misc changes

.gitattributes

@@ -1,4 +1,5 @@
 # Set the default behavior, in case people don't have core.autocrlf set.
+# Set
 * text=auto
 
 # Explicitly declare text files you want to always be normalized and converted

README.md

@@ -1,6 +1,6 @@
 # Welcome to <img src="logo-full.png" height="35"/>
 
-[![Build Status](https://travis-ci.org/biojava/biojava.svg?branch=master)](https://travis-ci.org/biojava/biojava) [![Version](http://img.shields.io/badge/version-5.3.0-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-5.2.0) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![Build Status](https://travis-ci.org/biojava/biojava.svg?branch=master)](https://travis-ci.org/biojava/biojava) [![Version](http://img.shields.io/badge/version-5.3.0-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-5.3.0) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
 
 BioJava is an open-source project dedicated to providing a Java framework for **processing biological data**. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.
@@ -34,6 +34,17 @@ If you are using Maven you can add the BioJava repository by adding the followin
     </dependencies>
 ```
 
+### Quick Demo
+
+on Linux, Mac, or in (git-bash)[https://gitforwindows.org/] run 
+
+```bash
+
+mvn install
+bin/biojava.sh
+```
+
+
 ### Snapshot builds
 
 To use the latest builds from BioJava, you can add the following config your project's pom.xml:

bin/biojava.sh

@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+# this runs any main function in the source tree.
+# to change the class to be run
+# EXECMAIN=org.biojava.not.demo.main bin/biojava.sh
+mkdir -p target/lib/                                          && {
+ln -s 2>/dev/null    $PWD/*/target{,/lib}/*jar  target/lib
+cp 2>/dev/null  -as  $PWD/*/src/main/resources/* target/
+}
+
+set -fx
+JDIR=$PWD/$(dirname $0)/../
+pushd target
+exec java  -classpath "$JDIR/target/*:$JDIR/target/lib/*"  ${EXECMAIN:=demo.DemoSixFrameTranslation} "$@"
+popd

biojava-aa-prop/pom.xml

@@ -20,15 +20,7 @@
 	<build>
 		<plugins>
 			<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <configuration>
-                    <excludes>
-                        <exclude>demo/**</exclude>
-                    </excludes>
-                </configuration>
-            </plugin>
+
 
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>

biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/AminoAcidProperties.java

@@ -43,7 +43,7 @@ public class AminoAcidProperties {
 	 * @param aa The one-letter amino acid code
 	 * @return true if amino acid is charged
 	 */
-	public static final boolean isCharged(char aa) {
+	public static boolean isCharged(char aa) {
 		if (negChargedAAs.contains(String.valueOf(aa))) {
 			return true;
 		}
@@ -60,7 +60,7 @@ else if (posChargedAAs.contains(String.valueOf(aa))) {
 	 * @param aa The one-letter amino acid code
 	 * @return the charge of amino acid (1 if positively charged, -1 if negatively charged, 0 if not charged)
 	 */
-	public static final int getChargeOfAminoAcid(char aa) {
+	public static int getChargeOfAminoAcid(char aa) {
 		if (negChargedAAs.contains(String.valueOf(aa))) {
 			return -1;
 		}
@@ -76,7 +76,7 @@ else if (posChargedAAs.contains(String.valueOf(aa))) {
 	 * @param aa The one-letter amino acid code
 	 * @return true if amino acid is polar
 	 */
-	public static final boolean isPolar(char aa) {
+	public static boolean isPolar(char aa) {
 		if (polarAAs.contains(String.valueOf(aa))) {
 			return true;
 		}
@@ -89,7 +89,7 @@ public static final boolean isPolar(char aa) {
 	 * @param aa The one-letter amino acid code
 	 * @return the polarity of amino acid (1 if polar, 0 if not polar)
 	 */
-	public static final int getPolarityOfAminoAcid(char aa) {
+	public static int getPolarityOfAminoAcid(char aa) {
 		if (polarAAs.contains(String.valueOf(aa))) {
 			return 1;
 		}

biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java

@@ -31,7 +31,6 @@
 
 import java.io.File;
 import java.io.FileInputStream;
-import java.io.IOException;
 import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
@@ -95,8 +94,8 @@ public static void run(String[] args) throws Exception{
 		/*
 		 * Parse input arguments
 		 */
-		List<Character> propertyList = new ArrayList<Character>();
-		List<Character> specificList = new ArrayList<Character>();
+		List<Character> propertyList = new ArrayList<>();
+		List<Character> specificList = new ArrayList<>();
 		String inputLocation = null;
 		String outputLocation = null;
 		String aminoAcidCompositionLocation = null;
