12 -9 -10 -6 -22 -10 8 -11 -10 -8 -23
-B -6 -11 7 7 -18 -6 -1 -6 -4 -9 -12 -5 -16 -14 -10 -4 -6 -13 -9 -11 7 -3 -8 -23
-Z -6 -7 -6 -1 -20 7 7 -8 -4 -9 -10 -6 -8 -20 -7 -8 -9 -21 -13 -10 -3 7 -8 -23
-X -6 -9 -6 -9 -13 -8 -8 -8 -8 -8 -9 -8 -9 -12 -8 -6 -7 -16 -11 -8 -8 -8 -8 -23
-* -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM100 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM100
deleted file mode 100644
index 2e33dd3..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM100
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 100 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -1.99, Entropy = 1.18 bits
-#
-# Lowest score = -9, Highest score = 12
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 4 -3 -1 -1 -3 -2 0 1 -3 -2 -3 -3 -2 -5 1 1 1 -7 -4 0 -1 -1 -1 -9
-R -3 7 -2 -4 -5 1 -3 -5 1 -3 -5 2 -1 -6 -1 -1 -3 1 -6 -4 -3 -1 -2 -9
-N -1 -2 5 3 -5 -1 1 -1 2 -3 -4 1 -4 -5 -2 1 0 -5 -2 -3 4 0 -1 -9
-D -1 -4 3 5 -7 0 4 -1 -1 -4 -6 -1 -5 -8 -3 -1 -2 -9 -6 -4 4 3 -2 -9
-C -3 -5 -5 -7 9 -8 -8 -5 -4 -3 -8 -8 -7 -7 -4 -1 -4 -9 -1 -3 -6 -8 -5 -9
-Q -2 1 -1 0 -8 6 2 -3 3 -4 -2 0 -2 -7 -1 -2 -2 -7 -6 -3 0 5 -2 -9
-E 0 -3 1 4 -8 2 5 -1 -1 -3 -5 -1 -4 -8 -2 -1 -2 -9 -5 -3 3 4 -2 -9
-G 1 -5 -1 -1 -5 -3 -1 5 -4 -5 -6 -3 -4 -6 -2 0 -2 -9 -7 -3 -1 -2 -2 -9
-H -3 1 2 -1 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -4 -1 -3 1 1 -2 -9
-I -2 -3 -3 -4 -3 -4 -3 -5 -4 6 1 -3 1 0 -4 -3 0 -7 -3 3 -3 -3 -2 -9
-L -3 -5 -4 -6 -8 -2 -5 -6 -3 1 6 -4 3 0 -4 -4 -3 -3 -3 0 -5 -4 -3 -9
-K -3 2 1 -1 -8 0 -1 -3 -2 -3 -4 5 0 -7 -3 -1 -1 -6 -6 -4 0 -1 -2 -9
-M -2 -1 -4 -5 -7 -2 -4 -4 -4 1 3 0 9 -1 -4 -3 -1 -6 -5 1 -4 -2 -2 -9
-F -5 -6 -5 -8 -7 -7 -8 -6 -3 0 0 -7 -1 8 -6 -4 -5 -1 4 -3 -6 -7 -4 -9
-P 1 -1 -2 -3 -4 -1 -2 -2 -1 -4 -4 -3 -4 -6 7 0 -1 -7 -7 -3 -3 -1 -2 -9
-S 1 -1 1 -1 -1 -2 -1 0 -2 -3 -4 -1 -3 -4 0 4 2 -3 -4 -2 0 -2 -1 -9
-T 1 -3 0 -2 -4 -2 -2 -2 -3 0 -3 -1 -1 -5 -1 2 5 -7 -4 0 -1 -2 -1 -9
-W -7 1 -5 -9 -9 -7 -9 -9 -4 -7 -3 -6 -6 -1 -7 -3 -7 12 -2 -9 -6 -8 -6 -9
-Y -4 -6 -2 -6 -1 -6 -5 -7 -1 -3 -3 -6 -5 4 -7 -4 -4 -2 9 -4 -4 -6 -4 -9
-V 0 -4 -3 -4 -3 -3 -3 -3 -3 3 0 -4 1 -3 -3 -2 0 -9 -4 5 -4 -3 -2 -9
-B -1 -3 4 4 -6 0 3 -1 1 -3 -5 0 -4 -6 -3 0 -1 -6 -4 -4 4 2 -2 -9
-Z -1 -1 0 3 -8 5 4 -2 1 -3 -4 -1 -2 -7 -1 -2 -2 -8 -6 -3 2 5 -2 -9
-X -1 -2 -1 -2 -5 -2 -2 -2 -2 -2 -3 -2 -2 -4 -2 -1 -1 -6 -4 -2 -2 -2 -2 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM110 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM110
deleted file mode 100644
index 25b2c01..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM110
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 110 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -1.81, Entropy = 1.07 bits
-#
-# Lowest score = -9, Highest score = 12
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 3 -3 -1 -1 -3 -1 0 1 -3 -1 -3 -3 -2 -4 1 1 1 -7 -4 0 -1 -1 -1 -9
-R -3 7 -1 -4 -4 1 -3 -4 1 -3 -4 2 -1 -5 -1 -1 -2 1 -5 -4 -2 -1 -2 -9
-N -1 -1 4 2 -5 0 1 0 2 -2 -4 1 -3 -4 -2 1 0 -5 -2 -3 3 0 -1 -9
-D -1 -4 2 5 -7 1 4 0 0 -3 -6 -1 -5 -7 -3 -1 -1 -8 -5 -4 4 3 -2 -9
-C -3 -4 -5 -7 9 -7 -7 -5 -4 -3 -8 -7 -7 -6 -4 -1 -3 -9 -1 -3 -6 -7 -4 -9
-Q -1 1 0 1 -7 6 2 -3 3 -3 -2 0 -1 -6 0 -2 -2 -6 -6 -3 0 4 -1 -9
-E 0 -3 1 4 -7 2 5 -1 -1 -3 -5 -1 -3 -7 -2 -1 -2 -9 -5 -3 3 4 -2 -9
-G 1 -4 0 0 -5 -3 -1 5 -4 -4 -6 -3 -4 -5 -2 0 -2 -8 -7 -2 0 -2 -2 -9
-H -3 1 2 0 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -4 -1 -3 1 1 -2 -9
-I -1 -3 -2 -3 -3 -3 -3 -4 -4 6 1 -3 1 0 -4 -3 0 -7 -2 3 -3 -3 -2 -9
-L -3 -4 -4 -6 -8 -2 -5 -6 -3 1 6 -4 3 0 -4 -4 -3 -3 -3 1 -5 -3 -2 -9
-K -3 2 1 -1 -7 0 -1 -3 -2 -3 -4 5 0 -7 -3 -1 -1 -5 -5 -4 0 -1 -2 -9
-M -2 -1 -3 -5 -7 -1 -3 -4 -4 1 3 0 8 -1 -4 -2 -1 -6 -5 1 -4 -2 -2 -9
-F -4 -5 -4 -7 -6 -6 -7 -5 -3 0 0 -7 -1 8 -6 -4 -4 -1 4 -3 -6 -7 -4 -9
-P 1 -1 -2 -3 -4 0 -2 -2 -1 -4 -4 -3 -4 -6 6 0 -1 -7 -7 -2 -2 -1 -2 -9
-S 1 -1 1 -1 -1 -2 -1 0 -2 -3 -4 -1 -2 -4 0 3 2 -3 -3 -2 0 -1 -1 -9
-T 1 -2 0 -1 -3 -2 -2 -2 -3 0 -3 -1 -1 -4 -1 2 5 -6 -3 0 -1 -2 -1 -9
-W -7 1 -5 -8 -9 -6 -9 -8 -4 -7 -3 -5 -6 -1 -7 -3 -6 12 -2 -8 -6 -7 -5 -9
-Y -4 -5 -2 -5 -1 -6 -5 -7 -1 -2 -3 -5 -5 4 -7 -3 -3 -2 8 -4 -3 -5 -3 -9
-V 0 -4 -3 -4 -3 -3 -3 -2 -3 3 1 -4 1 -3 -2 -2 0 -8 -4 5 -3 -3 -2 -9
-B -1 -2 3 4 -6 0 3 0 1 -3 -5 0 -4 -6 -2 0 -1 -6 -3 -3 4 2 -1 -9
-Z -1 -1 0 3 -7 4 4 -2 1 -3 -3 -1 -2 -7 -1 -1 -2 -7 -5 -3 2 4 -2 -9
-X -1 -2 -1 -2 -4 -1 -2 -2 -2 -2 -2 -2 -2 -4 -2 -1 -1 -5 -3 -2 -1 -2 -2 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM120 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM120
deleted file mode 100644
index 3cbb04b..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM120
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 120 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -1.64, Entropy = 0.979 bits
-#
-# Lowest score = -8, Highest score = 12
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 3 -3 -1 0 -3 -1 0 1 -3 -1 -3 -2 -2 -4 1 1 1 -7 -4 0 0 -1 -1 -8
-R -3 6 -1 -3 -4 1 -3 -4 1 -2 -4 2 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -2 -8
-N -1 -1 4 2 -5 0 1 0 2 -2 -4 1 -3 -4 -2 1 0 -4 -2 -3 3 0 -1 -8
-D 0 -3 2 5 -7 1 3 0 0 -3 -5 -1 -4 -7 -3 0 -1 -8 -5 -3 4 3 -2 -8
-C -3 -4 -5 -7 9 -7 -7 -4 -4 -3 -7 -7 -6 -6 -4 0 -3 -8 -1 -3 -6 -7 -4 -8
-Q -1 1 0 1 -7 6 2 -3 3 -3 -2 0 -1 -6 0 -2 -2 -6 -5 -3 0 4 -1 -8
-E 0 -3 1 3 -7 2 5 -1 -1 -3 -4 -1 -3 -7 -2 -1 -2 -8 -5 -3 3 4 -1 -8
-G 1 -4 0 0 -4 -3 -1 5 -4 -4 -5 -3 -4 -5 -2 1 -1 -8 -6 -2 0 -2 -2 -8
-H -3 1 2 0 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -3 -1 -3 1 1 -2 -8
-I -1 -2 -2 -3 -3 -3 -3 -4 -4 6 1 -3 1 0 -3 -2 0 -6 -2 3 -3 -3 -1 -8
-L -3 -4 -4 -5 -7 -2 -4 -5 -3 1 5 -4 3 0 -3 -4 -3 -3 -2 1 -4 -3 -2 -8
-K -2 2 1 -1 -7 0 -1 -3 -2 -3 -4 5 0 -7 -2 -1 -1 -5 -5 -4 0 -1 -2 -8
-M -2 -1 -3 -4 -6 -1 -3 -4 -4 1 3 0 8 -1 -3 -2 -1 -6 -4 1 -4 -2 -2 -8
-F -4 -5 -4 -7 -6 -6 -7 -5 -3 0 0 -7 -1 8 -5 -3 -4 -1 4 -3 -5 -6 -3 -8
-P 1 -1 -2 -3 -4 0 -2 -2 -1 -3 -3 -2 -3 -5 6 1 -1 -7 -6 -2 -2 -1 -2 -8
-S 1 -1 1 0 0 -2 -1 1 -2 -2 -4 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 -1 -8
-T 1 -2 0 -1 -3 -2 -2 -1 -3 0 -3 -1 -1 -4 -1 2 4 -6 -3 0 0 -2 -1 -8
-W -7 1 -4 -8 -8 -6 -8 -8 -3 -6 -3 -5 -6 -1 -7 -2 -6 12 -2 -8 -6 -7 -5 -8
-Y -4 -5 -2 -5 -1 -5 -5 -6 -1 -2 -2 -5 -4 4 -6 -3 -3 -2 8 -3 -3 -5 -3 -8
-V 0 -3 -3 -3 -3 -3 -3 -2 -3 3 1 -4 1 -3 -2 -2 0 -8 -3 5 -3 -3 -1 -8
-B 0 -2 3 4 -6 0 3 0 1 -3 -4 0 -4 -5 -2 0 0 -6 -3 -3 4 2 -1 -8
-Z -1 -1 0 3 -7 4 4 -2 1 -3 -3 -1 -2 -6 -1 -1 -2 -7 -5 -3 2 4 -1 -8
-X -1 -2 -1 -2 -4 -1 -1 -2 -2 -1 -2 -2 -2 -3 -2 -1 -1 -5 -3 -1 -1 -1 -2 -8
-* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM130 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM130
deleted file mode 100644
index 0b47a5d..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM130
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 130 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -1.48, Entropy = 0.895 bits
-#
-# Lowest score = -8, Highest score = 12
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 3 -3 0 0 -3 -1 0 1 -2 -1 -3 -2 -2 -4 1 1 1 -6 -4 0 0 0 -1 -8
-R -3 6 -1 -3 -4 1 -3 -4 1 -2 -4 2 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -2 -8
-N 0 -1 4 2 -4 0 1 0 2 -2 -3 1 -3 -4 -1 1 0 -4 -2 -3 3 0 -1 -8
-D 0 -3 2 5 -6 1 3 0 0 -3 -5 -1 -4 -7 -2 0 -1 -7 -5 -3 4 3 -1 -8
-C -3 -4 -4 -6 9 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -8 -1 -2 -5 -6 -4 -8
-Q -1 1 0 1 -6 5 2 -2 3 -3 -2 0 -1 -6 0 -1 -2 -6 -5 -3 0 4 -1 -8
-E 0 -3 1 3 -6 2 5 -1 0 -2 -4 -1 -3 -6 -2 -1 -1 -8 -5 -3 2 4 -1 -8
-G 1 -4 0 0 -4 -2 -1 5 -3 -4 -5 -3 -4 -5 -2 1 -1 -7 -6 -2 0 -1 -2 -8
-H -2 1 2 0 -4 3 0 -3 7 -3 -3 -1 -3 -2 -1 -2 -2 -3 0 -3 1 1 -1 -8
-I -1 -2 -2 -3 -3 -3 -2 -4 -3 5 1 -2 2 0 -3 -2 0 -6 -2 3 -3 -3 -1 -8
-L -3 -4 -3 -5 -7 -2 -4 -5 -3 1 5 -4 3 1 -3 -4 -2 -2 -2 1 -4 -3 -2 -8
-K -2 2 1 -1 -6 0 -1 -3 -1 -2 -4 5 0 -6 -2 -1 0 -5 -5 -4 0 0 -1 -8
-M -2 -1 -3 -4 -6 -1 -3 -4 -3 2 3 0 8 -1 -3 -2 -1 -5 -4 1 -3 -2 -1 -8
-F -4 -5 -4 -7 -5 -6 -6 -5 -2 0 1 -6 -1 7 -5 -3 -4 -1 4 -2 -5 -6 -3 -8
-P 1 -1 -1 -2 -3 0 -2 -2 -1 -3 -3 -2 -3 -5 6 1 -1 -6 -6 -2 -2 -1 -1 -8
-S 1 -1 1 0 0 -1 -1 1 -2 -2 -4 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 -1 -8
-T 1 -2 0 -1 -3 -2 -1 -1 -2 0 -2 0 -1 -4 -1 2 4 -6 -3 0 0 -2 -1 -8
-W -6 1 -4 -7 -8 -6 -8 -7 -3 -6 -2 -5 -5 -1 -6 -2 -6 12 -1 -7 -5 -7 -5 -8
-Y -4 -5 -2 -5 -1 -5 -5 -6 0 -2 -2 -5 -4 4 -6 -3 -3 -1 8 -3 -3 -5 -3 -8
-V 0 -3 -3 -3 -2 -3 -3 -2 -3 3 1 -4 1 -2 -2 -2 0 -7 -3 5 -3 -3 -1 -8
-B 0 -2 3 4 -5 0 2 0 1 -3 -4 0 -3 -5 -2 0 0 -5 -3 -3 3 2 -1 -8
-Z 0 -1 0 3 -6 4 4 -1 1 -3 -3 0 -2 -6 -1 -1 -2 -7 -5 -3 2 4 -1 -8
-X -1 -2 -1 -1 -4 -1 -1 -2 -1 -1 -2 -1 -1 -3 -1 -1 -1 -5 -3 -1 -1 -1 -1 -8
-* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM140 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM140
deleted file mode 100644
index 022c61b..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM140
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 140 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -1.35, Entropy = 0.820 bits
-#
-# Lowest score = -8, Highest score = 12
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 3 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -2 -4 1 1 1 -6 -4 0 0 0 -1 -8
-R -2 6 -1 -3 -4 1 -2 -4 1 -2 -4 3 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -1 -8
-N 0 -1 3 2 -4 0 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 3 1 -1 -8
-D 0 -3 2 4 -6 1 3 0 0 -3 -5 -1 -4 -6 -2 0 -1 -7 -5 -3 4 3 -1 -8
-C -2 -4 -4 -6 9 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -8 -1 -2 -5 -6 -4 -8
-Q -1 1 0 1 -6 5 2 -2 3 -3 -2 0 -1 -5 0 -1 -2 -5 -5 -2 1 4 -1 -8
-E 0 -2 1 3 -6 2 4 -1 0 -2 -4 -1 -3 -6 -1 -1 -1 -8 -4 -2 2 4 -1 -8
-G 1 -4 0 0 -4 -2 -1 5 -3 -4 -5 -3 -3 -5 -1 1 -1 -7 -6 -2 0 -1 -1 -8
-H -2 1 2 0 -4 3 0 -3 6 -3 -2 -1 -3 -2 -1 -1 -2 -3 0 -3 1 1 -1 -8
-I -1 -2 -2 -3 -3 -3 -2 -4 -3 5 1 -2 2 0 -3 -2 0 -6 -2 3 -2 -2 -1 -8
-L -2 -4 -3 -5 -7 -2 -4 -5 -2 1 5 -3 3 1 -3 -3 -2 -2 -2 1 -4 -3 -2 -8
-K -2 3 1 -1 -6 0 -1 -3 -1 -2 -3 5 0 -6 -2 -1 0 -4 -5 -3 0 0 -1 -8
-M -2 -1 -2 -4 -6 -1 -3 -3 -3 2 3 0 7 -1 -3 -2 -1 -5 -4 1 -3 -2 -1 -8
-F -4 -5 -4 -6 -5 -5 -6 -5 -2 0 1 -6 -1 7 -5 -3 -4 -1 4 -2 -5 -6 -3 -8
-P 1 -1 -1 -2 -3 0 -1 -1 -1 -3 -3 -2 -3 -5 6 1 0 -6 -6 -2 -2 -1 -1 -8
-S 1 -1 1 0 0 -1 -1 1 -1 -2 -3 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 0 -8
-T 1 -2 0 -1 -3 -2 -1 -1 -2 0 -2 0 -1 -4 0 2 4 -5 -3 0 0 -1 -1 -8
-W -6 1 -4 -7 -8 -5 -8 -7 -3 -6 -2 -4 -5 -1 -6 -2 -5 12 -1 -7 -5 -6 -5 -8
-Y -4 -5 -2 -5 -1 -5 -4 -6 0 -2 -2 -5 -4 4 -6 -3 -3 -1 8 -3 -3 -4 -3 -8
-V 0 -3 -2 -3 -2 -2 -2 -2 -3 3 1 -3 1 -2 -2 -2 0 -7 -3 5 -3 -2 -1 -8
-B 0 -2 3 4 -5 1 2 0 1 -2 -4 0 -3 -5 -2 0 0 -5 -3 -3 3 2 -1 -8
-Z 0 -1 1 3 -6 4 4 -1 1 -2 -3 0 -2 -6 -1 -1 -1 -6 -4 -2 2 4 -1 -8
-X -1 -1 -1 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 -1 -5 -3 -1 -1 -1 -1 -8
-* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM150 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM150
deleted file mode 100644
index c010eef..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM150
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 150 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -1.25, Entropy = 0.754 bits
-#
-# Lowest score = -7, Highest score = 12
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 3 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -1 -4 1 1 1 -6 -3 0 0 0 -1 -7
-R -2 6 -1 -2 -4 1 -2 -3 1 -2 -3 3 -1 -4 -1 -1 -2 1 -4 -3 -2 0 -1 -7
-N 0 -1 3 2 -4 0 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 3 1 -1 -7
-D 0 -2 2 4 -6 1 3 0 0 -3 -5 -1 -3 -6 -2 0 -1 -7 -4 -3 3 2 -1 -7
-C -2 -4 -4 -6 9 -6 -6 -4 -3 -2 -6 -6 -5 -5 -3 0 -3 -7 0 -2 -5 -6 -3 -7
-Q -1 1 0 1 -6 5 2 -2 3 -3 -2 0 -1 -5 0 -1 -1 -5 -4 -2 1 4 -1 -7
-E 0 -2 1 3 -6 2 4 -1 0 -2 -4 -1 -2 -6 -1 -1 -1 -7 -4 -2 2 4 -1 -7
-G 1 -3 0 0 -4 -2 -1 4 -3 -3 -4 -2 -3 -5 -1 1 -1 -7 -5 -2 0 -1 -1 -7
-H -2 1 2 0 -3 3 0 -3 6 -3 -2 -1 -3 -2 -1 -1 -2 -3 0 -3 1 1 -1 -7
-I -1 -2 -2 -3 -2 -3 -2 -3 -3 5 1 -2 2 0 -3 -2 0 -5 -2 3 -2 -2 -1 -7
-L -2 -3 -3 -5 -6 -2 -4 -4 -2 1 5 -3 3 1 -3 -3 -2 -2 -2 1 -4 -3 -2 -7
-K -2 3 1 -1 -6 0 -1 -2 -1 -2 -3 4 0 -6 -2 -1 0 -4 -4 -3 0 0 -1 -7
-M -1 -1 -2 -3 -5 -1 -2 -3 -3 2 3 0 7 -1 -3 -2 -1 -5 -3 1 -3 -2 -1 -7
-F -4 -4 -4 -6 -5 -5 -6 -5 -2 0 1 -6 -1 7 -5 -3 -3 -1 5 -2 -5 -5 -3 -7
-P 1 -1 -1 -2 -3 0 -1 -1 -1 -3 -3 -2 -3 -5 6 1 0 -6 -5 -2 -2 -1 -1 -7
-S 1 -1 1 0 0 -1 -1 1 -1 -2 -3 -1 -2 -3 1 2 1 -2 -3 -1 0 -1 0 -7
-T 1 -2 0 -1 -3 -1 -1 -1 -2 0 -2 0 -1 -3 0 1 4 -5 -3 0 0 -1 -1 -7
-W -6 1 -4 -7 -7 -5 -7 -7 -3 -5 -2 -4 -5 -1 -6 -2 -5 12 -1 -6 -5 -6 -4 -7
-Y -3 -4 -2 -4 0 -4 -4 -5 0 -2 -2 -4 -3 5 -5 -3 -3 -1 8 -3 -3 -4 -3 -7
-V 0 -3 -2 -3 -2 -2 -2 -2 -3 3 1 -3 1 -2 -2 -1 0 -6 -3 4 -2 -2 -1 -7
-B 0 -2 3 3 -5 1 2 0 1 -2 -4 0 -3 -5 -2 0 0 -5 -3 -2 3 2 -1 -7
-Z 0 0 1 2 -6 4 4 -1 1 -2 -3 0 -2 -5 -1 -1 -1 -6 -4 -2 2 4 -1 -7
-X -1 -1 -1 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 -1 -4 -3 -1 -1 -1 -1 -7
-* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM160 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM160
deleted file mode 100644
index f30d717..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM160
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 160 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -1.14, Entropy = 0.694 bits
-#
-# Lowest score = -7, Highest score = 12
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -1 -3 1 1 1 -5 -3 0 0 0 0 -7
-R -2 6 -1 -2 -3 1 -2 -3 1 -2 -3 3 -1 -4 -1 -1 -1 1 -4 -3 -1 0 -1 -7
-N 0 -1 3 2 -4 0 1 0 2 -2 -3 1 -2 -3 -1 1 0 -4 -2 -2 2 1 0 -7
-D 0 -2 2 4 -5 1 3 0 0 -3 -4 0 -3 -6 -2 0 -1 -6 -4 -3 3 2 -1 -7
-C -2 -3 -4 -5 9 -5 -5 -3 -3 -2 -6 -5 -5 -5 -3 0 -2 -7 0 -2 -4 -5 -3 -7
-Q -1 1 0 1 -5 5 2 -2 2 -2 -2 0 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -7
-E 0 -2 1 3 -5 2 4 0 0 -2 -3 -1 -2 -5 -1 0 -1 -7 -4 -2 2 3 -1 -7
-G 1 -3 0 0 -3 -2 0 4 -3 -3 -4 -2 -3 -4 -1 1 -1 -7 -5 -2 0 -1 -1 -7
-H -2 1 2 0 -3 2 0 -3 6 -3 -2 -1 -3 -2 -1 -1 -2 -3 0 -2 1 1 -1 -7
-I -1 -2 -2 -3 -2 -2 -2 -3 -3 5 2 -2 2 0 -2 -2 0 -5 -2 3 -2 -2 -1 -7
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 5 -3 3 1 -3 -3 -2 -2 -2 1 -4 -3 -2 -7
-K -2 3 1 0 -5 0 -1 -2 -1 -2 -3 4 0 -5 -2 -1 0 -4 -4 -3 0 0 -1 -7
-M -1 -1 -2 -3 -5 -1 -2 -3 -3 2 3 0 7 0 -2 -2 -1 -4 -3 1 -3 -2 -1 -7
-F -3 -4 -3 -6 -5 -5 -5 -4 -2 0 1 -5 0 7 -4 -3 -3 -1 5 -2 -4 -5 -3 -7
-P 1 -1 -1 -2 -3 0 -1 -1 -1 -2 -3 -2 -2 -4 5 1 0 -5 -5 -2 -1 -1 -1 -7
-S 1 -1 1 0 0 -1 0 1 -1 -2 -3 -1 -2 -3 1 2 1 -2 -3 -1 0 -1 0 -7
-T 1 -1 0 -1 -2 -1 -1 -1 -2 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -7
-W -5 1 -4 -6 -7 -5 -7 -7 -3 -5 -2 -4 -4 -1 -5 -2 -5 12 -1 -6 -5 -6 -4 -7
-Y -3 -4 -2 -4 0 -4 -4 -5 0 -2 -2 -4 -3 5 -5 -3 -3 -1 8 -3 -3 -4 -3 -7
-V 0 -3 -2 -3 -2 -2 -2 -2 -2 3 1 -3 1 -2 -2 -1 0 -6 -3 4 -2 -2 -1 -7
-B 0 -1 2 3 -4 1 2 0 1 -2 -4 0 -3 -4 -1 0 0 -5 -3 -2 3 2 -1 -7
-Z 0 0 1 2 -5 3 3 -1 1 -2 -3 0 -2 -5 -1 -1 -1 -6 -4 -2 2 3 -1 -7
-X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -4 -3 -1 -1 -1 -1 -7
-* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM170 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM170
deleted file mode 100644
index ca090d6..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM170
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 170 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -1.57, Entropy = 0.640 bits
-#
-# Lowest score = -10, Highest score = 18
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 3 -3 0 0 -3 -1 0 1 -3 -1 -3 -2 -2 -5 1 2 2 -8 -5 0 0 0 -1 -10
-R -3 8 -1 -3 -5 1 -2 -4 2 -3 -4 4 -1 -6 -1 -1 -2 2 -6 -4 -2 0 -2 -10
-N 0 -1 4 3 -5 0 2 0 2 -3 -4 1 -3 -5 -1 1 0 -5 -3 -3 3 1 -1 -10
-D 0 -3 3 6 -7 2 5 0 0 -4 -6 -1 -4 -8 -2 0 -1 -9 -6 -4 5 4 -1 -10
-C -3 -5 -5 -7 13 -8 -8 -5 -5 -3 -9 -8 -7 -6 -4 0 -3 -10 0 -3 -6 -8 -4 -10
-Q -1 1 0 2 -8 6 3 -2 4 -3 -2 0 -1 -7 0 -1 -2 -7 -6 -3 1 5 -1 -10
-E 0 -2 2 5 -8 3 6 0 0 -3 -5 -1 -3 -8 -1 -1 -1 -10 -6 -3 3 5 -1 -10
-G 1 -4 0 0 -5 -2 0 6 -4 -4 -6 -3 -4 -6 -2 1 -1 -9 -7 -2 0 -1 -2 -10
-H -3 2 2 0 -5 4 0 -4 9 -4 -3 -1 -4 -3 -1 -2 -2 -4 0 -3 1 2 -1 -10
-I -1 -3 -3 -4 -3 -3 -3 -4 -4 7 2 -3 2 1 -3 -2 0 -7 -2 5 -3 -3 -1 -10
-L -3 -4 -4 -6 -9 -2 -5 -6 -3 2 7 -4 4 1 -4 -4 -3 -3 -2 2 -5 -4 -2 -10
-K -2 4 1 -1 -8 0 -1 -3 -1 -3 -4 6 1 -8 -2 -1 0 -5 -6 -4 0 0 -2 -10
-M -2 -1 -3 -4 -7 -1 -3 -4 -4 2 4 1 10 0 -3 -2 -1 -6 -4 2 -4 -2 -1 -10
-F -5 -6 -5 -8 -6 -7 -8 -6 -3 1 1 -8 0 10 -6 -4 -5 -1 7 -2 -6 -7 -4 -10
-P 1 -1 -1 -2 -4 0 -1 -2 -1 -3 -4 -2 -3 -6 8 1 0 -8 -7 -2 -2 -1 -1 -10
-S 2 -1 1 0 0 -1 -1 1 -2 -2 -4 -1 -2 -4 1 3 2 -3 -4 -2 1 -1 0 -10
-T 2 -2 0 -1 -3 -2 -1 -1 -2 0 -3 0 -1 -5 0 2 5 -7 -4 0 0 -1 -1 -10
-W -8 2 -5 -9 -10 -7 -10 -9 -4 -7 -3 -5 -6 -1 -8 -3 -7 18 -1 -9 -7 -8 -6 -10
-Y -5 -6 -3 -6 0 -6 -6 -7 0 -2 -2 -6 -4 7 -7 -4 -4 -1 12 -4 -4 -6 -4 -10
-V 0 -4 -3 -4 -3 -3 -3 -2 -3 5 2 -4 2 -2 -2 -2 0 -9 -4 6 -3 -3 -1 -10
-B 0 -2 3 5 -6 1 3 0 1 -3 -5 0 -4 -6 -2 1 0 -7 -4 -3 4 3 -1 -10
-Z 0 0 1 4 -8 5 5 -1 2 -3 -4 0 -2 -7 -1 -1 -1 -8 -6 -3 3 5 -1 -10
-X -1 -2 -1 -1 -4 -1 -1 -2 -1 -1 -2 -2 -1 -4 -1 0 -1 -6 -4 -1 -1 -1 -2 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM180 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM180
deleted file mode 100644
index 84addeb..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM180
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 180 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -1.51, Entropy = 0.591 bits
-#
-# Lowest score = -10, Highest score = 18
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 3 -3 0 0 -3 -1 0 1 -2 -1 -3 -2 -2 -5 1 1 2 -8 -5 0 0 0 -1 -10
-R -3 8 -1 -3 -5 1 -2 -4 2 -3 -4 4 -1 -6 -1 -1 -2 2 -6 -4 -2 0 -2 -10
-N 0 -1 4 3 -5 0 2 0 2 -3 -4 1 -3 -5 -1 1 0 -5 -2 -3 3 1 -1 -10
-D 0 -3 3 5 -7 2 4 0 0 -3 -6 0 -4 -8 -2 0 -1 -9 -6 -3 4 3 -1 -10
-C -3 -5 -5 -7 13 -7 -7 -5 -4 -3 -8 -7 -7 -6 -4 0 -3 -10 0 -3 -6 -7 -4 -10
-Q -1 1 0 2 -7 6 3 -2 4 -3 -2 0 -1 -6 0 -1 -2 -6 -6 -3 1 5 -1 -10
-E 0 -2 2 4 -7 3 5 0 0 -3 -5 -1 -3 -7 -1 -1 -1 -9 -6 -3 3 5 -1 -10
-G 1 -4 0 0 -5 -2 0 6 -3 -4 -6 -3 -4 -6 -1 1 -1 -9 -7 -2 0 -1 -2 -10
-H -2 2 2 0 -4 4 0 -3 8 -4 -3 -1 -3 -3 -1 -2 -2 -4 0 -3 1 2 -1 -10
-I -1 -3 -3 -3 -3 -3 -3 -4 -4 6 2 -3 2 1 -3 -2 0 -7 -2 5 -3 -3 -1 -10
-L -3 -4 -4 -6 -8 -2 -5 -6 -3 2 7 -4 4 1 -4 -4 -3 -3 -2 2 -5 -3 -2 -10
-K -2 4 1 0 -7 0 -1 -3 -1 -3 -4 6 1 -7 -2 -1 0 -5 -6 -4 0 0 -1 -10
-M -2 -1 -3 -4 -7 -1 -3 -4 -3 2 4 1 9 0 -3 -2 -1 -6 -4 2 -3 -2 -1 -10
-F -5 -6 -5 -8 -6 -6 -7 -6 -3 1 1 -7 0 10 -6 -4 -4 0 7 -2 -6 -7 -3 -10
-P 1 -1 -1 -2 -4 0 -1 -1 -1 -3 -4 -2 -3 -6 8 1 0 -7 -7 -2 -2 -1 -1 -10
-S 1 -1 1 0 0 -1 -1 1 -2 -2 -4 -1 -2 -4 1 3 2 -3 -4 -2 1 -1 0 -10
-T 2 -2 0 -1 -3 -2 -1 -1 -2 0 -3 0 -1 -4 0 2 4 -7 -4 0 0 -1 -1 -10
-W -8 2 -5 -9 -10 -6 -9 -9 -4 -7 -3 -5 -6 0 -7 -3 -7 18 -1 -8 -7 -8 -6 -10
-Y -5 -6 -2 -6 0 -6 -6 -7 0 -2 -2 -6 -4 7 -7 -4 -4 -1 11 -4 -4 -6 -3 -10
-V 0 -4 -3 -3 -3 -3 -3 -2 -3 5 2 -4 2 -2 -2 -2 0 -8 -4 6 -3 -3 -1 -10
-B 0 -2 3 4 -6 1 3 0 1 -3 -5 0 -3 -6 -2 1 0 -7 -4 -3 4 3 -1 -10
-Z 0 0 1 3 -7 5 5 -1 2 -3 -3 0 -2 -7 -1 -1 -1 -8 -6 -3 3 5 -1 -10
-X -1 -2 -1 -1 -4 -1 -1 -2 -1 -1 -2 -1 -1 -3 -1 0 -1 -6 -3 -1 -1 -1 -1 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM190 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM190
deleted file mode 100644
index 6840cc4..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM190
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 190 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -1.35, Entropy = 0.547 bits
-#
-# Lowest score = -9, Highest score = 18
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 3 -2 0 0 -3 -1 0 1 -2 -1 -3 -2 -2 -5 1 1 2 -7 -4 0 0 0 0 -9
-R -2 8 -1 -2 -5 1 -2 -4 2 -3 -4 4 -1 -6 0 -1 -2 2 -5 -3 -1 0 -1 -9
-N 0 -1 3 3 -5 1 2 0 2 -2 -4 1 -3 -4 -1 1 0 -5 -2 -3 3 1 -1 -9
-D 0 -2 3 5 -7 2 4 0 0 -3 -5 0 -4 -7 -2 0 -1 -8 -5 -3 4 3 -1 -9
-C -3 -5 -5 -7 13 -7 -7 -4 -4 -3 -8 -7 -7 -6 -4 0 -3 -9 0 -3 -6 -7 -4 -9
-Q -1 1 1 2 -7 6 3 -2 3 -3 -2 1 -1 -6 0 -1 -1 -6 -5 -3 1 4 -1 -9
-E 0 -2 2 4 -7 3 5 0 0 -3 -4 -1 -3 -7 -1 0 -1 -9 -5 -3 3 4 -1 -9
-G 1 -4 0 0 -4 -2 0 6 -3 -4 -5 -3 -4 -6 -1 1 -1 -9 -7 -2 0 -1 -1 -9
-H -2 2 2 0 -4 3 0 -3 8 -3 -3 -1 -3 -2 -1 -1 -2 -3 0 -3 1 2 -1 -9
-I -1 -3 -2 -3 -3 -3 -3 -4 -3 6 2 -3 2 1 -3 -2 0 -7 -2 4 -3 -3 -1 -9
-L -3 -4 -4 -5 -8 -2 -4 -5 -3 2 7 -4 4 2 -3 -4 -2 -3 -2 2 -5 -3 -2 -9
-K -2 4 1 0 -7 1 -1 -3 -1 -3 -4 6 1 -7 -2 0 0 -5 -6 -3 0 0 -1 -9
-M -2 -1 -3 -4 -7 -1 -3 -4 -3 2 4 1 9 0 -3 -2 -1 -6 -4 2 -3 -2 -1 -9
-F -5 -6 -4 -7 -6 -6 -7 -6 -2 1 2 -7 0 10 -6 -4 -4 0 7 -2 -6 -7 -3 -9
-P 1 0 -1 -2 -4 0 -1 -1 -1 -3 -3 -2 -3 -6 7 1 0 -7 -6 -2 -1 -1 -1 -9
-S 1 -1 1 0 0 -1 0 1 -1 -2 -4 0 -2 -4 1 3 2 -3 -4 -2 1 -1 0 -9
-T 2 -2 0 -1 -3 -1 -1 -1 -2 0 -2 0 -1 -4 0 2 4 -6 -3 0 0 -1 0 -9
-W -7 2 -5 -8 -9 -6 -9 -9 -3 -7 -3 -5 -6 0 -7 -3 -6 18 -1 -8 -6 -7 -5 -9
-Y -4 -5 -2 -5 0 -5 -5 -7 0 -2 -2 -6 -4 7 -6 -4 -3 -1 11 -3 -4 -5 -3 -9
-V 0 -3 -3 -3 -3 -3 -3 -2 -3 4 2 -3 2 -2 -2 -2 0 -8 -3 6 -3 -3 -1 -9
-B 0 -1 3 4 -6 1 3 0 1 -3 -5 0 -3 -6 -1 1 0 -6 -4 -3 4 2 -1 -9
-Z 0 0 1 3 -7 4 4 -1 2 -3 -3 0 -2 -7 -1 -1 -1 -7 -5 -3 2 4 -1 -9
-X 0 -1 -1 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM20 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM20
deleted file mode 100644
index 58cc98c..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM20
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 20 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -6.18, Entropy = 2.95 bits
-#
-# Lowest score = -19, Highest score = 13
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 6 -8 -5 -4 -8 -5 -3 -3 -8 -6 -7 -8 -6 -9 -2 -1 -1 -16 -9 -3 -5 -4 -4 -19
-R -8 9 -7 -12 -9 -2 -11 -11 -3 -6 -10 -1 -5 -10 -5 -4 -8 -3 -11 -9 -9 -5 -7 -19
-N -5 -7 8 1 -13 -5 -3 -4 -1 -6 -8 -2 -11 -10 -7 -1 -3 -9 -5 -9 6 -4 -4 -19
-D -4 -12 1 8 -16 -4 2 -4 -5 -9 -15 -6 -13 -17 -9 -5 -6 -17 -13 -9 6 0 -7 -19
-C -8 -9 -13 -16 10 -16 -16 -11 -8 -7 -17 -16 -16 -15 -9 -4 -9 -18 -5 -7 -14 -16 -11 -19
-Q -5 -2 -5 -4 -16 9 0 -8 0 -9 -6 -4 -5 -15 -4 -6 -7 -15 -14 -8 -4 7 -6 -19
-E -3 -11 -3 2 -16 0 8 -5 -6 -6 -10 -5 -8 -16 -7 -5 -7 -19 -9 -8 0 6 -6 -19
-G -3 -11 -4 -4 -11 -8 -5 7 -10 -13 -12 -8 -10 -10 -7 -3 -7 -17 -16 -7 -4 -6 -6 -19
-H -8 -3 -1 -5 -8 0 -6 -10 9 -11 -7 -8 -13 -7 -5 -7 -8 -8 -4 -7 -2 -2 -6 -19
-I -6 -6 -6 -9 -7 -9 -6 -13 -11 9 -2 -7 -2 -3 -10 -8 -3 -16 -7 1 -7 -7 -6 -19
-L -7 -10 -8 -15 -17 -6 -10 -12 -7 -2 7 -9 0 -4 -8 -9 -8 -7 -8 -3 -10 -8 -7 -19
-K -8 -1 -2 -6 -16 -4 -5 -8 -8 -7 -9 7 -3 -16 -8 -5 -4 -14 -10 -10 -3 -5 -6 -19
-M -6 -5 -11 -13 -16 -5 -8 -10 -13 -2 0 -3 11 -5 -9 -6 -5 -15 -13 -2 -12 -6 -6 -19
-F -9 -10 -10 -17 -15 -15 -16 -10 -7 -3 -4 -16 -5 9 -11 -7 -10 -6 1 -9 -12 -16 -9 -19
-P -2 -5 -7 -9 -9 -4 -7 -7 -5 -10 -8 -8 -9 -11 8 -3 -5 -16 -16 -7 -8 -5 -6 -19
-S -1 -4 -1 -5 -4 -6 -5 -3 -7 -8 -9 -5 -6 -7 -3 7 0 -6 -8 -8 -2 -6 -4 -19
-T -1 -8 -3 -6 -9 -7 -7 -7 -8 -3 -8 -4 -5 -10 -5 0 7 -15 -7 -4 -4 -7 -5 -19
-W -16 -3 -9 -17 -18 -15 -19 -17 -8 -16 -7 -14 -15 -6 -16 -6 -15 13 -6 -18 -11 -17 -13 -19
-Y -9 -11 -5 -13 -5 -14 -9 -16 -4 -7 -8 -10 -13 1 -16 -8 -7 -6 10 -8 -7 -11 -9 -19
-V -3 -9 -9 -9 -7 -8 -8 -7 -7 1 -3 -10 -2 -9 -7 -8 -4 -18 -8 7 -9 -8 -6 -19
-B -5 -9 6 6 -14 -4 0 -4 -2 -7 -10 -3 -12 -12 -8 -2 -4 -11 -7 -9 6 -1 -6 -19
-Z -4 -5 -4 0 -16 7 6 -6 -2 -7 -8 -5 -6 -16 -5 -6 -7 -17 -11 -8 -1 6 -6 -19
-X -4 -7 -4 -7 -11 -6 -6 -6 -6 -6 -7 -6 -6 -9 -6 -4 -5 -13 -9 -6 -6 -6 -6 -19
-* -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM200 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM200
deleted file mode 100644
index d4edff2..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM200
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 200 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -1.23, Entropy = 0.507 bits
-#
-# Lowest score = -9, Highest score = 18
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 3 -2 0 0 -3 -1 0 1 -2 -1 -2 -2 -2 -4 1 1 1 -7 -4 0 0 0 0 -9
-R -2 7 0 -2 -4 1 -2 -4 2 -2 -4 4 -1 -5 0 -1 -1 2 -5 -3 -1 0 -1 -9
-N 0 0 3 3 -5 1 2 0 2 -2 -4 1 -2 -4 -1 1 0 -5 -2 -2 3 1 0 -9
-D 0 -2 3 5 -6 2 4 0 0 -3 -5 0 -4 -7 -2 0 0 -8 -5 -3 4 3 -1 -9
-C -3 -4 -5 -6 12 -7 -7 -4 -4 -3 -7 -7 -6 -6 -4 0 -3 -9 0 -2 -5 -7 -4 -9
-Q -1 1 1 2 -7 5 3 -2 3 -3 -2 1 -1 -6 0 -1 -1 -6 -5 -3 1 4 -1 -9
-E 0 -2 2 4 -7 3 5 0 0 -3 -4 0 -3 -7 -1 0 -1 -9 -5 -2 3 4 -1 -9
-G 1 -4 0 0 -4 -2 0 6 -3 -3 -5 -2 -4 -6 -1 1 0 -8 -6 -2 0 -1 -1 -9
-H -2 2 2 0 -4 3 0 -3 8 -3 -3 -1 -3 -2 -1 -1 -2 -3 0 -3 1 2 -1 -9
-I -1 -2 -2 -3 -3 -3 -3 -3 -3 6 2 -2 2 1 -3 -2 0 -6 -2 4 -3 -3 -1 -9
-L -2 -4 -4 -5 -7 -2 -4 -5 -3 2 7 -4 4 2 -3 -4 -2 -2 -2 2 -4 -3 -2 -9
-K -2 4 1 0 -7 1 0 -2 -1 -2 -4 6 1 -7 -2 0 0 -4 -5 -3 0 0 -1 -9
-M -2 -1 -2 -4 -6 -1 -3 -4 -3 2 4 1 8 0 -3 -2 -1 -5 -3 2 -3 -2 -1 -9
-F -4 -5 -4 -7 -6 -6 -7 -6 -2 1 2 -7 0 10 -6 -4 -4 0 7 -2 -6 -6 -3 -9
-P 1 0 -1 -2 -4 0 -1 -1 -1 -3 -3 -2 -3 -6 7 1 0 -7 -6 -2 -1 -1 -1 -9
-S 1 -1 1 0 0 -1 0 1 -1 -2 -4 0 -2 -4 1 2 2 -3 -3 -1 1 -1 0 -9
-T 1 -1 0 0 -3 -1 -1 0 -2 0 -2 0 -1 -4 0 2 4 -6 -3 0 0 -1 0 -9
-W -7 2 -5 -8 -9 -6 -9 -8 -3 -6 -2 -4 -5 0 -7 -3 -6 18 -1 -8 -6 -7 -5 -9
-Y -4 -5 -2 -5 0 -5 -5 -6 0 -2 -2 -5 -3 7 -6 -3 -3 -1 11 -3 -4 -5 -3 -9
-V 0 -3 -2 -3 -2 -3 -2 -2 -3 4 2 -3 2 -2 -2 -1 0 -8 -3 5 -3 -2 -1 -9
-B 0 -1 3 4 -5 1 3 0 1 -3 -4 0 -3 -6 -1 1 0 -6 -4 -3 3 2 -1 -9
-Z 0 0 1 3 -7 4 4 -1 2 -3 -3 0 -2 -6 -1 -1 -1 -7 -5 -2 2 4 -1 -9
-X 0 -1 0 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM210 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM210
deleted file mode 100644
index 0b49af5..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM210
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 210 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -1.12, Entropy = 0.470 bits
-#
-# Lowest score = -9, Highest score = 18
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -1 -4 1 1 1 -7 -4 0 0 0 0 -9
-R -2 7 0 -2 -4 1 -2 -3 2 -2 -4 4 -1 -5 0 0 -1 2 -5 -3 -1 0 -1 -9
-N 0 0 3 2 -4 1 2 0 2 -2 -3 1 -2 -4 -1 1 0 -5 -2 -2 3 1 0 -9
-D 0 -2 2 5 -6 2 4 0 1 -3 -5 0 -3 -7 -1 0 0 -8 -5 -3 4 3 -1 -9
-C -2 -4 -4 -6 12 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -9 0 -2 -5 -6 -4 -9
-Q -1 1 1 2 -6 5 3 -2 3 -3 -2 1 -1 -6 0 -1 -1 -6 -5 -2 1 4 -1 -9
-E 0 -2 2 4 -6 3 5 0 0 -2 -4 0 -3 -6 -1 0 -1 -8 -5 -2 3 4 -1 -9
-G 1 -3 0 0 -4 -2 0 5 -3 -3 -5 -2 -3 -5 -1 1 0 -8 -6 -2 0 -1 -1 -9
-H -2 2 2 1 -4 3 0 -3 8 -3 -2 0 -3 -2 0 -1 -2 -3 0 -3 1 2 -1 -9
-I -1 -2 -2 -3 -3 -3 -2 -3 -3 5 2 -2 2 1 -3 -2 0 -6 -1 4 -3 -3 -1 -9
-L -2 -4 -3 -5 -7 -2 -4 -5 -2 2 7 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -9
-K -2 4 1 0 -6 1 0 -2 0 -2 -3 5 1 -6 -2 0 0 -4 -5 -3 0 0 -1 -9
-M -1 -1 -2 -3 -6 -1 -3 -3 -3 2 4 1 8 0 -3 -2 -1 -5 -3 2 -3 -2 -1 -9
-F -4 -5 -4 -7 -5 -6 -6 -5 -2 1 2 -6 0 10 -5 -4 -4 0 7 -2 -5 -6 -3 -9
-P 1 0 -1 -1 -3 0 -1 -1 0 -3 -3 -2 -3 -5 7 1 0 -7 -6 -2 -1 0 -1 -9
-S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -4 1 2 2 -3 -3 -1 1 0 0 -9
-T 1 -1 0 0 -3 -1 -1 0 -2 0 -2 0 -1 -4 0 2 3 -6 -3 0 0 -1 0 -9
-W -7 2 -5 -8 -9 -6 -8 -8 -3 -6 -2 -4 -5 0 -7 -3 -6 18 -1 -7 -6 -7 -5 -9
-Y -4 -5 -2 -5 0 -5 -5 -6 0 -1 -1 -5 -3 7 -6 -3 -3 -1 11 -3 -4 -5 -3 -9
-V 0 -3 -2 -3 -2 -2 -2 -2 -3 4 2 -3 2 -2 -2 -1 0 -7 -3 5 -2 -2 -1 -9
-B 0 -1 3 4 -5 1 3 0 1 -3 -4 0 -3 -5 -1 1 0 -6 -4 -2 3 2 -1 -9
-Z 0 0 1 3 -6 4 4 -1 2 -3 -3 0 -2 -6 0 0 -1 -7 -5 -2 2 4 -1 -9
-X 0 -1 0 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM220 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM220
deleted file mode 100644
index 0834a92..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM220
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 220 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -1.06, Entropy = 0.437 bits
-#
-# Lowest score = -8, Highest score = 17
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
-R -2 7 0 -2 -4 1 -1 -3 2 -2 -3 4 -1 -5 0 0 -1 2 -5 -3 -1 0 -1 -8
-N 0 0 3 2 -4 1 2 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
-D 0 -2 2 4 -6 2 4 0 1 -3 -5 0 -3 -6 -1 0 0 -8 -5 -3 4 3 -1 -8
-C -2 -4 -4 -6 12 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -8 0 -2 -5 -6 -3 -8
-Q -1 1 1 2 -6 5 3 -2 3 -2 -2 1 -1 -5 0 -1 -1 -5 -5 -2 1 4 -1 -8
-E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 -1 0 -1 -8 -5 -2 3 4 -1 -8
-G 1 -3 0 0 -4 -2 0 5 -3 -3 -5 -2 -3 -5 -1 1 0 -8 -6 -2 0 -1 -1 -8
-H -2 2 2 1 -4 3 1 -3 7 -3 -2 0 -3 -2 0 -1 -2 -3 0 -3 1 2 -1 -8
-I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 2 -2 2 1 -2 -2 0 -6 -1 4 -2 -2 -1 -8
-L -2 -3 -3 -5 -7 -2 -4 -5 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -8
-K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 1 -6 -1 0 0 -4 -5 -3 0 0 -1 -8
-M -1 -1 -2 -3 -6 -1 -2 -3 -3 2 4 1 8 0 -2 -2 -1 -5 -3 2 -3 -2 -1 -8
-F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 2 -6 0 10 -5 -4 -4 0 7 -2 -5 -6 -3 -8
-P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 7 1 0 -6 -6 -1 -1 0 -1 -8
-S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -4 1 2 2 -3 -3 -1 0 0 0 -8
-T 1 -1 0 0 -3 -1 -1 0 -2 0 -2 0 -1 -4 0 2 3 -6 -3 0 0 -1 0 -8
-W -6 2 -4 -8 -8 -5 -8 -8 -3 -6 -2 -4 -5 0 -6 -3 -6 17 0 -7 -6 -7 -5 -8
-Y -4 -5 -2 -5 0 -5 -5 -6 0 -1 -1 -5 -3 7 -6 -3 -3 0 11 -3 -3 -5 -3 -8
-V 0 -3 -2 -3 -2 -2 -2 -2 -3 4 2 -3 2 -2 -1 -1 0 -7 -3 5 -2 -2 -1 -8
-B 0 -1 2 4 -5 1 3 0 1 -2 -4 0 -3 -5 -1 0 0 -6 -3 -2 3 2 -1 -8
-Z 0 0 1 3 -6 4 4 -1 2 -2 -3 0 -2 -6 0 0 -1 -7 -5 -2 2 4 -1 -8
-X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -8
-* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM230 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM230
deleted file mode 100644
index c9ff6db..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM230
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 230 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -0.991, Entropy = 0.407 bits
-#
-# Lowest score = -8, Highest score = 17
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
-R -2 7 0 -2 -4 1 -1 -3 2 -2 -3 4 -1 -5 0 0 -1 2 -5 -3 -1 0 -1 -8
-N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
-D 0 -2 2 4 -6 2 4 1 1 -3 -4 0 -3 -6 -1 0 0 -7 -5 -2 3 3 -1 -8
-C -2 -4 -4 -6 12 -6 -6 -4 -4 -2 -7 -6 -6 -5 -3 0 -2 -8 0 -2 -5 -6 -3 -8
-Q -1 1 1 2 -6 5 3 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 4 -1 -8
-E 0 -1 1 4 -6 3 4 0 1 -2 -4 0 -2 -6 -1 0 -1 -8 -5 -2 3 4 -1 -8
-G 1 -3 0 1 -4 -1 0 5 -2 -3 -4 -2 -3 -5 -1 1 0 -7 -6 -2 0 -1 -1 -8
-H -2 2 2 1 -4 3 1 -2 7 -3 -2 0 -2 -2 0 -1 -2 -3 0 -2 1 2 -1 -8
-I -1 -2 -2 -3 -2 -2 -2 -3 -3 5 2 -2 2 1 -2 -2 0 -6 -1 4 -2 -2 -1 -8
-L -2 -3 -3 -4 -7 -2 -4 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -8
-K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 0 -6 -1 0 0 -4 -5 -3 1 0 -1 -8
-M -1 -1 -2 -3 -6 -1 -2 -3 -2 2 4 0 7 0 -2 -2 -1 -5 -3 2 -2 -2 -1 -8
-F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 2 -6 0 9 -5 -3 -3 0 7 -1 -5 -6 -3 -8
-P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8
-S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -3 1 2 2 -3 -3 -1 0 0 0 -8
-T 1 -1 0 0 -2 -1 -1 0 -2 0 -2 0 -1 -3 0 2 3 -6 -3 0 0 -1 0 -8
-W -6 2 -4 -7 -8 -5 -8 -7 -3 -6 -2 -4 -5 0 -6 -3 -6 17 0 -7 -6 -6 -4 -8
-Y -4 -5 -2 -5 0 -4 -5 -6 0 -1 -1 -5 -3 7 -5 -3 -3 0 10 -3 -3 -5 -3 -8
-V 0 -3 -2 -2 -2 -2 -2 -2 -2 4 2 -3 2 -1 -1 -1 0 -7 -3 5 -2 -2 -1 -8
-B 0 -1 2 3 -5 1 3 0 1 -2 -4 1 -2 -5 -1 0 0 -6 -3 -2 3 2 -1 -8
-Z 0 0 1 3 -6 4 4 -1 2 -2 -3 0 -2 -6 0 0 -1 -6 -5 -2 2 4 -1 -8
-X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -4 -3 -1 -1 -1 -1 -8
-* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM240 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM240
deleted file mode 100644
index c17cdf8..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM240
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 240 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -0.923, Entropy = 0.379 bits
-#
-# Lowest score = -8, Highest score = 17
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
-R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -5 0 0 -1 2 -4 -3 -1 0 -1 -8
-N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
-D 0 -1 2 4 -5 2 4 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 -8
-C -2 -4 -4 -5 12 -6 -6 -4 -4 -2 -6 -6 -5 -5 -3 0 -2 -8 0 -2 -5 -6 -3 -8
-Q 0 1 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -8
-E 0 -1 1 4 -6 3 4 0 1 -2 -3 0 -2 -6 -1 0 0 -7 -4 -2 3 3 -1 -8
-G 1 -3 0 1 -4 -1 0 5 -2 -3 -4 -2 -3 -5 -1 1 0 -7 -5 -1 0 0 -1 -8
-H -1 2 2 1 -4 3 1 -2 7 -3 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -8
-I -1 -2 -2 -2 -2 -2 -2 -3 -3 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -8
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -1 -8
-K -1 3 1 0 -6 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -4 -5 -3 1 0 -1 -8
-M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 7 0 -2 -2 -1 -4 -3 2 -2 -2 -1 -8
-F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -5 -5 -2 -8
-P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8
-S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -3 -3 -1 0 0 0 -8
-T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8
-W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -4 -4 0 -6 -3 -5 17 0 -6 -5 -6 -4 -8
-Y -4 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -5 -3 7 -5 -3 -3 0 10 -3 -3 -4 -2 -8
-V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 2 -3 2 -1 -1 -1 0 -6 -3 4 -2 -2 -1 -8
-B 0 -1 2 3 -5 1 3 0 1 -2 -4 1 -2 -5 -1 0 0 -5 -3 -2 3 2 -1 -8
-Z 0 0 1 3 -6 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 -8
-X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 -8
-* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM250 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM250
deleted file mode 100644
index 17e9e60..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM250
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 250 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -0.844, Entropy = 0.354 bits
-#
-# Lowest score = -8, Highest score = 17
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8
-R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -8
-N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 2 1 0 -8
-D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 -8
-C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 0 -2 -4 -5 -3 -8
-Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -8
-E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 -1 0 0 -7 -4 -2 3 3 -1 -8
-G 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -7 -5 -1 0 0 -1 -8
-H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -8
-I -1 -2 -2 -2 -2 -2 -2 -3 -2 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -8
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -3 -3 -1 -8
-K -1 3 1 0 -5 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 0 -1 -8
-M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -2 -1 -4 -2 2 -2 -2 -1 -8
-F -3 -4 -3 -6 -4 -5 -5 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -4 -5 -2 -8
-P 1 0 0 -1 -3 0 -1 0 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8
-S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -2 -3 -1 0 0 0 -8
-T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8
-W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 -4 -8
-Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -8
-V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 -8
-B 0 -1 2 3 -4 1 3 0 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 -1 -8
-Z 0 0 1 3 -5 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 -8
-X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 -8
-* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM260 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM260
deleted file mode 100644
index 5098eb4..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM260
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 260 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -0.794, Entropy = 0.330 bits
-#
-# Lowest score = -7, Highest score = 17
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -1 0 0 -2 0 0 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -7
-R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -7
-N 0 0 2 2 -3 1 1 0 2 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 2 1 0 -7
-D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -2 -5 -1 0 0 -6 -4 -2 3 3 -1 -7
-C -2 -4 -3 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -7 0 -2 -4 -5 -3 -7
-Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -4 0 0 -1 -5 -4 -2 1 3 0 -7
-E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 0 0 0 -7 -4 -2 3 3 -1 -7
-G 1 -2 0 1 -3 -1 0 5 -2 -2 -4 -2 -3 -5 0 1 0 -7 -5 -1 1 0 -1 -7
-H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -7
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -7
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -2 -3 -2 -2 -1 2 -3 -2 -1 -7
-K -1 3 1 0 -5 1 0 -2 0 -2 -3 4 0 -5 -1 0 0 -3 -4 -2 1 0 -1 -7
-M -1 0 -2 -2 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -1 -1 -4 -2 2 -2 -2 -1 -7
-F -3 -4 -3 -5 -4 -4 -5 -5 -2 1 2 -5 0 9 -4 -3 -3 0 7 -1 -4 -5 -2 -7
-P 1 0 0 -1 -3 0 0 0 0 -2 -2 -1 -2 -4 6 1 0 -5 -5 -1 -1 0 -1 -7
-S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -1 -3 1 1 1 -2 -3 -1 0 0 0 -7
-T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 2 -5 -3 0 0 0 0 -7
-W -6 2 -4 -6 -7 -5 -7 -7 -3 -5 -2 -3 -4 0 -5 -2 -5 17 0 -6 -5 -6 -4 -7
-Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -7
-V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 -7
-B 0 -1 2 3 -4 1 3 1 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 0 -7
-Z 0 0 1 3 -5 3 3 0 2 -2 -2 0 -2 -5 0 0 0 -6 -4 -2 2 3 -1 -7
-X 0 -1 0 -1 -3 0 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 0 -1 -1 -7
-* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM270 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM270
deleted file mode 100644
index 322fcdb..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM270
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 270 substitution matrix, scale = ln(2)/4 = 0.173287
-#
-# Expected score = -0.969, Entropy = 0.309 bits
-#
-# Lowest score = -10, Highest score = 23
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 0 0 2 -2 -1 -2 -1 -1 -4 1 1 1 -7 -4 0 0 0 0 -10
-R -2 8 0 -1 -5 2 -1 -3 2 -2 -4 4 -1 -5 0 0 -1 3 -5 -3 -1 0 -1 -10
-N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 2 0 -10
-D 0 -1 2 5 -6 2 4 1 1 -3 -5 0 -3 -7 -1 0 0 -8 -5 -3 4 3 -1 -10
-C -2 -5 -4 -6 16 -7 -6 -4 -4 -3 -7 -7 -6 -5 -3 0 -3 -10 1 -2 -5 -7 -4 -10
-Q 0 2 1 2 -7 5 3 -1 4 -2 -2 1 -1 -6 0 -1 -1 -6 -5 -2 2 4 -1 -10
-E 0 -1 2 4 -6 3 5 0 1 -2 -4 0 -3 -7 -1 0 0 -9 -5 -2 3 4 -1 -10
-G 2 -3 1 1 -4 -1 0 6 -2 -3 -5 -2 -3 -6 0 1 0 -9 -6 -2 1 0 -1 -10
-H -2 2 2 1 -4 4 1 -2 8 -3 -3 0 -3 -2 0 -1 -1 -3 0 -3 1 2 -1 -10
-I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 3 -2 3 1 -2 -2 0 -6 -1 5 -3 -2 -1 -10
-L -2 -4 -3 -5 -7 -2 -4 -5 -3 3 8 -3 5 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -10
-K -1 4 1 0 -7 1 0 -2 0 -2 -3 6 0 -6 -1 0 0 -4 -5 -3 1 0 -1 -10
-M -1 -1 -2 -3 -6 -1 -3 -3 -3 3 5 0 8 0 -2 -2 -1 -5 -3 2 -3 -2 -1 -10
-F -4 -5 -4 -7 -5 -6 -7 -6 -2 1 2 -6 0 12 -6 -4 -4 1 9 -1 -6 -6 -3 -10
-P 1 0 0 -1 -3 0 -1 0 0 -2 -3 -1 -2 -6 7 1 0 -7 -6 -1 -1 0 -1 -10
-S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -4 1 2 2 -3 -4 -1 1 0 0 -10
-T 1 -1 1 0 -3 -1 0 0 -1 0 -2 0 -1 -4 0 2 3 -6 -3 0 0 -1 0 -10
-W -7 3 -5 -8 -10 -6 -9 -9 -3 -6 -2 -4 -5 1 -7 -3 -6 23 0 -8 -7 -7 -5 -10
-Y -4 -5 -3 -5 1 -5 -5 -6 0 -1 -1 -5 -3 9 -6 -4 -3 0 13 -3 -4 -5 -3 -10
-V 0 -3 -2 -3 -2 -2 -2 -2 -3 5 2 -3 2 -1 -1 -1 0 -8 -3 5 -2 -2 -1 -10
-B 0 -1 2 4 -5 2 3 1 1 -3 -4 1 -3 -6 -1 1 0 -7 -4 -2 3 3 -1 -10
-Z 0 0 2 3 -7 4 4 0 2 -2 -3 0 -2 -6 0 0 -1 -7 -5 -2 3 4 -1 -10
-X 0 -1 0 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM280 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM280
deleted file mode 100644
index 2b09bca..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM280
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 280 substitution matrix, scale = ln(2)/4 = 0.173287
-#
-# Expected score = -0.916, Entropy = 0.289 bits
-#
-# Lowest score = -9, Highest score = 22
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 0 0 2 -1 -1 -2 -1 -1 -4 1 1 1 -7 -4 0 0 0 0 -9
-R -2 7 0 -1 -4 2 -1 -3 2 -2 -3 4 0 -5 0 0 -1 3 -5 -3 -1 0 -1 -9
-N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 1 0 -9
-D 0 -1 2 4 -6 2 4 1 1 -3 -5 0 -3 -7 -1 0 0 -8 -5 -2 4 3 -1 -9
-C -2 -4 -4 -6 15 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -9 1 -2 -5 -6 -3 -9
-Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -6 -5 -2 2 4 -1 -9
-E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 4 -1 -9
-G 2 -3 1 1 -4 -1 0 6 -2 -3 -5 -2 -3 -6 0 1 0 -8 -6 -1 1 0 -1 -9
-H -1 2 2 1 -4 3 1 -2 8 -3 -2 0 -2 -2 0 -1 -1 -3 0 -3 1 2 -1 -9
-I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 3 -2 3 1 -2 -2 0 -6 -1 4 -2 -2 -1 -9
-L -2 -3 -3 -5 -7 -2 -4 -5 -2 3 7 -3 5 2 -3 -3 -2 -2 -1 2 -4 -3 -1 -9
-K -1 4 1 0 -6 1 0 -2 0 -2 -3 6 0 -6 -1 0 0 -4 -5 -3 1 1 -1 -9
-M -1 0 -2 -3 -6 -1 -2 -3 -2 3 5 0 7 0 -2 -2 -1 -5 -3 2 -2 -2 -1 -9
-F -4 -5 -4 -7 -5 -5 -6 -6 -2 1 2 -6 0 11 -5 -4 -4 1 9 -1 -5 -6 -3 -9
-P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 7 1 1 -7 -6 -1 -1 0 -1 -9
-S 1 0 1 0 0 0 0 1 -1 -2 -3 0 -2 -4 1 2 1 -3 -3 -1 1 0 0 -9
-T 1 -1 1 0 -3 -1 0 0 -1 0 -2 0 -1 -4 1 1 3 -6 -3 0 0 0 0 -9
-W -7 3 -5 -8 -9 -6 -8 -8 -3 -6 -2 -4 -5 1 -7 -3 -6 22 0 -7 -6 -7 -5 -9
-Y -4 -5 -3 -5 1 -5 -5 -6 0 -1 -1 -5 -3 9 -6 -3 -3 0 13 -3 -4 -5 -3 -9
-V 0 -3 -2 -2 -2 -2 -2 -1 -3 4 2 -3 2 -1 -1 -1 0 -7 -3 5 -2 -2 -1 -9
-B 0 -1 2 4 -5 2 3 1 1 -2 -4 1 -2 -5 -1 1 0 -6 -4 -2 3 2 -1 -9
-Z 0 0 1 3 -6 4 4 0 2 -2 -3 1 -2 -6 0 0 0 -7 -5 -2 2 4 -1 -9
-X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM290 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM290
deleted file mode 100644
index 6852c6a..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM290
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 290 substitution matrix, scale = ln(2)/4 = 0.173287
-#
-# Expected score = -0.877, Entropy = 0.271 bits
-#
-# Lowest score = -9, Highest score = 22
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 0 0 2 -1 -1 -2 -1 -1 -4 1 1 1 -7 -4 0 0 0 0 -9
-R -2 7 0 -1 -4 2 -1 -3 2 -2 -3 4 0 -5 0 0 -1 3 -5 -3 0 0 -1 -9
-N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 1 0 -9
-D 0 -1 2 4 -6 2 4 1 1 -3 -4 0 -3 -6 -1 0 0 -8 -5 -2 3 3 -1 -9
-C -2 -4 -4 -6 15 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -2 -9 1 -2 -5 -6 -3 -9
-Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -5 -5 -2 2 3 0 -9
-E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 4 -1 -9
-G 2 -3 1 1 -4 -1 0 5 -2 -3 -4 -2 -3 -6 0 1 0 -8 -6 -1 1 0 -1 -9
-H -1 2 2 1 -4 3 1 -2 7 -3 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -9
-I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 3 -2 3 1 -2 -1 0 -6 -1 4 -2 -2 -1 -9
-L -2 -3 -3 -4 -7 -2 -4 -4 -2 3 7 -3 5 3 -3 -3 -2 -2 -1 2 -4 -3 -1 -9
-K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 0 -6 -1 0 0 -4 -5 -3 1 1 -1 -9
-M -1 0 -2 -3 -6 -1 -2 -3 -2 3 5 0 7 0 -2 -2 -1 -5 -2 2 -2 -2 -1 -9
-F -4 -5 -4 -6 -5 -5 -6 -6 -2 1 3 -6 0 11 -5 -4 -3 1 9 -1 -5 -6 -3 -9
-P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 7 1 1 -6 -6 -1 -1 0 -1 -9
-S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -2 -4 1 2 1 -3 -3 -1 1 0 0 -9
-T 1 -1 1 0 -2 -1 0 0 -1 0 -2 0 -1 -3 1 1 3 -6 -3 0 0 0 0 -9
-W -7 3 -5 -8 -9 -5 -8 -8 -3 -6 -2 -4 -5 1 -6 -3 -6 22 0 -7 -6 -7 -5 -9
-Y -4 -5 -3 -5 1 -5 -5 -6 0 -1 -1 -5 -2 9 -6 -3 -3 0 13 -3 -4 -5 -2 -9
-V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 2 -3 2 -1 -1 -1 0 -7 -3 5 -2 -2 -1 -9
-B 0 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 -1 1 0 -6 -4 -2 3 2 0 -9
-Z 0 0 1 3 -6 3 4 0 2 -2 -3 1 -2 -6 0 0 0 -7 -5 -2 2 4 -1 -9
-X 0 -1 0 -1 -3 0 -1 -1 -1 -1 -1 -1 -1 -3 -1 0 0 -5 -2 -1 0 -1 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM30 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM30
deleted file mode 100644
index 8a01c88..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM30
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 30 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -5.06, Entropy = 2.57 bits
-#
-# Lowest score = -17, Highest score = 13
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 6 -7 -4 -3 -6 -4 -2 -2 -7 -5 -6 -7 -5 -8 -2 0 -1 -13 -8 -2 -3 -3 -3 -17
-R -7 8 -6 -10 -8 -2 -9 -9 -2 -5 -8 0 -4 -9 -4 -3 -6 -2 -10 -8 -7 -4 -6 -17
-N -4 -6 8 2 -11 -3 -2 -3 0 -5 -7 -1 -9 -9 -6 0 -2 -8 -4 -8 6 -3 -3 -17
-D -3 -10 2 8 -14 -2 2 -3 -4 -7 -12 -4 -11 -15 -8 -4 -5 -15 -11 -8 6 1 -5 -17
-C -6 -8 -11 -14 10 -14 -14 -9 -7 -6 -15 -14 -13 -13 -8 -3 -8 -15 -4 -6 -12 -14 -9 -17
-Q -4 -2 -3 -2 -14 8 1 -7 1 -8 -5 -3 -4 -13 -3 -5 -5 -13 -12 -7 -3 6 -5 -17
-E -2 -9 -2 2 -14 1 8 -4 -5 -5 -9 -4 -7 -14 -5 -4 -6 -17 -8 -6 1 6 -5 -17
-G -2 -9 -3 -3 -9 -7 -4 6 -9 -11 -10 -7 -8 -9 -6 -2 -6 -15 -14 -5 -3 -5 -5 -17
-H -7 -2 0 -4 -7 1 -5 -9 9 -9 -6 -6 -10 -6 -4 -6 -7 -7 -3 -6 -1 -1 -5 -17
-I -5 -5 -5 -7 -6 -8 -5 -11 -9 8 -1 -6 -1 -2 -8 -7 -2 -14 -6 2 -6 -6 -5 -17
-L -6 -8 -7 -12 -15 -5 -9 -10 -6 -1 7 -8 1 -3 -7 -8 -7 -6 -7 -2 -9 -7 -6 -17
-K -7 0 -1 -4 -14 -3 -4 -7 -6 -6 -8 7 -2 -14 -6 -4 -3 -12 -9 -9 -2 -4 -5 -17
-M -5 -4 -9 -11 -13 -4 -7 -8 -10 -1 1 -2 11 -4 -8 -5 -4 -13 -11 -1 -10 -5 -5 -17
-F -8 -9 -9 -15 -13 -13 -14 -9 -6 -2 -3 -14 -4 9 -10 -6 -9 -4 2 -8 -10 -13 -8 -17
-P -2 -4 -6 -8 -8 -3 -5 -6 -4 -8 -7 -6 -8 -10 8 -2 -4 -14 -13 -6 -7 -4 -5 -17
-S 0 -3 0 -4 -3 -5 -4 -2 -6 -7 -8 -4 -5 -6 -2 6 0 -5 -7 -6 -1 -5 -3 -17
-T -1 -6 -2 -5 -8 -5 -6 -6 -7 -2 -7 -3 -4 -9 -4 0 7 -13 -6 -3 -3 -6 -4 -17
-W -13 -2 -8 -15 -15 -13 -17 -15 -7 -14 -6 -12 -13 -4 -14 -5 -13 13 -5 -15 -10 -14 -11 -17
-Y -8 -10 -4 -11 -4 -12 -8 -14 -3 -6 -7 -9 -11 2 -13 -7 -6 -5 10 -7 -6 -9 -7 -17
-V -2 -8 -8 -8 -6 -7 -6 -5 -6 2 -2 -9 -1 -8 -6 -6 -3 -15 -7 7 -8 -6 -5 -17
-B -3 -7 6 6 -12 -3 1 -3 -1 -6 -9 -2 -10 -10 -7 -1 -3 -10 -6 -8 6 0 -5 -17
-Z -3 -4 -3 1 -14 6 6 -5 -1 -6 -7 -4 -5 -13 -4 -5 -6 -14 -9 -6 0 6 -5 -17
-X -3 -6 -3 -5 -9 -5 -5 -5 -5 -5 -6 -5 -5 -8 -5 -3 -4 -11 -7 -5 -5 -5 -5 -17
-* -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM300 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM300
deleted file mode 100644
index 5d1a5a8..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM300
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 300 substitution matrix, scale = ln(2)/4 = 0.173287
-#
-# Expected score = -0.835, Entropy = 0.254 bits
-#
-# Lowest score = -9, Highest score = 22
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -1 0 0 -2 0 0 2 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -9
-R -1 7 0 -1 -4 2 -1 -2 2 -2 -3 4 0 -5 0 0 -1 3 -5 -3 0 0 -1 -9
-N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -5 -2 -2 2 1 0 -9
-D 0 -1 2 4 -6 2 4 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -5 -2 3 3 -1 -9
-C -2 -4 -4 -6 15 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -2 -9 1 -2 -5 -6 -3 -9
-Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -5 -4 -2 2 3 0 -9
-E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 3 -1 -9
-G 2 -2 1 1 -4 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -8 -6 -1 1 0 -1 -9
-H -1 2 2 1 -4 3 1 -2 7 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -9
-I 0 -2 -2 -2 -3 -2 -2 -3 -2 5 3 -2 3 1 -2 -1 0 -6 -1 4 -2 -2 -1 -9
-L -2 -3 -3 -4 -7 -2 -4 -4 -2 3 7 -3 4 3 -3 -3 -2 -2 0 2 -4 -3 -1 -9
-K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 0 -6 -1 0 0 -4 -5 -2 1 1 -1 -9
-M -1 0 -2 -3 -6 -1 -2 -3 -2 3 4 0 6 1 -2 -2 -1 -5 -2 2 -2 -2 -1 -9
-F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 3 -6 1 11 -5 -4 -3 1 9 -1 -5 -5 -2 -9
-P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 -1 -9
-S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -9
-W -6 3 -5 -7 -9 -5 -8 -8 -3 -6 -2 -4 -5 1 -6 -3 -6 22 0 -7 -6 -6 -4 -9
-Y -4 -5 -2 -5 1 -4 -5 -6 0 -1 0 -5 -2 9 -5 -3 -3 0 12 -3 -4 -5 -2 -9
-V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -7 -3 5 -2 -2 0 -9
-B 0 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -6 -4 -2 3 2 0 -9
-Z 0 0 1 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -5 -2 2 3 -1 -9
-X 0 -1 0 -1 -3 0 -1 -1 0 -1 -1 -1 -1 -2 -1 0 0 -4 -2 0 0 -1 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM310 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM310
deleted file mode 100644
index cd0e5b0..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM310
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 310 substitution matrix, scale = ln(2)/4 = 0.173287
-#
-# Expected score = -0.779, Entropy = 0.238 bits
-#
-# Lowest score = -9, Highest score = 22
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -1 0 0 -2 0 0 1 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -9
-R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 4 0 -5 0 0 -1 3 -4 -2 0 0 -1 -9
-N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -4 -2 -2 2 1 0 -9
-D 0 -1 2 4 -5 2 4 1 1 -2 -4 0 -2 -6 -1 0 0 -7 -5 -2 3 3 -1 -9
-C -2 -4 -4 -5 15 -6 -6 -3 -4 -2 -6 -6 -6 -4 -3 0 -2 -9 1 -2 -5 -6 -3 -9
-Q 0 1 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -5 -4 -2 2 3 0 -9
-E 0 -1 2 4 -6 3 4 1 1 -2 -3 0 -2 -6 0 0 0 -7 -5 -2 3 3 -1 -9
-G 1 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -3 -5 0 1 0 -8 -6 -1 1 0 -1 -9
-H -1 2 2 1 -4 3 1 -2 7 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -9
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 1 -2 -1 0 -5 -1 4 -2 -2 -1 -9
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -3 -3 -2 -2 0 2 -3 -3 -1 -9
-K -1 4 1 0 -6 1 0 -1 0 -2 -3 5 0 -5 -1 0 0 -3 -5 -2 1 1 -1 -9
-M -1 0 -2 -2 -6 -1 -2 -3 -2 3 4 0 6 1 -2 -2 -1 -4 -2 2 -2 -2 -1 -9
-F -4 -5 -4 -6 -4 -5 -6 -5 -2 1 3 -5 1 11 -5 -4 -3 1 9 -1 -5 -5 -2 -9
-P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -9
-S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -9
-W -6 3 -4 -7 -9 -5 -7 -8 -3 -5 -2 -3 -4 1 -6 -3 -6 22 0 -7 -6 -6 -4 -9
-Y -4 -4 -2 -5 1 -4 -5 -6 0 -1 0 -5 -2 9 -5 -3 -3 0 12 -2 -4 -4 -2 -9
-V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -7 -2 4 -2 -2 0 -9
-B 0 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 3 2 0 -9
-Z 0 0 1 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -4 -2 2 3 0 -9
-X 0 -1 0 -1 -3 0 -1 -1 0 -1 -1 -1 -1 -2 0 0 0 -4 -2 0 0 0 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM320 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM320
deleted file mode 100644
index d7fbbd2..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM320
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 320 substitution matrix, scale = ln(2)/4 = 0.173287
-#
-# Expected score = -0.741, Entropy = 0.224 bits
-#
-# Lowest score = -8, Highest score = 22
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 0 1 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
-R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 4 0 -5 0 0 -1 3 -4 -2 0 0 -1 -8
-N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -4 -2 -2 2 1 0 -8
-D 1 -1 2 4 -5 2 3 1 1 -2 -4 0 -2 -6 0 0 0 -7 -5 -2 3 3 -1 -8
-C -2 -4 -4 -5 15 -5 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -8 1 -2 -4 -5 -3 -8
-Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 0 0 -5 -4 -2 2 3 0 -8
-E 0 -1 2 3 -5 2 4 1 1 -2 -3 0 -2 -5 0 0 0 -7 -5 -2 3 3 0 -8
-G 1 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -3 -5 0 1 0 -7 -5 -1 1 0 -1 -8
-H -1 2 2 1 -4 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -8
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 0 -8
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -2 -3 -2 -2 0 2 -3 -3 -1 -8
-K -1 4 1 0 -6 1 0 -1 0 -2 -3 5 0 -5 -1 0 0 -3 -5 -2 1 1 -1 -8
-M -1 0 -2 -2 -5 -1 -2 -3 -2 2 4 0 6 1 -2 -1 -1 -4 -2 2 -2 -2 0 -8
-F -4 -5 -4 -6 -4 -5 -5 -5 -2 1 3 -5 1 11 -5 -3 -3 1 9 -1 -5 -5 -2 -8
-P 1 0 0 0 -3 0 0 0 0 -2 -2 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -8
-S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
-T 1 -1 0 0 -2 0 0 0 -1 0 -2 0 -1 -3 1 1 2 -5 -3 0 0 0 0 -8
-W -6 3 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 1 -6 -3 -5 22 1 -6 -6 -6 -4 -8
-Y -4 -4 -2 -5 1 -4 -5 -5 0 -1 0 -5 -2 9 -5 -3 -3 1 12 -2 -3 -4 -2 -8
-V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 0 -8
-B 0 0 2 3 -4 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -3 -2 2 2 0 -8
-Z 0 0 1 3 -5 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -4 -2 2 3 0 -8
-X 0 -1 0 -1 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -4 -2 0 0 0 -1 -8
-* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM330 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM330
deleted file mode 100644
index 77db35e..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM330
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 330 substitution matrix, scale = ln(2)/4 = 0.173287
-#
-# Expected score = -0.693, Entropy = 0.210 bits
-#
-# Lowest score = -8, Highest score = 22
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 0 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8
-R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 4 0 -4 0 0 -1 3 -4 -2 0 0 -1 -8
-N 0 0 2 2 -4 1 2 1 1 -2 -3 1 -1 -3 0 1 0 -4 -2 -1 2 1 0 -8
-D 1 -1 2 3 -5 2 3 1 1 -2 -4 0 -2 -5 0 0 0 -7 -4 -2 3 3 0 -8
-C -2 -4 -4 -5 15 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 1 -2 -4 -5 -3 -8
-Q 0 1 1 2 -5 3 2 -1 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -2 1 3 0 -8
-E 0 -1 2 3 -5 2 3 1 1 -2 -3 0 -2 -5 0 0 0 -7 -4 -2 2 3 0 -8
-G 1 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -2 -5 0 1 0 -7 -5 -1 1 0 -1 -8
-H -1 2 1 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -8
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 2 1 -2 -1 0 -5 0 4 -2 -2 0 -8
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 6 -3 4 3 -2 -3 -1 -2 0 2 -3 -2 -1 -8
-K -1 4 1 0 -5 1 0 -1 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 1 -1 -8
-M -1 0 -1 -2 -5 -1 -2 -2 -2 2 4 0 5 1 -2 -1 0 -4 -2 2 -2 -1 0 -8
-F -3 -4 -3 -5 -4 -4 -5 -5 -2 1 3 -5 1 10 -5 -3 -3 1 9 -1 -4 -5 -2 -8
-P 1 0 0 0 -3 0 0 0 0 -2 -2 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -8
-S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
-T 1 -1 0 0 -2 0 0 0 -1 0 -1 0 0 -3 1 1 2 -5 -3 0 0 0 0 -8
-W -6 3 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 1 -6 -3 -5 22 1 -6 -5 -6 -4 -8
-Y -3 -4 -2 -4 1 -4 -4 -5 0 0 0 -4 -2 9 -5 -3 -3 1 12 -2 -3 -4 -2 -8
-V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 0 -8
-B 0 0 2 3 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 0 -5 -3 -2 2 2 0 -8
-Z 0 0 1 3 -5 3 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -2 2 3 0 -8
-X 0 -1 0 0 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -4 -2 0 0 0 -1 -8
-* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM340 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM340
deleted file mode 100644
index 02c8540..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM340
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 340 substitution matrix, scale = ln(2)/4 = 0.173287
-#
-# Expected score = -0.680, Entropy = 0.198 bits
-#
-# Lowest score = -8, Highest score = 22
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 0 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8
-R -1 6 0 -1 -4 1 0 -2 2 -2 -3 4 0 -4 0 0 0 3 -4 -2 0 0 -1 -8
-N 0 0 1 2 -3 1 1 1 1 -2 -3 1 -1 -3 0 1 0 -4 -2 -1 2 1 0 -8
-D 1 -1 2 3 -5 2 3 1 1 -2 -4 0 -2 -5 0 0 0 -7 -4 -2 3 3 0 -8
-C -2 -4 -3 -5 15 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 1 -2 -4 -5 -3 -8
-Q 0 1 1 2 -5 3 2 -1 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -2 1 3 0 -8
-E 0 0 1 3 -5 2 3 1 1 -2 -3 0 -2 -5 0 0 0 -7 -4 -1 2 3 0 -8
-G 1 -2 1 1 -3 -1 1 4 -2 -2 -4 -1 -2 -5 0 1 0 -7 -5 -1 1 0 -1 -8
-H -1 2 1 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 0 -1 -2 0 -2 1 2 0 -8
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 2 1 -2 -1 0 -5 0 3 -2 -2 0 -8
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 6 -3 4 3 -2 -2 -1 -2 0 2 -3 -2 -1 -8
-K -1 4 1 0 -5 1 0 -1 0 -2 -3 4 0 -5 -1 0 0 -3 -4 -2 1 1 0 -8
-M -1 0 -1 -2 -5 -1 -2 -2 -2 2 4 0 5 1 -2 -1 0 -4 -2 2 -2 -1 0 -8
-F -3 -4 -3 -5 -4 -4 -5 -5 -2 1 3 -5 1 10 -4 -3 -3 1 9 -1 -4 -5 -2 -8
-P 1 0 0 0 -3 0 0 0 0 -2 -2 -1 -2 -4 5 1 1 -5 -5 -1 0 0 0 -8
-S 1 0 1 0 0 0 0 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
-T 1 0 0 0 -2 0 0 0 -1 0 -1 0 0 -3 1 1 2 -5 -3 0 0 0 0 -8
-W -6 3 -4 -7 -8 -5 -7 -7 -2 -5 -2 -3 -4 1 -5 -3 -5 22 1 -6 -5 -6 -4 -8
-Y -3 -4 -2 -4 1 -4 -4 -5 0 0 0 -4 -2 9 -5 -3 -3 1 12 -2 -3 -4 -2 -8
-V 0 -2 -1 -2 -2 -2 -1 -1 -2 3 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 0 -8
-B 0 0 2 3 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 0 -5 -3 -2 2 2 0 -8
-Z 0 0 1 3 -5 3 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -2 2 3 0 -8
-X 0 -1 0 0 -3 0 0 -1 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -8
-* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM350 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM350
deleted file mode 100644
index 140a6f2..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM350
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 350 substitution matrix, scale = ln(2)/5 = 0.138629
-#
-# Expected score = -0.701, Entropy = 0.186 bits
-#
-# Lowest score = -10, Highest score = 27
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
-R -1 7 1 -1 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 -1 4 -5 -3 0 1 -1 -10
-N 0 1 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 2 0 -10
-D 1 -1 2 4 -6 2 4 1 1 -2 -4 1 -3 -6 0 1 0 -8 -5 -2 3 3 -1 -10
-C -2 -4 -4 -6 18 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -2 -10 1 -2 -5 -6 -3 -10
-Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -5 -2 2 3 0 -10
-E 1 0 2 4 -6 3 4 1 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 3 0 -10
-G 2 -2 1 1 -4 -1 1 5 -2 -2 -4 -1 -3 -6 0 1 1 -8 -6 -1 1 0 -1 -10
-H -1 2 2 1 -4 3 1 -2 7 -2 -2 1 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -10
-I 0 -2 -2 -2 -3 -2 -2 -2 -2 5 4 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -10
-L -2 -3 -3 -4 -7 -2 -4 -4 -2 4 8 -3 5 3 -3 -3 -2 -2 0 3 -4 -3 -1 -10
-K -1 4 1 1 -6 1 0 -1 1 -2 -3 5 0 -6 -1 0 0 -4 -5 -2 1 1 -1 -10
-M -1 0 -2 -3 -6 -1 -2 -3 -2 3 5 0 6 1 -2 -2 -1 -5 -2 2 -2 -2 0 -10
-F -4 -5 -4 -6 -5 -5 -6 -6 -2 2 3 -6 1 13 -5 -4 -3 1 11 -1 -5 -6 -2 -10
-P 1 0 0 0 -3 1 0 0 0 -2 -3 -1 -2 -5 6 1 1 -7 -6 -1 0 0 0 -10
-S 1 0 1 1 0 0 0 1 -1 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -10
-T 1 -1 1 0 -2 0 0 1 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -10
-W -7 4 -5 -8 -10 -5 -8 -8 -3 -6 -2 -4 -5 1 -7 -3 -6 27 1 -7 -6 -7 -5 -10
-Y -4 -5 -3 -5 1 -5 -5 -6 0 0 0 -5 -2 11 -6 -3 -3 1 14 -2 -4 -5 -2 -10
-V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 3 -2 2 -1 -1 -1 0 -7 -2 5 -2 -2 0 -10
-B 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -6 -4 -2 3 2 0 -10
-Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -2 -6 0 0 0 -7 -5 -2 2 3 0 -10
-X 0 -1 0 -1 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -5 -2 0 0 0 -1 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM360 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM360
deleted file mode 100644
index 5f6cd46..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM360
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 360 substitution matrix, scale = ln(2)/5 = 0.138629
-#
-# Expected score = -0.697, Entropy = 0.175 bits
-#
-# Lowest score = -9, Highest score = 27
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -9
-R -1 6 1 -1 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 -1 -9
-N 0 1 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 2 0 -9
-D 1 -1 2 4 -6 2 4 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -9
-C -2 -4 -4 -6 18 -6 -6 -4 -4 -3 -7 -6 -6 -4 -3 0 -2 -9 1 -2 -5 -6 -3 -9
-Q 0 2 1 2 -6 3 3 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -9
-E 1 0 2 4 -6 3 4 1 1 -2 -3 0 -2 -6 0 0 0 -8 -5 -2 3 3 0 -9
-G 2 -2 1 1 -4 -1 1 5 -2 -2 -4 -1 -3 -6 0 1 1 -8 -6 -1 1 0 -1 -9
-H -1 2 2 1 -4 3 1 -2 7 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9
-I 0 -2 -2 -2 -3 -2 -2 -2 -2 4 3 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -9
-L -2 -3 -3 -4 -7 -2 -3 -4 -2 3 7 -3 5 3 -3 -3 -2 -2 0 3 -4 -3 -1 -9
-K -1 4 1 1 -6 1 0 -1 1 -2 -3 5 0 -6 -1 0 0 -4 -5 -2 1 1 -1 -9
-M -1 0 -2 -2 -6 -1 -2 -3 -2 3 5 0 6 1 -2 -2 -1 -4 -2 2 -2 -2 0 -9
-F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 3 -6 1 12 -5 -4 -3 2 11 -1 -5 -5 -2 -9
-P 1 0 0 0 -3 1 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -9
-S 1 0 1 1 0 0 0 1 0 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 1 0 -2 0 0 1 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -9
-W -7 4 -5 -8 -9 -5 -8 -8 -3 -6 -2 -4 -4 2 -6 -3 -6 27 1 -7 -6 -7 -4 -9
-Y -4 -5 -3 -5 1 -4 -5 -6 0 0 0 -5 -2 11 -5 -3 -3 1 14 -2 -4 -5 -2 -9
-V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 3 -2 2 -1 -1 -1 0 -7 -2 4 -2 -2 0 -9
-B 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9
-Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -7 -5 -2 2 3 0 -9
-X 0 -1 0 0 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM370 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM370
deleted file mode 100644
index f72261f..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM370
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 370 substitution matrix, scale = ln(2)/5 = 0.138629
-#
-# Expected score = -0.649, Entropy = 0.165 bits
-#
-# Lowest score = -9, Highest score = 27
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -9
-R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 3 -4 -2 0 1 -1 -9
-N 0 1 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -5 -3 -1 2 1 0 -9
-D 1 0 2 4 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -7 -5 -2 3 3 0 -9
-C -2 -4 -4 -5 18 -6 -6 -3 -4 -2 -6 -6 -6 -4 -3 0 -2 -9 1 -2 -5 -6 -3 -9
-Q 0 2 1 2 -6 3 2 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -9
-E 1 0 2 3 -6 2 3 1 1 -2 -3 1 -2 -6 0 0 0 -8 -5 -2 3 3 0 -9
-G 2 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -3 -5 0 1 1 -8 -6 -1 1 0 -1 -9
-H -1 2 2 1 -4 3 1 -2 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 2 -2 -1 0 -5 0 4 -2 -2 0 -9
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 5 3 -3 -3 -1 -2 0 3 -3 -3 -1 -9
-K -1 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -6 -1 0 0 -3 -5 -2 1 1 0 -9
-M -1 0 -2 -2 -6 -1 -2 -3 -2 3 5 0 5 1 -2 -1 0 -4 -2 2 -2 -2 0 -9
-F -4 -5 -4 -6 -4 -5 -6 -5 -2 2 3 -6 1 12 -5 -4 -3 2 11 0 -5 -5 -2 -9
-P 1 0 0 0 -3 1 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -9
-S 1 0 1 1 0 0 0 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 2 -6 -3 0 0 0 0 -9
-W -7 3 -5 -7 -9 -5 -8 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 27 1 -7 -6 -6 -4 -9
-Y -4 -4 -3 -5 1 -4 -5 -6 0 0 0 -5 -2 11 -5 -3 -3 1 14 -2 -4 -5 -2 -9
-V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -2 -2 0 -9
-B 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9
-Z 0 1 1 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -5 -2 2 3 0 -9
-X 0 -1 0 0 -3 0 0 -1 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM380 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM380
deleted file mode 100644
index cbcf063..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM380
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 380 substitution matrix, scale = ln(2)/5 = 0.138629
-#
-# Expected score = -0.612, Entropy = 0.156 bits
-#
-# Lowest score = -9, Highest score = 26
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 1 0 0 -9
-R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 3 -4 -2 0 1 0 -9
-N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -9
-D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -7 -5 -2 3 3 0 -9
-C -2 -4 -4 -5 17 -5 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9
-Q 0 2 1 2 -5 3 2 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -9