@@ -179,15 +178,15 @@ private static LinkedHashMap<String, ProteinSequence> readInputFile(String input
 		}
 		LinkedHashMap<String, ProteinSequence> ret;
 		if ( inputLocation.toLowerCase().contains(".gb")) {
-			GenbankReader<ProteinSequence, AminoAcidCompound> genbankReader = new GenbankReader<ProteinSequence, AminoAcidCompound>(
-					inStream, new GenericGenbankHeaderParser<ProteinSequence, AminoAcidCompound>(),
+			GenbankReader<ProteinSequence, AminoAcidCompound> genbankReader = new GenbankReader<>(
+					inStream, new GenericGenbankHeaderParser<>(),
 					new ProteinSequenceCreator(set));
 			ret = genbankReader.process();
 
 
 		} else {
-			FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
-					inStream, new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
+			FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<>(
+					inStream, new GenericFastaHeaderParser<>(),
 					new ProteinSequenceCreator(set));
 			ret = fastaReader.process();
 
@@ -198,9 +197,9 @@ private static LinkedHashMap<String, ProteinSequence> readInputFile(String input
 	public enum PropertyName{MolecularWeight, Absorbance_True, Absorbance_False, ExtinctionCoefficient_True, ExtinctionCoefficient_False,
 		InstabilityIndex, ApliphaticIndex, AverageHydropathyValue, IsoelectricPoint, NetCharge_pH_7, A, R,
 		N, D, C, E, Q, G, H, I, L,
-		K, M, F, P, S, T, W, Y, V};
+		K, M, F, P, S, T, W, Y, V}
 
-	private static void printHeader(PrintStream output, List<Character> propertyList, List<Character> specificList, String delimiter) throws IOException{
+	private static void printHeader(PrintStream output, List<Character> propertyList, List<Character> specificList, String delimiter) {
 		int specificCount = 0;
 		/*
 		 * 1 Molecular weight
@@ -214,7 +213,7 @@ private static void printHeader(PrintStream output, List<Character> propertyList
 		 * 9 Composition of the 20 standard amino acid
 		 * 0 Composition of the specific amino acid
 		 */
-		List<String> sList = new ArrayList<String>();
+		List<String> sList = new ArrayList<>();
 		sList.add("SequenceName");
 		for(Character c:propertyList){
 			switch(c){
@@ -238,7 +237,7 @@ private static void printHeader(PrintStream output, List<Character> propertyList
 				sList.add(PropertyName.T.toString()); sList.add(PropertyName.W.toString());
 				sList.add(PropertyName.Y.toString()); sList.add(PropertyName.V.toString());
 				break;
-			case '0': sList.add("" + specificList.get(specificCount++)); break;
+			case '0': sList.add(String.valueOf(specificList.get(specificCount++))); break;
 			}
 		}
 		for(int i = 0; i < sList.size(); i++){
@@ -272,19 +271,16 @@ private static void compute(PrintStream output, String header, String sequence,
 		}else{
 			sequence = Utils.checkSequence(sequence);
 			pSequence = new ProteinSequence(sequence);
-			aaSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+            aaSet = AminoAcidCompoundSet.aminoAcidCompoundSet;
 		}
 		IPeptideProperties pp = new PeptidePropertiesImpl();
 
 		int specificCount = 0;
-		List<Double> dList = new ArrayList<Double>();
+		List<Double> dList = new ArrayList<>();
 		for(Character c:propertyList){
 			switch(c){
 			case '1':
-				if(aaTable == null)
-					dList.add(pp.getMolecularWeight(pSequence));
-				else
-					dList.add(pp.getMolecularWeight(pSequence));
+				dList.add(pp.getMolecularWeight(pSequence));
 				break;
 			case '2':
 				dList.add(pp.getAbsorbance(pSequence, true));
@@ -323,7 +319,7 @@ private static void compute(PrintStream output, String header, String sequence,
 				dList.add(aaCompound2Double.get(Constraints.Y));
 				dList.add(aaCompound2Double.get(Constraints.V));
 				break;
-			case '0': dList.add(pp.getEnrichment(pSequence, aaSet.getCompoundForString("" + specificList.get(specificCount++)))); break;
+			case '0': dList.add(pp.getEnrichment(pSequence, aaSet.getCompoundForString(String.valueOf(specificList.get(specificCount++))))); break;
 			}
 		}
 		output.print(header.replace(delimiter, "_"));

biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java

@@ -41,37 +41,37 @@
  * @see IPeptideProperties
  */
 public class Constraints {
-	private static AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
+	private static final AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
 	//A, R, N, D, C, E, Q, G, H, I, L, K, M, F, P, S, T, W, Y, V
-	public static AminoAcidCompound A = aaSet.getCompoundForString("A");
-	public static AminoAcidCompound R = aaSet.getCompoundForString("R");