-E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 0 0 -7 -5 -2 3 3 0 -9
-G 2 -2 1 1 -3 -1 1 5 -1 -2 -4 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9
-H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 2 -2 -1 0 -5 0 4 -2 -2 0 -9
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -2 -3 -1 -2 0 3 -3 -3 -1 -9
-K -1 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
-M -1 0 -1 -2 -5 -1 -2 -2 -2 3 4 0 5 1 -2 -1 0 -4 -2 2 -2 -1 0 -9
-F -4 -5 -4 -6 -4 -5 -5 -5 -2 2 3 -5 1 12 -5 -4 -3 2 10 0 -5 -5 -2 -9
-P 1 0 0 0 -3 1 0 0 0 -2 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -9
-S 1 0 1 1 0 0 0 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 2 -6 -3 0 0 0 0 -9
-W -6 3 -5 -7 -9 -5 -7 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 26 1 -6 -6 -6 -4 -9
-Y -4 -4 -3 -5 1 -4 -5 -5 0 0 0 -5 -2 10 -5 -3 -3 1 13 -2 -4 -4 -2 -9
-V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -6 -2 4 -2 -2 0 -9
-B 1 0 2 3 -4 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9
-Z 0 1 1 3 -5 3 3 0 2 -2 -3 1 -1 -5 0 0 0 -6 -4 -2 2 3 0 -9
-X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM390 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM390
deleted file mode 100644
index 8206530..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM390
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 390 substitution matrix, scale = ln(2)/5 = 0.138629
-#
-# Expected score = -0.581, Entropy = 0.147 bits
-#
-# Lowest score = -9, Highest score = 26
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -4 0 1 0 0 -9
-R -1 6 1 0 -4 1 0 -2 2 -2 -3 4 0 -5 0 0 0 3 -4 -2 0 1 0 -9
-N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -4 -3 -1 2 1 0 -9
-D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -7 -5 -2 3 3 0 -9
-C -2 -4 -4 -5 17 -5 -5 -3 -4 -2 -6 -5 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9
-Q 0 1 1 2 -5 3 2 0 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -1 2 3 0 -9
-E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 0 0 -7 -5 -1 2 3 0 -9
-G 1 -2 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -5 0 1 1 -7 -5 -1 1 0 0 -9
-H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 2 -1 -1 0 -5 0 4 -2 -2 0 -9
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -2 -2 -1 -2 0 3 -3 -2 -1 -9
-K -1 4 1 1 -5 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
-M -1 0 -1 -2 -5 -1 -2 -2 -2 3 4 0 5 1 -2 -1 0 -4 -1 2 -2 -1 0 -9
-F -3 -5 -4 -5 -4 -4 -5 -5 -2 2 3 -5 1 12 -5 -3 -3 2 10 0 -5 -5 -2 -9
-P 1 0 0 0 -3 0 0 0 0 -1 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -9
-S 1 0 1 1 0 0 0 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -9
-W -6 3 -4 -7 -9 -5 -7 -7 -3 -5 -2 -3 -4 2 -6 -3 -5 26 1 -6 -6 -6 -4 -9
-Y -4 -4 -3 -5 1 -4 -5 -5 0 0 0 -5 -1 10 -5 -3 -3 1 13 -2 -4 -4 -2 -9
-V 0 -2 -1 -2 -2 -1 -1 -1 -2 4 3 -2 2 0 -1 -1 0 -6 -2 4 -2 -1 0 -9
-B 1 0 2 3 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9
-Z 0 1 1 3 -5 3 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 3 0 -9
-X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM40 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM40
deleted file mode 100644
index e0df4f6..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM40
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 40 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -4.27, Entropy = 2.26 bits
-#
-# Lowest score = -15, Highest score = 13
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 6 -6 -3 -3 -6 -3 -2 -1 -6 -4 -5 -6 -4 -7 -1 0 0 -12 -7 -2 -3 -2 -3 -15
-R -6 8 -5 -9 -7 -1 -8 -8 -1 -5 -8 1 -3 -8 -3 -2 -5 -1 -9 -7 -6 -3 -5 -15
-N -3 -5 7 2 -9 -3 -1 -2 1 -4 -6 0 -7 -8 -5 0 -1 -7 -4 -7 6 -2 -3 -15
-D -3 -9 2 7 -12 -2 3 -3 -3 -6 -11 -4 -9 -13 -7 -3 -4 -13 -10 -7 6 2 -5 -15
-C -6 -7 -9 -12 9 -12 -12 -8 -7 -5 -13 -12 -12 -11 -7 -2 -7 -14 -3 -5 -11 -12 -8 -15
-Q -3 -1 -3 -2 -12 8 2 -6 1 -7 -4 -2 -3 -11 -2 -4 -5 -11 -10 -6 -2 6 -4 -15
-E -2 -8 -1 3 -12 2 7 -3 -4 -5 -8 -4 -6 -12 -5 -4 -5 -15 -8 -6 2 6 -4 -15
-G -1 -8 -2 -3 -8 -6 -3 6 -8 -9 -9 -6 -7 -8 -5 -1 -5 -13 -12 -5 -2 -4 -4 -15
-H -6 -1 1 -3 -7 1 -4 -8 9 -8 -5 -5 -9 -5 -3 -5 -6 -6 -3 -6 -1 0 -4 -15
-I -4 -5 -4 -6 -5 -7 -5 -9 -8 8 -1 -5 0 -2 -7 -6 -2 -12 -5 2 -5 -5 -4 -15
-L -5 -8 -6 -11 -13 -4 -8 -9 -5 -1 7 -7 1 -2 -6 -7 -6 -5 -6 -2 -8 -6 -5 -15
-K -6 1 0 -4 -12 -2 -4 -6 -5 -5 -7 6 -1 -12 -6 -3 -2 -10 -8 -8 -2 -3 -4 -15
-M -4 -3 -7 -9 -12 -3 -6 -7 -9 0 1 -1 11 -3 -7 -5 -3 -11 -10 -1 -8 -4 -4 -15
-F -7 -8 -8 -13 -11 -11 -12 -8 -5 -2 -2 -12 -3 9 -9 -6 -8 -4 2 -7 -9 -12 -7 -15
-P -1 -3 -5 -7 -7 -2 -5 -5 -3 -7 -6 -6 -7 -9 8 -1 -3 -12 -12 -5 -6 -3 -4 -15
-S 0 -2 0 -3 -2 -4 -4 -1 -5 -6 -7 -3 -5 -6 -1 6 1 -4 -6 -5 -1 -4 -2 -15
-T 0 -5 -1 -4 -7 -5 -5 -5 -6 -2 -6 -2 -3 -8 -3 1 7 -11 -6 -2 -2 -5 -3 -15
-W -12 -1 -7 -13 -14 -11 -15 -13 -6 -12 -5 -10 -11 -4 -12 -4 -11 13 -4 -14 -9 -13 -9 -15
-Y -7 -9 -4 -10 -3 -10 -8 -12 -3 -5 -6 -8 -10 2 -12 -6 -6 -4 10 -6 -6 -8 -7 -15
-V -2 -7 -7 -7 -5 -6 -6 -5 -6 2 -2 -8 -1 -7 -5 -5 -2 -14 -6 7 -7 -6 -4 -15
-B -3 -6 6 6 -11 -2 2 -2 -1 -5 -8 -2 -8 -9 -6 -1 -2 -9 -6 -7 6 1 -4 -15
-Z -2 -3 -2 2 -12 6 6 -4 0 -5 -6 -3 -4 -12 -3 -4 -5 -13 -8 -6 1 6 -4 -15
-X -3 -5 -3 -5 -8 -4 -4 -4 -4 -4 -5 -4 -4 -7 -4 -2 -3 -9 -7 -4 -4 -4 -4 -15
-* -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM400 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM400
deleted file mode 100644
index 4d99c84..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM400
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 400 substitution matrix, scale = ln(2)/5 = 0.138629
-#
-# Expected score = -0.521, Entropy = 0.139 bits
-#
-# Lowest score = -8, Highest score = 26
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 1 0 0 -8
-R -1 5 1 0 -4 1 0 -2 2 -2 -3 4 0 -4 0 0 0 3 -4 -2 0 1 0 -8
-N 0 1 1 2 -3 1 2 1 1 -1 -3 1 -1 -3 0 1 0 -4 -3 -1 2 1 0 -8
-D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -4 -2 2 2 0 -8
-C -2 -4 -3 -5 17 -5 -5 -3 -3 -2 -6 -5 -5 -4 -2 0 -2 -8 1 -2 -4 -5 -3 -8
-Q 0 1 1 2 -5 3 2 0 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -1 2 2 0 -8
-E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 0 0 -7 -4 -1 2 3 0 -8
-G 1 -2 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 0 1 1 -7 -5 -1 1 0 0 -8
-H -1 2 1 1 -3 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -2 0 -2 1 2 0 -8
-I 0 -2 -1 -2 -2 -2 -2 -2 -2 4 3 -2 2 2 -1 -1 0 -5 0 3 -2 -2 0 -8
-L -2 -3 -3 -3 -6 -2 -3 -3 -2 3 7 -2 4 3 -2 -2 -1 -2 0 3 -3 -2 -1 -8
-K -1 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -4 -2 1 1 0 -8
-M -1 0 -1 -2 -5 -1 -2 -2 -1 2 4 0 5 1 -1 -1 0 -4 -1 2 -2 -1 0 -8
-F -3 -4 -3 -5 -4 -4 -5 -5 -2 2 3 -5 1 11 -4 -3 -3 2 10 0 -4 -5 -2 -8
-P 1 0 0 0 -2 0 0 0 0 -1 -2 0 -1 -4 5 1 1 -6 -5 -1 0 0 0 -8
-S 1 0 1 1 0 0 0 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
-T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -8
-W -6 3 -4 -7 -8 -5 -7 -7 -2 -5 -2 -3 -4 2 -6 -3 -5 26 1 -6 -5 -6 -4 -8
-Y -3 -4 -3 -4 1 -4 -4 -5 0 0 0 -4 -1 10 -5 -3 -3 1 13 -2 -3 -4 -2 -8
-V 0 -2 -1 -2 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 4 -1 -1 0 -8
-B 1 0 2 2 -4 2 2 1 1 -2 -3 1 -2 -4 0 1 0 -5 -3 -1 2 2 0 -8
-Z 0 1 1 2 -5 2 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 3 0 -8
-X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -8
-* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM410 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM410
deleted file mode 100644
index b7c9bfd..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM410
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 410 substitution matrix, scale = ln(2)/6 = 0.115525
-#
-# Expected score = -0.617, Entropy = 0.131 bits
-#
-# Lowest score = -10, Highest score = 31
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
-R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 0 -10
-N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 1 -5 -3 -1 2 2 0 -10
-D 1 0 2 3 -6 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
-C -2 -4 -4 -6 20 -6 -6 -4 -4 -3 -7 -6 -6 -4 -3 0 -2 -10 1 -2 -5 -6 -3 -10
-Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -10
-E 1 0 2 3 -6 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
-G 2 -2 1 1 -4 0 1 5 -1 -2 -4 -1 -3 -6 0 1 1 -8 -6 -1 1 0 0 -10
-H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -10
-I 0 -2 -2 -2 -3 -2 -2 -2 -2 4 4 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -10
-L -2 -3 -3 -4 -7 -2 -3 -4 -2 4 8 -3 5 4 -3 -3 -1 -2 1 3 -3 -3 -1 -10
-K -1 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -6 0 0 0 -3 -5 -2 1 1 0 -10
-M -1 0 -2 -2 -6 -1 -2 -3 -2 3 5 0 5 1 -2 -1 0 -4 -2 2 -2 -2 0 -10
-F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 4 -6 1 14 -5 -4 -3 2 12 0 -5 -5 -2 -10
-P 1 0 0 0 -3 1 0 0 0 -2 -3 0 -2 -5 6 1 1 -7 -5 -1 0 0 0 -10
-S 1 0 1 1 0 0 1 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -10
-T 1 0 1 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 2 -6 -3 0 0 0 0 -10
-W -7 4 -5 -8 -10 -5 -8 -8 -3 -6 -2 -3 -4 2 -7 -3 -6 31 2 -7 -6 -7 -4 -10
-Y -4 -5 -3 -5 1 -4 -5 -6 0 0 1 -5 -2 12 -5 -3 -3 2 15 -2 -4 -5 -2 -10
-V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -2 -2 0 -10
-B 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -10
-Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -7 -5 -2 2 3 0 -10
-X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM420 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM420
deleted file mode 100644
index 53e0caf..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM420
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 420 substitution matrix, scale = ln(2)/6 = 0.115525
-#
-# Expected score = -0.599, Entropy = 0.124 bits
-#
-# Lowest score = -10, Highest score = 31
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
-R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 0 -10
-N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 2 0 -10
-D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
-C -2 -4 -4 -5 20 -6 -6 -3 -4 -3 -7 -6 -6 -4 -3 0 -2 -10 1 -2 -5 -6 -3 -10
-Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -10
-E 1 0 2 3 -6 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
-G 2 -2 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -6 0 1 1 -8 -6 -1 1 0 0 -10
-H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -10
-I 0 -2 -2 -2 -3 -2 -2 -2 -2 4 4 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -10
-L -2 -3 -3 -4 -7 -2 -3 -4 -2 4 7 -3 5 4 -2 -3 -1 -2 1 3 -3 -3 -1 -10
-K 0 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -6 0 0 0 -3 -5 -2 1 1 0 -10
-M -1 0 -1 -2 -6 -1 -2 -2 -2 3 5 0 5 1 -2 -1 0 -4 -1 2 -2 -1 0 -10
-F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 4 -6 1 13 -5 -4 -3 2 12 0 -5 -5 -2 -10
-P 1 0 0 0 -3 1 0 0 0 -2 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -10
-S 1 0 1 1 0 0 1 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -10
-T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -10
-W -7 4 -5 -8 -10 -5 -8 -8 -3 -6 -2 -3 -4 2 -6 -3 -6 31 2 -7 -6 -7 -4 -10
-Y -4 -5 -3 -5 1 -4 -5 -6 0 0 1 -5 -1 12 -5 -3 -3 2 15 -2 -4 -5 -2 -10
-V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -2 -2 0 -10
-B 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -10
-Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -1 -5 0 0 0 -7 -5 -2 2 3 0 -10
-X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM430 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM430
deleted file mode 100644
index 2450215..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM430
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 430 substitution matrix, scale = ln(2)/6 = 0.115525
-#
-# Expected score = -0.543, Entropy = 0.117 bits
-#
-# Lowest score = -9, Highest score = 31
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -9
-R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -9
-N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -9
-D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -7 -5 -2 3 3 0 -9
-C -2 -4 -4 -5 20 -6 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9
-Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -1 2 3 0 -9
-E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -1 2 3 0 -9
-G 2 -2 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9
-H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -3 0 -2 1 2 0 -9
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 4 -2 -2 0 -9
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 4 7 -3 5 4 -2 -2 -1 -2 1 3 -3 -3 -1 -9
-K 0 4 1 1 -6 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
-M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 5 1 -2 -1 0 -4 -1 2 -2 -1 0 -9
-F -4 -5 -4 -6 -4 -5 -6 -5 -2 2 4 -5 1 13 -5 -4 -3 2 12 0 -5 -5 -2 -9
-P 1 0 0 0 -3 1 0 0 0 -1 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -9
-S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9
-W -7 4 -5 -7 -9 -5 -8 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 31 2 -7 -6 -6 -4 -9
-Y -4 -4 -3 -5 1 -4 -5 -5 0 0 1 -5 -1 12 -5 -3 -3 2 15 -2 -4 -5 -2 -9
-V 0 -2 -1 -2 -2 -1 -1 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -1 -1 0 -9
-B 1 0 2 3 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -9
-Z 0 1 1 3 -5 3 3 0 2 -2 -3 1 -1 -5 0 0 0 -6 -5 -1 2 3 0 -9
-X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM440 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM440
deleted file mode 100644
index 0429e87..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM440
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 440 substitution matrix, scale = ln(2)/6 = 0.115525
-#
-# Expected score = -0.529, Entropy = 0.111 bits
-#
-# Lowest score = -9, Highest score = 30
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -6 -4 0 1 0 0 -9
-R -1 5 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -9
-N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -9
-D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -7 -5 -2 2 2 0 -9
-C -2 -4 -4 -5 20 -5 -5 -3 -4 -2 -6 -5 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9
-Q 0 2 1 2 -5 3 2 0 3 -2 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9
-E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 3 0 -9
-G 2 -2 1 1 -3 0 1 4 -1 -2 -4 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9
-H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -3 0 -2 1 2 0 -9
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9
-L -2 -3 -3 -3 -6 -2 -3 -4 -2 4 7 -3 5 4 -2 -2 -1 -2 1 3 -3 -2 -1 -9
-K 0 4 1 1 -5 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
-M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9
-F -4 -5 -4 -6 -4 -4 -5 -5 -2 2 4 -5 1 13 -5 -4 -3 2 12 0 -5 -5 -2 -9
-P 1 0 0 0 -3 1 0 0 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 0 0 -9
-S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9
-W -6 4 -5 -7 -9 -5 -7 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 30 2 -6 -6 -6 -4 -9
-Y -4 -4 -3 -5 1 -4 -5 -5 0 0 1 -5 -1 12 -5 -3 -3 2 15 -2 -4 -4 -2 -9
-V 0 -2 -1 -2 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 4 -1 -1 0 -9
-B 1 0 2 2 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -9
-Z 0 1 1 2 -5 2 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 3 0 -9
-X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM450 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM450
deleted file mode 100644
index 30cc7a2..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM450
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 450 substitution matrix, scale = ln(2)/6 = 0.115525
-#
-# Expected score = -0.476, Entropy = 0.105 bits
-#
-# Lowest score = -9, Highest score = 30
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 1 -1 0 -2 0 -1 -3 1 1 1 -6 -4 0 1 0 0 -9
-R -1 5 1 0 -4 2 0 -1 2 -2 -3 4 0 -4 0 0 0 4 -4 -2 0 1 0 -9
-N 0 1 1 2 -4 1 2 1 1 -1 -2 1 -1 -4 0 1 0 -4 -3 -1 1 1 0 -9
-D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9
-C -2 -4 -4 -5 20 -5 -5 -3 -4 -2 -6 -5 -5 -4 -2 0 -2 -9 1 -2 -4 -5 -2 -9
-Q 0 2 1 2 -5 3 2 0 3 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9
-E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 3 0 -9
-G 1 -1 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9
-H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -2 0 -2 1 2 0 -9
-I 0 -2 -1 -2 -2 -1 -2 -2 -2 4 3 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9
-L -2 -3 -2 -3 -6 -2 -3 -3 -2 3 7 -2 4 4 -2 -2 -1 -1 1 3 -3 -2 -1 -9
-K 0 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
-M -1 0 -1 -2 -5 -1 -2 -2 -1 3 4 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9
-F -3 -4 -4 -5 -4 -4 -5 -5 -2 2 4 -5 1 13 -5 -3 -3 2 12 0 -4 -5 -2 -9
-P 1 0 0 0 -2 1 0 0 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 0 0 -9
-S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -9
-W -6 4 -4 -7 -9 -5 -7 -8 -2 -5 -1 -3 -4 2 -6 -3 -5 30 2 -6 -6 -6 -4 -9
-Y -4 -4 -3 -5 1 -4 -5 -5 0 0 1 -5 -1 12 -5 -3 -3 2 14 -2 -4 -4 -2 -9
-V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 3 -1 -1 0 -9
-B 1 0 1 2 -4 2 2 1 1 -2 -3 1 -2 -4 0 1 0 -6 -4 -1 2 2 0 -9
-Z 0 1 1 2 -5 2 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 2 0 -9
-X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM460 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM460
deleted file mode 100644
index 7491d6c..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM460
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 460 substitution matrix, scale = ln(2)/6 = 0.115525
-#
-# Expected score = -0.429, Entropy = 0.0994 bits
-#
-# Lowest score = -9, Highest score = 30
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 1 0 0 -1 0 -1 -3 1 1 1 -6 -3 0 1 0 0 -9
-R -1 5 1 0 -4 1 0 -1 2 -2 -2 4 0 -4 0 0 0 4 -4 -2 0 1 0 -9
-N 0 1 1 2 -3 1 1 1 1 -1 -2 1 -1 -3 0 1 0 -4 -3 -1 1 1 0 -9
-D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -4 -1 2 2 0 -9
-C -2 -4 -3 -5 19 -5 -5 -3 -3 -2 -6 -5 -5 -3 -2 0 -2 -9 2 -2 -4 -5 -2 -9
-Q 0 1 1 2 -5 2 2 0 2 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 1 2 0 -9
-E 1 0 1 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -4 -1 2 2 0 -9
-G 1 -1 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 1 1 1 -7 -5 -1 1 0 0 -9
-H 0 2 1 1 -3 2 1 -1 5 -2 -2 1 -1 -2 0 0 0 -2 0 -2 1 2 0 -9
-I 0 -2 -1 -2 -2 -1 -2 -2 -2 3 3 -2 2 2 -1 -1 0 -5 0 3 -2 -2 0 -9
-L -1 -2 -2 -3 -6 -2 -3 -3 -2 3 7 -2 4 3 -2 -2 -1 -1 1 3 -3 -2 -1 -9
-K 0 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -4 -2 1 1 0 -9
-M -1 0 -1 -2 -5 -1 -2 -2 -1 2 4 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9
-F -3 -4 -3 -5 -3 -4 -5 -5 -2 2 3 -5 1 12 -4 -3 -3 2 11 0 -4 -5 -2 -9
-P 1 0 0 0 -2 1 0 1 0 -1 -2 0 -1 -4 4 1 1 -6 -5 -1 0 0 0 -9
-S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -9
-W -6 4 -4 -7 -9 -5 -7 -7 -2 -5 -1 -3 -4 2 -6 -3 -5 30 2 -6 -6 -6 -4 -9
-Y -3 -4 -3 -4 2 -4 -4 -5 0 0 1 -4 -1 11 -5 -3 -3 2 14 -2 -4 -4 -2 -9
-V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 3 -1 -1 0 -9
-B 1 0 1 2 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 0 -6 -4 -1 2 2 0 -9
-Z 0 1 1 2 -5 2 2 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 2 0 -9
-X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM470 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM470
deleted file mode 100644
index 9d5e333..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM470
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 470 substitution matrix, scale = ln(2)/7 = 0.0990210
-#
-# Expected score = -0.520, Entropy = 0.0942 bits
-#
-# Lowest score = -10, Highest score = 35
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 1 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
-R -1 6 1 0 -4 2 0 -1 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 0 -10
-N 1 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -10
-D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
-C -2 -4 -4 -5 22 -6 -5 -3 -4 -2 -6 -6 -6 -4 -3 0 -2 -10 2 -2 -5 -6 -3 -10
-Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -1 2 2 0 -10
-E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -1 2 3 0 -10
-G 2 -1 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -6 1 1 1 -8 -6 -1 1 1 0 -10
-H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 0 -3 0 -2 1 2 0 -10
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -10
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 4 8 -3 5 4 -2 -2 -1 -2 1 3 -3 -3 -1 -10
-K 0 4 1 1 -6 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -10
-M -1 0 -1 -2 -6 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -10
-F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 4 -5 1 14 -5 -4 -3 3 13 0 -5 -5 -2 -10
-P 1 0 0 0 -3 1 0 1 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 1 0 -10
-S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -4 -3 -1 1 0 0 -10
-T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -10
-W -7 4 -5 -8 -10 -5 -8 -8 -3 -5 -2 -3 -4 3 -6 -4 -6 35 2 -7 -6 -7 -4 -10
-Y -4 -5 -3 -5 2 -4 -5 -6 0 0 1 -5 -1 13 -5 -3 -3 2 16 -2 -4 -5 -2 -10
-V 0 -2 -1 -2 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -7 -2 4 -1 -1 0 -10
-B 1 0 2 3 -5 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -10
-Z 0 1 1 3 -6 2 3 1 2 -2 -3 1 -1 -5 1 0 0 -7 -5 -1 2 3 0 -10
-X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM480 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM480
deleted file mode 100644
index c777c62..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM480
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 480 substitution matrix, scale = ln(2)/7 = 0.0990210
-#
-# Expected score = -0.494, Entropy = 0.0893 bits
-#
-# Lowest score = -10, Highest score = 35
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 1 1 -2 0 1 2 0 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
-R -1 5 1 0 -4 2 0 -1 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -10
-N 1 1 1 2 -4 1 2 1 1 -1 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -10
-D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -7 -5 -1 2 2 0 -10
-C -2 -4 -4 -5 22 -5 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -10 2 -2 -4 -5 -3 -10
-Q 0 2 1 2 -5 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -1 2 2 0 -10
-E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -8 -5 -1 2 3 0 -10
-G 2 -1 1 1 -3 0 1 4 -1 -2 -4 -1 -2 -5 1 1 1 -8 -5 -1 1 1 0 -10
-H 0 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 0 -3 0 -2 1 2 0 -10
-I 0 -2 -1 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -10
-L -2 -3 -3 -3 -6 -2 -3 -4 -2 4 7 -3 5 4 -2 -2 -1 -2 1 3 -3 -3 -1 -10
-K 0 4 1 1 -6 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -10
-M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -10
-F -4 -5 -4 -6 -4 -5 -5 -5 -2 2 4 -5 1 14 -5 -4 -3 3 13 0 -5 -5 -2 -10
-P 1 0 0 0 -3 1 0 1 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 1 0 -10
-S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -10
-T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -10
-W -7 4 -5 -7 -10 -5 -8 -8 -3 -5 -2 -3 -4 3 -6 -3 -6 35 2 -7 -6 -6 -4 -10
-Y -4 -4 -3 -5 2 -4 -5 -5 0 0 1 -5 -1 13 -5 -3 -3 2 16 -2 -4 -5 -2 -10
-V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -7 -2 3 -1 -1 0 -10
-B 1 0 2 2 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -10
-Z 0 1 1 2 -5 2 3 1 2 -2 -3 1 -1 -5 1 0 0 -6 -5 -1 2 2 0 -10
-X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM490 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM490
deleted file mode 100644
index 107a0c8..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM490
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 490 substitution matrix, scale = ln(2)/7 = 0.0990210
-#
-# Expected score = -0.431, Entropy = 0.0847 bits
-#
-# Lowest score = -9, Highest score = 34
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 2 0 0 -1 0 -1 -3 1 1 1 -6 -4 0 1 0 0 -9
-R -1 5 1 0 -4 2 0 -1 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -9
-N 0 1 1 2 -4 1 2 1 1 -1 -2 1 -1 -4 0 1 0 -5 -3 -1 1 1 0 -9
-D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9
-C -2 -4 -4 -5 22 -5 -5 -3 -4 -2 -6 -5 -5 -4 -3 0 -2 -9 2 -2 -4 -5 -2 -9
-Q 0 2 1 2 -5 2 2 0 2 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9
-E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9
-G 2 -1 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 1 1 1 -8 -5 -1 1 1 0 -9
-H 0 2 1 1 -4 2 1 -1 5 -2 -2 1 -1 -2 0 0 0 -3 0 -2 1 2 0 -9
-I 0 -2 -1 -2 -2 -1 -2 -2 -2 3 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9
-L -1 -3 -2 -3 -6 -2 -3 -3 -2 4 7 -2 5 4 -2 -2 -1 -1 1 3 -3 -2 -1 -9
-K 0 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
-M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9
-F -3 -5 -4 -5 -4 -4 -5 -5 -2 2 4 -5 1 14 -5 -4 -3 3 13 0 -5 -5 -2 -9
-P 1 0 0 0 -3 1 0 1 0 -1 -2 0 -1 -5 4 1 1 -6 -5 -1 0 1 0 -9
-S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9
-W -6 4 -5 -7 -9 -5 -7 -8 -3 -5 -1 -3 -4 3 -6 -3 -6 34 2 -6 -6 -6 -4 -9
-Y -4 -4 -3 -5 2 -4 -5 -5 0 0 1 -5 -1 13 -5 -3 -3 2 15 -2 -4 -4 -2 -9
-V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 3 -1 -1 0 -9
-B 1 0 1 2 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -9
-Z 0 1 1 2 -5 2 2 1 2 -2 -2 1 -1 -5 1 0 0 -6 -4 -1 2 2 0 -9
-X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM50 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM50
deleted file mode 100644
index 6d37d4b..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM50
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 50 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -3.70, Entropy = 2.00 bits
-#
-# Lowest score = -13, Highest score = 13
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -5 -2 -2 -5 -3 -1 -1 -5 -3 -5 -5 -4 -7 0 0 0 -11 -6 -1 -2 -2 -2 -13
-R -5 8 -4 -7 -6 0 -7 -7 0 -4 -7 1 -3 -8 -3 -2 -5 -1 -8 -6 -5 -2 -4 -13
-N -2 -4 7 2 -8 -2 -1 -2 1 -4 -6 0 -6 -7 -4 1 -1 -7 -3 -6 5 -1 -2 -13
-D -2 -7 2 7 -11 -1 3 -2 -2 -6 -10 -3 -8 -12 -6 -2 -3 -12 -9 -6 6 2 -4 -13
-C -5 -6 -8 -11 9 -11 -11 -7 -6 -5 -12 -11 -11 -10 -6 -2 -6 -13 -3 -5 -9 -11 -7 -13
-Q -3 0 -2 -1 -11 8 2 -5 2 -6 -4 -2 -3 -10 -2 -4 -4 -10 -9 -5 -2 6 -3 -13
-E -1 -7 -1 3 -11 2 7 -3 -3 -4 -7 -3 -5 -11 -4 -3 -4 -13 -7 -5 2 6 -3 -13
-G -1 -7 -2 -2 -7 -5 -3 6 -7 -8 -9 -6 -7 -8 -4 -1 -4 -12 -11 -4 -2 -4 -4 -13
-H -5 0 1 -2 -6 2 -3 -7 9 -7 -5 -4 -8 -5 -3 -4 -5 -6 -2 -5 0 0 -4 -13
-I -3 -4 -4 -6 -5 -6 -4 -8 -7 8 0 -5 0 -1 -7 -5 -1 -11 -5 3 -5 -5 -3 -13
-L -5 -7 -6 -10 -12 -4 -7 -9 -5 0 6 -6 2 -1 -6 -7 -5 -5 -5 -1 -7 -5 -5 -13
-K -5 1 0 -3 -11 -2 -3 -6 -4 -5 -6 6 -1 -11 -5 -3 -2 -9 -8 -7 -1 -2 -4 -13
-M -4 -3 -6 -8 -11 -3 -5 -7 -8 0 2 -1 10 -3 -6 -4 -3 -10 -8 0 -7 -4 -4 -13
-F -7 -8 -7 -12 -10 -10 -11 -8 -5 -1 -1 -11 -3 9 -8 -5 -7 -3 3 -6 -9 -11 -6 -13
-P 0 -3 -4 -6 -6 -2 -4 -4 -3 -7 -6 -5 -6 -8 8 -1 -3 -11 -11 -4 -5 -3 -4 -13
-S 0 -2 1 -2 -2 -4 -3 -1 -4 -5 -7 -3 -4 -5 -1 6 1 -4 -5 -4 -1 -3 -2 -13
-T 0 -5 -1 -3 -6 -4 -4 -4 -5 -1 -5 -2 -3 -7 -3 1 6 -10 -5 -2 -2 -4 -2 -13
-W -11 -1 -7 -12 -13 -10 -13 -12 -6 -11 -5 -9 -10 -3 -11 -4 -10 13 -4 -12 -8 -11 -9 -13
-Y -6 -8 -3 -9 -3 -9 -7 -11 -2 -5 -5 -8 -8 3 -11 -5 -5 -4 9 -6 -5 -8 -6 -13
-V -1 -6 -6 -6 -5 -5 -5 -4 -5 3 -1 -7 0 -6 -4 -4 -2 -12 -6 7 -6 -5 -3 -13
-B -2 -5 5 6 -9 -2 2 -2 0 -5 -7 -1 -7 -9 -5 -1 -2 -8 -5 -6 5 1 -3 -13
-Z -2 -2 -1 2 -11 6 6 -4 0 -5 -5 -2 -4 -11 -3 -3 -4 -11 -8 -5 1 6 -3 -13
-X -2 -4 -2 -4 -7 -3 -3 -4 -4 -3 -5 -4 -4 -6 -4 -2 -2 -9 -6 -3 -3 -3 -4 -13
-* -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM500 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM500
deleted file mode 100644
index 617c3f1..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM500
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 500 substitution matrix, scale = ln(2)/7 = 0.0990210
-#
-# Expected score = -0.401, Entropy = 0.0803 bits
-#
-# Lowest score = -9, Highest score = 34
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 1 0 0 -1 0 -1 -3 1 1 1 -6 -3 0 1 0 0 -9
-R -1 5 1 0 -4 2 0 -1 2 -2 -2 4 0 -4 0 0 0 4 -4 -2 0 1 0 -9
-N 0 1 1 2 -3 1 1 1 1 -1 -2 1 -1 -4 0 1 0 -5 -3 -1 1 1 0 -9
-D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9
-C -2 -4 -3 -5 22 -5 -5 -3 -4 -2 -6 -5 -5 -3 -2 0 -2 -9 2 -2 -4 -5 -2 -9
-Q 0 2 1 2 -5 2 2 0 2 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9
-E 1 0 1 3 -5 2 3 1 1 -2 -3 1 -1 -5 0 1 0 -7 -5 -1 2 2 0 -9
-G 1 -1 1 1 -3 0 1 4 -1 -2 -3 0 -2 -5 1 1 1 -8 -5 -1 1 1 0 -9
-H 0 2 1 1 -4 2 1 -1 4 -2 -2 1 -1 -2 0 0 0 -2 0 -2 1 2 0 -9
-I 0 -2 -1 -2 -2 -1 -2 -2 -2 3 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9
-L -1 -2 -2 -3 -6 -2 -3 -3 -2 4 7 -2 4 4 -2 -2 -1 -1 1 3 -3 -2 -1 -9
-K 0 4 1 1 -5 1 1 0 1 -2 -2 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
-M -1 0 -1 -2 -5 -1 -1 -2 -1 3 4 0 4 1 -1 -1 0 -4 -1 2 -1 -1 0 -9
-F -3 -4 -4 -5 -3 -4 -5 -5 -2 2 4 -5 1 13 -4 -3 -3 3 13 0 -4 -5 -2 -9
-P 1 0 0 0 -2 1 0 1 0 -1 -2 0 -1 -4 4 1 1 -6 -5 -1 0 1 0 -9
-S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9
-W -6 4 -5 -7 -9 -5 -7 -8 -2 -5 -1 -3 -4 3 -6 -3 -6 34 2 -6 -6 -6 -4 -9
-Y -3 -4 -3 -5 2 -4 -5 -5 0 0 1 -5 -1 13 -5 -3 -3 2 15 -1 -4 -4 -2 -9
-V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -1 3 -1 -1 0 -9
-B 1 0 1 2 -4 2 2 1 1 -2 -3 1 -1 -4 0 1 0 -6 -4 -1 2 2 0 -9
-Z 0 1 1 2 -5 2 2 1 2 -2 -2 1 -1 -5 1 0 0 -6 -4 -1 2 2 0 -9
-X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM60 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM60
deleted file mode 100644
index fba70b9..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM60
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 60 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -3.21, Entropy = 1.79 bits
-#
-# Lowest score = -12, Highest score = 13
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -5 -2 -2 -5 -3 -1 0 -5 -3 -4 -5 -3 -6 0 1 1 -10 -6 -1 -2 -2 -2 -12
-R -5 8 -3 -6 -6 0 -6 -7 0 -4 -6 2 -2 -7 -2 -2 -4 0 -8 -5 -5 -2 -4 -12
-N -2 -3 6 2 -7 -2 0 -1 1 -4 -5 0 -6 -6 -4 1 -1 -6 -3 -5 5 -1 -2 -12
-D -2 -6 2 7 -10 -1 3 -2 -2 -5 -9 -2 -7 -11 -5 -2 -3 -11 -8 -6 5 2 -3 -12
-C -5 -6 -7 -10 9 -10 -10 -7 -6 -4 -11 -10 -10 -9 -6 -1 -5 -12 -2 -4 -9 -10 -6 -12
-Q -3 0 -2 -1 -10 7 2 -5 2 -5 -3 -1 -2 -9 -1 -3 -4 -9 -8 -5 -1 6 -3 -12
-E -1 -6 0 3 -10 2 7 -2 -3 -4 -7 -3 -5 -10 -3 -2 -4 -12 -7 -4 2 5 -3 -12
-G 0 -7 -1 -2 -7 -5 -2 6 -6 -7 -8 -5 -6 -7 -4 0 -3 -11 -10 -4 -2 -3 -3 -12
-H -5 0 1 -2 -6 2 -3 -6 8 -6 -4 -4 -7 -4 -2 -4 -5 -5 -2 -5 0 0 -3 -12
-I -3 -4 -4 -5 -4 -5 -4 -7 -6 7 0 -4 1 -1 -6 -4 -1 -10 -4 3 -4 -4 -3 -12
-L -4 -6 -5 -9 -11 -3 -7 -8 -4 0 6 -6 2 -1 -5 -6 -5 -4 -5 -1 -7 -5 -4 -12
-K -5 2 0 -2 -10 -1 -3 -5 -4 -4 -6 6 0 -10 -4 -2 -2 -8 -7 -6 -1 -2 -3 -12
-M -3 -2 -6 -7 -10 -2 -5 -6 -7 1 2 0 10 -2 -6 -4 -2 -9 -7 0 -6 -4 -3 -12
-F -6 -7 -6 -11 -9 -9 -10 -7 -4 -1 -1 -10 -2 8 -7 -5 -6 -3 3 -5 -8 -10 -5 -12
-P 0 -2 -4 -5 -6 -1 -3 -4 -2 -6 -5 -4 -6 -7 7 0 -2 -10 -10 -4 -4 -2 -3 -12
-S 1 -2 1 -2 -1 -3 -2 0 -4 -4 -6 -2 -4 -5 0 5 1 -4 -5 -4 0 -3 -2 -12
-T 1 -4 -1 -3 -5 -4 -4 -3 -5 -1 -5 -2 -2 -6 -2 1 6 -9 -5 -1 -2 -4 -2 -12
-W -10 0 -6 -11 -12 -9 -12 -11 -5 -10 -4 -8 -9 -3 -10 -4 -9 13 -3 -11 -8 -11 -8 -12
-Y -6 -8 -3 -8 -2 -8 -7 -10 -2 -4 -5 -7 -7 3 -10 -5 -5 -3 9 -5 -5 -7 -5 -12
-V -1 -5 -5 -6 -4 -5 -4 -4 -5 3 -1 -6 0 -5 -4 -4 -1 -11 -5 6 -5 -5 -3 -12
-B -2 -5 5 5 -9 -1 2 -2 0 -4 -7 -1 -6 -8 -4 0 -2 -8 -5 -5 5 1 -3 -12
-Z -2 -2 -1 2 -10 6 5 -3 0 -4 -5 -2 -4 -10 -2 -3 -4 -11 -7 -5 1 5 -3 -12
-X -2 -4 -2 -3 -6 -3 -3 -3 -3 -3 -4 -3 -3 -5 -3 -2 -2 -8 -5 -3 -3 -3 -3 -12
-* -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM70 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM70
deleted file mode 100644
index b20cdf0..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM70
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 70 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -2.77, Entropy = 1.60 bits
-#
-# Lowest score = -11, Highest score = 13
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -4 -2 -1 -4 -2 -1 0 -4 -2 -4 -4 -3 -6 0 1 1 -9 -5 -1 -1 -1 -2 -11
-R -4 8 -3 -6 -5 0 -5 -6 0 -3 -6 2 -2 -7 -2 -1 -4 0 -7 -5 -4 -2 -3 -11
-N -2 -3 6 3 -7 -1 0 -1 1 -3 -5 0 -5 -6 -3 1 0 -6 -3 -5 5 -1 -2 -11
-D -1 -6 3 6 -9 0 3 -1 -1 -5 -8 -2 -7 -10 -4 -1 -2 -10 -7 -5 5 2 -3 -11
-C -4 -5 -7 -9 9 -9 -9 -6 -5 -4 -10 -9 -9 -8 -5 -1 -5 -11 -2 -4 -8 -9 -6 -11
-Q -2 0 -1 0 -9 7 2 -4 2 -5 -3 -1 -2 -9 -1 -3 -3 -8 -8 -4 -1 5 -2 -11
-E -1 -5 0 3 -9 2 6 -2 -2 -4 -6 -2 -4 -9 -3 -2 -3 -11 -6 -4 2 5 -3 -11
-G 0 -6 -1 -1 -6 -4 -2 6 -6 -6 -7 -5 -6 -7 -3 0 -3 -10 -9 -3 -1 -3 -3 -11
-H -4 0 1 -1 -5 2 -2 -6 8 -6 -4 -3 -6 -4 -2 -3 -4 -5 -1 -4 0 1 -3 -11
-I -2 -3 -3 -5 -4 -5 -4 -6 -6 7 1 -4 1 0 -5 -4 -1 -9 -4 3 -4 -4 -3 -11
-L -4 -6 -5 -8 -10 -3 -6 -7 -4 1 6 -5 2 -1 -5 -6 -4 -4 -4 0 -6 -4 -4 -11
-K -4 2 0 -2 -9 -1 -2 -5 -3 -4 -5 6 0 -9 -4 -2 -1 -7 -7 -6 -1 -2 -3 -11
-M -3 -2 -5 -7 -9 -2 -4 -6 -6 1 2 0 10 -2 -5 -3 -2 -8 -7 0 -6 -3 -3 -11
-F -6 -7 -6 -10 -8 -9 -9 -7 -4 0 -1 -9 -2 8 -7 -4 -6 -2 4 -5 -7 -9 -5 -11
-P 0 -2 -3 -4 -5 -1 -3 -3 -2 -5 -5 -4 -5 -7 7 0 -2 -9 -9 -3 -4 -2 -3 -11
-S 1 -1 1 -1 -1 -3 -2 0 -3 -4 -6 -2 -3 -4 0 5 2 -3 -5 -3 0 -2 -1 -11
-T 1 -4 0 -2 -5 -3 -3 -3 -4 -1 -4 -1 -2 -6 -2 2 6 -8 -4 -1 -1 -3 -2 -11
-W -9 0 -6 -10 -11 -8 -11 -10 -5 -9 -4 -7 -8 -2 -9 -3 -8 13 -3 -10 -7 -10 -7 -11
-Y -5 -7 -3 -7 -2 -8 -6 -9 -1 -4 -4 -7 -7 4 -9 -5 -4 -3 9 -5 -4 -7 -5 -11
-V -1 -5 -5 -5 -4 -4 -4 -3 -4 3 0 -6 0 -5 -3 -3 -1 -10 -5 6 -5 -4 -2 -11
-B -1 -4 5 5 -8 -1 2 -1 0 -4 -6 -1 -6 -7 -4 0 -1 -7 -4 -5 5 1 -2 -11
-Z -1 -2 -1 2 -9 5 5 -3 1 -4 -4 -2 -3 -9 -2 -2 -3 -10 -7 -4 1 5 -3 -11
-X -2 -3 -2 -3 -6 -2 -3 -3 -3 -3 -4 -3 -3 -5 -3 -1 -2 -7 -5 -2 -2 -3 -3 -11
-* -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM80 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM80
deleted file mode 100644
index 55aa043..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM80
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 80 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -2.55, Entropy = 1.44 bits
-#
-# Lowest score = -11, Highest score = 13
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 4 -4 -1 -1 -4 -2 -1 0 -4 -2 -4 -4 -3 -5 0 1 1 -8 -5 0 -1 -1 -1 -11
-R -4 7 -2 -5 -5 0 -4 -6 0 -3 -5 2 -2 -6 -2 -1 -3 0 -7 -5 -3 -1 -3 -11
-N -1 -2 5 3 -6 -1 0 -1 2 -3 -5 0 -4 -5 -3 1 0 -5 -3 -4 4 0 -1 -11
-D -1 -5 3 6 -9 0 4 -1 -1 -4 -7 -2 -6 -9 -4 -1 -2 -10 -7 -5 5 2 -3 -11
-C -4 -5 -6 -9 9 -9 -9 -6 -5 -4 -9 -9 -8 -8 -5 -1 -4 -10 -2 -3 -7 -9 -5 -11
-Q -2 0 -1 0 -9 7 2 -4 2 -4 -3 -1 -2 -8 -1 -3 -3 -8 -7 -4 0 5 -2 -11
-E -1 -4 0 4 -9 2 6 -2 -2 -3 -6 -2 -4 -9 -3 -2 -3 -11 -6 -4 2 5 -2 -11
-G 0 -6 -1 -1 -6 -4 -2 6 -5 -6 -7 -4 -5 -6 -3 0 -2 -10 -8 -3 -1 -2 -3 -11
-H -4 0 2 -1 -5 2 -2 -5 8 -5 -4 -3 -5 -3 -2 -3 -4 -4 -1 -4 0 1 -2 -11
-I -2 -3 -3 -4 -4 -4 -3 -6 -5 7 1 -4 1 0 -5 -4 -1 -8 -3 3 -4 -4 -2 -11
-L -4 -5 -5 -7 -9 -3 -6 -7 -4 1 6 -5 2 0 -4 -5 -4 -3 -4 0 -6 -4 -3 -11
-K -4 2 0 -2 -9 -1 -2 -4 -3 -4 -5 6 0 -9 -4 -2 -1 -7 -6 -5 -1 -1 -3 -11
-M -3 -2 -4 -6 -8 -2 -4 -5 -5 1 2 0 9 -2 -5 -3 -2 -7 -6 1 -5 -3 -2 -11
-F -5 -6 -5 -9 -8 -8 -9 -6 -3 0 0 -9 -2 8 -7 -4 -5 -2 4 -4 -7 -8 -5 -11
-P 0 -2 -3 -4 -5 -1 -3 -3 -2 -5 -4 -4 -5 -7 7 0 -2 -9 -8 -3 -3 -2 -2 -11
-S 1 -1 1 -1 -1 -3 -2 0 -3 -4 -5 -2 -3 -4 0 4 2 -3 -4 -3 0 -2 -1 -11
-T 1 -3 0 -2 -4 -3 -3 -2 -4 -1 -4 -1 -2 -5 -2 2 5 -8 -4 -1 -1 -3 -1 -11
-W -8 0 -5 -10 -10 -8 -11 -10 -4 -8 -3 -7 -7 -2 -9 -3 -8 13 -2 -10 -7 -9 -7 -11
-Y -5 -7 -3 -7 -2 -7 -6 -8 -1 -3 -4 -6 -6 4 -8 -4 -4 -2 9 -5 -4 -6 -4 -11
-V 0 -5 -4 -5 -3 -4 -4 -3 -4 3 0 -5 1 -4 -3 -3 -1 -10 -5 6 -4 -4 -2 -11
-B -1 -3 4 5 -7 0 2 -1 0 -4 -6 -1 -5 -7 -3 0 -1 -7 -4 -4 5 2 -2 -11
-Z -1 -1 0 2 -9 5 5 -2 1 -4 -4 -1 -3 -8 -2 -2 -3 -9 -6 -4 2 5 -2 -11
-X -1 -3 -1 -3 -5 -2 -2 -3 -2 -2 -3 -3 -2 -5 -2 -1 -1 -7 -4 -2 -2 -2 -3 -11
-* -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM90 b/maven-src/target/classes/java/jaligner/matrix/matrices/PAM90
deleted file mode 100644
index fa2d5b3..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/matrices/PAM90
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 90 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -2.26, Entropy = 1.30 bits
-#
-# Lowest score = -10, Highest score = 13
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 4 -4 -1 -1 -3 -2 0 0 -4 -2 -3 -3 -2 -5 0 1 1 -8 -5 0 -1 -1 -1 -10
-R -4 7 -2 -5 -5 0 -4 -5 1 -3 -5 2 -2 -6 -1 -1 -3 0 -6 -4 -3 -1 -2 -10
-N -1 -2 5 3 -6 -1 0 -1 2 -3 -4 1 -4 -5 -2 1 0 -5 -2 -4 4 0 -1 -10
-D -1 -5 3 6 -8 0 4 -1 -1 -4 -7 -2 -5 -8 -4 -1 -2 -9 -6 -4 5 3 -2 -10
-C -3 -5 -6 -8 9 -8 -8 -5 -5 -3 -9 -8 -8 -7 -5 -1 -4 -10 -1 -3 -7 -8 -5 -10
-Q -2 0 -1 0 -8 6 2 -3 2 -4 -3 -1 -2 -7 -1 -2 -3 -7 -6 -4 0 5 -2 -10
-E 0 -4 0 4 -8 2 6 -1 -1 -3 -5 -2 -4 -8 -2 -2 -2 -10 -6 -3 2 5 -2 -10
-G 0 -5 -1 -1 -5 -3 -1 5 -5 -5 -6 -4 -5 -6 -3 0 -2 -9 -8 -3 -1 -2 -2 -10
-H -4 1 2 -1 -5 2 -1 -5 8 -5 -3 -2 -5 -3 -2 -3 -3 -4 -1 -4 1 1 -2 -10
-I -2 -3 -3 -4 -3 -4 -3 -5 -5 6 1 -3 1 0 -4 -3 0 -8 -3 3 -3 -3 -2 -10
-L -3 -5 -4 -7 -9 -3 -5 -6 -3 1 6 -5 2 0 -4 -5 -3 -3 -3 0 -5 -4 -3 -10
-K -3 2 1 -2 -8 -1 -2 -4 -2 -3 -5 5 0 -8 -3 -1 -1 -6 -6 -5 0 -1 -2 -10
-M -2 -2 -4 -5 -8 -2 -4 -5 -5 1 2 0 9 -1 -4 -3 -2 -7 -6 1 -5 -3 -2 -10
-F -5 -6 -5 -8 -7 -7 -8 -6 -3 0 0 -8 -1 8 -6 -4 -5 -2 4 -4 -6 -8 -4 -10
-P 0 -1 -2 -4 -5 -1 -2 -3 -2 -4 -4 -3 -4 -6 7 0 -1 -8 -8 -3 -3 -2 -2 -10
-S 1 -1 1 -1 -1 -2 -2 0 -3 -3 -5 -1 -3 -4 0 4 2 -3 -4 -3 0 -2 -1 -10
-T 1 -3 0 -2 -4 -3 -2 -2 -3 0 -3 -1 -2 -5 -1 2 5 -7 -4 -1 -1 -2 -1 -10
-W -8 0 -5 -9 -10 -7 -10 -9 -4 -8 -3 -6 -7 -2 -8 -3 -7 13 -2 -9 -7 -8 -6 -10
-Y -5 -6 -2 -6 -1 -6 -6 -8 -1 -3 -3 -6 -6 4 -8 -4 -4 -2 9 -4 -4 -6 -4 -10
-V 0 -4 -4 -4 -3 -4 -3 -3 -4 3 0 -5 1 -4 -3 -3 -1 -9 -4 6 -4 -3 -2 -10
-B -1 -3 4 5 -7 0 2 -1 1 -3 -5 0 -5 -6 -3 0 -1 -7 -4 -4 4 2 -2 -10
-Z -1 -1 0 3 -8 5 5 -2 1 -3 -4 -1 -3 -8 -2 -2 -2 -8 -6 -3 2 5 -2 -10
-X -1 -2 -1 -2 -5 -2 -2 -2 -2 -2 -3 -2 -2 -4 -2 -1 -1 -6 -4 -2 -2 -2 -2 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/maven-src/target/classes/java/jaligner/matrix/package.html b/maven-src/target/classes/java/jaligner/matrix/package.html
deleted file mode 100644
index d5583c2..0000000
--- a/maven-src/target/classes/java/jaligner/matrix/package.html
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
-
-
-Scoring matrices package.
-@author Ahmed Moustafa (ahmed@users.sf.net)
-
-
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/package.html b/maven-src/target/classes/java/jaligner/package.html
deleted file mode 100644
index 614c03d..0000000
--- a/maven-src/target/classes/java/jaligner/package.html
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
-
-
-Core classes for the implementation of Smith-Waterman-Gotoh algorithm
-@author Ahmed Moustafa (ahmed@users.sf.net)
-
-
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/test/AlignmentScoreChecker.java b/maven-src/target/classes/java/jaligner/test/AlignmentScoreChecker.java
deleted file mode 100644
index 4a57cc5..0000000
--- a/maven-src/target/classes/java/jaligner/test/AlignmentScoreChecker.java
+++ /dev/null
@@ -1,131 +0,0 @@
-/*
- * $Id: AlignmentScoreChecker.java,v 1.2 2005/04/18 14:06:15 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.test;
-
-import jaligner.Alignment;
-import jaligner.Sequence;
-import jaligner.SmithWatermanGotoh;
-import jaligner.formats.Format;
-import jaligner.formats.Pair;
-import jaligner.matrix.Matrix;
-import jaligner.matrix.MatrixLoader;
-
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.Random;
-
-/**
- * Testing the scores of the alignments of the SmithWaterman algorithm
- *
- * @author Bram Minnaert
- */
-
-public class AlignmentScoreChecker {
-
- public static void main(String[] args) {
-
- int numberOfTests = Integer.parseInt(args[0]);
- int sequencesSize = Integer.parseInt(args[1]);
- Random random = new Random();
- Format format = new Pair();
-
- try {
- ArrayList matrices = new ArrayList();
- for (Iterator i = MatrixLoader.list().iterator(); i.hasNext();) {
- matrices.add(i.next());
- }
- int countOfMatrices = matrices.size();
-
- int i = 1;
- while (i <= numberOfTests) {
-
- System.gc();
-
- String s1 = RandomSequenceGenerator.generate(sequencesSize);
- String s2 = RandomSequenceGenerator.generate(sequencesSize);
-
- int o = random.nextInt(50);
- int e = random.nextInt(10);
-
- if (s1.length() > 0 && s2.length() > 0 && o >= e) {
-
- Matrix matrix = (Matrix) MatrixLoader
- .load((String) matrices.get(random
- .nextInt(countOfMatrices)));
- Sequence seq1 = new Sequence(s1);
- Sequence seq2 = new Sequence(s2);
-
- Alignment alignment1 = SmithWatermanGotoh.align(seq1, seq2,
- matrix, o, e);
-
- if (!alignment1.checkScore()) {
- System.err.println("Invalid alignment found:");
- System.err.println("Sequence 1 = " + s1);
- System.err.println("Sequence 2 = " + s2);
- System.err.println(format.format(alignment1));
- System.err.println(alignment1.getSummary());
- System.err
- .println("The score of the alignment above is: "
- + alignment1.calculateScore());
- System.exit(1);
- }
-
- Alignment alignment2 = SmithWatermanGotoh.align(seq2, seq1,
- matrix, o, e);
- if (!alignment1.checkScore()) {
- System.err.println("Invalid alignment found:");
- System.err.println("Sequence 1 = " + s2);
- System.err.println("Sequence 2 = " + s1);
- System.err.println(format.format(alignment2));
- System.err.println(alignment2.getSummary());
- System.err
- .println("The score of the alignment above is: "
- + alignment2.calculateScore());
- System.exit(1);
- }
-
- if (alignment1.getScore() != alignment2.getScore()) {
- System.err.println("Not symmetric alignment:");
-
- System.err.println("Alignment #1: ");
- System.err.println("Sequence 1 = " + s1);
- System.err.println("Sequence 2 = " + s2);
- System.err.println(format.format(alignment1));
- System.err.println(alignment1.getSummary());
-
- System.err.println();
-
- System.err.println("Alignment #2: ");
- System.err.println("Sequence 1 = " + s2);
- System.err.println("Sequence 2 = " + s1);
- System.err.println(format.format(alignment2));
- System.err.println(alignment2.getSummary());
-
- System.exit(1);
- }
- }
- System.out.println("Processed " + i + "/" + numberOfTests);
- i++;
- }
- } catch (Exception e) {
- e.printStackTrace();
- System.exit(1);
- }
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/test/RandomSequenceGenerator.java b/maven-src/target/classes/java/jaligner/test/RandomSequenceGenerator.java
deleted file mode 100644
index 0701d80..0000000
--- a/maven-src/target/classes/java/jaligner/test/RandomSequenceGenerator.java
+++ /dev/null
@@ -1,75 +0,0 @@
-/*
- * $Id: RandomSequenceGenerator.java,v 1.1 2005/04/03 19:38:21 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.test;
-
-import java.util.Random;
-
-/**
- * This class contains a random generator for smithwaterman sequences.
- *
- * @author Bram Minnaert
- */
-
-public class RandomSequenceGenerator {
-
- /**
- * All possible characters
- */
- private static final char[] CHARS = {
- 'A', 'R', 'N', 'D', 'C', 'Q', 'E',
- 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P',
- 'S', 'T', 'W', 'Y', 'V', 'B', 'Z', 'X'};
-
- /**
- * Number of possible characters
- */
- private static final int NUMBER_OF_CHARS = CHARS.length;
-
- /**
- * Random generator
- */
- private static Random random = new Random();
-
- /**
- * Returns random sequence
- * @param length Size of the sequence
- * @return Random sequence
- */
- public static String generate(int length) {
- StringBuffer buffer = new StringBuffer();
- char randomChar;
- int randomInt;
- for (int i = 0; i < length ; i++) {
- randomInt = random.nextInt(NUMBER_OF_CHARS);
- randomChar = CHARS[randomInt];
- buffer.append(randomChar);
- }
- return buffer.toString();
- }
-
- /**
- * Displays 10 random smithwaterman sequences with length 50.
- * @param args no args
- */
- public static void main(String[] args) {
- for (int i = 0; i < 10; i++) {
- System.out.println("S" + i + " = " + generate(50));
- }
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/test/package.html b/maven-src/target/classes/java/jaligner/test/package.html
deleted file mode 100644
index 56c88e4..0000000
--- a/maven-src/target/classes/java/jaligner/test/package.html
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
-
-
-Testing package.
-@author Bram Minnaert
-
-
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/AlignCommandLine.java b/maven-src/target/classes/java/jaligner/ui/AlignCommandLine.java
deleted file mode 100644
index bdc0df8..0000000
--- a/maven-src/target/classes/java/jaligner/ui/AlignCommandLine.java
+++ /dev/null
@@ -1,93 +0,0 @@
-/*
- * $Id: AlignCommandLine.java,v 1.7 2005/04/18 05:37:52 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui;
-
-import jaligner.Alignment;
-import jaligner.Sequence;
-import jaligner.SmithWatermanGotoh;
-import jaligner.formats.Pair;
-import jaligner.matrix.Matrix;
-import jaligner.matrix.MatrixLoader;
-import jaligner.util.Commons;
-import jaligner.util.SequenceParser;
-
-import java.io.File;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-/**
- * Command line interface for JAligner.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-public class AlignCommandLine {
-
- private static final Logger logger = Logger.getLogger(AlignCommandLine.class.getName());
-
- /**
- * @param args The command line arguments
- */
- public static void main(String[] args) {
- logger.info( Commons.getJAlignerInfo() );
-
- if (args.length == 0) {
- new AlignWindow().setVisible(true);
- } else {
- if (args.length == 5) {
- try {
-
- String f1 = args[0]; // file name of sequence #1
- String f2 = args[1]; // file name of sequence #1
- String m = args[2]; // scoring matrix id or file name user-defined scoring matrix
- float o = Float.parseFloat(args[3]); // open gap penalty
- float e = Float.parseFloat(args[4]); // extend gap penalty
-
- Sequence s1 = SequenceParser.parse(new File(f1));
- Sequence s2 = SequenceParser.parse(new File(f2));
- Matrix matrix = MatrixLoader.load(m);
- Alignment alignment = SmithWatermanGotoh.align (s1, s2, matrix, o, e);
- System.out.println (alignment.getSummary());
- System.out.println (new Pair().format(alignment));
- } catch (Exception e) {
- logger.log(Level.SEVERE, "Failed processing the command line: " + e.getMessage(), e);
- System.exit(1);
- }
- } else {
- logger.severe( "Invalid number of arguments: " + args.length );
- printUsage();
- System.exit(1);
- }
- }
-
- }
-
- /**
- * Prints the syntax for using JAligner
- */
- private static void printUsage( ) {
- StringBuffer buffer = new StringBuffer();
- buffer.append ( "\n" );
- buffer.append ( "Usage:\n" );
- buffer.append ( "------\n" );
- buffer.append ( "[1] java -jar jaligner.jar \n" );
- buffer.append ( "[2] java -jar jaligner.jar\n" );
- buffer.append ( "\n" ) ;
- logger.info(buffer.toString());
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/AlignWindow.form b/maven-src/target/classes/java/jaligner/ui/AlignWindow.form
deleted file mode 100644
index 20c67ee..0000000
--- a/maven-src/target/classes/java/jaligner/ui/AlignWindow.form
+++ /dev/null
@@ -1,896 +0,0 @@
-
-
-
diff --git a/maven-src/target/classes/java/jaligner/ui/AlignWindow.java b/maven-src/target/classes/java/jaligner/ui/AlignWindow.java
deleted file mode 100644
index 6f099cf..0000000
--- a/maven-src/target/classes/java/jaligner/ui/AlignWindow.java
+++ /dev/null
@@ -1,1663 +0,0 @@
-
-
-package jaligner.ui;
-
-import jaligner.Alignment;
-import jaligner.Sequence;
-import jaligner.SmithWatermanGotoh;
-import jaligner.example.Example;
-import jaligner.formats.CLUSTAL;
-import jaligner.formats.FASTA;
-import jaligner.formats.FormatFactory;
-import jaligner.formats.Pair;
-import jaligner.matrix.Matrix;
-import jaligner.matrix.MatrixLoader;
-import jaligner.ui.clipboard.ClipboardListener;
-import jaligner.ui.clipboard.ClipboardPoller;
-import jaligner.ui.filechooser.FileChooserFactory;
-import jaligner.ui.filechooser.NamedInputStream;
-import jaligner.ui.images.ToolbarIcons;
-import jaligner.ui.logging.DocumentHandler;
-import jaligner.ui.util.TextComponentUtil;
-import jaligner.ui.util.TextComponentUtilException;
-import jaligner.util.Commons;
-import jaligner.util.SequenceParser;
-
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Cursor;
-import java.awt.Image;
-import java.awt.event.ActionEvent;
-import java.awt.event.MouseEvent;
-import java.net.URL;
-import java.text.DecimalFormat;
-import java.util.Collection;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-import javax.swing.AbstractAction;
-import javax.swing.AbstractButton;
-import javax.swing.Action;
-import javax.swing.JComboBox;
-import javax.swing.JFormattedTextField;
-import javax.swing.JOptionPane;
-import javax.swing.JTextArea;
-import javax.swing.KeyStroke;
-import javax.swing.event.CaretEvent;
-import javax.swing.event.DocumentEvent;
-import javax.swing.event.DocumentListener;
-import javax.swing.text.JTextComponent;
-
-/**
- * Graphical user inteface for JAligner.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class AlignWindow extends javax.swing.JFrame implements ClipboardListener, DocumentListener {
- /**
- *
- */
- private static final long serialVersionUID = 3257844376876364850L;
-
- /**
- * Window width
- */
- private static final int WINDOW_WIDTH = 800;
-
- /**
- * Window height
- */
- private static final int WINDOW_HEIGHT = 600;
-
- /**
- * Default open gap penalty
- */
- private static final float DEFAULT_OPEN_GAP_PENALTY = 10f;
-
- /**
- * Default extend gap penalty
- */
- private static final float DEFAULT_EXTEND_GAP_PENALTY = 0.5f;
-
- /**
- * Default scoring matrix
- */
- private static final String DEFAULT_SCORING_MATRIX = "BLOSUM62";
-
- /**
- * Logger
- */
- private static final Logger logger = Logger.getLogger(AlignWindow.class.getName());
-
- /**
- * Clipboard poller thread
- */
- private ClipboardPoller clipboardPoller = null;
-
- /**
- * Loaded scoring matrices
- */
- private HashMap matrices = new HashMap();
-
- /**
- * Current text component
- */
- private JTextComponent currentTextComponent = null;
-
- // The actions
- public Action nextFocusAction = new AbstractAction("Move Focus Forwards") {
- /**
- *
- */
- private static final long serialVersionUID = 3763091972940183858L;
-
- public void actionPerformed(ActionEvent evt) {
- ((Component)evt.getSource()).transferFocus();
- }
- };
-
- public Action prevFocusAction = new AbstractAction("Move Focus Backwards") {
- /**
- *
- */
- private static final long serialVersionUID = 3257844402628997943L;
-
- public void actionPerformed(ActionEvent evt) {
- ((Component)evt.getSource()).transferFocusBackward();
- }
- };
-
- /**
- * Constructor
- */
- public AlignWindow() {
- initComponents();
-
- logger.addHandler(new DocumentHandler(jTextPaneConsole));
-
- try {
- // Set the icon for the frame
- URL url = getClass().getResource( ToolbarIcons.GIFS_HOME + "jaligner.gif");
- if (url != null) {
- Image image = java.awt.Toolkit.getDefaultToolkit().getImage(url);
- setIconImage(image);
- } else {
- logger.warning("Image URL is NULL");
- }
- } catch (Exception e) {
- logger.log(Level.WARNING, "Failed setting the frame image: " + e.getMessage(), e);
- }
-
- jMenuItemFileOpen.setVisible(false);
-
- jFormattedTextFieldGapOpen.setValue(new Float(DEFAULT_OPEN_GAP_PENALTY));
- jFormattedTextFieldGapExtend.setValue(new Float(DEFAULT_EXTEND_GAP_PENALTY));
-
- Collection matrices = null;
- try {
- matrices = MatrixLoader.list(false);
- } catch (Exception e) {
- logger.log(Level.WARNING, "Failed getting list of scoring matrices: " + e.getMessage(), e);
- }
- if (matrices != null) {
- populateComboBox(jComboBoxScoringMatrix, matrices, DEFAULT_SCORING_MATRIX);
- }
-
- FormatFactory.getInstance().registerFormat(new CLUSTAL());
- FormatFactory.getInstance().registerFormat(new Pair());
- FormatFactory.getInstance().registerFormat(new FASTA());
-
- Collection formats = FormatFactory.getInstance().getFormats();
- String[] outputFormats = new String[formats.size()];
- Iterator i = formats.iterator();
- for (int j = 0; i.hasNext(); j++) {
- outputFormats[j] = (String) i.next();
- }
- populateComboBox(jComboBoxOutputFormat, outputFormats, null);
-
- jTextAreaSequence1.getDocument().addDocumentListener(this);
- jTextAreaSequence2.getDocument().addDocumentListener(this);
- jTextAreaAlignment.getDocument().addDocumentListener(this);
-
- // Add actions
- jTextAreaSequence1.getInputMap().put(KeyStroke.getKeyStroke("TAB"), nextFocusAction.getClass().getName());
- jTextAreaSequence1.getActionMap().put(nextFocusAction.getClass().getName(), nextFocusAction);
- jTextAreaSequence1.getInputMap().put(KeyStroke.getKeyStroke("shift TAB"), prevFocusAction.getClass().getName());
- jTextAreaSequence1.getActionMap().put(prevFocusAction.getClass().getName(), prevFocusAction);
-
- jTextAreaSequence2.getInputMap().put(KeyStroke.getKeyStroke("TAB"), nextFocusAction.getClass().getName());
- jTextAreaSequence2.getActionMap().put(nextFocusAction.getClass().getName(), nextFocusAction);
- jTextAreaSequence2.getInputMap().put(KeyStroke.getKeyStroke("shift TAB"), prevFocusAction.getClass().getName());
- jTextAreaSequence2.getActionMap().put(prevFocusAction.getClass().getName(), prevFocusAction);
-
- // Add radio buttons to group
- buttonGroupSequences.add(jRadioButtonSequence1);
- buttonGroupSequences.add(jRadioButtonSequence2);
- buttonGroupSequences.add(jRadioButtonAlignment);
- buttonGroupSequences.add(jRadioButtonConsole);
-
- // Split the space
- jSplitPaneBody.setResizeWeight(.9D);
- jSplitPaneIO.setResizeWeight(.5D);
- jSplitPaneSequences.setResizeWeight(.5D);
-
- // Set the focus on the text area for sequence #1
- jTextAreaSequence1.requestFocus();
-
- // Start the clipboard checker
- clipboardPoller = new ClipboardPoller(this);
- clipboardPoller.start();
-
- // Hide the print menu item in under the File menu
- jMenuItemFilePrint.setVisible(false);
-
- // Set the frame size
- this.setSize(WINDOW_WIDTH, WINDOW_HEIGHT);
- }
-
- private void initComponents() {//GEN-BEGIN:initComponents
- jPopup = new javax.swing.JPopupMenu();
- jPopupOpen = new javax.swing.JMenuItem();
- jPopupSave = new javax.swing.JMenuItem();
- jPopupSeparator1 = new javax.swing.JSeparator();
- jPopupCut = new javax.swing.JMenuItem();
- jPopupCopy = new javax.swing.JMenuItem();
- jPopupPaste = new javax.swing.JMenuItem();
- jPopupDelete = new javax.swing.JMenuItem();
- jPopupSeparator2 = new javax.swing.JSeparator();
- jPopupPrint = new javax.swing.JMenuItem();
- jPopupSeparator3 = new javax.swing.JSeparator();
- jPopupSelectAll = new javax.swing.JMenuItem();
- buttonGroupSequences = new javax.swing.ButtonGroup();
- jToolBar = new javax.swing.JToolBar();
- jButtonOpen = new javax.swing.JButton();
- jButtonSave = new javax.swing.JButton();
- jButtonCut = new javax.swing.JButton();
- jButtonCopy = new javax.swing.JButton();
- jButtonPaste = new javax.swing.JButton();
- jButtonDelete = new javax.swing.JButton();
- jButtonPrint = new javax.swing.JButton();
- jButtonExit = new javax.swing.JButton();
- jSplitPaneBody = new javax.swing.JSplitPane();
- jSplitPaneIO = new javax.swing.JSplitPane();
- jSplitPaneSequences = new javax.swing.JSplitPane();
- jPanelSequence1 = new javax.swing.JPanel();
- jScrollPaneSequence1 = new javax.swing.JScrollPane();
- jTextAreaSequence1 = new JTextArea();
- jRadioButtonSequence1 = new javax.swing.JRadioButton();
- jPanelSequence2 = new javax.swing.JPanel();
- jScrollPaneSequence2 = new javax.swing.JScrollPane();
- jTextAreaSequence2 = new JTextArea();
- jRadioButtonSequence2 = new javax.swing.JRadioButton();
- jPanelAlignment = new javax.swing.JPanel();
- jRadioButtonAlignment = new javax.swing.JRadioButton();
- jScrollPaneAlignment = new javax.swing.JScrollPane();
- jTextAreaAlignment = new JTextArea();
- jPanelConsole = new javax.swing.JPanel();
- jRadioButtonConsole = new javax.swing.JRadioButton();
- jScrollPaneConsole = new javax.swing.JScrollPane();
- jTextPaneConsole = new javax.swing.JTextPane();
- jPanelControls = new javax.swing.JPanel();
- jPanelScoringMatrix = new javax.swing.JPanel();
- jLabelScoringMatrix = new javax.swing.JLabel();
- jComboBoxScoringMatrix = new JComboBox();
- jPanelGapOpen = new javax.swing.JPanel();
- jLabelOpenGapPenalty = new javax.swing.JLabel();
- jFormattedTextFieldGapOpen = new JFormattedTextField(new DecimalFormat("##0.0##"));
- jPanelGapExtend = new javax.swing.JPanel();
- jLabelExtendGapPenalty = new javax.swing.JLabel();
- jFormattedTextFieldGapExtend = new JFormattedTextField(new DecimalFormat("##0.0##"));
- jPanelOutputFormat = new javax.swing.JPanel();
- jLabelOutputFormat = new javax.swing.JLabel();
- jComboBoxOutputFormat = new JComboBox();
- jPanelGo = new javax.swing.JPanel();
- jButtonGo = new javax.swing.JButton();
- jMenuBar = new javax.swing.JMenuBar();
- jMenuFile = new javax.swing.JMenu();
- jMenuItemFileOpen = new javax.swing.JMenuItem();
- jMenuItemFileLoadSequence1 = new javax.swing.JMenuItem();
- jMenuItemFileLoadSequence2 = new javax.swing.JMenuItem();
- jMenuItemFileLoadMatrix = new javax.swing.JMenuItem();
- jSeparatorFile = new javax.swing.JSeparator();
- jMenuItemFileExit = new javax.swing.JMenuItem();
- jMenuItemFilePrint = new javax.swing.JMenuItem();
- jMenuEdit = new javax.swing.JMenu();
- jMenuItemEditCut = new javax.swing.JMenuItem();
- jMenuItemEditCopy = new javax.swing.JMenuItem();
- jMenuItemEditPaste = new javax.swing.JMenuItem();
- jMenuItemEditDelete = new javax.swing.JMenuItem();
- jMenuItemEditSelectAll = new javax.swing.JMenuItem();
- jMenuTools = new javax.swing.JMenu();
- jMenuItemToolsRunExample = new javax.swing.JMenuItem();
- jMenuHelp = new javax.swing.JMenu();
- jMenuItemAbout = new javax.swing.JMenuItem();
-
- jPopupOpen.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_O, java.awt.event.InputEvent.CTRL_MASK));
- jPopupOpen.setIcon(ToolbarIcons.OPEN);
- jPopupOpen.setMnemonic('O');
- jPopupOpen.setText("Open...");
- jPopupOpen.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jPopupOpenActionPerformed(evt);
- }
- });
-
- jPopup.add(jPopupOpen);
-
- jPopupSave.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_S, java.awt.event.InputEvent.CTRL_MASK));
- jPopupSave.setIcon(ToolbarIcons.SAVE);
- jPopupSave.setMnemonic('S');
- jPopupSave.setText("Save...");
- jPopupSave.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jPopupSaveActionPerformed(evt);
- }
- });
-
- jPopup.add(jPopupSave);
-
- jPopup.add(jPopupSeparator1);
-
- jPopupCut.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_X, java.awt.event.InputEvent.CTRL_MASK));
- jPopupCut.setIcon(ToolbarIcons.CUT);
- jPopupCut.setMnemonic('t');
- jPopupCut.setText("Cut");
- jPopupCut.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jPopupCutActionPerformed(evt);
- }
- });
-
- jPopup.add(jPopupCut);
-
- jPopupCopy.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_C, java.awt.event.InputEvent.CTRL_MASK));
- jPopupCopy.setIcon(ToolbarIcons.COPY);
- jPopupCopy.setMnemonic('C');
- jPopupCopy.setText("Copy");
- jPopupCopy.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jPopupCopyActionPerformed(evt);
- }
- });
-
- jPopup.add(jPopupCopy);
-
- jPopupPaste.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_V, java.awt.event.InputEvent.CTRL_MASK));
- jPopupPaste.setIcon(ToolbarIcons.PASTE);
- jPopupPaste.setMnemonic('P');
- jPopupPaste.setText("Paste");
- jPopupPaste.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jPopupPasteActionPerformed(evt);
- }
- });
-
- jPopup.add(jPopupPaste);
-
- jPopupDelete.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_DELETE, 0));
- jPopupDelete.setIcon(ToolbarIcons.DELETE);
- jPopupDelete.setMnemonic('D');
- jPopupDelete.setText("Delete");
- jPopupDelete.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jPopupDeleteActionPerformed(evt);
- }
- });
-
- jPopup.add(jPopupDelete);
-
- jPopup.add(jPopupSeparator2);
-
- jPopupPrint.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_P, java.awt.event.InputEvent.CTRL_MASK));
- jPopupPrint.setIcon(ToolbarIcons.PRINT);
- jPopupPrint.setMnemonic('D');
- jPopupPrint.setText("Print");
- jPopupPrint.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jPopupPrintActionPerformed(evt);
- }
- });
-
- jPopup.add(jPopupPrint);
-
- jPopup.add(jPopupSeparator3);
-
- jPopupSelectAll.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_A, java.awt.event.InputEvent.CTRL_MASK));
- jPopupSelectAll.setMnemonic('A');
- jPopupSelectAll.setText("Select All");
- jPopupSelectAll.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jPopupSelectAllActionPerformed(evt);
- }
- });
-
- jPopup.add(jPopupSelectAll);
-
- setDefaultCloseOperation(javax.swing.WindowConstants.DO_NOTHING_ON_CLOSE);
- setTitle("JAligner - biological pairwise sequence alignment ");
- setName("AlignWindow");
- addWindowListener(new java.awt.event.WindowAdapter() {
- public void windowClosing(java.awt.event.WindowEvent evt) {
- exitForm(evt);
- }
- });
-
- jButtonOpen.setIcon(ToolbarIcons.OPEN);
- jButtonOpen.setToolTipText("Open...");
- jButtonOpen.setFocusable(false);
- jButtonOpen.setPreferredSize(new java.awt.Dimension(24, 24));
- jButtonOpen.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jButtonOpenActionPerformed(evt);
- }
- });
-
- jToolBar.add(jButtonOpen);
-
- jButtonSave.setIcon(ToolbarIcons.SAVE);
- jButtonSave.setToolTipText("Save...");
- jButtonSave.setFocusable(false);
- jButtonSave.setPreferredSize(new java.awt.Dimension(24, 24));
- jButtonSave.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jButtonSaveActionPerformed(evt);
- }
- });
-
- jToolBar.add(jButtonSave);
-
- jButtonCut.setIcon(ToolbarIcons.CUT);
- jButtonCut.setToolTipText("Cut");
- jButtonCut.setFocusable(false);
- jButtonCut.setPreferredSize(new java.awt.Dimension(24, 24));
- jButtonCut.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jButtonCutActionPerformed(evt);
- }
- });
-
- jToolBar.add(jButtonCut);
-
- jButtonCopy.setIcon(ToolbarIcons.COPY);
- jButtonCopy.setToolTipText("Copy");
- jButtonCopy.setFocusable(false);
- jButtonCopy.setPreferredSize(new java.awt.Dimension(24, 24));
- jButtonCopy.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jButtonCopyActionPerformed(evt);
- }
- });
-
- jToolBar.add(jButtonCopy);
-
- jButtonPaste.setIcon(ToolbarIcons.PASTE);
- jButtonPaste.setToolTipText("Paste");
- jButtonPaste.setFocusable(false);
- jButtonPaste.setPreferredSize(new java.awt.Dimension(24, 24));
- jButtonPaste.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jButtonPasteActionPerformed(evt);
- }
- });
-
- jToolBar.add(jButtonPaste);
-
- jButtonDelete.setIcon(ToolbarIcons.DELETE);
- jButtonDelete.setToolTipText("Delete");
- jButtonDelete.setFocusable(false);
- jButtonDelete.setPreferredSize(new java.awt.Dimension(24, 24));
- jButtonDelete.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jButtonDeleteActionPerformed(evt);
- }
- });
-
- jToolBar.add(jButtonDelete);
-
- jButtonPrint.setIcon(ToolbarIcons.PRINT);
- jButtonPrint.setToolTipText("Print");
- jButtonPrint.setFocusable(false);
- jButtonPrint.setPreferredSize(new java.awt.Dimension(24, 24));
- jButtonPrint.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jButtonPrintActionPerformed(evt);
- }
- });
-
- jToolBar.add(jButtonPrint);
-
- jButtonExit.setIcon(ToolbarIcons.CLOSE);
- jButtonExit.setToolTipText("Exit");
- jButtonExit.setFocusable(false);
- jButtonExit.setPreferredSize(new java.awt.Dimension(24, 24));
- jButtonExit.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jButtonExitActionPerformed(evt);
- }
- });
-
- jToolBar.add(jButtonExit);
-
- getContentPane().add(jToolBar, java.awt.BorderLayout.NORTH);
-
- jSplitPaneBody.setOrientation(javax.swing.JSplitPane.VERTICAL_SPLIT);
- jSplitPaneBody.setOneTouchExpandable(true);
- jSplitPaneIO.setOneTouchExpandable(true);
- jSplitPaneSequences.setOrientation(javax.swing.JSplitPane.VERTICAL_SPLIT);
- jSplitPaneSequences.setOneTouchExpandable(true);
- jPanelSequence1.setLayout(new java.awt.BorderLayout());