-	public static AminoAcidCompound N = aaSet.getCompoundForString("N");
-	public static AminoAcidCompound D = aaSet.getCompoundForString("D");
-	public static AminoAcidCompound C = aaSet.getCompoundForString("C");
-	public static AminoAcidCompound E = aaSet.getCompoundForString("E");
-	public static AminoAcidCompound Q = aaSet.getCompoundForString("Q");
-	public static AminoAcidCompound G = aaSet.getCompoundForString("G");
-	public static AminoAcidCompound H = aaSet.getCompoundForString("H");
-	public static AminoAcidCompound I = aaSet.getCompoundForString("I");
-	public static AminoAcidCompound L = aaSet.getCompoundForString("L");
-	public static AminoAcidCompound K = aaSet.getCompoundForString("K");
-	public static AminoAcidCompound M = aaSet.getCompoundForString("M");
-	public static AminoAcidCompound F = aaSet.getCompoundForString("F");
-	public static AminoAcidCompound P = aaSet.getCompoundForString("P");
-	public static AminoAcidCompound S = aaSet.getCompoundForString("S");
-	public static AminoAcidCompound T = aaSet.getCompoundForString("T");
-	public static AminoAcidCompound W = aaSet.getCompoundForString("W");
-	public static AminoAcidCompound Y = aaSet.getCompoundForString("Y");
-	public static AminoAcidCompound V = aaSet.getCompoundForString("V");
+	public static final AminoAcidCompound A = aaSet.getCompoundForString("A");
+	public static final AminoAcidCompound R = aaSet.getCompoundForString("R");
+	public static final AminoAcidCompound N = aaSet.getCompoundForString("N");
+	public static final AminoAcidCompound D = aaSet.getCompoundForString("D");
+	public static final AminoAcidCompound C = aaSet.getCompoundForString("C");
+	public static final AminoAcidCompound E = aaSet.getCompoundForString("E");
+	public static final AminoAcidCompound Q = aaSet.getCompoundForString("Q");
+	public static final AminoAcidCompound G = aaSet.getCompoundForString("G");
+	public static final AminoAcidCompound H = aaSet.getCompoundForString("H");
+	public static final AminoAcidCompound I = aaSet.getCompoundForString("I");
+	public static final AminoAcidCompound L = aaSet.getCompoundForString("L");
+	public static final AminoAcidCompound K = aaSet.getCompoundForString("K");
+	public static final AminoAcidCompound M = aaSet.getCompoundForString("M");
+	public static final AminoAcidCompound F = aaSet.getCompoundForString("F");
+	public static final AminoAcidCompound P = aaSet.getCompoundForString("P");
+	public static final AminoAcidCompound S = aaSet.getCompoundForString("S");
+	public static final AminoAcidCompound T = aaSet.getCompoundForString("T");
+	public static final AminoAcidCompound W = aaSet.getCompoundForString("W");
+	public static final AminoAcidCompound Y = aaSet.getCompoundForString("Y");
+	public static final AminoAcidCompound V = aaSet.getCompoundForString("V");
 
-	public static Map<AminoAcidCompound, Double> aa2ExtinctionCoefficient = new HashMap<AminoAcidCompound, Double>();
-	public static Map<AminoAcidCompound, Double> aa2MolecularWeight = new HashMap<AminoAcidCompound, Double>();
-	public static Map<AminoAcidCompound, Double> aa2Hydrophathicity = new HashMap<AminoAcidCompound, Double>();
-	public static Map<AminoAcidCompound, Double> aa2PKa = new HashMap<AminoAcidCompound, Double>();
-	public static Map<String, Double> diAA2Instability = new HashMap<String, Double>();
+	public static final Map<AminoAcidCompound, Double> aa2ExtinctionCoefficient = new HashMap<>();
+	public static final Map<AminoAcidCompound, Double> aa2MolecularWeight = new HashMap<>();
+	public static final Map<AminoAcidCompound, Double> aa2Hydrophathicity = new HashMap<>();
+	public static final Map<AminoAcidCompound, Double> aa2PKa = new HashMap<>();
+	public static final Map<String, Double> diAA2Instability = new HashMap<>();
 
-	public static Map<AminoAcidCompound, Double> aa2NTerminalPka = new HashMap<AminoAcidCompound, Double>();
-	public static Map<AminoAcidCompound, Double> aa2CTerminalPka = new HashMap<AminoAcidCompound, Double>();
+	public static final Map<AminoAcidCompound, Double> aa2NTerminalPka = new HashMap<>();
+	public static final Map<AminoAcidCompound, Double> aa2CTerminalPka = new HashMap<>();
 
 	static{
 		initMolecularWeight();
@@ -287,7 +287,7 @@ private static void initInstability(){
 		SingleLetterAACode[] aa = SingleLetterAACode.values();
 		for(int i = 0; i < aa.length; i++){
 			for(int j = 0; j < aa.length; j++){
-				diAA2Instability.put("" + aa[i] + aa[j], instability[i][j]);
+				diAA2Instability.put(String.valueOf(aa[i]) + aa[j], instability[i][j]);
 			}
 		}
 	}