-
- jScrollPaneSequence1.setPreferredSize(new java.awt.Dimension(400, 50));
- jTextAreaSequence1.setFont(new java.awt.Font("DialogInput", 0, 12));
- jTextAreaSequence1.addFocusListener(new java.awt.event.FocusAdapter() {
- public void focusGained(java.awt.event.FocusEvent evt) {
- jTextAreaSequence1FocusGained(evt);
- }
- });
- jTextAreaSequence1.addMouseListener(new java.awt.event.MouseAdapter() {
- public void mouseClicked(MouseEvent evt) {
- jTextAreaSequence1MouseClicked(evt);
- }
- });
- jTextAreaSequence1.addCaretListener(new javax.swing.event.CaretListener() {
- public void caretUpdate(CaretEvent evt) {
- jTextAreaSequence1CaretUpdate(evt);
- }
- });
-
- jScrollPaneSequence1.setViewportView(jTextAreaSequence1);
-
- jPanelSequence1.add(jScrollPaneSequence1, java.awt.BorderLayout.CENTER);
-
- jRadioButtonSequence1.setMnemonic('1');
- jRadioButtonSequence1.setText("Sequence #1");
- jRadioButtonSequence1.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jRadioButtonSequence1ActionPerformed(evt);
- }
- });
-
- jPanelSequence1.add(jRadioButtonSequence1, java.awt.BorderLayout.NORTH);
-
- jSplitPaneSequences.setTopComponent(jPanelSequence1);
-
- jPanelSequence2.setLayout(new java.awt.BorderLayout());
-
- jScrollPaneSequence2.setPreferredSize(new java.awt.Dimension(400, 50));
- jTextAreaSequence2.setFont(new java.awt.Font("DialogInput", 0, 12));
- jTextAreaSequence2.addFocusListener(new java.awt.event.FocusAdapter() {
- public void focusGained(java.awt.event.FocusEvent evt) {
- jTextAreaSequence2FocusGained(evt);
- }
- });
- jTextAreaSequence2.addMouseListener(new java.awt.event.MouseAdapter() {
- public void mouseClicked(MouseEvent evt) {
- jTextAreaSequence2MouseClicked(evt);
- }
- });
- jTextAreaSequence2.addCaretListener(new javax.swing.event.CaretListener() {
- public void caretUpdate(CaretEvent evt) {
- jTextAreaSequence2CaretUpdate(evt);
- }
- });
-
- jScrollPaneSequence2.setViewportView(jTextAreaSequence2);
-
- jPanelSequence2.add(jScrollPaneSequence2, java.awt.BorderLayout.CENTER);
-
- jRadioButtonSequence2.setMnemonic('2');
- jRadioButtonSequence2.setText("Sequence #2");
- jRadioButtonSequence2.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jRadioButtonSequence2ActionPerformed(evt);
- }
- });
-
- jPanelSequence2.add(jRadioButtonSequence2, java.awt.BorderLayout.NORTH);
-
- jSplitPaneSequences.setBottomComponent(jPanelSequence2);
-
- jSplitPaneIO.setLeftComponent(jSplitPaneSequences);
-
- jPanelAlignment.setLayout(new java.awt.BorderLayout());
-
- jRadioButtonAlignment.setMnemonic('A');
- jRadioButtonAlignment.setText("Alignment");
- jRadioButtonAlignment.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jRadioButtonAlignmentActionPerformed(evt);
- }
- });
-
- jPanelAlignment.add(jRadioButtonAlignment, java.awt.BorderLayout.NORTH);
-
- jScrollPaneAlignment.setPreferredSize(new java.awt.Dimension(400, 50));
- jTextAreaAlignment.setEditable(false);
- jTextAreaAlignment.setFont(new java.awt.Font("DialogInput", 0, 12));
- jTextAreaAlignment.setTabSize(0);
- jTextAreaAlignment.addFocusListener(new java.awt.event.FocusAdapter() {
- public void focusGained(java.awt.event.FocusEvent evt) {
- jTextAreaAlignmentFocusGained(evt);
- }
- });
- jTextAreaAlignment.addMouseListener(new java.awt.event.MouseAdapter() {
- public void mouseClicked(MouseEvent evt) {
- jTextAreaAlignmentMouseClicked(evt);
- }
- });
- jTextAreaAlignment.addCaretListener(new javax.swing.event.CaretListener() {
- public void caretUpdate(CaretEvent evt) {
- jTextAreaAlignmentCaretUpdate(evt);
- }
- });
-
- jScrollPaneAlignment.setViewportView(jTextAreaAlignment);
-
- jPanelAlignment.add(jScrollPaneAlignment, java.awt.BorderLayout.CENTER);
-
- jSplitPaneIO.setRightComponent(jPanelAlignment);
-
- jSplitPaneBody.setTopComponent(jSplitPaneIO);
-
- jPanelConsole.setLayout(new java.awt.BorderLayout());
-
- jRadioButtonConsole.setMnemonic('C');
- jRadioButtonConsole.setText("Console");
- jRadioButtonConsole.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jRadioButtonConsoleActionPerformed(evt);
- }
- });
-
- jPanelConsole.add(jRadioButtonConsole, java.awt.BorderLayout.NORTH);
-
- jScrollPaneConsole.setPreferredSize(new java.awt.Dimension(400, 50));
- jTextPaneConsole.setEditable(false);
- jTextPaneConsole.addFocusListener(new java.awt.event.FocusAdapter() {
- public void focusGained(java.awt.event.FocusEvent evt) {
- jTextPaneConsoleFocusGained(evt);
- }
- });
- jTextPaneConsole.addMouseListener(new java.awt.event.MouseAdapter() {
- public void mouseClicked(MouseEvent evt) {
- jTextPaneConsoleMouseClicked(evt);
- }
- });
- jTextPaneConsole.addCaretListener(new javax.swing.event.CaretListener() {
- public void caretUpdate(CaretEvent evt) {
- jTextPaneConsoleCaretUpdate(evt);
- }
- });
-
- jScrollPaneConsole.setViewportView(jTextPaneConsole);
-
- jPanelConsole.add(jScrollPaneConsole, java.awt.BorderLayout.CENTER);
-
- jSplitPaneBody.setBottomComponent(jPanelConsole);
-
- getContentPane().add(jSplitPaneBody, java.awt.BorderLayout.CENTER);
-
- jPanelControls.setLayout(new java.awt.GridLayout(1, 0));
-
- jPanelControls.setAutoscrolls(true);
- jLabelScoringMatrix.setDisplayedMnemonic('M');
- jLabelScoringMatrix.setHorizontalAlignment(javax.swing.SwingConstants.CENTER);
- jLabelScoringMatrix.setLabelFor(jComboBoxScoringMatrix);
- jLabelScoringMatrix.setText("Matrix");
- jPanelScoringMatrix.add(jLabelScoringMatrix);
-
- jComboBoxScoringMatrix.setToolTipText("Scoring matrix");
- jComboBoxScoringMatrix.setPrototypeDisplayValue("BLOSUMXXX");
- jPanelScoringMatrix.add(jComboBoxScoringMatrix);
-
- jPanelControls.add(jPanelScoringMatrix);
-
- jLabelOpenGapPenalty.setDisplayedMnemonic('O');
- jLabelOpenGapPenalty.setHorizontalAlignment(javax.swing.SwingConstants.CENTER);
- jLabelOpenGapPenalty.setLabelFor(jFormattedTextFieldGapOpen);
- jLabelOpenGapPenalty.setText("Open");
- jPanelGapOpen.add(jLabelOpenGapPenalty);
-
- jFormattedTextFieldGapOpen.setColumns(3);
- jFormattedTextFieldGapOpen.setToolTipText("Gap open penalty");
- jPanelGapOpen.add(jFormattedTextFieldGapOpen);
-
- jPanelControls.add(jPanelGapOpen);
-
- jLabelExtendGapPenalty.setDisplayedMnemonic('E');
- jLabelExtendGapPenalty.setHorizontalAlignment(javax.swing.SwingConstants.CENTER);
- jLabelExtendGapPenalty.setLabelFor(jFormattedTextFieldGapExtend);
- jLabelExtendGapPenalty.setText("Extend");
- jPanelGapExtend.add(jLabelExtendGapPenalty);
-
- jFormattedTextFieldGapExtend.setColumns(3);
- jFormattedTextFieldGapExtend.setToolTipText("Gap extend penalty");
- jPanelGapExtend.add(jFormattedTextFieldGapExtend);
-
- jPanelControls.add(jPanelGapExtend);
-
- jLabelOutputFormat.setDisplayedMnemonic('F');
- jLabelOutputFormat.setLabelFor(jComboBoxOutputFormat);
- jLabelOutputFormat.setText("Format");
- jPanelOutputFormat.add(jLabelOutputFormat);
-
- jComboBoxOutputFormat.setToolTipText("Alignment output format");
- jComboBoxOutputFormat.setOpaque(false);
- jPanelOutputFormat.add(jComboBoxOutputFormat);
-
- jPanelControls.add(jPanelOutputFormat);
-
- jButtonGo.setMnemonic('G');
- jButtonGo.setText("Go");
- jButtonGo.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jButtonGoActionPerformed(evt);
- }
- });
-
- jPanelGo.add(jButtonGo);
-
- jPanelControls.add(jPanelGo);
-
- getContentPane().add(jPanelControls, java.awt.BorderLayout.SOUTH);
-
- jMenuFile.setMnemonic('F');
- jMenuFile.setText("File");
- jMenuItemFileOpen.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_O, java.awt.event.InputEvent.CTRL_MASK));
- jMenuItemFileOpen.setIcon(ToolbarIcons.OPEN);
- jMenuItemFileOpen.setMnemonic('O');
- jMenuItemFileOpen.setText("Open...");
- jMenuItemFileOpen.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jMenuItemFileOpenActionPerformed(evt);
- }
- });
-
- jMenuFile.add(jMenuItemFileOpen);
-
- jMenuItemFileLoadSequence1.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_1, java.awt.event.InputEvent.CTRL_MASK));
- jMenuItemFileLoadSequence1.setIcon(ToolbarIcons.OPEN);
- jMenuItemFileLoadSequence1.setMnemonic('1');
- jMenuItemFileLoadSequence1.setText("Load sequence #1...");
- jMenuItemFileLoadSequence1.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jMenuItemFileLoadSequence1ActionPerformed(evt);
- }
- });
-
- jMenuFile.add(jMenuItemFileLoadSequence1);
-
- jMenuItemFileLoadSequence2.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_2, java.awt.event.InputEvent.CTRL_MASK));
- jMenuItemFileLoadSequence2.setIcon(ToolbarIcons.OPEN);
- jMenuItemFileLoadSequence2.setMnemonic('2');
- jMenuItemFileLoadSequence2.setText("Load sequence #2...");
- jMenuItemFileLoadSequence2.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jMenuItemFileLoadSequence2ActionPerformed(evt);
- }
- });
-
- jMenuFile.add(jMenuItemFileLoadSequence2);
-
- jMenuItemFileLoadMatrix.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_M, java.awt.event.InputEvent.CTRL_MASK));
- jMenuItemFileLoadMatrix.setIcon(ToolbarIcons.OPEN);
- jMenuItemFileLoadMatrix.setMnemonic('M');
- jMenuItemFileLoadMatrix.setText("Load scoring matrix...");
- jMenuItemFileLoadMatrix.setToolTipText("Load user-defined scoring matrix from file system");
- jMenuItemFileLoadMatrix.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jMenuItemFileLoadMatrixActionPerformed(evt);
- }
- });
-
- jMenuFile.add(jMenuItemFileLoadMatrix);
-
- jMenuFile.add(jSeparatorFile);
-
- jMenuItemFileExit.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_X, java.awt.event.InputEvent.ALT_MASK));
- jMenuItemFileExit.setIcon(ToolbarIcons.CLOSE);
- jMenuItemFileExit.setMnemonic('X');
- jMenuItemFileExit.setText("Exit");
- jMenuItemFileExit.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jMenuItemFileExitActionPerformed(evt);
- }
- });
-
- jMenuFile.add(jMenuItemFileExit);
-
- jMenuItemFilePrint.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_P, java.awt.event.InputEvent.CTRL_MASK));
- jMenuItemFilePrint.setIcon(ToolbarIcons.PRINT);
- jMenuItemFilePrint.setText("Print...");
- jMenuItemFilePrint.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jMenuItemFilePrintActionPerformed(evt);
- }
- });
-
- jMenuFile.add(jMenuItemFilePrint);
-
- jMenuBar.add(jMenuFile);
-
- jMenuEdit.setMnemonic('E');
- jMenuEdit.setText("Edit");
- jMenuItemEditCut.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_X, java.awt.event.InputEvent.CTRL_MASK));
- jMenuItemEditCut.setIcon(ToolbarIcons.CUT);
- jMenuItemEditCut.setMnemonic('t');
- jMenuItemEditCut.setText("Cut");
- jMenuItemEditCut.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jMenuItemEditCutActionPerformed(evt);
- }
- });
-
- jMenuEdit.add(jMenuItemEditCut);
-
- jMenuItemEditCopy.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_C, java.awt.event.InputEvent.CTRL_MASK));
- jMenuItemEditCopy.setIcon(ToolbarIcons.COPY);
- jMenuItemEditCopy.setMnemonic('C');
- jMenuItemEditCopy.setText("Copy");
- jMenuItemEditCopy.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jMenuItemEditCopyActionPerformed(evt);
- }
- });
-
- jMenuEdit.add(jMenuItemEditCopy);
-
- jMenuItemEditPaste.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_V, java.awt.event.InputEvent.CTRL_MASK));
- jMenuItemEditPaste.setIcon(ToolbarIcons.PASTE);
- jMenuItemEditPaste.setMnemonic('P');
- jMenuItemEditPaste.setText("Paste");
- jMenuItemEditPaste.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jMenuItemEditPasteActionPerformed(evt);
- }
- });
-
- jMenuEdit.add(jMenuItemEditPaste);
-
- jMenuItemEditDelete.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_DELETE, 0));
- jMenuItemEditDelete.setIcon(ToolbarIcons.DELETE);
- jMenuItemEditDelete.setMnemonic('D');
- jMenuItemEditDelete.setText("Delete");
- jMenuItemEditDelete.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jMenuItemEditDeleteActionPerformed(evt);
- }
- });
-
- jMenuEdit.add(jMenuItemEditDelete);
-
- jMenuItemEditSelectAll.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_A, java.awt.event.InputEvent.CTRL_MASK));
- jMenuItemEditSelectAll.setMnemonic('A');
- jMenuItemEditSelectAll.setText("Select All");
- jMenuItemEditSelectAll.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jMenuItemEditSelectAllActionPerformed(evt);
- }
- });
-
- jMenuEdit.add(jMenuItemEditSelectAll);
-
- jMenuBar.add(jMenuEdit);
-
- jMenuTools.setMnemonic('T');
- jMenuTools.setText("Tools");
- jMenuItemToolsRunExample.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_F5, 0));
- jMenuItemToolsRunExample.setMnemonic('E');
- jMenuItemToolsRunExample.setText("Example");
- jMenuItemToolsRunExample.setToolTipText("Aligns P53 human and P53 mouse");
- jMenuItemToolsRunExample.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jMenuItemToolsRunExampleActionPerformed(evt);
- }
- });
-
- jMenuTools.add(jMenuItemToolsRunExample);
-
- jMenuBar.add(jMenuTools);
-
- jMenuHelp.setMnemonic('H');
- jMenuHelp.setText("Help");
- jMenuItemAbout.setAccelerator(KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_F1, 0));
- jMenuItemAbout.setIcon(ToolbarIcons.ABOUT);
- jMenuItemAbout.setMnemonic('A');
- jMenuItemAbout.setText("About...");
- jMenuItemAbout.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- jMenuItemAboutActionPerformed(evt);
- }
- });
-
- jMenuHelp.add(jMenuItemAbout);
-
- jMenuBar.add(jMenuHelp);
-
- setJMenuBar(jMenuBar);
-
- pack();
- }//GEN-END:initComponents
-
- private void jPopupPrintActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jPopupPrintActionPerformed
- print();
- }//GEN-LAST:event_jPopupPrintActionPerformed
-
- private void jMenuItemToolsRunExampleActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jMenuItemToolsRunExampleActionPerformed
- try {
- logger.info("Running the example...");
- jTextAreaSequence1.setText(Example.loadP53Human());
- jTextAreaSequence2.setText(Example.loadP53Mouse());
- align();
- jTextAreaAlignment.requestFocus();
- logger.info("Finished running the example...");
- } catch (Exception e) {
- logger.log(Level.SEVERE, "Failed running the example: " + e.getMessage(), e);
- }
-
- }//GEN-LAST:event_jMenuItemToolsRunExampleActionPerformed
-
- private void jMenuItemFilePrintActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jMenuItemFilePrintActionPerformed
- print();
- }//GEN-LAST:event_jMenuItemFilePrintActionPerformed
-
- private void jButtonPrintActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jButtonPrintActionPerformed
- print();
- }//GEN-LAST:event_jButtonPrintActionPerformed
-
- private void jTextPaneConsoleCaretUpdate(CaretEvent evt) {//GEN-FIRST:event_jTextPaneConsoleCaretUpdate
- handleCaretUpdateEvent(evt);
- }//GEN-LAST:event_jTextPaneConsoleCaretUpdate
-
- private void jTextPaneConsoleMouseClicked(MouseEvent evt) {//GEN-FIRST:event_jTextPaneConsoleMouseClicked
- jTextPaneConsole.requestFocus();
- if (evt.getButton() == MouseEvent.BUTTON3) {
- jPopup.show(evt.getComponent(), evt.getX(), evt.getY());
- }
- }//GEN-LAST:event_jTextPaneConsoleMouseClicked
-
- private void jTextPaneConsoleFocusGained(java.awt.event.FocusEvent evt) {//GEN-FIRST:event_jTextPaneConsoleFocusGained
- currentTextComponent = jTextPaneConsole;
- jRadioButtonConsole.setSelected(true);
- handleMoveToTextComponent();
- }//GEN-LAST:event_jTextPaneConsoleFocusGained
-
- private void jRadioButtonConsoleActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jRadioButtonConsoleActionPerformed
- jTextPaneConsole.requestFocus();
- }//GEN-LAST:event_jRadioButtonConsoleActionPerformed
-
- private void jTextAreaAlignmentFocusGained(java.awt.event.FocusEvent evt) {//GEN-FIRST:event_jTextAreaAlignmentFocusGained
- currentTextComponent = jTextAreaAlignment;
- jRadioButtonAlignment.setSelected(true);
- handleMoveToTextComponent();
- }//GEN-LAST:event_jTextAreaAlignmentFocusGained
-
- private void jTextAreaSequence2FocusGained(java.awt.event.FocusEvent evt) {//GEN-FIRST:event_jTextAreaSequence2FocusGained
- currentTextComponent = jTextAreaSequence2;
- jRadioButtonSequence2.setSelected(true);
- handleMoveToTextComponent();
- }//GEN-LAST:event_jTextAreaSequence2FocusGained
-
- private void jTextAreaSequence1FocusGained(java.awt.event.FocusEvent evt) {//GEN-FIRST:event_jTextAreaSequence1FocusGained
- currentTextComponent = jTextAreaSequence1;
- jRadioButtonSequence1.setSelected(true);
- handleMoveToTextComponent();
- }//GEN-LAST:event_jTextAreaSequence1FocusGained
-
- private void jRadioButtonAlignmentActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jRadioButtonAlignmentActionPerformed
- jTextAreaAlignment.requestFocus();
- }//GEN-LAST:event_jRadioButtonAlignmentActionPerformed
-
- private void jRadioButtonSequence2ActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jRadioButtonSequence2ActionPerformed
- jTextAreaSequence2.requestFocus();
- }//GEN-LAST:event_jRadioButtonSequence2ActionPerformed
-
- private void jRadioButtonSequence1ActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jRadioButtonSequence1ActionPerformed
- jTextAreaSequence1.requestFocus();
- }//GEN-LAST:event_jRadioButtonSequence1ActionPerformed
-
- private void jMenuItemEditCopyActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jMenuItemEditCopyActionPerformed
- copy();
- }//GEN-LAST:event_jMenuItemEditCopyActionPerformed
-
- private void jMenuItemEditDeleteActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jMenuItemEditDeleteActionPerformed
- delete();
- }//GEN-LAST:event_jMenuItemEditDeleteActionPerformed
-
- private void jMenuItemEditPasteActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jMenuItemEditPasteActionPerformed
- paste();
- }//GEN-LAST:event_jMenuItemEditPasteActionPerformed
-
- private void jMenuItemFileOpenActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jMenuItemFileOpenActionPerformed
- loadFileToTextArea("", currentTextComponent);
- }//GEN-LAST:event_jMenuItemFileOpenActionPerformed
-
- private void jMenuItemEditCutActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jMenuItemEditCutActionPerformed
- cut();
- }//GEN-LAST:event_jMenuItemEditCutActionPerformed
-
- private void jMenuItemEditSelectAllActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jMenuItemEditSelectAllActionPerformed
- selectAll();
- }//GEN-LAST:event_jMenuItemEditSelectAllActionPerformed
-
- private void jTextAreaSequence2MouseClicked(MouseEvent evt) {//GEN-FIRST:event_jTextAreaSequence2MouseClicked
- jTextAreaSequence2.requestFocus();
- if (evt.getButton() == MouseEvent.BUTTON3) {
- jPopup.show(evt.getComponent(), evt.getX(), evt.getY());
- }
- }//GEN-LAST:event_jTextAreaSequence2MouseClicked
-
- private void jTextAreaSequence2CaretUpdate(CaretEvent evt) {//GEN-FIRST:event_jTextAreaSequence2CaretUpdate
- handleCaretUpdateEvent(evt);
- }//GEN-LAST:event_jTextAreaSequence2CaretUpdate
-
- private void jButtonExitActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jButtonExitActionPerformed
- exitForm(null);
- }//GEN-LAST:event_jButtonExitActionPerformed
-
- private void jButtonGoActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jButtonGoActionPerformed
- align();
- }//GEN-LAST:event_jButtonGoActionPerformed
-
- private void jMenuItemFileLoadSequence2ActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jMenuItemFileLoadSequence2ActionPerformed
- loadFileToTextArea("sequence #2", jTextAreaSequence2);
- }//GEN-LAST:event_jMenuItemFileLoadSequence2ActionPerformed
-
- private void jMenuItemFileLoadSequence1ActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jMenuItemFileLoadSequence1ActionPerformed
- loadFileToTextArea("sequence #1", jTextAreaSequence1);
- }//GEN-LAST:event_jMenuItemFileLoadSequence1ActionPerformed
-
- private void jMenuItemFileLoadMatrixActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jMenuItemFileLoadMatrixActionPerformed
- NamedInputStream selectedInputStream = null;
- try {
- logger.info("Loading scoring matrix...");
- selectedInputStream = FileChooserFactory.getFileChooser().open();
- if (selectedInputStream != null) {
- Matrix matrix = MatrixLoader.load(selectedInputStream);
-
- // Put the loaded matrix in the matrices hashmap
- matrices.put(selectedInputStream.getName(), matrix);
-
- boolean found = false;
- int index = 0;
- int count = jComboBoxScoringMatrix.getItemCount();
- while (index < count && !found) {
- if (((String)jComboBoxScoringMatrix.getItemAt(index)).equalsIgnoreCase(selectedInputStream.getName())) {
- found = true;
- } else {
- index++;
- }
- }
- if (!found) {
- // Add the loaded matrix to the scoring matrices dropdown menu
- jComboBoxScoringMatrix.addItem(selectedInputStream.getName());
- index = jComboBoxScoringMatrix.getItemCount()-1;
- }
- // Set the selected item to the new loaded matrix
- jComboBoxScoringMatrix.setSelectedIndex(index);
-
- logger.info("Finished loading scoring matrix");
- } else {
- logger.info("Canceled loading scoring matrix");
- }
- } catch (Exception e) {
- String message = "Failed loading scoring matrix: " + e.getMessage();
- logger.log(Level.SEVERE, message, e);
- showErrorMessage(message);
- } finally {
- if (selectedInputStream != null) {
- try {
- selectedInputStream.getInputStream().close();
- } catch(Exception e) {
- logger.log(Level.WARNING, "Failed closing input stream: " + e.getMessage(), e);
- }
- }
- }
- }//GEN-LAST:event_jMenuItemFileLoadMatrixActionPerformed
-
- private void jTextAreaAlignmentMouseClicked(MouseEvent evt) {//GEN-FIRST:event_jTextAreaAlignmentMouseClicked
- jTextAreaAlignment.requestFocus();
- if (evt.getButton() == MouseEvent.BUTTON3) {
- jPopup.show(evt.getComponent(), evt.getX(), evt.getY());
- }
- }//GEN-LAST:event_jTextAreaAlignmentMouseClicked
-
- private void jPopupSaveActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jPopupSaveActionPerformed
- saveTextAreaToFile((JTextArea) jPopup.getInvoker());
- }//GEN-LAST:event_jPopupSaveActionPerformed
-
- private void jButtonSaveActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jButtonSaveActionPerformed
- saveTextAreaToFile(currentTextComponent);
- }//GEN-LAST:event_jButtonSaveActionPerformed
-
- private void jTextAreaAlignmentCaretUpdate(CaretEvent evt) {//GEN-FIRST:event_jTextAreaAlignmentCaretUpdate
- handleCaretUpdateEvent(evt);
- }//GEN-LAST:event_jTextAreaAlignmentCaretUpdate
-
- private void jPopupOpenActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jPopupOpenActionPerformed
- loadFileToTextArea("", (JTextArea) jPopup.getInvoker());
- }//GEN-LAST:event_jPopupOpenActionPerformed
-
- private void jPopupSelectAllActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jPopupSelectAllActionPerformed
- selectAll();
- }//GEN-LAST:event_jPopupSelectAllActionPerformed
-
- private void jPopupDeleteActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jPopupDeleteActionPerformed
- delete();
- }//GEN-LAST:event_jPopupDeleteActionPerformed
-
- private void jPopupPasteActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jPopupPasteActionPerformed
- paste();
- }//GEN-LAST:event_jPopupPasteActionPerformed
-
- private void jPopupCopyActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jPopupCopyActionPerformed
- copy();
- }//GEN-LAST:event_jPopupCopyActionPerformed
-
- private void jPopupCutActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jPopupCutActionPerformed
- cut();
- }//GEN-LAST:event_jPopupCutActionPerformed
-
- private void jTextAreaSequence1CaretUpdate(CaretEvent evt) {//GEN-FIRST:event_jTextAreaSequence1CaretUpdate
- handleCaretUpdateEvent(evt);
- }//GEN-LAST:event_jTextAreaSequence1CaretUpdate
-
- private void jButtonDeleteActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jButtonDeleteActionPerformed
- delete();
- }//GEN-LAST:event_jButtonDeleteActionPerformed
-
- private void jButtonPasteActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jButtonPasteActionPerformed
- paste();
- }//GEN-LAST:event_jButtonPasteActionPerformed
-
- private void jButtonCopyActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jButtonCopyActionPerformed
- copy();
- }//GEN-LAST:event_jButtonCopyActionPerformed
-
- private void jButtonCutActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jButtonCutActionPerformed
- cut();
- }//GEN-LAST:event_jButtonCutActionPerformed
-
- private void jButtonOpenActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jButtonOpenActionPerformed
- loadFileToTextArea("", currentTextComponent);
- }//GEN-LAST:event_jButtonOpenActionPerformed
-
- private void jTextAreaSequence1MouseClicked(MouseEvent evt) {//GEN-FIRST:event_jTextAreaSequence1MouseClicked
- jTextAreaSequence1.requestFocus();
- if (evt.getButton() == MouseEvent.BUTTON3) {
- jPopup.show(evt.getComponent(), evt.getX(), evt.getY());
- }
- }//GEN-LAST:event_jTextAreaSequence1MouseClicked
-
- private void jMenuItemAboutActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jMenuItemAboutActionPerformed
- String message = "JAligner "
- + Commons.getLineSeparator() + Commons.getLineSeparator()
- + "Open source Java implementation"
- + Commons.getLineSeparator()
- + "of the Smith-Waterman algorithm"
- + Commons.getLineSeparator()
- + "for biological sequence alignment."
- + Commons.getLineSeparator() + Commons.getLineSeparator()
- + "Build: " + Commons.getCurrentRelease()
- + Commons.getLineSeparator() + Commons.getLineSeparator()
- + "By: Ahmed Moustafa ";
- JOptionPane.showMessageDialog(this, message, "About JAligner",
- JOptionPane.INFORMATION_MESSAGE);
- }//GEN-LAST:event_jMenuItemAboutActionPerformed
-
- private void jMenuItemFileExitActionPerformed(ActionEvent evt) {//GEN-FIRST:event_jMenuItemFileExitActionPerformed
- exitForm(null);
- }//GEN-LAST:event_jMenuItemFileExitActionPerformed
-
- /** Exit the Application */
- private void exitForm(java.awt.event.WindowEvent evt) {//GEN-FIRST:event_exitForm
- logger.info("Quitting...");
- if (JOptionPane.showConfirmDialog(this, "Are you sure you want to exit JAligner?", "JAligner - confirmation", JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) {
- logger.info("Thank you for using JAligner!");
- System.exit(0);
- } else {
- logger.info("Canceled quitting");
- currentTextComponent.requestFocus();
- }
- }//GEN-LAST:event_exitForm
-
- // Variables declaration - do not modify//GEN-BEGIN:variables
- private javax.swing.ButtonGroup buttonGroupSequences;
- private javax.swing.JButton jButtonCopy;
- private javax.swing.JButton jButtonCut;
- private javax.swing.JButton jButtonDelete;
- private javax.swing.JButton jButtonExit;
- private javax.swing.JButton jButtonGo;
- private javax.swing.JButton jButtonOpen;
- private javax.swing.JButton jButtonPaste;
- private javax.swing.JButton jButtonPrint;
- private javax.swing.JButton jButtonSave;
- private JComboBox jComboBoxOutputFormat;
- private JComboBox jComboBoxScoringMatrix;
- private JFormattedTextField jFormattedTextFieldGapExtend;
- private JFormattedTextField jFormattedTextFieldGapOpen;
- private javax.swing.JLabel jLabelExtendGapPenalty;
- private javax.swing.JLabel jLabelOpenGapPenalty;
- private javax.swing.JLabel jLabelOutputFormat;
- private javax.swing.JLabel jLabelScoringMatrix;
- private javax.swing.JMenuBar jMenuBar;
- private javax.swing.JMenu jMenuEdit;
- private javax.swing.JMenu jMenuFile;
- private javax.swing.JMenu jMenuHelp;
- private javax.swing.JMenuItem jMenuItemAbout;
- private javax.swing.JMenuItem jMenuItemEditCopy;
- private javax.swing.JMenuItem jMenuItemEditCut;
- private javax.swing.JMenuItem jMenuItemEditDelete;
- private javax.swing.JMenuItem jMenuItemEditPaste;
- private javax.swing.JMenuItem jMenuItemEditSelectAll;
- private javax.swing.JMenuItem jMenuItemFileExit;
- private javax.swing.JMenuItem jMenuItemFileLoadMatrix;
- private javax.swing.JMenuItem jMenuItemFileLoadSequence1;
- private javax.swing.JMenuItem jMenuItemFileLoadSequence2;
- private javax.swing.JMenuItem jMenuItemFileOpen;
- private javax.swing.JMenuItem jMenuItemFilePrint;
- private javax.swing.JMenuItem jMenuItemToolsRunExample;
- private javax.swing.JMenu jMenuTools;
- private javax.swing.JPanel jPanelAlignment;
- private javax.swing.JPanel jPanelConsole;
- private javax.swing.JPanel jPanelControls;
- private javax.swing.JPanel jPanelGapExtend;
- private javax.swing.JPanel jPanelGapOpen;
- private javax.swing.JPanel jPanelGo;
- private javax.swing.JPanel jPanelOutputFormat;
- private javax.swing.JPanel jPanelScoringMatrix;
- private javax.swing.JPanel jPanelSequence1;
- private javax.swing.JPanel jPanelSequence2;
- private javax.swing.JPopupMenu jPopup;
- private javax.swing.JMenuItem jPopupCopy;
- private javax.swing.JMenuItem jPopupCut;
- private javax.swing.JMenuItem jPopupDelete;
- private javax.swing.JMenuItem jPopupOpen;
- private javax.swing.JMenuItem jPopupPaste;
- private javax.swing.JMenuItem jPopupPrint;
- private javax.swing.JMenuItem jPopupSave;
- private javax.swing.JMenuItem jPopupSelectAll;
- private javax.swing.JSeparator jPopupSeparator1;
- private javax.swing.JSeparator jPopupSeparator2;
- private javax.swing.JSeparator jPopupSeparator3;
- private javax.swing.JRadioButton jRadioButtonAlignment;
- private javax.swing.JRadioButton jRadioButtonConsole;
- private javax.swing.JRadioButton jRadioButtonSequence1;
- private javax.swing.JRadioButton jRadioButtonSequence2;
- private javax.swing.JScrollPane jScrollPaneAlignment;
- private javax.swing.JScrollPane jScrollPaneConsole;
- private javax.swing.JScrollPane jScrollPaneSequence1;
- private javax.swing.JScrollPane jScrollPaneSequence2;
- private javax.swing.JSeparator jSeparatorFile;
- private javax.swing.JSplitPane jSplitPaneBody;
- private javax.swing.JSplitPane jSplitPaneIO;
- private javax.swing.JSplitPane jSplitPaneSequences;
- private JTextArea jTextAreaAlignment;
- private JTextArea jTextAreaSequence1;
- private JTextArea jTextAreaSequence2;
- private javax.swing.JTextPane jTextPaneConsole;
- private javax.swing.JToolBar jToolBar;
- // End of variables declaration//GEN-END:variables
-
- /**
- * Populates a combobox with an array of strings and selects the default
- * @param combobox combobox to be populated
- * @param items array of strings to be added to the combobox
- * @param selected the default selected item
- */
- private void populateComboBox(JComboBox combobox, String[] items, String selected) {
- for (int i = 0; i < items.length; i++) {
- combobox.addItem(items[i]);
- if (items[i].equals(selected)) {
- combobox.setSelectedIndex(i);
- }
- }
- }
-
- /**
- * Populates a combobox with an array of strings and selects the default
- * @param combobox combobox to be populated
- * @param items array of strings to be added to the combobox
- * @param selected the default selected item
- */
- private void populateComboBox(JComboBox combobox, Collection items, String selected) {
- String item;
- Iterator i = items.iterator();
- int index = 0;
- while (i.hasNext()) {
- item = (String) i.next();
- combobox.addItem(item);
- if (item.equals(selected)) {
- combobox.setSelectedIndex(index);
- }
- index++;
- }
- }
-
- /**
- * Displays an error message
- * @param message the error message to be displayed
- */
- private void showErrorMessage(String message) {
- JOptionPane.showMessageDialog(this, message, "JAligner - error message", JOptionPane.ERROR_MESSAGE);
- }
-
- /**
- * Loads the contents of a selected file into a text component.
- * @param id
- * @param textComponent
- */
- private void loadFileToTextArea(String id, JTextComponent textComponent) {
- logger.info("Loading " + id + "...");
- try {
- if (TextComponentUtil.open(textComponent)) {
- textComponent.requestFocus();
- textComponent.setCaretPosition(0);
- logger.info("Finished loading " + id);
- } else {
- logger.info("Canceled loading " + id);
- }
- } catch (Exception e) {
- String message = "Failed loading " + id + ": " + e.getMessage();
- logger.log(Level.SEVERE, message, e);
- showErrorMessage(message);
- }
- }
-
- /**
- * Saves a text component to a file.
- * @param textComponent
- */
- private void saveTextAreaToFile(JTextComponent textComponent) {
- try {
- logger.info("Saving...");
- if (TextComponentUtil.save(textComponent)) {
- logger.info("Finished saving");
- } else {
- logger.info("Canceled saving");
- }
- } catch (Exception e) {
- String message = "Failed saving: " + e.getMessage();
- logger.log(Level.SEVERE, message, e);
- showErrorMessage(message);
- }
- }
-
- /**
- *
- *
- */
- private void cut() {
- TextComponentUtil.cut(currentTextComponent);
- }
-
- /**
- *
- *
- */
- private void copy() {
- TextComponentUtil.copy(currentTextComponent);
- }
-
- /**
- *
- *
- */
- private void paste() {
- TextComponentUtil.paste(currentTextComponent);
- }
-
- /**
- *
- *
- */
- private void delete() {
- TextComponentUtil.delete(currentTextComponent);
- }
-
- /**
- *
- *
- */
- private void selectAll() {
- TextComponentUtil.selectAll(currentTextComponent);
- }
-
- /**
- * Prints the contents of a text component
- *
- */
- private void print() {
- try {
- logger.info("Printing...");
- TextComponentUtil.print(currentTextComponent);
- logger.info("Finished printing.");
- } catch (TextComponentUtilException textComponentUtilException) {
- logger.log(Level.SEVERE, "Failed printing: " + textComponentUtilException.getMessage(), textComponentUtilException);
- }
- }
-
- /**
- * Implements insertUpdate of {@link DocumentListener}
- */
- public void insertUpdate(DocumentEvent e) {
- if (e.getDocument() == currentTextComponent.getDocument()) {
- setSaveControlsEnabled(true);
- setSelectAllControlsEnabled(true);
- setPrintControlsEnabled(true);
- }
- }
-
- /**
- * Implements removeUpdate of {@link DocumentListener}
- */
- public void removeUpdate(DocumentEvent e) {
- if (e.getDocument() == currentTextComponent.getDocument()) {
- if (e.getDocument().getLength() == 0) {
- setSaveControlsEnabled(false);
- setSelectAllControlsEnabled(false);
- setPrintControlsEnabled(false);
- }
- }
- }
-
- /**
- * Implements changedUpdate of {@link DocumentListener}
- */
- public void changedUpdate(DocumentEvent e) {}
-
- /**
- * Implements the notify method of the interface {@link ClipboardListener}
- */
- public void clipboardCheck(String clipboardContents) {
- setPasteControlsEnabled(clipboardContents != null && currentTextComponent != null && currentTextComponent.isEditable());
- }
-
- /**
- * Sets the status of the open controls
- * @param enabled
- */
- private void setOpenControlsEnabled(boolean enabled) {
- jMenuItemFileOpen.setEnabled(enabled);
- jButtonOpen.setEnabled(enabled);
- jPopupOpen.setEnabled(enabled);
- }
-
- /**
- * Sets the status of the save controls
- * @param enabled
- */
- private void setSaveControlsEnabled(boolean enabled) {
- jButtonSave.setEnabled(enabled);
- jPopupSave.setEnabled(enabled);
- }
-
- /**
- * Sets the status of the cut controls
- * @param enabled
- */
- private void setCutControlsEnabled(boolean enabled) {
- jMenuItemEditCut.setEnabled(enabled);
- jButtonCut.setEnabled(enabled);
- jPopupCut.setEnabled(enabled);
- }
-
- /**
- * Sets the status of the copy controls
- * @param enabled
- */
- private void setCopyControlsEnabled(boolean enabled) {
- jMenuItemEditCopy.setEnabled(enabled);
- jButtonCopy.setEnabled(enabled);
- jPopupCopy.setEnabled(enabled);
- }
-
- /**
- * Sets the status of the paste controls
- * @param enabled
- */
- private void setPasteControlsEnabled(boolean enabled) {
- jMenuItemEditPaste.setEnabled(enabled);
- jButtonPaste.setEnabled(enabled);
- jPopupPaste.setEnabled(enabled);
- }
-
- /**
- * Sets the status of the delete controls
- * @param enabled
- */
- private void setDeleteControlsEnabled(boolean enabled) {
- jMenuItemEditDelete.setEnabled(enabled);
- jButtonDelete.setEnabled(enabled);
- jPopupDelete.setEnabled(enabled);
- }
-
- /**
- * Sets the status of the select all controls
- * @param enabled
- */
- private void setSelectAllControlsEnabled(boolean enabled) {
- jMenuItemEditSelectAll.setEnabled(enabled);
- jPopupSelectAll.setEnabled(enabled);
- }
-
- /**
- * Sets the status of the print controls
- * @param enabled
- */
- private void setPrintControlsEnabled(boolean enabled) {
- jButtonPrint.setEnabled(enabled);
- jPopupPrint.setEnabled(enabled);
- }
-
- /**
- *
- * @param event
- */
- private void handleCaretUpdateEvent(CaretEvent event) {
- if (event.getSource() == currentTextComponent) {
- boolean enabled = event.getDot() != event.getMark();
- // Read controls
- setCopyControlsEnabled(enabled);
-
- // Write controls
- enabled &= currentTextComponent.isEditable();
- setCutControlsEnabled(enabled);
- setDeleteControlsEnabled(enabled);
- }
- }
-
- /**
- *
- *
- */
- private void handleMoveToTextComponent( ) {
- boolean enabled;
-
- enabled = currentTextComponent.getSelectedText() != null;
- setCopyControlsEnabled(enabled);
-
- if (currentTextComponent.isEditable()) {
- setOpenControlsEnabled(true);
-
- setCutControlsEnabled(enabled);
- setDeleteControlsEnabled(enabled);
- } else {
- setPasteControlsEnabled(false);
-
- setOpenControlsEnabled(false);
-
- setCutControlsEnabled(false);
- setDeleteControlsEnabled(false);
- }
-
- enabled = currentTextComponent.getText().length() > 0;
- setSaveControlsEnabled(enabled);
- setSelectAllControlsEnabled(enabled);
- setPrintControlsEnabled(enabled);
-
- // Adjust background of the radio buttons
- Enumeration buttons = buttonGroupSequences.getElements();
- AbstractButton button = null;
- while (buttons.hasMoreElements()) {
- button = (AbstractButton) buttons.nextElement();
- if (button.isSelected()) {
- button.setForeground(Color.blue);
- } else {
- button.setForeground(Color.black);
- }
- }
-
- }
-
- /**
- *
- *
- */
- private void align() {
- jTextAreaAlignment.setText("");
-
- String matrixId = (String) jComboBoxScoringMatrix.getSelectedItem();
- float open = ((Number)jFormattedTextFieldGapOpen.getValue()).floatValue();
- float extend = ((Number)jFormattedTextFieldGapExtend.getValue()).floatValue();
-
- Sequence sequence1 = null;
- try {
- logger.info("Processing sequence #1...");
- sequence1 = SequenceParser.parse(jTextAreaSequence1.getText());
- logger.info("Finished processing sequence #1");
- } catch (Exception e) {
- String message = "Failed parsing sequence #1: " + e.getMessage();
- logger.log(Level.SEVERE, message, e);
- showErrorMessage(message);
- jTextAreaSequence1.requestFocus();
- return;
- }
-
- Sequence sequence2 = null;
- try {
- logger.info("Processing sequence #2...");
- sequence2 = SequenceParser.parse(jTextAreaSequence2.getText());
- logger.info("Finished processing sequence #2");
- } catch (Exception e) {
- String message = "Failed parsing sequence #2: " + e.getMessage();
- logger.log(Level.SEVERE, message, e);
- showErrorMessage(message);
- jTextAreaSequence2.requestFocus();
- return;
- }
-
- logger.info("Aliging...");
- try {
- setCursor(new Cursor(Cursor.WAIT_CURSOR));
-
- long start = System.currentTimeMillis();
- Matrix matrix = null;
- if (!matrices.containsKey(matrixId)) {
- matrix = MatrixLoader.load(matrixId);
- matrices.put(matrixId, matrix);
- } else {
- matrix = (Matrix) matrices.get(matrixId);
- }
- Alignment alignment = SmithWatermanGotoh.align(sequence1, sequence2, matrix, open, extend);
- long end = System.currentTimeMillis();
- logger.info("Finished aligning in " + (end - start) + " milliseconds");
-
- StringBuffer buffer = new StringBuffer();
-
- buffer.append(alignment.getSummary());
- buffer.append(Commons.getLineSeparator());
-
- String formatId = (String) jComboBoxOutputFormat.getSelectedItem();
- String formattedAlignment = FormatFactory.getInstance().getFormat(formatId).format(alignment);
- buffer.append(formattedAlignment);
-
- jTextAreaAlignment.setText("");
- jTextAreaAlignment.append(buffer.toString());
- jTextAreaAlignment.setCaretPosition(0);
- } catch (Error error) {
- String message = "Failed aligning: " + error.getMessage();
- logger.log(Level.SEVERE, message, error);
- showErrorMessage(message);
- } catch (Exception exception) {
- String message = "Failed aligning: " + exception.getMessage();
- logger.log(Level.SEVERE, message, exception);
- showErrorMessage(message);
- } finally {
- setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
- }
- }
-
- /**
- *
- * @param args
- */
- public static void main(String[] args) {
- logger.info( Commons.getJAlignerInfo() );
- new AlignWindow().setVisible(true);
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/clipboard/ClipboardHandler.java b/maven-src/target/classes/java/jaligner/ui/clipboard/ClipboardHandler.java
deleted file mode 100644
index e5020e7..0000000
--- a/maven-src/target/classes/java/jaligner/ui/clipboard/ClipboardHandler.java
+++ /dev/null
@@ -1,42 +0,0 @@
-/*
- * $Id: ClipboardHandler.java,v 1.4 2004/11/30 05:10:29 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.clipboard;
-
-/**
- * Abstract class to handle setting and getting "text" contents of
- * the system clipboard.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public interface ClipboardHandler {
- /**
- * Returns the contents of the system of the clipboard
- *
- * @return String
- */
- public String getContents();
-
- /**
- * Sets the contents of the system of the clipboard
- *
- * @param s the clipboard contents to set
- */
- public void setContents(String s);
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/clipboard/ClipboardHandlerAWT.java b/maven-src/target/classes/java/jaligner/ui/clipboard/ClipboardHandlerAWT.java
deleted file mode 100644
index 95859b7..0000000
--- a/maven-src/target/classes/java/jaligner/ui/clipboard/ClipboardHandlerAWT.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * $Id: ClipboardHandlerAWT.java,v 1.3 2004/12/19 08:00:48 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.clipboard;
-
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-
-/**
- * Sets and gets the contents of the system clipboard.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class ClipboardHandlerAWT implements ClipboardHandler {
- private static Logger logger = Logger.getLogger(ClipboardHandlerAWT.class.getName());
-
- /**
- * Gets the contents of the system clipboard
- *
- * @return The text contents of the system clipboard
- */
- public String getContents() {
- String contents = null;
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
- Transferable data = c.getContents(null);
- if (data != null && data.isDataFlavorSupported(DataFlavor.stringFlavor)) {
- try {
- contents = ((String)(data.getTransferData(DataFlavor.stringFlavor)));
- } catch (Exception e) {
- logger.log(Level.WARNING, "Failed getting tranfer data: " + e.getMessage(), e);
- }
- }
- return contents;
- }
-
- /**
- * Sets the contents of the system clipboard
- *
- * @param s the clipboard contents to set
- */
- public void setContents(String s) {
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
- c.setContents(new StringSelection(s), null);
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/clipboard/ClipboardHandlerFactory.java b/maven-src/target/classes/java/jaligner/ui/clipboard/ClipboardHandlerFactory.java
deleted file mode 100644
index 772d57e..0000000
--- a/maven-src/target/classes/java/jaligner/ui/clipboard/ClipboardHandlerFactory.java
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * $Id: ClipboardHandlerFactory.java,v 1.2 2004/11/30 05:10:29 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.clipboard;
-
-import jaligner.util.Commons;
-
-/**
- * A factory for {@link ClipboardHandler}.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class ClipboardHandlerFactory {
- /**
- * Instance of a concrete {@link ClipboardHandlerFactory}.
- */
- private static ClipboardHandler instance = null;
-
- /**
- * Constructor
- */
- private ClipboardHandlerFactory ( ) {
- super();
- }
-
- /**
- * Returns an instance of a concrete {@link ClipboardHandler}.
- * @return Concrete {@link ClipboardHandler}.
- */
- public static ClipboardHandler getClipboardHandler( ) {
- if (instance == null) {
- if (Commons.isJnlp()) {
- instance = new ClipboardHandlerJNLP();
- } else {
- instance = new ClipboardHandlerAWT();
- }
- }
- return instance;
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/clipboard/ClipboardHandlerJNLP.java b/maven-src/target/classes/java/jaligner/ui/clipboard/ClipboardHandlerJNLP.java
deleted file mode 100644
index e31ee47..0000000
--- a/maven-src/target/classes/java/jaligner/ui/clipboard/ClipboardHandlerJNLP.java
+++ /dev/null
@@ -1,71 +0,0 @@
-/*
- * $Id: ClipboardHandlerJNLP.java,v 1.3 2004/12/19 08:00:48 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.clipboard;
-
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-import javax.jnlp.ClipboardService;
-import javax.jnlp.ServiceManager;
-
-/**
- * Sets and gets the contents of the system clipboard.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class ClipboardHandlerJNLP implements ClipboardHandler {
- private static Logger logger = Logger.getLogger(ClipboardHandlerJNLP.class.getName());
-
- /**
- * Gets the contents of the system clipboard
- *
- * @return The text system clipboad contents
- */
- public String getContents() {
- String contents = null;
- try {
- ClipboardService cs = (ClipboardService)ServiceManager.lookup(ClipboardService.class.getName());
- Transferable data = cs.getContents();
- if (data != null && data.isDataFlavorSupported(DataFlavor.stringFlavor)) {
- contents = ((String)(data.getTransferData(DataFlavor.stringFlavor)));
- }
- } catch (Exception e) {
- logger.log(Level.WARNING, "Failed getting the clipboard contents: " + e.getMessage(), e );
- }
- return contents;
- }
-
- /**
- * Sets the contents of the system clipboard
- *
- * @param s clipboard contents to set
- */
- public void setContents(String s) {
- try {
- ClipboardService cs = (ClipboardService)ServiceManager.lookup(ClipboardService.class.getName());
- cs.setContents(new StringSelection(s));
- } catch (Exception e) {
- logger.log(Level.WARNING, "Failed setting the clipboard contents: " + e.getMessage(), e );
- }
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/clipboard/ClipboardListener.java b/maven-src/target/classes/java/jaligner/ui/clipboard/ClipboardListener.java
deleted file mode 100644
index 1716596..0000000
--- a/maven-src/target/classes/java/jaligner/ui/clipboard/ClipboardListener.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * $Id: ClipboardListener.java,v 1.5 2004/12/23 17:06:47 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.clipboard;
-
-/**
- * Listener interface to get notified with the clipboard contents.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public interface ClipboardListener {
-
- /**
- * Notifies the listener with the current contents of the clipboard.
- * @param contents The current contents of the clipboard
- */
- public void clipboardCheck(String contents);
-
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/clipboard/ClipboardPoller.java b/maven-src/target/classes/java/jaligner/ui/clipboard/ClipboardPoller.java
deleted file mode 100644
index 0b4daf0..0000000
--- a/maven-src/target/classes/java/jaligner/ui/clipboard/ClipboardPoller.java
+++ /dev/null
@@ -1,94 +0,0 @@
-/*
- * $Id: ClipboardPoller.java,v 1.5 2004/12/23 17:06:47 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.clipboard;
-
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-/**
- * Checks the system clipboard to notifies a listener with current contents.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class ClipboardPoller extends Thread {
- /**
- * Sleeping interval
- */
- private static final int SLEEPING_TIME_IN_MILLISECONDS = 1500;
-
- /**
- * Clipboard listener {@link ClipboardListener}
- */
- private ClipboardListener listener = null;
-
- /**
- * Running flag
- */
- private boolean running = false;
-
- /**
- * Logger
- */
- private Logger logger = null;
-
- /**
- * Constructor
- * @param listener
- */
- public ClipboardPoller(ClipboardListener listener) {
- logger = Logger.getLogger(this.getClass().getName());
- this.listener = listener;
- }
-
- /**
- * Runs the thread
- */
- public void run() {
- logger.info("Started");
- while (running) {
- String contents = ClipboardHandlerFactory.getClipboardHandler().getContents();
- listener.clipboardCheck(contents);
- try {
- Thread.sleep(SLEEPING_TIME_IN_MILLISECONDS);
- } catch (Exception e){
- logger.log(Level.SEVERE, "Failed sleeping: " + e.getMessage(), e);
- running = false;
- }
- }
- logger.info("Stopped");
- }
-
- /**
- * Starts the thread
- */
- public void start() {
- logger.info("Starting...");
- if (!running) {
- if (listener != null) {
- running = true;
- } else {
- logger.warning("No listener");
- }
- } else {
- logger.warning("Already started");
- }
- super.start();
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/clipboard/package.html b/maven-src/target/classes/java/jaligner/ui/clipboard/package.html
deleted file mode 100644
index d3f3582..0000000
--- a/maven-src/target/classes/java/jaligner/ui/clipboard/package.html
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
-
-
-Clipboard handling for JNLP and AWT.
-@author Ahmed Moustafa (ahmed@users.sf.net)
-
-
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/filechooser/FileChooser.java b/maven-src/target/classes/java/jaligner/ui/filechooser/FileChooser.java
deleted file mode 100644
index a7a1a5b..0000000
--- a/maven-src/target/classes/java/jaligner/ui/filechooser/FileChooser.java
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- * $Id: FileChooser.java,v 1.10 2005/01/10 15:01:01 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.filechooser;
-
-import java.io.InputStream;
-
-/**
- * Opens and saves files.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public abstract class FileChooser {
- /**
- * Buffer size while reading from or write to a file (4 KB)
- */
- public static final int BUFFER_SIZE = 4096;
-
- private String userDir = null;
-
- /**
- * Shows a dialog to select a file
- *
- * @return InputStream
- * @throws FileChooserException
- */
- public abstract NamedInputStream open() throws FileChooserException;
-
- /**
- * Saves an input stream to a file
- *
- * @param is
- * @param fileName
- * @return boolean
- * @throws FileChooserException
- */
- public abstract boolean save(InputStream is, String fileName) throws FileChooserException;
-
- /**
- * Gets the current user working directory
- * @return current working directory
- */
- public String getUserDirectory ( ) {
- if (userDir == null) {
- userDir = System.getProperty("user.home");
- }
- return userDir;
- }
-
- /**
- * Sets the user working directory
- * @param userDir The user directory to set
- */
- public void setUserDirectory (String userDir) {
- this.userDir = userDir;
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/filechooser/FileChooserException.java b/maven-src/target/classes/java/jaligner/ui/filechooser/FileChooserException.java
deleted file mode 100644
index 3882735..0000000
--- a/maven-src/target/classes/java/jaligner/ui/filechooser/FileChooserException.java
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * $Id: FileChooserException.java,v 1.2 2005/04/14 14:44:43 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.filechooser;
-
-/**
- * File chooser exception
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class FileChooserException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 3258408434931086648L;
-
- /**
- * @param message
- */
- public FileChooserException(String message) {
- super(message);
- }
-}
diff --git a/maven-src/target/classes/java/jaligner/ui/filechooser/FileChooserFactory.java b/maven-src/target/classes/java/jaligner/ui/filechooser/FileChooserFactory.java
deleted file mode 100644
index ef6abf3..0000000
--- a/maven-src/target/classes/java/jaligner/ui/filechooser/FileChooserFactory.java
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * $Id: FileChooserFactory.java,v 1.3 2005/01/11 15:23:25 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.filechooser;
-
-import jaligner.util.Commons;
-
-/**
- * A factory for {@link FileChooser}.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class FileChooserFactory {
- /**
- * Instance of a concrete {@link FileChooser}.
- */
- private static FileChooser instance = null;
-
- /**
- * Constructor
- */
- private FileChooserFactory ( ) {
- super();
- }
-
- /**
- * Returns an instance of a concrete {@link FileChooser}.
- * @return Concrete {@link FileChooser}.
- */
- public static FileChooser getFileChooser( ) {
- if (instance == null) {
- if (Commons.isJnlp()) {
- instance = new FileChooserJNLP();
- } else {
- instance = new FileChooserTrusted();
- }
- }
- return instance;
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/filechooser/FileChooserJNLP.java b/maven-src/target/classes/java/jaligner/ui/filechooser/FileChooserJNLP.java
deleted file mode 100644
index 8a4e443..0000000
--- a/maven-src/target/classes/java/jaligner/ui/filechooser/FileChooserJNLP.java
+++ /dev/null
@@ -1,86 +0,0 @@
-/*
- * $Id: FileChooserJNLP.java,v 1.11 2005/01/10 15:01:01 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.filechooser;
-
-import java.io.InputStream;
-import java.util.logging.Logger;
-
-import javax.jnlp.FileContents;
-import javax.jnlp.FileOpenService;
-import javax.jnlp.FileSaveService;
-import javax.jnlp.ServiceManager;
-
-
-/**
- * Opens and saves files.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class FileChooserJNLP extends FileChooser {
- private static final Logger logger = Logger.getLogger(FileChooserJNLP.class.getName());
-
- /**
- * Shows a dialog to select a file.
- *
- * @return InputStream
- * @throws FileChooserException
- */
- public NamedInputStream open() throws FileChooserException {
- try {
- FileOpenService fos = (FileOpenService) ServiceManager.lookup(FileOpenService.class.getName());
- FileContents fc = null;
- if ((fc = fos.openFileDialog(getUserDirectory(), null)) != null) {
- logger.info("Loaded: " + fc.getName());
- return new NamedInputStream(fc.getName(), fc.getInputStream());
- } else {
- return null;
- }
- } catch (Exception e) {
- String message = "Failed open: " + e.getMessage();
- logger.warning(message);
- throw new FileChooserException(message);
- }
- }
-
- /**
- * Saves an input stream to a file.
- *
- * @param is
- * @param fileName
- * @return Boolean
- * @throws FileChooserException
- */
- public boolean save(InputStream is, String fileName) throws FileChooserException {
- try {
- FileSaveService fss = (FileSaveService) ServiceManager.lookup(FileSaveService.class.getName());
- FileContents fc = fss.saveFileDialog(getUserDirectory(), null, is, fileName);
- if (fc != null) {
- logger.info("Saved: " + fc.getName());
- return true;
- } else {
- return false;
- }
- } catch (Exception e) {
- String message = "Failed save: " + e.getMessage();
- logger.warning(message);
- throw new FileChooserException(message);
- }
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/filechooser/FileChooserTrusted.java b/maven-src/target/classes/java/jaligner/ui/filechooser/FileChooserTrusted.java
deleted file mode 100644
index 5ebd6ff..0000000
--- a/maven-src/target/classes/java/jaligner/ui/filechooser/FileChooserTrusted.java
+++ /dev/null
@@ -1,104 +0,0 @@
-/*
- * $Id: FileChooserTrusted.java,v 1.12 2005/01/10 15:01:01 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.filechooser;
-
-
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.InputStream;
-import java.util.logging.Logger;
-
-import javax.swing.JFileChooser;
-
-/**
- * Opens and saves files.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class FileChooserTrusted extends FileChooser {
- private static final Logger logger = Logger.getLogger(FileChooserJNLP.class.getName());
-
- /**
- * Shows a dialog to select a file.
- * @return input stream
- * @throws FileChooserException
- * @see NamedInputStream
- */
- public NamedInputStream open() throws FileChooserException {
- try {
- JFileChooser chooser = new JFileChooser( );
- chooser.setCurrentDirectory(new File(getUserDirectory()));
- int returnVal = chooser.showOpenDialog(null);
- if (returnVal == JFileChooser.APPROVE_OPTION) {
- setUserDirectory(chooser.getCurrentDirectory().toString());
- logger.info("Loaded: " + chooser.getSelectedFile().getName());
- return new NamedInputStream(chooser.getSelectedFile().getName(),
- new FileInputStream(chooser.getSelectedFile()));
- } else {
- return null;
- }
- } catch (Exception e) {
- String message = "Failed open: " + e.getMessage();
- logger.warning(message);
- throw new FileChooserException(message);
- }
- }
-
- /**
- * Saves an input stream to a file.
- *
- * @param is
- * @param fileName
- * @return boolean
- * @throws FileChooserException
- */
- public boolean save(InputStream is, String fileName) throws FileChooserException {
- try {
- JFileChooser chooser = new JFileChooser( );
- chooser.setCurrentDirectory(new File(getUserDirectory()));
- if (fileName != null) {
- chooser.setSelectedFile(new File(fileName));
- }
- int returnVal = chooser.showSaveDialog(null);
- if (returnVal == JFileChooser.APPROVE_OPTION) {
- setUserDirectory(chooser.getCurrentDirectory().toString());
- File file = chooser.getSelectedFile();
- logger.info("Saved: " + file.getName());
- FileOutputStream fos = new FileOutputStream(file);
- byte[] buffer = new byte[BUFFER_SIZE];
- int len;
- while ((len = is.read(buffer)) != -1) {
- fos.write(buffer, 0, len);
- }
- fos.close();
- is.close();
- return true;
- } else {
- return false;
- }
- } catch (Exception e) {
- String message = "Failed save: " + e.getMessage();
- logger.warning(message);
- throw new FileChooserException(message);
- }
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/filechooser/NamedInputStream.java b/maven-src/target/classes/java/jaligner/ui/filechooser/NamedInputStream.java
deleted file mode 100644
index 6ee46ac..0000000
--- a/maven-src/target/classes/java/jaligner/ui/filechooser/NamedInputStream.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * $Id: NamedInputStream.java,v 1.2 2005/04/14 14:44:43 ahmed Exp $
- *
- * This program inputStream free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program inputStream distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.filechooser;
-
-import java.io.InputStream;
-import java.io.Serializable;
-
-/**
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class NamedInputStream extends Object implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 3256441404384686387L;
-
- /**
- * Name.
- */
- private String name = null;
-
- /**
- * Input stream.
- */
- private InputStream inputStream = null;
-
- /**
- *
- */
- public NamedInputStream(String name, InputStream inputStream) {
- this.name = name;
- this.inputStream = inputStream;
- }
-
- /**
- * @return Returns the inputStream.
- */
- public InputStream getInputStream() {
- return this.inputStream;
- }
-
- /**
- * @return Returns the name.
- */
- public String getName() {
- return this.name;
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/filechooser/package.html b/maven-src/target/classes/java/jaligner/ui/filechooser/package.html
deleted file mode 100644
index 437cb06..0000000
--- a/maven-src/target/classes/java/jaligner/ui/filechooser/package.html
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
-
-
-File loading and storing.
-@author Ahmed Moustafa (ahmed@users.sf.net)
-
-
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/images/ToolbarIcons.java b/maven-src/target/classes/java/jaligner/ui/images/ToolbarIcons.java
deleted file mode 100644
index 4864d27..0000000
--- a/maven-src/target/classes/java/jaligner/ui/images/ToolbarIcons.java
+++ /dev/null
@@ -1,79 +0,0 @@
-/*
- * $Id: ToolbarIcons.java,v 1.3 2005/02/17 07:14:56 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.images;
-
-import javax.swing.ImageIcon;
-
-/**
- * Toolbar icons
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public abstract class ToolbarIcons {
- /**
- * Path to the gifs folder
- */
- public static final String GIFS_HOME = "/jaligner/ui/images/gifs/";
-
- /**
- * Open icon
- */
- public static final ImageIcon OPEN = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "open.gif"));
-
- /**
- * Save icon
- */
- public static final ImageIcon SAVE = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "save.gif"));
-
- /**
- * Cut icon
- */
- public static final ImageIcon CUT = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "cut.gif"));
-
- /**
- * Copy icon
- */
- public static final ImageIcon COPY = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "copy.gif"));
-
- /**
- * Paste icon
- */
- public static final ImageIcon PASTE = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "paste.gif"));
-
- /**
- * Delete icon
- */
- public static final ImageIcon DELETE = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "delete.gif"));
-
- /**
- * Close icon
- */
- public static final ImageIcon CLOSE = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "close.gif"));
-
- /**
- * About icon
- */
- public static final ImageIcon ABOUT = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "about.gif"));
-
-
- /**
- * Print icon
- */
- public static final ImageIcon PRINT = new ImageIcon(ToolbarIcons.class.getResource(GIFS_HOME + "print.gif"));
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/images/gifs/about.gif b/maven-src/target/classes/java/jaligner/ui/images/gifs/about.gif
deleted file mode 100644
index 04da95e..0000000
Binary files a/maven-src/target/classes/java/jaligner/ui/images/gifs/about.gif and /dev/null differ
diff --git a/maven-src/target/classes/java/jaligner/ui/images/gifs/close.gif b/maven-src/target/classes/java/jaligner/ui/images/gifs/close.gif
deleted file mode 100644
index 064202b..0000000
Binary files a/maven-src/target/classes/java/jaligner/ui/images/gifs/close.gif and /dev/null differ
diff --git a/maven-src/target/classes/java/jaligner/ui/images/gifs/copy.gif b/maven-src/target/classes/java/jaligner/ui/images/gifs/copy.gif
deleted file mode 100644
index fa98681..0000000
Binary files a/maven-src/target/classes/java/jaligner/ui/images/gifs/copy.gif and /dev/null differ
diff --git a/maven-src/target/classes/java/jaligner/ui/images/gifs/cut.gif b/maven-src/target/classes/java/jaligner/ui/images/gifs/cut.gif
deleted file mode 100644
index 14b73a8..0000000
Binary files a/maven-src/target/classes/java/jaligner/ui/images/gifs/cut.gif and /dev/null differ
diff --git a/maven-src/target/classes/java/jaligner/ui/images/gifs/delete.gif b/maven-src/target/classes/java/jaligner/ui/images/gifs/delete.gif
deleted file mode 100644
index d9d1a33..0000000
Binary files a/maven-src/target/classes/java/jaligner/ui/images/gifs/delete.gif and /dev/null differ
diff --git a/maven-src/target/classes/java/jaligner/ui/images/gifs/jaligner.gif b/maven-src/target/classes/java/jaligner/ui/images/gifs/jaligner.gif
deleted file mode 100644
index 4711572..0000000
Binary files a/maven-src/target/classes/java/jaligner/ui/images/gifs/jaligner.gif and /dev/null differ
diff --git a/maven-src/target/classes/java/jaligner/ui/images/gifs/open.gif b/maven-src/target/classes/java/jaligner/ui/images/gifs/open.gif
deleted file mode 100644
index fabd567..0000000
Binary files a/maven-src/target/classes/java/jaligner/ui/images/gifs/open.gif and /dev/null differ
diff --git a/maven-src/target/classes/java/jaligner/ui/images/gifs/paste.gif b/maven-src/target/classes/java/jaligner/ui/images/gifs/paste.gif
deleted file mode 100644
index f118c7e..0000000
Binary files a/maven-src/target/classes/java/jaligner/ui/images/gifs/paste.gif and /dev/null differ
diff --git a/maven-src/target/classes/java/jaligner/ui/images/gifs/print.gif b/maven-src/target/classes/java/jaligner/ui/images/gifs/print.gif
deleted file mode 100644
index 7eb8299..0000000
Binary files a/maven-src/target/classes/java/jaligner/ui/images/gifs/print.gif and /dev/null differ
diff --git a/maven-src/target/classes/java/jaligner/ui/images/gifs/save.gif b/maven-src/target/classes/java/jaligner/ui/images/gifs/save.gif
deleted file mode 100644
index 8d3929c..0000000
Binary files a/maven-src/target/classes/java/jaligner/ui/images/gifs/save.gif and /dev/null differ
diff --git a/maven-src/target/classes/java/jaligner/ui/images/package.html b/maven-src/target/classes/java/jaligner/ui/images/package.html
deleted file mode 100644
index 5c792c9..0000000
--- a/maven-src/target/classes/java/jaligner/ui/images/package.html
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
-
-
-Images used in the toolbar.
-@author Ahmed Moustafa (ahmed@users.sf.net)
-
-
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/logging/DocumentHandler.java b/maven-src/target/classes/java/jaligner/ui/logging/DocumentHandler.java
deleted file mode 100644
index 5ac9a33..0000000
--- a/maven-src/target/classes/java/jaligner/ui/logging/DocumentHandler.java
+++ /dev/null
@@ -1,118 +0,0 @@
-/*
- * $Id: DocumentHandler.java,v 1.6 2005/02/22 06:11:58 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.logging;
-
-import java.awt.Color;
-import java.util.logging.ErrorManager;
-import java.util.logging.Handler;
-import java.util.logging.Level;
-import java.util.logging.LogRecord;
-
-import javax.swing.JTextPane;
-import javax.swing.text.Style;
-import javax.swing.text.StyleConstants;
-import javax.swing.text.StyledDocument;
-
-/**
- * Logging handler of {@link JTextPane}.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class DocumentHandler extends Handler {
- /**
- * Maximum document size
- */
- private static final int MAXIMUM_DOCUMENT_SIZE = 524288; // 0.5 MB
-
- private JTextPane textPane = null;
- private Style infoStyle = null;
- private Style severStyle = null;
-
- /**
- * Constructor
- * @param textPane
- */
- public DocumentHandler(JTextPane textPane) {
- this.textPane = textPane;
- setFormatter(new RecordFormatter());
-
- StyledDocument document = (StyledDocument) this.textPane.getDocument();
-
- infoStyle = document.addStyle("INFO", null);
- StyleConstants.setFontFamily(infoStyle,"Monospaced");
- StyleConstants.setBackground(infoStyle, Color.white);
- StyleConstants.setForeground(infoStyle, Color.blue);
-
- severStyle = document.addStyle("SEVER", null);
- StyleConstants.setFontFamily(severStyle,"Monospaced");
- StyleConstants.setBackground(severStyle, Color.white);
- StyleConstants.setForeground(severStyle, Color.red);
- }
-
-
- /**
- *
- */
- public void close() {
- }
-
- /**
- *
- */
- public void flush() {
- }
-
- /**
- *
- */
- public void publish(LogRecord record) {
- if (!isLoggable(record)) {
- return;
- }
-
- String message;
-
- try {
- message = getFormatter().format(record);
- } catch (Exception exception) {
- reportError(null, exception, ErrorManager.FORMAT_FAILURE);
- return;
- }
-
- synchronized(textPane) {
- if (textPane.getDocument().getLength() >= MAXIMUM_DOCUMENT_SIZE) {
- // Delete the contents of the text pane.
- textPane.setText("");
- }
-
- try {
- if (record.getLevel() == Level.SEVERE) {
- textPane.getDocument().insertString(textPane.getDocument().getLength(), message, severStyle);
- } else {
- textPane.getDocument().insertString(textPane.getDocument().getLength(), message, infoStyle);
- }
- textPane.setCaretPosition(textPane.getDocument().getLength());
- } catch (Exception ex) {
- reportError(null, ex, ErrorManager.WRITE_FAILURE);
- }
- }
-
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/logging/RecordFormatter.java b/maven-src/target/classes/java/jaligner/ui/logging/RecordFormatter.java
deleted file mode 100644
index bae1955..0000000
--- a/maven-src/target/classes/java/jaligner/ui/logging/RecordFormatter.java
+++ /dev/null
@@ -1,70 +0,0 @@
-/*
- * $Id: RecordFormatter.java,v 1.6 2005/02/19 14:58:10 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.logging;
-
-import java.util.Date;
-import java.util.logging.Formatter;
-import java.util.logging.Handler;
-import java.util.logging.LogRecord;
-
-/**
- * Logging record formatter
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class RecordFormatter extends Formatter {
-
- /**
- * This method is called for every log records
- *
- * @param record
- */
- public String format(LogRecord record) {
- StringBuffer buffer = new StringBuffer( );
- buffer.append ( new Date().toString() );
- buffer.append ( " " );
- buffer.append ( record.getLevel() );
- buffer.append ( "\t" );
- buffer.append ( record.getMessage() );
- buffer.append ( "\n" );
-
- return buffer.toString();
- }
-
- /**
- * This method is called just after the handler using this
- * formatter is created
- *
- * @param handler
- */
- public String getHead(Handler handler) {
- return "";
- }
-
- /**
- * This method is called just after the handler using this
- * formatter is closed
- *
- * @param handler
- */
- public String getTail(Handler handler) {
- return "\n";
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/logging/package.html b/maven-src/target/classes/java/jaligner/ui/logging/package.html
deleted file mode 100644
index 4506adc..0000000
--- a/maven-src/target/classes/java/jaligner/ui/logging/package.html
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
-
-
-Logging package.
-@author Ahmed Moustafa (ahmed@users.sf.net)
-
-
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/package.html b/maven-src/target/classes/java/jaligner/ui/package.html
deleted file mode 100644
index cf56259..0000000
--- a/maven-src/target/classes/java/jaligner/ui/package.html
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
-
-
-Command line and graphical user interface.
-@author Ahmed Moustafa (ahmed@users.sf.net)
-
-
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/util/PrintJobMointor.java b/maven-src/target/classes/java/jaligner/ui/util/PrintJobMointor.java
deleted file mode 100644
index 8329caa..0000000
--- a/maven-src/target/classes/java/jaligner/ui/util/PrintJobMointor.java
+++ /dev/null
@@ -1,89 +0,0 @@
-/*
- * $Id: PrintJobMointor.java,v 1.2 2005/02/19 14:58:10 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.util;
-
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-import javax.print.DocPrintJob;
-import javax.print.event.PrintJobAdapter;
-import javax.print.event.PrintJobEvent;
-
-/**
- * Mointor for print job.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class PrintJobMointor {
- /**
- * Logger
- */
- private static final Logger logger = Logger.getLogger(TextComponentUtil.class.getName());
-
- // True iff it is safe to close the print job's input stream
- private boolean done = false;
-
- PrintJobMointor(DocPrintJob job) {
- // Add a listener to the print job
- job.addPrintJobListener(new PrintJobAdapter() {
- public void printJobCanceled(PrintJobEvent printJobEvent) {
- logger.info("Print job canceled");
- allDone();
- }
-
- public void printJobCompleted(PrintJobEvent printJobEvent) {
- logger.info("Print job completed");
- allDone();
- }
-
- public void printJobFailed(PrintJobEvent printJobEvent) {
- logger.info("Print job failed");
- allDone();
- }
-
- public void printJobNoMoreEvents(PrintJobEvent printJobEvent) {
- allDone();
- }
-
- void allDone() {
- synchronized (PrintJobMointor.this) {
- done = true;
- PrintJobMointor.this.notify();
- }
- }
- });
- }
-
- /**
- * Waits for print job
- *
- */
- public synchronized void waitForPrintJob() {
- try {
- logger.info("Waiting for print job...");
- while (!done) {
- wait();
- }
- logger.info("Finished waiting for print");
- } catch (InterruptedException e) {
- logger.log(Level.SEVERE, "Failed waiting for print job: " + e.getMessage(), e);
- }
- }
-}
diff --git a/maven-src/target/classes/java/jaligner/ui/util/TextComponentUtil.java b/maven-src/target/classes/java/jaligner/ui/util/TextComponentUtil.java
deleted file mode 100644
index 954f64b..0000000
--- a/maven-src/target/classes/java/jaligner/ui/util/TextComponentUtil.java
+++ /dev/null
@@ -1,281 +0,0 @@
-/*
- * $Id: TextComponentUtil.java,v 1.14 2005/04/15 15:03:15 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.util;
-
-import jaligner.ui.clipboard.ClipboardHandlerFactory;
-import jaligner.ui.filechooser.FileChooserFactory;
-import jaligner.ui.filechooser.NamedInputStream;
-import jaligner.util.Commons;
-
-import java.io.BufferedReader;
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-import javax.print.Doc;
-import javax.print.DocFlavor;
-import javax.print.DocPrintJob;
-import javax.print.PrintService;
-import javax.print.PrintServiceLookup;
-import javax.print.ServiceUI;
-import javax.print.SimpleDoc;
-import javax.print.attribute.HashDocAttributeSet;
-import javax.print.attribute.HashPrintRequestAttributeSet;
-import javax.print.attribute.PrintRequestAttributeSet;
-import javax.print.attribute.standard.DocumentName;
-import javax.print.attribute.standard.JobName;
-import javax.swing.text.Document;
-import javax.swing.text.JTextComponent;
-
-/**
- * Text component (e.g. {@link javax.swing.JTextArea}or
- * {@link javax.swing.JTextPane}) editing helper class.
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class TextComponentUtil {
- /**
- * Empty string
- */
- private static final String EMPTY = "";
-
- /**
- * Logger
- */
- private static final Logger logger = Logger
- .getLogger(TextComponentUtil.class.getName());
-
- /**
- * Copies the selected text to the system clipboad and then deletes it from
- * the text component.
- *
- * @param textComponent
- */
- public static void cut(JTextComponent textComponent) {
- copy(textComponent);
- delete(textComponent);
- }
-
- /**
- * Copies the selected text to the system clipboard.
- *
- * @param textComponent
- */
- public static void copy(JTextComponent textComponent) {
- ClipboardHandlerFactory.getClipboardHandler().setContents(
- textComponent.getSelectedText());
- }
-
- /**
- * Copies the text contents of the system clipboard to the text component.
- *
- * @param textComponent
- */
- public static void paste(JTextComponent textComponent) {
- String contents = ClipboardHandlerFactory.getClipboardHandler()
- .getContents();
- if (contents != null) {
- StringBuffer buffer = new StringBuffer();
- char c;
- for (int i = 0, n = contents.length(); i < n; i++) {
- c = contents.charAt(i);
- // Not to copy a null character
- if (c != 0) {
- buffer.append(c);
- }
- }
- textComponent.replaceSelection(buffer.toString());
- }
- if (!textComponent.hasFocus()) {
- textComponent.requestFocus();
- }
- }
-
- /**
- * Deletes the selected text in a text component.
- *
- * @param textComponent
- */
- public static void delete(JTextComponent textComponent) {
- textComponent.replaceSelection(EMPTY);
- }
-
- /**
- * Selects all contents of a text component.
- *
- * @param textComponent
- */
- public static void selectAll(JTextComponent textComponent) {
- if (!textComponent.hasFocus()) {
- textComponent.requestFocus();
- }
- textComponent.selectAll();
- }
-
- /**
- * Opens a file and puts the contents of the file in a text component.
- *
- * @param textComponent
- * @throws TextComponentUtilException
- */
- public static boolean open(JTextComponent textComponent)
- throws TextComponentUtilException {
- InputStream is = null;
- BufferedReader reader = null;
- try {
- NamedInputStream selectedInputStream = FileChooserFactory
- .getFileChooser().open();
- if (selectedInputStream != null) {
- is = selectedInputStream.getInputStream();
- textComponent.setText(EMPTY);
-
- reader = new BufferedReader(new InputStreamReader(is));
- String line;
- Document document = textComponent.getDocument();
- while ((line = reader.readLine()) != null) {
- document.insertString(document.getLength(), line
- + Commons.getLineSeparator(), null);
- }
- if (!textComponent.hasFocus()) {
- textComponent.requestFocus();
- }
- return true;
- } else {
- return false;
- }
- } catch (Exception e) {
- throw new TextComponentUtilException(e.getMessage());
- } finally {
- if (is != null) {
- try {
- is.close();
- } catch (Exception e) {
- logger.log(Level.WARNING, "Failed closing input stream: "
- + e.getMessage(), e);
- }
- }
- if (reader != null) {
- try {
- reader.close();
- } catch (Exception e) {
- logger.log(Level.WARNING, "Failed closing reader: "
- + e.getMessage(), e);
- }
- }
- }
- }
-
- /**
- * Saves the contents of a text component to a file.
- *
- * @param textComponent
- * @param fileName
- * @return true if a file has been chosen or false otherwise
- * @throws TextComponentUtilException
- */
- public static boolean save(JTextComponent textComponent, String fileName)
- throws TextComponentUtilException {
- InputStream is = null;
- try {
- is = new ByteArrayInputStream(textComponent.getText().getBytes());
- return FileChooserFactory.getFileChooser().save(is, fileName);
- } catch (Exception e) {
- throw new TextComponentUtilException(e.getMessage());
- } finally {
- try {
- is.close();
- } catch (Exception e) {
- logger.log(Level.WARNING, "Failed closing input stream: "
- + e.getMessage(), e);
- }
- }
- }
-
- /**
- * Saves the contents of a text component to a file.
- *
- * @param textComponent
- * @return true if a file has been chosen or false otherwise
- * @throws TextComponentUtilException
- */
- public static boolean save(JTextComponent textComponent)
- throws TextComponentUtilException {
- return save(textComponent, null);
- }
-
- /**
- * Prints the contents of a text component.
- *
- * @param textComponent
- */
- public static void print(JTextComponent textComponent)
- throws TextComponentUtilException {
- InputStream is = null;
- try {
- PrintService[] printServices = PrintServiceLookup
- .lookupPrintServices(DocFlavor.INPUT_STREAM.AUTOSENSE, null);
- if (printServices.length > 0) {
-
- PrintRequestAttributeSet printRequestAttributeSet = new HashPrintRequestAttributeSet();
- printRequestAttributeSet.add(new JobName("JAligner", null));
- PrintService service = ServiceUI.printDialog(null, 50, 50,
- printServices, PrintServiceLookup
- .lookupDefaultPrintService(),
- DocFlavor.INPUT_STREAM.AUTOSENSE,
- printRequestAttributeSet);
-
- if (service != null) {
- DocPrintJob printJob = service.createPrintJob();
- PrintJobMointor printJobMointor = new PrintJobMointor(
- printJob);
-
- is = new ByteArrayInputStream(textComponent.getText()
- .getBytes());
-
- DocumentName documentName = new DocumentName("JAligner",
- null);
- HashDocAttributeSet docAttributeSet = new HashDocAttributeSet();
- docAttributeSet.add(documentName);
- Doc doc = new SimpleDoc(is,
- DocFlavor.INPUT_STREAM.AUTOSENSE, docAttributeSet);
-
- printJob.print(doc, printRequestAttributeSet);
- printJobMointor.waitForPrintJob();
- }
- } else {
- throw new TextComponentUtilException("No print service found!");
- }
- } catch (Exception e) {
- throw new TextComponentUtilException(e.getMessage());
- } finally {
- if (is != null) {
- try {
- is.close();
- } catch (IOException e) {
- logger.log(Level.WARNING, "Failed closing input stream: "
- + e.getMessage(), e);
- }
- }
- }
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/ui/util/TextComponentUtilException.java b/maven-src/target/classes/java/jaligner/ui/util/TextComponentUtilException.java
deleted file mode 100644
index d99df09..0000000
--- a/maven-src/target/classes/java/jaligner/ui/util/TextComponentUtilException.java
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * $Id: TextComponentUtilException.java,v 1.2 2005/04/14 14:44:44 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.util;
-
-/**
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class TextComponentUtilException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 4050763797251567922L;
-
- /**
- * @param message
- */
- public TextComponentUtilException(String message) {
- super(message);
- }
-}
diff --git a/maven-src/target/classes/java/jaligner/ui/util/package.html b/maven-src/target/classes/java/jaligner/ui/util/package.html
deleted file mode 100644
index a98316d..0000000
--- a/maven-src/target/classes/java/jaligner/ui/util/package.html
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
-
-
-Text component utilites package.
-@author Ahmed Moustafa (ahmed@users.sf.net)
-
-
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/util/Commons.java b/maven-src/target/classes/java/jaligner/util/Commons.java
deleted file mode 100644
index 1e07b29..0000000
--- a/maven-src/target/classes/java/jaligner/util/Commons.java
+++ /dev/null
@@ -1,217 +0,0 @@
-/*
- * $Id: Commons.java,v 1.27 2005/04/18 05:37:52 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.util;
-
-import java.net.JarURLConnection;
-import java.net.URL;
-import java.util.jar.Attributes;
-import java.util.jar.JarFile;
-import java.util.jar.Manifest;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-/**
- * Global constants/varilables/settings
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public abstract class Commons {
- /**
- * Logger
- */
- private static final Logger logger = Logger.getLogger(Commons.class
- .getName());
-
- /**
- * Build timestamp attribute in the manifest in the jar
- */
- private static final String BUILD_TIMESTAMP = "Created-At";
-
- /**
- *
- */
- private static final String currentRelease = getManifestBuildTimestamp();
-
- /**
- * Default home directory
- */
- private static final String DEFAULT_USER_DIRECTORY = ".";
-
- /**
- * Default file separator
- */
- private static final String DEFAULT_FILE_SEPARATOR = "/";
-
- /**
- * Default line separator
- */
- private static final String DEFAULT_LINE_SEPARATOR = "\r\n";
-
- /**
- * User home directory
- */
- private static String userDirectory = DEFAULT_USER_DIRECTORY;
- static {
- try {
- userDirectory = System.getProperty("user.dir");
- } catch (Exception e) {
- /*logger.log(Level.WARNING, "Failed getting user current directory: "
- + e.getMessage(), e);*/
- }
- }
-
- /**
- * Line separator
- */
- private static String fileSeparator = DEFAULT_FILE_SEPARATOR;
- static {
- try {
- fileSeparator = System.getProperty("file.separator");
- } catch (Exception e) {
- /*logger.log(Level.WARNING, "Failed getting system file separator: "
- + e.getMessage(), e);*/
- }
- }
-
- /**
- * Line separator
- */
- private static String lineSeparator = DEFAULT_LINE_SEPARATOR;
-
- static {
- try {
- lineSeparator = System.getProperty("line.separator");
- } catch (Exception e) {
- /*logger.log(Level.WARNING, "Failed getting system line separator: "
- + e.getMessage(), e);*/
- }
- }
-
- /**
- * JNLP enabled
- */
- private static boolean jnlp = false;
- static {
- try {
- jnlp = "true".equalsIgnoreCase(System.getProperty("jnlp.enabled"));
- } catch (Exception e) {
- /*logger.log(Level.WARNING, "Failed getting jnlp enabled property: "
- + e.getMessage(), e);*/
- }
- setJnlp(jnlp);
- }
-
- /**
- * Returns system file separator.
- *
- * @return file separator
- */
- public static String getFileSeparator() {
- return fileSeparator;
- }
-
- /**
- * Returns system line separator.
- *
- * @return line separator
- */
- public static String getLineSeparator() {
- return lineSeparator;
- }
-
- /**
- * Returns user's current directory.
- *
- * @return user's current directory
- */
- public static String getUserDirectory() {
- return userDirectory;
- }
-
- /**
- * Sets the JNLP flag to true of false
- *
- * @param jnlp
- * true or false
- */
- public static void setJnlp(boolean jnlp) {
- Commons.jnlp = jnlp;
- }
-
- /**
- * Returns true if jnlp is enabled
- *
- * @return true if jnlp is enabled, otherwise returns false
- */
- public static boolean isJnlp() {
- return jnlp;
- }
-
- /**
- * Gets the build teimstamp from the jar manifest
- *
- * @return build timestamp
- */
- private static String getManifestBuildTimestamp() {
- JarURLConnection connection = null;
- JarFile jarFile = null;
- URL url = Commons.class.getClassLoader().getResource("jaligner");
- try {
- // Get jar connection
- connection = (JarURLConnection) url.openConnection();
-
- // Get the jar file
- jarFile = connection.getJarFile();
-
- // Get the manifest
- Manifest manifest = jarFile.getManifest();
-
- // Get the manifest entries
- Attributes attributes = manifest.getMainAttributes();
-
- Attributes.Name name = new Attributes.Name(BUILD_TIMESTAMP);
- return attributes.getValue(name);
- } catch (Exception e) {
- String message = "Failed getting the current release info: "
- + e.getMessage();
- /*logger.log(Level.WARNING, message);*/
- }
- return null;
- }
-
- /**
- * Returns the current release version of JAligner
- *
- * @return current release
- */
- public static String getCurrentRelease() {
- return currentRelease;
- }
-
- /**
- * Returns information about JAligner
- *
- * @return information about JAligner
- */
- public static String getJAlignerInfo() {
- return "JAligner - Build: " + getCurrentRelease()
- + " - By: Ahmed Moustafa (ahmed@users.sf.net)";
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/util/SequenceParser.java b/maven-src/target/classes/java/jaligner/util/SequenceParser.java
deleted file mode 100644
index 27ee681..0000000
--- a/maven-src/target/classes/java/jaligner/util/SequenceParser.java
+++ /dev/null
@@ -1,215 +0,0 @@
-/*
- * @author Ahmed Moustafa (ahmed at users.sourceforge.net)
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.util;
-
-
-import jaligner.Sequence;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.InputStreamReader;
-import java.util.StringTokenizer;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-/**
- * SequenceParser to sequences from different formats.
- *
- * Currently the supported formats are:
- *
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class SequenceParser {
-
- /**
- * Logger
- */
- private static final Logger logger = Logger.getLogger(SequenceParser.class.getName());
-
- /**
- * Returns a parsed Sequence from a string.
- * @param sequence string to parse
- * @return parsed sequence
- * @throws SequenceParserException
- * @see Sequence
- */
- public static Sequence parse (String sequence) throws SequenceParserException {
- if (sequence == null) {
- throw new SequenceParserException ( "Null sequence" );
- }
-
- if (sequence.trim().length() == 0) {
- throw new SequenceParserException ( "Empty sequence" );
- }
-
- sequence = sequence.replaceAll("\r\n", "\n");
-
- String sequenceName = null;
- String sequenceDescription = null;
-
- if (sequence.startsWith(">")) {
- // FASTA format
- int index = sequence.indexOf("\n");
-
- if (index == -1) {
- throw new SequenceParserException ( "Invalid sequence format" );
- }
-
- String first = sequence.substring(1, index);
- sequence = sequence.substring(index);
-
- index = 0;
- for (int i = 0; i < first.length() && first.charAt(i) != ' ' && first.charAt(i) != '\t'; i++, index++) {
- // Skip white spaces
- }
- sequenceName = first.substring(0, index);
- StringTokenizer stringTokenizer = new StringTokenizer(sequenceName, "|");
- while (stringTokenizer.hasMoreTokens()) {
- sequenceName = stringTokenizer.nextToken();
- }
- sequenceDescription = index + 1 > first.length() ? "" : first.substring(index + 1);
- } else {
- // Plain format ... nothing to do here
- }
-
- Sequence s = new Sequence(prepare(sequence), sequenceName, sequenceDescription, Sequence.PROTEIN);
-
- return s;
- }
-
- /**
- * Returns a Sequence parsed and loaded from a file
- * @param file to parse
- * @return parsed sequence
- * @throws SequenceParserException
- * @see Sequence
- */
- public static Sequence parse (File file) throws SequenceParserException {
- String sequenceName = null;
- String sequenceDescription = null;
- BufferedReader reader = null;
- try {
- reader = new BufferedReader(new InputStreamReader(new FileInputStream(file)));
- StringBuffer buffer = new StringBuffer();
-
- // Read & parse the first line
- String line = reader.readLine();
-
- if (line.startsWith(">")) {
- // FASTA sequence
-
- line = line.substring(1).trim();
- int index = 0;
- for (int i = 0; i < line.length() && line.charAt(i) != ' ' && line.charAt(i) != '\t'; i++, index++) {
- // Skip white spaces
- }
-
- sequenceName = line.substring(0, index);
- StringTokenizer stringTokenizer = new StringTokenizer(sequenceName, "|");
- while (stringTokenizer.hasMoreTokens()) {
- sequenceName = stringTokenizer.nextToken();
- }
- sequenceDescription = index + 1 > line.length() ? "" : line.substring(index + 1);
- } else {
- // Plain sequence
- buffer.append(prepare(line));
- }
-
- // Read the remaining the file (the actual sequence)
- while ((line = reader.readLine()) != null) {
- buffer.append(prepare(line));
- }
- reader.close();
-
- Sequence s = new Sequence(buffer.toString(), sequenceName, sequenceDescription, Sequence.PROTEIN);
- return s;
- } catch (Exception e) {
- throw new SequenceParserException(e.getMessage());
- } finally {
- if (reader != null) {
- try {
- reader.close();
- } catch (Exception silent) {
- logger.log(Level.WARNING, "Failed closing reader: " + silent.getMessage(), silent);
- }
- }
- }
-
- }
-
- /**
- * Removes whitespaces from a sequence and validates other characters.
- * @param sequence sequence to be prepared
- * @return prepared array of characters
- * @throws SequenceParserException
- */
- private static String prepare (String sequence) throws SequenceParserException {
- StringBuffer buffer = new StringBuffer();
- String copy = sequence.trim().toUpperCase();
-
- for (int i = 0, n = copy.length(); i < n; i++) {
- switch ( copy.charAt(i) ) {
- // skip whitespaces
- case 9:
- case 10:
- case 13:
- case 32: break;
-
- // add a valid character
- case 'A':
- case 'B':
- case 'C':
- case 'D':
- case 'E':
- case 'F':
- case 'G':
- case 'H':
- case 'I':
- case 'K':
- case 'L':
- case 'M':
- case 'N':
- case 'P':
- case 'Q':
- case 'R':
- case 'S':
- case 'T':
- case 'U':
- case 'V':
- case 'W':
- case 'Y':
- case 'Z':
- case 'X':
-
- case '-':
- case '*': buffer.append(copy.charAt(i)); break;
-
- // throw an exception for anything else
- default: throw new SequenceParserException( "Invalid sequence character: '" + copy.charAt(i) + "'");
- }
- }
- return buffer.toString();
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/util/SequenceParserException.java b/maven-src/target/classes/java/jaligner/util/SequenceParserException.java
deleted file mode 100644
index 450169f..0000000
--- a/maven-src/target/classes/java/jaligner/util/SequenceParserException.java
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * @author Ahmed Moustafa (ahmed at users.sourceforge.net)
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.util;
-
-/**
- *
- * @author Ahmed Moustafa (ahmed@users.sf.net)
- */
-
-public class SequenceParserException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 3258417248288191543L;
-
- /**
- * @param message
- */
- public SequenceParserException(String message) {
- super(message);
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/jaligner/util/package.html b/maven-src/target/classes/java/jaligner/util/package.html
deleted file mode 100644
index 9223585..0000000
--- a/maven-src/target/classes/java/jaligner/util/package.html
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
-
-
-Utility classes for helping core and GUI classes.
-@author Ahmed Moustafa (ahmed@users.sf.net)
-
-
\ No newline at end of file
diff --git a/maven-src/target/classes/java/main.java b/maven-src/target/classes/java/main.java
deleted file mode 100644
index e49dc5d..0000000
--- a/maven-src/target/classes/java/main.java
+++ /dev/null
@@ -1,174 +0,0 @@
-import halign.centerstar.MatrixMSA;
-import halign.centerstar.TreeMSA;
-import halign.kband.KbandMSA;
-import halign.suffixtree.ExtremeMSA;
-import halign.suffixtree.SparkDNAMSA;
-import halign.smithwaterman.LocalProteinMSA;
-import halign.smithwaterman.SparkProteinMSA;
-import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.JavaSparkContext;
-import tree.MSATree;
-import tree.SparkTree;
-
-import java.util.Objects;
-
-public class main {
-
- public static void main(String[] args) {
- long start = System.currentTimeMillis();
- String inputFile;
- String outputFile;
- String outputDFS;
- int method;
- try {
- if (args.length == 0) {
- errorNote();
- return;
- }
- if (Objects.equals(args[0], "-localMSA")) { // msa mode, Single mode
- inputFile = args[1];
- outputFile = args[2];
- method = Integer.parseInt(args[3]);
- switch (method) {
- case 0:
- // suffix tree algorithm, which is the fastest, but only for DNA/RNA
- System.out.println("Running suffix alignment as single mode");
- new ExtremeMSA().start(inputFile, outputFile, null);
- break;
- case 1:
- // kband algorithm based on BLOSUM62 scoring matrix, only for Protein
- System.out.println("Running smithwaterman alignment as single mode");
- new LocalProteinMSA().start(inputFile, outputFile);
- break;
- case 2:
- // kband algorithm based on affine gap penalty, only for DNA/RNA
- System.out.println("Running kband alignment as single mode");
- new KbandMSA().start(inputFile, outputFile, null);
- break;
- case 3:
- // trie tree alignment algorithm which is slower and only for DNA/RNA
- System.out.println("Running trie tree alignment as single mode");
- new TreeMSA().start(inputFile, outputFile, null);
- break;
- case 4:
- // basic algorithm based on the similarity matrix, the slowest and only for DNA/RNA
- // but it is the most accurate in the case of lower sequences similarity
- System.out.println("Running similarity matrix alignment as single mode");
- new MatrixMSA().start(inputFile, outputFile, null);
- break;
- }
- long end = System.currentTimeMillis();
- System.out.println("Cost time: " + (end - start) + "ms");
- System.out.println("Successfully! The result is saved as: " + outputFile);
- } else if (Objects.equals(args[0], "-hadoopMSA")) { //Hadoop mode
- inputFile = args[1];
- outputFile = args[2];
- outputDFS = args[3];
- method = Integer.parseInt(args[4]);
- switch (method) {
- case 0:
- System.out.println("Running suffix tree alignment as hadoop mode");
- new ExtremeMSA().start(inputFile, outputFile, outputDFS);
- break;
- case 1:
- System.out.println("Sorry, smithwaterman alignment as hadoop mode had been canceled. " +
- "You may use Spark mode instead.");
- break;
- case 2:
- System.out.println("Running kband alignment as hadoop mode");
- new KbandMSA().start(inputFile, outputFile, outputDFS);
- break;
- case 3:
- System.out.println("Running trie tree alignment as hadoop mode");
- new TreeMSA().start(inputFile, outputFile, outputDFS);
- break;
- case 4:
- System.out.println("Running similarity matrix alignment as hadoop mode");
- new MatrixMSA().start(inputFile, outputFile, outputDFS);
- break;
- }
- long end = System.currentTimeMillis();
- System.out.println("Cost time: " + (end - start) + "ms");
- System.out.println("Successfully! The result is saved as: " + outputFile);
- } else if (Objects.equals(args[0], "-sparkMSA")) {
- inputFile = args[1];
- outputFile = args[2];
- method = Integer.parseInt(args[3]);
- switch (method) {
- case 0:
- System.out.println("Running suffix tree alignment as spark mode");
- SparkConf conf = new SparkConf().setAppName("SparkSuffixAutomation");
- conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
- conf.set("spark.kryoserializer.buffer.max", "2000m");
- conf.registerKryoClasses(new Class[]{SparkDNAMSA.class});
- JavaSparkContext jsc = new JavaSparkContext(conf);
- new SparkDNAMSA().start(jsc, inputFile, outputFile);
- jsc.stop();
- break;
- case 1:
- System.out.println("Running smithwaterman alignment as spark mode");
- conf = new SparkConf().setAppName("SparkProteinMSA");
- conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
- conf.set("spark.kryoserializer.buffer.max", "2000m");
- conf.registerKryoClasses(new Class[]{SparkProteinMSA.class});
- jsc = new JavaSparkContext(conf);
- new SparkProteinMSA().start(jsc, inputFile, outputFile);
- jsc.stop();
- break;
- }
- long end = System.currentTimeMillis();
- System.out.println("Cost time: " + (end - start) + "ms");
- System.out.println("Successfully! The result is saved as: " + outputFile);
- } else if (Objects.equals(args[0], "-localTree")) {
- inputFile = args[1];
- outputFile = args[2];
- System.out.println("Generating phylogenetic trees as local mode");
- new MSATree().start(inputFile, outputFile);
- long end = System.currentTimeMillis();
- System.out.println("Cost time: " + (end - start) + "ms");
- System.out.println("Successfully! The result is saved as: " + outputFile);
- } else if (Objects.equals(args[0], "-sparkTree")) {
- inputFile = args[1];
- outputFile = args[2];
- System.out.println("Generating phylogenetic trees as spark mode");
- SparkConf conf = new SparkConf().setAppName("SparkMSATree");
- conf.setMaster("local[16]");
- conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
- conf.set("spark.kryoserializer.buffer.max", "2000m");
- conf.registerKryoClasses(new Class[]{SparkTree.class});
- JavaSparkContext jsc = new JavaSparkContext(conf);
- new SparkTree().GenerateTree(jsc, inputFile, outputFile);
- jsc.stop();
- } else
- errorNote();
- } catch (Exception e) {
- e.printStackTrace();
- }
- }
-
- private static void errorNote() {
- String version = "HAlign2.1.jar";
- String suffix = " ";
- System.out.println("Kindly note: error params.");
- System.out.println();
- System.out.println("1. if you are a single core user, command is: java -jar " + version + suffix);
- System.out.println("mode: -localMSA, -localTree.");
- System.out.println("input-file: local fasta format file, required.");
- System.out.println("output-file: local fasta format file, just a file name, required.");
- System.out.println("algorithm: 0, 1, 2, 3, or 4, optional.");
- System.out.println();
- System.out.println("2. if you are a hadoop user, command is: hadoop jar " + version + suffix);
- System.out.println("mode: -hadoopMSA.");
- System.out.println("input-file: local fasta format file, required.");
- System.out.println("output-file: local fasta format file, just a file name, required.");
- System.out.println("algorithm: 0, 1, 2, 3, or 4, optional.");
- System.out.println();
- System.out.println("3. if you are a spark user, command is: spark-submit --class main " + version + suffix);
- System.out.println("mode: -sparkMSA, -sparkTree.");
- System.out.println("input-file: local fasta format file, required.");
- System.out.println("output-file: local fasta format file, just a file name, required.");
- System.out.println("algorithm: 0, 1, required for '-sparkMSA' mode.");
- System.out.println();
- System.out.println("Visit https://github.com/ShixiangWan/HAlign2.0 for detailed usages. Thanks.");
- }
-}
diff --git a/maven-src/target/classes/java/tree/ClusterProcess.java b/maven-src/target/classes/java/tree/ClusterProcess.java
deleted file mode 100644
index ea61b24..0000000
--- a/maven-src/target/classes/java/tree/ClusterProcess.java
+++ /dev/null
@@ -1,106 +0,0 @@
-package tree;
-
-import java.io.*;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.Set;
-
-public class ClusterProcess {
-
- public static Set sum_set = new HashSet<>();
-
- class cluster_data {
- String label;
- String name;
- String sequence;
- }
-
- public void preProcess(String filename) throws IOException {
- BufferedReader br = new BufferedReader(new FileReader(filename));
- int first_set_flag = 0;
- String pre_label = "";
- String cur_label;
- Set pre_set = new HashSet<>();
- while (br.ready()) {
- String str[] = br.readLine().split("\t");
- cur_label = str[0];
- if (first_set_flag == 0) { // add the first data
- first_set_flag = 1;
- pre_label = cur_label;
- cluster_data clusterdata = new cluster_data();
- clusterdata.label = str[0];
- clusterdata.name = str[1];
- clusterdata.sequence = str[2];
- pre_set.add(clusterdata);
- continue;
- }
- // if the current label no equal to the pre label add the set to sum-set
- if (!cur_label.equals(pre_label)) {
- sum_set.add(pre_set);
- pre_label = cur_label;
- pre_set = new HashSet<>();
- cluster_data clusterdata = new cluster_data();
- clusterdata.label = str[0];
- clusterdata.name = str[1];
- clusterdata.sequence = str[2];
- pre_set.add(clusterdata);
- } else {
- cluster_data clusterdata = new cluster_data();
- clusterdata.label = str[0];
- clusterdata.name = str[1];
- clusterdata.sequence = str[2];
- pre_set.add(clusterdata);
- }
- }// end while
- sum_set.add(pre_set);
- br.close();
- }
-
- public void kvProcess(String inputKVFile, String outputClusterFile) throws IOException {
- BufferedReader bufferedReader = new BufferedReader(new FileReader(inputKVFile));
- BufferedWriter bufferedWriter = new BufferedWriter(new FileWriter(outputClusterFile));
-
- String value;
- while (bufferedReader.ready()) {
- value = bufferedReader.readLine().trim();
- String[] value_temp = value.split("\t");
- String name = value_temp[0];
- String sequence = value_temp[1];
- String label = "";
- double min_distance = 100000;
- for (Set set : sum_set) {
- Iterator iter = set.iterator();
- cluster_data clusterdata = (cluster_data) iter.next(); // random select one sample to calculate the distance
- double p = JukeCantor(sequence, clusterdata.sequence);
- p = 1.0 - 0.75 * p;
- double distance = (double) (int) (-0.75 * Math.log(p) * 1000) / 1000; //根据公式计算距离
- if (distance < min_distance) {
- min_distance = distance;
- label = clusterdata.label;
- }
- }
- bufferedWriter.write(label + "\t" + name + "\t" + sequence+"\n");
- }
- bufferedReader.close();
- bufferedWriter.close();
- }
-
- /*input two sequences, return differ parts rate of them.*/
- public static double JukeCantor(String gene1, String gene2) {
- int rate = 0;
- int i;
- double result;
- int length = gene1.length();
- if (gene1.length() > gene2.length()) {
- length = gene2.length();
- }
- for (i = 0; i < length; i++) {
- if (gene1.charAt(i) != gene2.charAt(i)) {
- rate++;
- }
- }
- result = (double) rate / (double) gene1.length();
- return result;
- }
-
-}
diff --git a/maven-src/target/classes/java/tree/MSATree.java b/maven-src/target/classes/java/tree/MSATree.java
deleted file mode 100644
index f6356ee..0000000
--- a/maven-src/target/classes/java/tree/MSATree.java
+++ /dev/null
@@ -1,123 +0,0 @@
-package tree;
-
-import utils.IOUtils;
-import utils.HDFSUtils;
-
-import java.io.*;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-
-public class MSATree {
- public static void main(String[] args) throws Exception {
- String inputFile = "/home/shixiang/out.fasta";
- String outputFile = "/home/shixiang/tree.tre";
- new MSATree().start(inputFile, outputFile);
- }
-
- public void start(String inputFile, String outputFile) throws Exception {
-
- String localPath = "";
- if (inputFile.contains("/")) {
- localPath = inputFile.substring(0, inputFile.lastIndexOf("/")+1);
- inputFile = inputFile.substring(inputFile.lastIndexOf("/")+1);
- }
- HDFSUtils utils = new HDFSUtils();
- utils.clear_local_path(new File(localPath + "HPTree_OutPut"));
-
- System.out.println(">>(Local mode for tree) loading data ...");
- long startTime = System.currentTimeMillis();
- IOUtils formatUtils = new IOUtils();
- formatUtils.formatKVFasta(localPath + inputFile, localPath + "inputKV");
- int allNum = formatUtils.getAllNum();
- System.out.println("total number: " + allNum);
- System.out.println((System.currentTimeMillis() - startTime) + "ms");
-
- System.out.println(">>clustering process ...");
- String reduce_number = "2";
- Pre_Cluster_process cluster = new Pre_Cluster_process(localPath + "inputKV", reduce_number);
- cluster.Get_Cluster(localPath + "single_cluster_output", allNum);
-
- ////////////////////////////////////////////////////////////////////////////////////////
- ClusterProcess clusterProcess = new ClusterProcess();
- clusterProcess.preProcess(localPath + "single_cluster_output");
- new File(localPath + "single_cluster_output").delete();
- clusterProcess.kvProcess(localPath + "inputKV", localPath + "Cluster_OutPut");
- new File(localPath + "inputKV").delete();
- System.out.println((System.currentTimeMillis() - startTime) + "ms");
-
- /*local_path: Cluster_OutPut -> OnBalance_OutPut*/
- int cluster_number = 3;
- OnBalance onbalance = new OnBalance(localPath + "Cluster_OutPut");
- onbalance.Balance(cluster_number, localPath);
- new File(localPath + "Cluster_OutPut").delete();
-
- System.out.println(">>construct phylogenetic tree ...");
- ////////////////////////////////////////////////////////////////////////////////////////
- new File(localPath + "HPTree_OutPut").mkdir();
- BufferedReader bufferedReader = new BufferedReader(new FileReader(localPath + "OnBalance_OutPut"));
- String value;
- List balanceKey = new ArrayList<>();
- List balanceVal = new ArrayList<>();
- while (bufferedReader.ready()) {
- value = bufferedReader.readLine();
- String [] list = value.split("\t");// 把三个字段分离出来
- balanceKey.add(list[1]);
- balanceVal.add(list[2]);
- }
- bufferedReader.close();
-
- int loop;
- if (allNum < 100) loop = 4;
- else loop = 32;
- int loopNum = allNum/loop;
- int position = 0;
- ExecutorService pool = Executors.newFixedThreadPool(loop);
- for (int i = 0; i < loop; i++) {
- int position2 = position+loopNum;
- if (i == loop-1) position2 = allNum;
- List key = balanceKey.subList(position, position2);
- List val = balanceVal.subList(position, position2);
- GetSubTreeThread getSubTreeThread = new GetSubTreeThread(key, val, localPath + "HPTree_OutPut/"+i+".txt");
- pool.execute(new Thread(getSubTreeThread));
- position = position2;
- }
- pool.shutdown();
- while (!pool.isTerminated());
- new File(localPath + "OnBalance_OutPut").delete();
- System.out.println((System.currentTimeMillis() - startTime) + "ms");
-
- System.out.println(">>merge and save phylogenetic tree ...");
- NeighbourJoining_Summary nj_summary = new NeighbourJoining_Summary(localPath+"HPTree_OutPut", outputFile);
- nj_summary.Merge();
- nj_summary.Summary();
-
- utils.clear_local_path(new File(localPath + "HPTree_OutPut"));
- }
-
- public class GetSubTreeThread implements Runnable {
- private List Key;
- private List Val;
- private String outputFile;
- GetSubTreeThread(List Key, List Val, String outputFile) {
- this.Key = Key;
- this.Val = Val;
- this.outputFile = outputFile;
- }
- @Override
- public void run() {
- try {
- BufferedWriter bufferedWriter = new BufferedWriter(new FileWriter(outputFile));
- NeighbourJoining nj = new NeighbourJoining();//开启进化树构建算法
- nj.construct(Key, Val);
- String sub_tree = nj.getSubTree();
- String present_seq = nj.getPresentNode();
- bufferedWriter.write(present_seq+"\t"+sub_tree);
- bufferedWriter.close();
- } catch (IOException e) {
- e.printStackTrace();
- }
- }
- }
-}
diff --git a/maven-src/target/classes/java/tree/MinDistance.java b/maven-src/target/classes/java/tree/MinDistance.java
deleted file mode 100644
index 03dff9c..0000000
--- a/maven-src/target/classes/java/tree/MinDistance.java
+++ /dev/null
@@ -1,30 +0,0 @@
-package tree;
-
-public class MinDistance{//这个类用来保存在迭代查找的最小值信息
- private double mindistance;
- private int i;
- private int j;
- public MinDistance(double mindistance,int i,int j){
- this.mindistance=mindistance; //保存最小值
- this.i=i;//最小值的下标
- this.j=j;
- }
- public void setDistance(double mindistance){
- this.mindistance=mindistance;
- }
- public void seti(int i){
- this.i=i;
- }
- public void setj(int j){
- this.j=j;
- }
- public double getDistance(){
- return mindistance;
- }
- public int geti(){
- return i;
- }
- public int getj(){
- return j;
- }
-}
\ No newline at end of file
diff --git a/maven-src/target/classes/java/tree/NeighbourJoining.java b/maven-src/target/classes/java/tree/NeighbourJoining.java
deleted file mode 100644
index f420034..0000000
--- a/maven-src/target/classes/java/tree/NeighbourJoining.java
+++ /dev/null
@@ -1,309 +0,0 @@
-package tree;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-class NeighbourJoining_Node {
- private NeighbourJoining_Node ParentNode;
- private NeighbourJoining_Node LNode;
- private NeighbourJoining_Node RNode;
- private String Tree;
- private int index;
-
- public NeighbourJoining_Node(int index, NeighbourJoining_Node ParentNode, NeighbourJoining_Node LNode, NeighbourJoining_Node RNode, String Tree) {
- this.ParentNode = ParentNode;
- this.LNode = LNode;
- this.RNode = RNode;
- this.index = index;
- this.Tree = Tree;
- }
-
- public void Reset(int index, NeighbourJoining_Node ParentNode, NeighbourJoining_Node LNode, NeighbourJoining_Node RNode, String Tree) {
- this.ParentNode = ParentNode;
- this.LNode = LNode;
- this.RNode = RNode;
- this.index = index;
- this.Tree = Tree;
- }
-
- // reset function
- public void Reset_ParentNode(NeighbourJoining_Node ParentNode) {
- this.ParentNode = ParentNode;
- }
-
- public void Reset_LNode(NeighbourJoining_Node LNode) {
- this.LNode = LNode;
- }
-
- public void Reset_RNode(NeighbourJoining_Node RNode) {
- this.RNode = RNode;
- }
-
- public void Reset_index(int index) {
- this.index = index;
- }
-
- public void Reset_Tree(String Tree) {
- this.Tree = Tree;
- }
-
- // get function
- public NeighbourJoining_Node Get_ParentNode() {
- return this.ParentNode;
- }
-
- public NeighbourJoining_Node Get_LNode() {
- return this.LNode;
- }
-
- public NeighbourJoining_Node Get_RNode() {
- return this.RNode;
- }
-
- public int Get_index() {
- return this.index;
- }
-
- public String Get_Tree() {
- return this.Tree;
- }
-
-}
-
-public class NeighbourJoining {
-
- String subTree;// 返回进化子树
- String present_seq;
-
- public void construct(List seq_name, List seq) throws IOException {//把子集合的序列名和序列数组作为参数传进来
-
- int setsize = seq.size();//获取序列的条数
- double[][] distance = new double[setsize][setsize]; //设置子集合的距离矩阵
- double[] A = new double[setsize];//距离矩阵每行的和
- ArrayList LeaveNode_list = new ArrayList<>();
- for (int i = 0; i < setsize; i++) {//构建叶子节点列表
- LeaveNode_list.add(new NeighbourJoining_Node(i, null, null, null, ""));
- }
-
- CountTheDistance(seq, seq.size(), distance, A);//计算距离矩阵以及A
- MinDistance min_distance = new MinDistance(10000.0, 0, 0);
- AmendTheDistance(distance, A, setsize, min_distance);//对距离矩阵进行修正
- Set Already_set = new HashSet();
- int iter = 0;
- while (iter != setsize - 1) {//依次合并两个节点
- //System.out.println("iter time is:" + iter);
- iter++;
- double Li = 0.0, Lj = 0.0;
- for (int z = 0; z < setsize; z++) {
- Li = Li + distance[min_distance.geti()][z] - distance[min_distance.getj()][z];
- }
- Lj = -Li;
- Li = (min_distance.getDistance() + Li) / 2;//分枝长度计算的时候是全总再加min_distance
- Lj = (min_distance.getDistance() + Lj) / 2; //获取了i , j 到父节点的分枝长度
-
- for (int k = 0; k < setsize; k++) { //更新矩阵
- if (k != min_distance.geti() && k != min_distance.getj()) {//当不是扫描到对正轴的时候
- if (distance[k][min_distance.geti()] == 0) {
- continue;
- }
- distance[min_distance.geti()][k] = (distance[min_distance.geti()][k] + distance[min_distance.getj()][k]
- - min_distance.getDistance()) / 2;
- distance[min_distance.getj()][k] = 0;//然后把下标大的横和列全部都变成0
- distance[k][min_distance.getj()] = 0;
- distance[k][min_distance.geti()] = distance[min_distance.geti()][k];
- } else { //要么k=i ,或者k=j
- distance[min_distance.geti()][k] = 0;
- distance[min_distance.getj()][k] = 0;
- distance[k][min_distance.getj()] = 0;
- distance[k][min_distance.geti()] = 0;
- }
- }
-
- //更新完矩阵后，合并这两个节点， 1、两个均未出现过 2、一个出现过一个未出现过
- if (!Already_set.contains(min_distance.geti()) && !Already_set.contains(min_distance.getj())) {
- LeaveNode_list.get(min_distance.geti()).Reset_Tree(seq_name.get(min_distance.geti()));//叶子节点添加子结构
- LeaveNode_list.get(min_distance.getj()).Reset_Tree(seq_name.get(min_distance.getj()));
- NeighbourJoining_Node InternalNode = new NeighbourJoining_Node(-1,//构建一个内部节点
- null,
- LeaveNode_list.get(min_distance.geti()),
- LeaveNode_list.get(min_distance.getj()),
- "(" + LeaveNode_list.get(min_distance.geti()).Get_Tree() + ":" + Li + "," + LeaveNode_list.get(min_distance.getj()).Get_Tree() + ":" + Lj + ")"
- );
- LeaveNode_list.get(min_distance.geti()).Reset_ParentNode(InternalNode);//叶子节修改父节点
- LeaveNode_list.get(min_distance.getj()).Reset_ParentNode(InternalNode);
- InternalNode.Get_LNode().Reset_Tree(null);// 设置左右子树节点为空，减小空间消耗
- InternalNode.Get_RNode().Reset_Tree(null);
- Already_set.add(min_distance.geti());// 记录已处理节点
- Already_set.add(min_distance.getj());
- } else if (Already_set.contains(min_distance.geti()) && !Already_set.contains(min_distance.getj())) { // i 节点已经被处理了
- NeighbourJoining_Node CurrentNode = LeaveNode_list.get(min_distance.geti());
- while (CurrentNode.Get_ParentNode() != null) {
- CurrentNode = CurrentNode.Get_ParentNode(); //回溯到i节点的根节点
- }
- LeaveNode_list.get(min_distance.getj()).Reset_Tree(seq_name.get(min_distance.getj()));
- NeighbourJoining_Node InternalNode = new NeighbourJoining_Node(-1,//构建一个内部节点
- null,
- CurrentNode,
- LeaveNode_list.get(min_distance.getj()),
- "(" + CurrentNode.Get_Tree() + ":" + Li + "," + LeaveNode_list.get(min_distance.getj()).Get_Tree() + ":" + Lj + ")"
- );
- CurrentNode.Reset_ParentNode(InternalNode);
- LeaveNode_list.get(min_distance.getj()).Reset_ParentNode(InternalNode);
- InternalNode.Get_LNode().Reset_Tree(null);// 设置左右子树节点为空，减小空间消耗
- InternalNode.Get_RNode().Reset_Tree(null);
- Already_set.add(min_distance.getj());// 记录已处理节点
- }//end if i contain
- else if (Already_set.contains(min_distance.getj()) && !Already_set.contains(min_distance.geti())) { // j 节点已经被处理了
- NeighbourJoining_Node CurrentNode = LeaveNode_list.get(min_distance.getj());
- while (CurrentNode.Get_ParentNode() != null) {
- CurrentNode = CurrentNode.Get_ParentNode(); //回溯到i节点的根节点
- }
- LeaveNode_list.get(min_distance.geti()).Reset_Tree(seq_name.get(min_distance.geti()));//叶子节点添加子结构
- NeighbourJoining_Node InternalNode = new NeighbourJoining_Node(-1,//构建一个内部节点
- null,
- CurrentNode,
- LeaveNode_list.get(min_distance.geti()),
- "(" + LeaveNode_list.get(min_distance.geti()).Get_Tree() + ":" + Li + "," + CurrentNode.Get_Tree() + ":" + Lj + ")"
- );
- CurrentNode.Reset_ParentNode(InternalNode);
- LeaveNode_list.get(min_distance.geti()).Reset_ParentNode(InternalNode);
- InternalNode.Get_LNode().Reset_Tree(null);// 设置左右子树节点为空，减小空间消耗
- InternalNode.Get_RNode().Reset_Tree(null);
- Already_set.add(min_distance.geti());// 记录已处理节点
- }//end if j contain
- else if (Already_set.contains(min_distance.geti()) && Already_set.contains(min_distance.getj())) {
- NeighbourJoining_Node CurrentNodei = LeaveNode_list.get(min_distance.geti());
- while (CurrentNodei.Get_ParentNode() != null) {
- CurrentNodei = CurrentNodei.Get_ParentNode(); //回溯到i节点的根节点
- }
- NeighbourJoining_Node CurrentNodej = LeaveNode_list.get(min_distance.getj());
- while (CurrentNodej.Get_ParentNode() != null) {
- CurrentNodej = CurrentNodej.Get_ParentNode(); //回溯到i节点的根节点
- }
- NeighbourJoining_Node InternalNode = new NeighbourJoining_Node(-1,//构建一个内部节点
- null,
- CurrentNodei,
- CurrentNodej,
- "(" + CurrentNodei.Get_Tree() + ":" + Li + "," + CurrentNodej.Get_Tree() + ":" + Lj + ")"
- );
- CurrentNodei.Reset_ParentNode(InternalNode);
- CurrentNodej.Reset_ParentNode(InternalNode);
- CurrentNodei.Reset_Tree(null);
- CurrentNodej.Reset_Tree(null);
- }
- // 合并节点过程完成
-
- // 再次寻找最小值
- min_distance.setDistance(10000.0);//重新设置最小值的下标，后面的代码用来找新构建的最小值,因为扫描是从上到下从左到右，所以x一定是比y更小
- min_distance.seti(0);
- min_distance.setj(0);
- for (int i = 0; i < setsize; i++) { // 重新修改净分枝度
- A[i] = 0;
- for (int j = 0; j < setsize; j++) {
- A[i] = A[i] + distance[i][j];
- }
- }
- for (int i = 0; i < setsize; i++) {
- for (int j = i + 1; j < setsize; j++) {
- if (distance[i][j] == 0) {
- continue;
- }
- distance[i][j] = distance[i][j] - (A[i] + A[j]) / (setsize - 2);//修正的时候根据公式要用到A 和distance
- distance[j][i] = distance[i][j];
- if (distance[i][j] < min_distance.getDistance() && distance[i][j] != 0) {//获取矩阵中最小的距离
- min_distance.setDistance(distance[i][j]);
- min_distance.seti(i);
- min_distance.setj(j);
- }// end if
- }//end for
- } //end for
- }//end while(Already_set.size()!=setsize)
-
- // 获取子树
- NeighbourJoining_Node CurrentNode = LeaveNode_list.get(0);
- while (CurrentNode.Get_ParentNode() != null) {
- CurrentNode = CurrentNode.Get_ParentNode(); //回溯到i节点的根节点
- }
- subTree = CurrentNode.Get_Tree();
- // 获取代表序列
- while (CurrentNode.Get_LNode() != null) {
- CurrentNode = CurrentNode.Get_LNode();
- }
- present_seq = seq.get(CurrentNode.Get_index());
- }
-
- public String getSubTree() {//用来获取子树
- return subTree;
- }
-
- public String getPresentNode() {//获取代表序列
- return present_seq;
- }
-
- public static void AmendTheDistance(double[][] distance, double[] A, int lineNumber, MinDistance min_distance) {//在进化树构建的时候用来修正距离
- int i, j;
- for (i = 0; i < lineNumber; i++) {
- for (j = i + 1; j < lineNumber; j++) {
- distance[i][j] = distance[i][j] - (A[i] + A[j]) / (lineNumber - 2);//修正的时候根据公式要用到A 和distance
- distance[j][i] = distance[i][j];
- if (distance[i][j] < min_distance.getDistance() && distance[i][j] != 0) {//获取矩阵中最小的距离
- min_distance.setDistance(distance[i][j]);
- min_distance.seti(i);
- min_distance.setj(j);
- }
- }
- }
- }
-
- public static void CountTheDistance(List sequences, int lineNumber, double[][] distance, double[] A) throws IOException {//这个函数用来计算距离矩阵
- int i, j;
- double p;
- double temp;
- double distance_temp = 0;//这个在计算方差和均值的时候有用
-
- for (i = 0; i < lineNumber; i++) {
- for (j = 0; j < lineNumber; j++) {
-
- if (i < j) {
- p = JukeCantor(sequences.get(i), sequences.get(j));
- p = 1.0 - 0.75 * p;
- temp = Math.log(p);
- distance_temp = -0.75 * temp; //根据公式计算距离
- distance[i][j] = distance_temp;
- } else if (i == j) {
- distance[i][j] = 0;//对角线上为0
- } else {
- distance[i][j] = distance[j][i];
- }
- // System.out.print(distance_temp+"\t"); //这里打印出距离矩阵可以在屏幕上显示
- A[i] += distance[i][j];//计算A数组
- }
- // System.out.println();
- }
- }
-
- public static double JukeCantor(String gene1, String gene2) {
- int rate = 0;
- int i;
- double result = 0.0;
- int length = gene1.length();
- if (gene1.length() > gene2.length()) {
- length = gene2.length();
- }
- for (i = 0; i < length; i++) {
- //System.out.print(gene1.charAt(i)+" ");
- if (gene1.charAt(i) != gene2.charAt(i)) {
- rate++;
- }
- }
- result = (double) rate / (double) gene1.length();
- //System.out.print(result+" ");
- return result;
- }
-
-
-}
-
\ No newline at end of file
diff --git a/maven-src/target/classes/java/tree/NeighbourJoining_Summary.java b/maven-src/target/classes/java/tree/NeighbourJoining_Summary.java
deleted file mode 100644
index a1dd7cb..0000000
--- a/maven-src/target/classes/java/tree/NeighbourJoining_Summary.java
+++ /dev/null
@@ -1,319 +0,0 @@
-package tree;
-
-import java.io.*;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.Set;
-
-class NeighbourJoiningSummary_Node{
- private NeighbourJoiningSummary_Node ParentNode;
- private NeighbourJoiningSummary_Node LNode;
- private NeighbourJoiningSummary_Node RNode;
- private String Tree;
- private int index;
-
- public NeighbourJoiningSummary_Node(int index, NeighbourJoiningSummary_Node ParentNode, NeighbourJoiningSummary_Node LNode, NeighbourJoiningSummary_Node RNode , String Tree){
- this.ParentNode = ParentNode;
- this.LNode = LNode;
- this.RNode = RNode;
- this.index = index;
- this.Tree = Tree;
- }
- public void Reset(int index, NeighbourJoiningSummary_Node ParentNode, NeighbourJoiningSummary_Node LNode, NeighbourJoiningSummary_Node RNode , String Tree){
- this.ParentNode = ParentNode;
- this.LNode = LNode;
- this.RNode = RNode;
- this.index = index;
- this.Tree = Tree;
- }
-//reset function
- public void Reset_ParentNode(NeighbourJoiningSummary_Node ParentNode){
- this.ParentNode = ParentNode;
- }
- public void Reset_LNode(NeighbourJoiningSummary_Node LNode){
- this.LNode = LNode;
- }
- public void Reset_RNode(NeighbourJoiningSummary_Node RNode){
- this.RNode = RNode;
- }
- public void Reset_index(int index){
- this.index = index;
- }
- public void Reset_Tree(String Tree){
- this.Tree = Tree;
- }
-// get function
- public NeighbourJoiningSummary_Node Get_ParentNode(){
- return this.ParentNode;
- }
- public NeighbourJoiningSummary_Node Get_LNode(){
- return this.LNode;
- }
- public NeighbourJoiningSummary_Node Get_RNode(){
- return this.RNode;
- }
- public int Get_index(){
- return this.index;
- }
- public String Get_Tree(){
- return this.Tree;
- }
-
-}
-
-public class NeighbourJoining_Summary {
-
- String input_Directory;
- String HPTree_OutPut;
- ArrayList LeaveNode_list = new ArrayList();
- //列表用于保存所有的子树
- ArrayList seq = new ArrayList();
- //列表用于保存所有的代表节点
-
- public NeighbourJoining_Summary(String input_Directory , String HPTree_OutPut){
- this.input_Directory = input_Directory;
- this.HPTree_OutPut = HPTree_OutPut;
- }
-
- public void Merge() throws IOException{ //合并文件夹下的所有reduce输出结果
- File NeighbourJoining_subTree_Directory = new File(input_Directory);//获取本地文件目录
- if (!NeighbourJoining_subTree_Directory.isDirectory()){
- System.out.println(NeighbourJoining_subTree_Directory + " is not a directory ");
- System.exit(0);
- }
- else{//操作文件夹下的每个文件
- String[] filelist = NeighbourJoining_subTree_Directory.list();
-
- for(int i=0;i Already_set = new HashSet();
-
- int iter=0;
- while(iter!=setsize-1){//依次合并两个节点
- iter++;
- double Li=0.0 , Lj=0.0;
- for(int z=0;zsequences,int lineNumber,double[][] distance,double[] A) throws IOException{//这个函数用来计算距离矩阵
- int i,j;
- double p;
- double temp;
- double distance_temp = 0;//这个在计算方差和均值的时候有用
-
- for(i=0;igene2.length()){
- length=gene2.length();
- }
- for(i=0;i set_info_list = new ArrayList<>();
- for (int i = 0; i < cluster_num; i++) {
- set_info_list.add(new set_info(String.valueOf(i), 0));
- }
-
- while (br.ready()) {
- String[] line = br.readLine().split("\t");
- set_info_list.get(Integer.parseInt(line[0])).Reset_size(
- set_info_list.get(Integer.parseInt(line[0])).Get_size() + 1);
-
- }//end while
- br.close();
-
- /*
- * 以上获取正确的集合类别信息,所有集合的信息被保存到list当中
- */
- int balance_value = 0;
- Comparator comparator = (obj1, obj2) -> {
- set_info test1 = obj1;
- set_info test2 = obj2;
- if (test1.size > test2.size) {
- return 1;
- } else if (test1.size < test2.size) {
- return -1;
- } else {
- return 0;
- }
- };
-
- Collections.sort(set_info_list, comparator); //首先需要对set_info_list 根据size的大小进行排序
-
- ArrayList new_list = new ArrayList<>();
- for (int i = 0; i < set_info_list.size() - 1; i++) { //排序后计算balance value
- balance_value = balance_value + (set_info_list.get(i).size - set_info_list.get(i + 1).size);
- new_list.add(set_info_list.get(i).size);
- }
- new_list.add(set_info_list.get(set_info_list.size() - 1).size);////把 set_info_list 中的size 复制给new_list
- new_list.set(1, new_list.get(0) + new_list.get(1));
- new_list.set(0, new_list.get(new_list.size() - 1) / 2);
- new_list.set(new_list.size() - 1, new_list.get(new_list.size() - 1) / 2);
-
- Collections.sort(new_list); //对new_list 进行排序，并计算其balance value
-
- int new_balance_value = 0;
- for (int i = 0; i < set_info_list.size() - 1; i++) { //排序后计算 new balance value
- new_balance_value = new_balance_value + (new_list.get(i) - new_list.get(i + 1));
- }
- if (balance_value < 0) balance_value = -balance_value;
- if (new_balance_value < 0) new_balance_value = -new_balance_value;//由于是从小到大，所有balance value 的正负号需要调整
-
-
- if (new_balance_value < balance_value) {
- flag = 0;//flag等于0的时候表明有改进，需要继续迭代
- //重写数据
- String splitLabel = set_info_list.get(set_info_list.size() - 1).label;
- String splitToLable = set_info_list.get(0).label;
- int splitSize = set_info_list.get(set_info_list.size() - 1).size / 2;
- String combineLabel = set_info_list.get(0).label;
- String combineToLabel = set_info_list.get(1).label;
- iteratorTime++;
- inputfile = ReWriterFile(splitLabel, splitToLable, combineLabel, combineToLabel, splitSize, inputfile, iteratorTime);
- } else {
- flag = 1;//flag等于1的时候说明没有改进，退出while循环
- break;
- }
- }//end while
-
- BufferedReader br = new BufferedReader(new FileReader(inputfile));
- BufferedWriter bw = new BufferedWriter(new FileWriter(local_path + "/OnBalance_OutPut"));
- while (br.ready()) {
- bw.write(br.readLine());
- bw.newLine();
- bw.flush();
- }
- br.close();
- bw.close();
- }// end Balance
-
- public String ReWriterFile(String splitLabel, String splitToLabel,
- String combineLabel, String combineToLabel, int splitSize, String inputfile, int iteratorTime) throws IOException {
- String fw = "tmp-" + iteratorTime;
- BufferedReader br = new BufferedReader(new FileReader(inputfile));
- BufferedWriter bw = new BufferedWriter(new FileWriter(fw));
- while (br.ready()) {
- String[] line = br.readLine().split("\t");
- if (line[0].equals(splitLabel) && splitSize > 0) {
- splitSize--;
- bw.write(line[0] + "\t" + line[1] + "\t" + line[2]);
- bw.newLine();
- bw.flush();
- } else if (line[0].equals(splitLabel) && splitSize <= 0) {
- bw.write(splitToLabel + "\t" + line[1] + "\t" + line[2]);
- bw.newLine();
- bw.flush();
- } else if (line[0].equals(combineLabel)) {
- bw.write(combineToLabel + "\t" + line[1] + "\t" + line[2]);
- bw.newLine();
- bw.flush();
- } else {
- bw.write(line[0] + "\t" + line[1] + "\t" + line[2]);
- bw.newLine();
- bw.flush();
- }
- }
- br.close();
- bw.close();
- return fw;
- }
-}
diff --git a/maven-src/target/classes/java/tree/Pre_Cluster_process.java b/maven-src/target/classes/java/tree/Pre_Cluster_process.java
deleted file mode 100644
index 2f277e3..0000000
--- a/maven-src/target/classes/java/tree/Pre_Cluster_process.java
+++ /dev/null
@@ -1,524 +0,0 @@
-package tree;
-
-import java.io.*;
-import java.util.*;
-
-class Point {
- double meature;
- int i;
- int j;
-
- Point(double meature, int i, int j) {
- this.meature = meature;
- this.i = i;
- this.j = j;
- }
-}
-
-class Node {
- private String ID;
- private int Lnum;
- private int Rnum;
- private Node ParentNode;
- private Node LNode;
- private Node RNode;
- private int index;
- private Boolean HaveClass;
-
- public Node(String ID, int Lnum, int Rnum, Node ParentNode, Node LNode, Node RNode, int index, Boolean HaveClass) {
- this.ID = ID;
- this.Lnum = Lnum;
- this.Rnum = Rnum;
- this.ParentNode = ParentNode;
- this.LNode = LNode;
- this.RNode = RNode;
- this.index = index;
- this.HaveClass = HaveClass;
- }
-
- public void Reset(String ID, int Lnum, int Rnum, Node ParentNode, Node LNode, Node RNode, int index, Boolean HaveClass) {
- this.ID = ID;
- this.Lnum = Lnum;
- this.Rnum = Rnum;
- this.ParentNode = ParentNode;
- this.LNode = LNode;
- this.RNode = RNode;
- this.index = index;
- this.HaveClass = HaveClass;
- }
-
- // reset function
- public void Reset_Lnum(int Lnum) {
- this.Lnum = Lnum;
- }
-
- public void Reset_Rnum(int Rnum) {
- this.Rnum = Rnum;
- }
-
- public void Reset_ParentNode(Node ParentNode) {
- this.ParentNode = ParentNode;
- }
-
- public void Reset_LNode(Node LNode) {
- this.LNode = LNode;
- }
-
- public void Reset_RNode(Node RNode) {
- this.RNode = RNode;
- }
-
- public void Reset_index(int index) {
- this.index = index;
- }
-
- public void Reset_HaveClass(Boolean HaveClass) {
- this.HaveClass = HaveClass;
- }
-
- // get function
- public int Get_Lnum() {
- return this.Lnum;
- }
-
- public int Get_Rnum() {
- return this.Rnum;
- }
-
- public Node Get_ParentNode() {
- return this.ParentNode;
- }
-
- public Node Get_LNode() {
- return this.LNode;
- }
-
- public Node Get_RNode() {
- return this.RNode;
- }
-
- public int Get_index() {
- return this.index;
- }
-
- public Boolean Get_HaveClass() {
- return this.HaveClass;
- }
-}
-
-public class Pre_Cluster_process {
- private String inputFile = new String();
- private int rdNum = 0;
- private static int cluster_num;
-
- public Pre_Cluster_process(String inputFile, String reduceNumber) {
- // TODO Auto-generated constructor stub
- this.inputFile = inputFile;
- this.rdNum = Integer.parseInt(reduceNumber);
- }
-
- public static String ClusterFromMatrix(double[][] distance, String output, ArrayList cluster_list, int cluster_list_size, int k) {
- try {
- Comparator comparator = (obj1, obj2) -> { // for the sort
- Point point = obj2;
- if (point.meature > point.meature) {
- return 1;
- } else if (point.meature < point.meature) {
- return -1;
- } else {
- return 0;
- }
- };
- ArrayList distance_list = new ArrayList<>();
- Set Already_set = new HashSet(); // this set save the whole index of data
- for (int i = 0; i < cluster_list_size; i++) { // translate the matrix to the list
- for (int j = i + 1; j < cluster_list_size; j++) {
- Point point = new Point(distance[i][j], i, j);
- distance_list.add(point);
- }
- }
- Collections.sort(distance_list, comparator); // sort the list
- Set Root_set = new HashSet();
- Set Sum_set = new HashSet();
- ArrayList LeaveNode_list = new ArrayList();//用于保存叶子节点的数组
- for (int i = 0; i < cluster_list_size; i++) {
- LeaveNode_list.add(new Node("leave", 0, 0, null, null, null, i, null));
- }
- int Index = 0;
- while (Already_set.size() != cluster_list_size) {
- //i和j都未被处理过
- if (!Already_set.contains(distance_list.get(Index).i) && !Already_set.contains(distance_list.get(Index).j)) {
- Set new_set = new HashSet();// 申请新的集合用于存放i,j
- new_set.add(distance_list.get(Index).i); //新集合添加i ,j
- new_set.add(distance_list.get(Index).j);
- Sum_set.add(new_set); //全总集合添加新集合
- Already_set.add(distance_list.get(Index).i);
- Already_set.add(distance_list.get(Index).j);
- Node InternalNode = new Node("Internal", 1, 1, null, LeaveNode_list.get(distance_list.get(Index).i),
- LeaveNode_list.get(distance_list.get(Index).j), -1, null); //申请一个内部节点，左右节点指向叶子节点，Parent节点为null
- LeaveNode_list.get(distance_list.get(Index).i).Reset("leave", 0, 0, InternalNode,
- null, null, distance_list.get(Index).i, true); //修改叶子节点的信息
- LeaveNode_list.get(distance_list.get(Index).j).Reset("leave", 0, 0, InternalNode,
- null, null, distance_list.get(Index).j, true);
- Root_set.add(InternalNode); //将当前的根节点添加到根节点集合
- }// end if //i和j有一个被处理过
- else if (Already_set.contains(distance_list.get(Index).i) && !Already_set.contains(distance_list.get(Index).j)) {
- for (Set seti : Sum_set) {
- if (seti.contains(distance_list.get(Index).i)) {
- seti.add(distance_list.get(Index).j);
- Already_set.add(distance_list.get(Index).j);
- break;
- }
- }// end for
- Node CurrentNode = LeaveNode_list.get(distance_list.get(Index).i); // current node
- while (CurrentNode.Get_ParentNode() != null) {
- CurrentNode = CurrentNode.Get_ParentNode(); //回溯到i节点的根节点
- }
- // now the CurrentNode is the root
- Node InternalNode = new Node("Internal", CurrentNode.Get_Lnum() + CurrentNode.Get_Rnum(), 1, null, CurrentNode,
- LeaveNode_list.get(distance_list.get(Index).j), -1, null); //申请一个内部节点，
- LeaveNode_list.get(distance_list.get(Index).j).Reset("leave", 0, 0, InternalNode,
- null, null, distance_list.get(Index).j, true); //设置右子节点
- CurrentNode.Reset_ParentNode(InternalNode); //修改左节点的父节点
- Root_set.add(InternalNode); //添加新的根节点
- Root_set.remove(CurrentNode); //移除旧的根节点
- }// end if //i和j有一个被处理过
- else if (!Already_set.contains(distance_list.get(Index).i) && Already_set.contains(distance_list.get(Index).j)) {
- for (Set setj : Sum_set) {
- if (setj.contains(distance_list.get(Index).j)) {
- setj.add(distance_list.get(Index).i);
- Already_set.add(distance_list.get(Index).i);
- break;
- }
- }//end for
- Node CurrentNode = LeaveNode_list.get(distance_list.get(Index).j); // current node
- while (CurrentNode.Get_ParentNode() != null) {
- CurrentNode = CurrentNode.Get_ParentNode(); //回溯到i节点的根节点
- }
- // now the CurrentNode is the root
- Node InternalNode = new Node("Internal", CurrentNode.Get_Lnum() + CurrentNode.Get_Rnum(), 1, null, CurrentNode,
- LeaveNode_list.get(distance_list.get(Index).i), -1, null); //申请一个内部节点，
- LeaveNode_list.get(distance_list.get(Index).i).Reset("leave", 0, 0, InternalNode,
- null, null, distance_list.get(Index).i, true); //设置右子节点
- CurrentNode.Reset_ParentNode(InternalNode); //修改左节点的父节点
- Root_set.add(InternalNode); //添加新的根节点
- Root_set.remove(CurrentNode); //移除旧的根节点
- }// end if
- else { // in this part the Already_set no add element
- Set seti = new HashSet();
- Set setj = new HashSet();
- for (Set set : Sum_set) {
- if (set.contains(distance_list.get(Index).i)) {
- seti = set;
- break;
- }
- }
- for (Set set : Sum_set) {
- if (set.contains(distance_list.get(Index).j)) {
- setj = set;
- break;
- }
- }
- if (seti.equals(setj)) { // if i and j in the same set
- Index++;
- continue;
- }
- Set combine_set = new HashSet(); // combine the two set
- for (Integer item : seti) { // get the set's elements
- combine_set.add(item);
- }
- for (Integer item : setj) {
- combine_set.add(item);
- }
-
- Set tmp_set = new HashSet();////为了确保能够删除seti和setj
- tmp_set.add(combine_set);
- for (Set set : Sum_set) {
- if (set.equals(seti)) {
- continue;
- }
- if (set.equals(setj)) {
- continue;
- }
- tmp_set.add(set);
- }
- Sum_set = null;
- Sum_set = tmp_set;
-
- Node CurrentNodei = LeaveNode_list.get(distance_list.get(Index).i); // current node i
- Node CurrentNodej = LeaveNode_list.get(distance_list.get(Index).j); // current node i
- while (CurrentNodei.Get_ParentNode() != null) {
- CurrentNodei = CurrentNodei.Get_ParentNode(); //回溯到i节点的根节点
- }
- while (CurrentNodej.Get_ParentNode() != null) {
- CurrentNodej = CurrentNodej.Get_ParentNode(); //回溯到i节点的根节点
- }
- Node InternalNode = new Node("Internal", CurrentNodei.Get_Lnum() + CurrentNodei.Get_Rnum(),
- CurrentNodej.Get_Lnum() + CurrentNodej.Get_Rnum(), null, CurrentNodei,
- CurrentNodej, -1, null); //申请一个内部节点，
- CurrentNodei.Reset_ParentNode(InternalNode); //修改 父节点
- CurrentNodej.Reset_ParentNode(InternalNode); //修改 父节点
- Root_set.add(InternalNode); //添加新的根节点
- Root_set.remove(CurrentNodei); //移除旧的根节点
- Root_set.remove(CurrentNodej); //移除旧的根节点
- } // end else
- Index++;
- } // end while
- // now the Sum_set contains the class of the data
-
- /*
- * This should have the on load balance to the sum_set to make the set size==rdNum
- * Root_set.size() == Sum_set.size()
- */
- if (Sum_set.size() > 3 * k) {
- while (Sum_set.size() > 3 * k) {
- ArrayList set_list = new ArrayList(); //用于存储集合的列表
- for (Set set : Sum_set) {
- set_list.add(set); //向列表中添加元素
- }
- Comparator comparator2 = new Comparator() { //比较函数
- public int compare(Set obj1, Set obj2) { // for the sort
- Set test1 = (Set) obj1;
- Set test2 = (Set) obj2;
- if (test1.size() > test2.size()) {
- return 1;
- } else if (test1.size() < test2.size()) {
- return -1;
- } else {
- return 0;
- }
- }
- };
- Collections.sort(set_list, comparator2);//对集合列表进行排序
- Set tmp = set_list.get(0);
- set_list.get(0).addAll(set_list.get(1));//合并最小的两个集合
- Sum_set.remove(tmp);//删除总集合中的最小两个
- Sum_set.remove(set_list.get(1));//并添加新的集合进总集合中
- }
- int label = 0;
- BufferedWriter bw = new BufferedWriter(new FileWriter(output)); // write the class the the output file
- for (Set set : Sum_set) {
- for (int item : set) {
- bw.write(label + "\t" + cluster_list.get(item)); // output is label \t name \t seq
- bw.newLine();
- bw.flush();
- }
- label++;
- }//end for
- cluster_num = Sum_set.size();
- //System.out.println("Sum_set.size()>3k the class number is " + Sum_set.size());
- }// end Sum_set.size()>3*rdNum
- else if (Sum_set.size() >= k && Sum_set.size() <= 3 * k) {
- int label = 0;
- BufferedWriter bw = new BufferedWriter(new FileWriter(output)); // write the class the the output file
- for (Set set : Sum_set) {
- for (int item : set) {
- bw.write(label + "\t" + cluster_list.get(item)); // output is label \t name \t seq
- bw.newLine();
- bw.flush();
- }
- label++;
- }//end for
-
- //System.out.println("rdNum Root_set = new HashSet();
- int max_size = 0; //记录最大树
- Node max_node = null;
- for (Node root : Root_set) {//遍历所有的根节点获取节点数目最多的树
- int node_number = root.Get_Lnum() + root.Get_Rnum();
- if (node_number > max_size) {
- max_size = node_number;
- max_node = root;
- }
- }//end for
- double LRrate = (double) max_node.Get_Lnum() / (double) max_node.Get_Rnum();
- if (LRrate >= 0.5 && LRrate <= 2) {//左右子分支个数满足拆分条件，直接拆分根节点
- max_node.Get_LNode().Reset_ParentNode(null);
- max_node.Get_RNode().Reset_ParentNode(null);
- Root_set.remove(max_node);
- Root_set.add(max_node.Get_LNode());
- Root_set.add(max_node.Get_RNode());
- } else if (LRrate > 2) {
- while (LRrate > 2) {
- max_node = max_node.Get_LNode(); //修改节点及其分支数目
- max_node.Reset_Rnum(max_node.Get_ParentNode().Get_Rnum() + max_node.Get_Rnum());
- LRrate = (double) max_node.Get_Lnum() / (double) max_node.Get_Rnum();
- }
- max_node.Get_LNode().Reset_ParentNode(null);
- max_node.Get_ParentNode().Reset_LNode(max_node.Get_RNode());
- max_node.Get_RNode().Reset_ParentNode(max_node.Get_ParentNode());
- Root_set.add(max_node.Get_LNode());//设置当前节点的左分支为根节点
- while (max_node.Get_ParentNode() != null) {
- max_node = max_node.Get_ParentNode();//向根节点回溯
- max_node.Reset_Lnum(max_node.Get_LNode().Get_Lnum() + max_node.Get_LNode().Get_Rnum());
- max_node.Reset_Rnum(max_node.Get_RNode().Get_Lnum() + max_node.Get_RNode().Get_Rnum());
- }
- }//end else
- else if (LRrate < 0.5) {
- while (LRrate < 0.5) {
- max_node = max_node.Get_RNode();
- max_node.Reset_Lnum(max_node.Get_ParentNode().Get_Lnum() + max_node.Get_Lnum());
- LRrate = (double) max_node.Get_Lnum() / (double) max_node.Get_Rnum();
- }
- max_node.Get_RNode().Reset_ParentNode(null);
- max_node.Get_ParentNode().Reset_RNode(max_node.Get_LNode());
- max_node.Get_LNode().Reset_ParentNode(max_node.Get_ParentNode());
- Root_set.add(max_node.Get_RNode());
- while (max_node.Get_ParentNode() != null) {
- max_node = max_node.Get_ParentNode();
- max_node.Reset_Lnum(max_node.Get_LNode().Get_Lnum() + max_node.Get_LNode().Get_Rnum());
- max_node.Reset_Rnum(max_node.Get_RNode().Get_Lnum() + max_node.Get_RNode().Get_Rnum());
- }
- } //end else
- }// end while
- // now the Root_set.size > rdNum 遍历每棵子树，写出聚类信息
- int label = 0;
- BufferedWriter bw = new BufferedWriter(new FileWriter(output));
- for (Node root : Root_set) {
- Queue queue = new LinkedList(); //用队列实现层序遍历
- queue.add(root);
- Node current_node;
- while (!queue.isEmpty()) {
- current_node = queue.poll();
- if (current_node.Get_LNode().Get_index() != -1) { //不等于-1为叶子节点
- bw.write(label + "\t" + cluster_list.get(current_node.Get_LNode().Get_index())); // output is label \t name \t seq
- bw.newLine();
- bw.flush();
- } else {
- queue.add(current_node.Get_LNode());
- }// end if
- if (current_node.Get_RNode().Get_index() != -1) { //不等于-1为叶子节点
- bw.write(label + "\t" + cluster_list.get(current_node.Get_RNode().Get_index())); // output is label \t name \t seq
- bw.newLine();
- bw.flush();
- } else {
- queue.add(current_node.Get_RNode());
- }//end if
- }// end while
- label++;
- }
- //System.out.println("Sum_set.size() sequences, int lineNumber, double[][] distance, double[] A) {//这个函数用来计算距离矩阵
- int i, j;
- double p;
- double temp;
- double distance_temp = 0;//这个在计算方差和均值的时候有用
-
- for (i = 0; i < lineNumber; i++) {
- for (j = 0; j < lineNumber; j++) {
-
- if (i < j) {
- p = JukeCantor(sequences.get(i).split("\t")[1], sequences.get(j).split("\t")[1]);
- p = 1.0 - 0.75 * p;
- temp = Math.log(p);
- distance_temp = -0.75 * temp; //根据公式计算距离
- distance[i][j] = distance_temp;
- } else if (i == j) {
- distance[i][j] = 0;//对角线上为0
- } else {
- distance[i][j] = distance[j][i];
- }
- //System.out.print(distance_temp+"\t"); //这里打印出距离矩阵可以在屏幕上显示
- A[i] += distance[i][j];//计算A数组
- }
- }
- }
-
- public double JukeCantor(String gene1, String gene2) {
- int rate = 0;
- int i;
- double result = 0.0;
- int length = gene1.length();
- if (gene1.length() > gene2.length()) {
- length = gene2.length();
- }
- for (i = 0; i < length; i++) {
- if (gene1.charAt(i) != gene2.charAt(i)) {
- rate++;
- }
- }
- result = (double) rate / (double) gene1.length();
- return result;
- }
-
- public static void AmendTheDistance(double[][] distance, double[] A, int lineNumber) {//在进化树构建的时候用来修正距离
- int i, j;
- for (i = 0; i < lineNumber; i++) {
- for (j = i + 1; j < lineNumber; j++) {
- distance[i][j] = distance[i][j] - (A[i] + A[j]) / (lineNumber - 2);//修正的时候根据公式要用到A 和distance
- distance[j][i] = distance[i][j];
- }
- }
- }
-
-
- public void Get_Cluster(String output, int line_number) throws IOException {
- int select_number = 0;
- if (line_number < 100) { // if the totle number is bigger than 100000 , we random select 10000 sequences
- select_number = line_number / 2;
- } else if (line_number < 10000) { // if the totle number is bigger than 100000 , we random select 10000 sequences
- select_number = line_number / 10;
- } else if (10000 <= line_number && line_number <= 100000) { // if the number is less than 100000 , we random select 1 of the 10 number sequences
- select_number = 1000;
- } else if (line_number > 100000) {
- select_number = 3000;
- }
-
- ArrayList cluster_list = new ArrayList<>(); //用于保存样本序列
- ArrayList random_list = new ArrayList<>(); // the index of the samples
- Set random_set = new HashSet();
- Random random = new Random();
- int count = 0;
- while (count < select_number) {
- int ran_num = random.nextInt(line_number);
- if (!random_set.contains(ran_num)) {
- count++;
- random_set.add(ran_num);
- random_list.add(ran_num);
- }
- }
- Collections.sort(random_list);
-
- // get the random data to cluster
- BufferedReader br = new BufferedReader(new FileReader(inputFile)); // the input data is key value format
- count = 0;
- int index_random_list = 0;
- String current_line;
- while (br.ready() && index_random_list < random_list.size()) {
- current_line = br.readLine();
- if (count == random_list.get(index_random_list)) {
- cluster_list.add(current_line); // the current_line is key value format
- index_random_list++;
- }
- count++;
- }
- br.close();
-
- // the cluster_list is the key value format
- int cluster_list_size = cluster_list.size();
- double[][] distance = new double[cluster_list_size][cluster_list_size];
-// double[] A = new double[cluster_list_size];
-// CountTheDistance(cluster_list, cluster_list_size, distance, A);//计算距离矩阵以及A
-// AmendTheDistance(distance, A, cluster_list_size);//对距离矩阵进行修正
- String flag;
- flag = ClusterFromMatrix(distance, output, cluster_list, cluster_list_size, rdNum);
-// do {
-// } while (flag.equals(null));
- }
-}
diff --git a/maven-src/target/classes/java/tree/SparkTree.java b/maven-src/target/classes/java/tree/SparkTree.java
deleted file mode 100644
index 21a5c02..0000000
--- a/maven-src/target/classes/java/tree/SparkTree.java
+++ /dev/null
@@ -1,170 +0,0 @@
-package tree;
-
-import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.JavaPairRDD;
-import org.apache.spark.api.java.JavaSparkContext;
-import org.apache.spark.api.java.function.Function;
-import org.apache.spark.api.java.function.PairFunction;
-import scala.Tuple2;
-import utils.IOUtils;
-import utils.HDFSUtils;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Set;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-
-public class SparkTree {
- public static void main(String[] args) throws Exception {
- String filename = "/home/shixiang/out.fasta";
-// filename = "/home/shixiang/genome-out2.fasta";
- String outputFile = "/home/shixiang/tree.tre";
-
- SparkConf conf = new SparkConf().setAppName("SparkMSATree");
- conf.setMaster("local[16]");
- conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
- conf.set("spark.kryoserializer.buffer.max", "2000m");
- conf.registerKryoClasses(new Class[]{SparkTree.class});
- JavaSparkContext jsc = new JavaSparkContext(conf);
- new SparkTree().GenerateTree(jsc, filename, outputFile);
- jsc.stop();
- }
-
- public void GenerateTree(JavaSparkContext jsc, String inputFile, String outputFile) throws Exception {
-
- String localPath = "";
- if (inputFile.contains("/")) {
- localPath = inputFile.substring(0, inputFile.lastIndexOf("/")+1);
- inputFile = inputFile.substring(inputFile.lastIndexOf("/")+1);
- }
-
- HDFSUtils utils = new HDFSUtils();
- utils.clear_local_path(new File(localPath + "HPTree_OutPut"));
-
- System.out.println(">> (Spark mode for tree) loading data ...");
- long startTime = System.currentTimeMillis();
- IOUtils formatUtils = new IOUtils();
- formatUtils.formatKVFasta(localPath + inputFile, localPath + "inputKV");
- int allNum = formatUtils.getAllNum();
- System.out.println("total number: " + allNum);
- System.out.println((System.currentTimeMillis() - startTime) + "ms");
-
- System.out.println(">>clustering process ...");
- String reduce_number = "2";
- Pre_Cluster_process cluster = new Pre_Cluster_process(localPath + "inputKV", reduce_number);
- cluster.Get_Cluster(localPath + "single_cluster_output", allNum);
-
- ////////////////////////////////////////////////////////////////////////////////////////
- ClusterProcess clusterProcess = new ClusterProcess();
- clusterProcess.preProcess(localPath + "single_cluster_output");
- new File(localPath + "single_cluster_output").delete();
- //clusterProcess.kvProcess(local_path + "inputKV", local_path + "Cluster_OutPut");
-
- BufferedWriter bufferedWriter = new BufferedWriter(new FileWriter(localPath + "Cluster_OutPut"));
- jsc.textFile("file://"+localPath + "inputKV").map(
- (Function) f -> {
- String value = f.trim();
- String[] value_temp = value.split("\t");
- String name = value_temp[0];
- String sequence = value_temp[1];
- String label = "";
- double min_distance = 100000;
- for (Set set : ClusterProcess.sum_set) {
- Iterator iter = set.iterator();
- ClusterProcess.cluster_data data = (ClusterProcess.cluster_data) iter.next();
- double p = ClusterProcess.JukeCantor(sequence, data.sequence);
- p = 1.0 - 0.75 * p;
- double distance = (double) (int) (-0.75 * Math.log(p) * 1000) / 1000;
- if (distance < min_distance) {
- min_distance = distance;
- label = data.label;
- }
- }
- return label + "\t" + name + "\t" + sequence+"\n";
- }).collect().forEach(l -> {
- try {
- bufferedWriter.write(l);
- } catch (IOException e) {
- e.printStackTrace();
- }
- });
- bufferedWriter.close();
- new File(localPath + "inputKV").delete();
- System.out.println((System.currentTimeMillis() - startTime) + "ms");
-
- /*local_path: Cluster_OutPut -> OnBalance_OutPut*/
- int cluster_number = 3;
- OnBalance onbalance = new OnBalance(localPath + "Cluster_OutPut");
- onbalance.Balance(cluster_number, localPath);
- new File(localPath + "Cluster_OutPut").delete();
-
- System.out.println(">>construct phylogenetic tree ...");
- ////////////////////////////////////////////////////////////////////////////////////////
- new File(localPath + "HPTree_OutPut").mkdir();
- JavaPairRDD balancePairRDD = jsc.textFile("file://"+localPath + "OnBalance_OutPut").mapToPair(
- (PairFunction) s -> {
- String [] list = s.split("\t");
- return new Tuple2(list[1], list[2]);
- });
- List balanceKey = balancePairRDD.keys().collect();
- List balanceVal = balancePairRDD.values().collect();
-
- int loop;
- if (allNum < 100) loop = 8;
- else loop = 32;
- int loopNum = allNum/loop;
- int position = 0;
- ExecutorService pool = Executors.newFixedThreadPool(loop);
- for (int i = 0; i < loop; i++) {
- int position2 = position+loopNum;
- if (i == loop-1) position2 = allNum;
- List key = balanceKey.subList(position, position2);
- List val = balanceVal.subList(position, position2);
- GetSubTreeThread getSubTreeThread = new GetSubTreeThread(key, val, localPath + "HPTree_OutPut/"+i+".txt");
- pool.execute(new Thread(getSubTreeThread));
- position = position2;
- }
- pool.shutdown();
- while (!pool.isTerminated());
- new File(localPath + "OnBalance_OutPut").delete();
- System.out.println((System.currentTimeMillis() - startTime) + "ms");
-
- System.out.println(">>merge and save phylogenetic tree ...");
- NeighbourJoining_Summary nj_summary = new NeighbourJoining_Summary(localPath+"HPTree_OutPut", outputFile);
- nj_summary.Merge();
- nj_summary.Summary();
-
- utils.clear_local_path(new File(localPath + "HPTree_OutPut"));
- System.out.println(">>success! time cost: " + (System.currentTimeMillis() - startTime) + "ms");
- }
-
- public class GetSubTreeThread implements Runnable {
- private List Key;
- private List Val;
- private String outputFile;
- GetSubTreeThread(List Key, List Val, String outputFile) {
- this.Key = Key;
- this.Val = Val;
- this.outputFile = outputFile;
- }
- @Override
- public void run() {
- try {
- BufferedWriter bufferedWriter = new BufferedWriter(new FileWriter(outputFile));
- NeighbourJoining nj = new NeighbourJoining();//开启进化树构建算法
- nj.construct(Key, Val);
- String sub_tree = nj.getSubTree();
- String present_seq = nj.getPresentNode();
- bufferedWriter.write(present_seq+"\t"+sub_tree);
- bufferedWriter.close();
- } catch (IOException e) {
- e.printStackTrace();
- }
- }
- }
-}
diff --git a/maven-src/target/classes/java/utils/HDFSUtils.java b/maven-src/target/classes/java/utils/HDFSUtils.java
deleted file mode 100644
index 460fed1..0000000
--- a/maven-src/target/classes/java/utils/HDFSUtils.java
+++ /dev/null
@@ -1,71 +0,0 @@
-package utils;
-
-import java.io.File;
-import java.io.IOException;
-import java.net.URI;
-
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-
-public class HDFSUtils {
- public void local_to_dfs(String local_file, String dfs_file) {
- try {
- Configuration conf = new Configuration();
- FileSystem fs = FileSystem.get(URI.create(dfs_file), conf);
- Path src = new Path(local_file);
- Path dst = new Path(dfs_file);
- fs.copyFromLocalFile(src, dst);
- } catch (IOException e) {
- e.printStackTrace();
- }
- }
-
- public void dfs_to_local(String dfs_file, String local_file) {
- try {
- Configuration conf = new Configuration();
- FileSystem fs = FileSystem.get(URI.create(dfs_file), conf);
- Path src = new Path(local_file);
- Path dst = new Path(dfs_file);
- fs.copyToLocalFile(true, dst, src);
- } catch (IOException e) {
- e.printStackTrace();
- }
- }
-
- public void clear_dfs_path(String dfs_path) {
- try {
- Configuration conf = new Configuration();
- FileSystem fs = FileSystem.get(URI.create(dfs_path), conf);
- fs.delete(new Path(dfs_path), true);
- } catch (Exception e) {
- e.printStackTrace();
- }
- }
-
- public boolean clear_local_path(File local_path) {
- if (local_path.isFile() && local_path.exists()) {
- local_path.delete();
- return true;
- }
- if (local_path.isDirectory()) {
- String[] children = local_path.list();
- for (String child : children) {
- boolean success = clear_local_path(new File(local_path, child));
- if (!success) {
- return false;
- }
- }
- }
- return local_path.delete();
- }
-
- public static String check_input_path(String path) {
- if (!path.contains("/")) {
- System.out.println("Error: Please set full input file path, such as '/home/user/input.txt'");
- System.exit(0);
- }
- return path.substring(0, path.lastIndexOf("/"));
- }
-
-}
diff --git a/maven-src/target/classes/java/utils/IOUtils.java b/maven-src/target/classes/java/utils/IOUtils.java
deleted file mode 100644
index f0ab63b..0000000
--- a/maven-src/target/classes/java/utils/IOUtils.java
+++ /dev/null
@@ -1,124 +0,0 @@
-package utils;
-
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Objects;
-
-public class IOUtils {
- private List s_key = new ArrayList<>();
- private List s_val = new ArrayList<>();
- private int maxLength;
- private int allNum;
-
- public int getMaxLength() {
- return maxLength;
- }
-
- public int getAllNum() {
- return allNum;
- }
-
- public List getS_key() {
- return s_key;
- }
-
- public List getS_val() {
- return s_val;
- }
-
- public void readFasta(String input, boolean isDNA) {
- try {
- BufferedReader brReader = new BufferedReader(new FileReader(input));
- StringBuilder stringBuilder = new StringBuilder();
- int max = 0;
- int all = 0;
- while(brReader.ready()) {
- String line = brReader.readLine();
- if (line.equals("")) continue;
- line = line.trim();
- if (line.charAt(0) == '>') {
- s_key.add(line);
- all++;
- if (stringBuilder.length() != 0) {
- String sbString;
- if (isDNA) sbString = formatDNA(stringBuilder.toString());
- else sbString = stringBuilder.toString();
- int len = sbString.length();
- if (max < len) max = len;
- s_val.add(sbString);
- stringBuilder.setLength(0);
- }
- } else {
- stringBuilder.append(line);
- }
- }
- if (stringBuilder.length() != 0) {
- String sbString;
- if (isDNA) sbString = formatDNA(stringBuilder.toString());
- else sbString = stringBuilder.toString();
- int len = sbString.length();
- if (max < len) max = len;
- s_val.add(sbString);
- }
- maxLength = max;
- allNum = all;
- brReader.close();
- } catch (Exception e) {
- e.printStackTrace();
- }
- }
-
- public List deleteSimilarityOutput(List in_key, List in_val,
- List out_key, List out_val) {
- List deleteIndex = new ArrayList<>();
- for (int i=0; i