diff --git a/.classpath b/.classpath
index 6cae17e..149cb3c 100644
--- a/.classpath
+++ b/.classpath
@@ -11,65 +11,6 @@
-
-
-
-
-
-
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-
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diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs
index 714351a..b8947ec 100644
--- a/.settings/org.eclipse.jdt.core.prefs
+++ b/.settings/org.eclipse.jdt.core.prefs
@@ -2,4 +2,5 @@ eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/pom.xml b/pom.xml
index b70a027..6fba82a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -25,11 +25,6 @@
poi-ooxml
3.9
-
- ontologizer
- ontologizer
- 0.0.3-SNAPSHOT
-
javautil_pheno
javautil_pheno
diff --git a/src/de/phenomics/Obo2Xls.java b/src/de/phenomics/Obo2Xls.java
index 41172d8..c972563 100644
--- a/src/de/phenomics/Obo2Xls.java
+++ b/src/de/phenomics/Obo2Xls.java
@@ -7,9 +7,6 @@
import java.util.Arrays;
import java.util.stream.Collectors;
-import ontologizer.go.Ontology;
-import ontologizer.go.Term;
-
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.DefaultParser;
@@ -27,6 +24,8 @@
import org.apache.poi.xssf.usermodel.XSSFFont;
import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+import ontologizer.ontology.Ontology;
+import ontologizer.ontology.Term;
import sonumina.math.graph.SlimDirectedGraphView;
import util.OntologyUtil;
@@ -53,7 +52,8 @@ public static void main(String[] args) throws IOException, ParseException {
options.addOption(ontologyOpt);
// the folder where the output is written to...
- Option classOpt = new Option("c", "class", true, "The ontology class for which the excel file shall be created.");
+ Option classOpt = new Option("c", "class", true,
+ "The ontology class for which the excel file shall be created.");
options.addOption(classOpt);
/*
@@ -68,14 +68,16 @@ public static void main(String[] args) throws IOException, ParseException {
// check that required parameters are set
String parameterError = null;
if (oboFilePath == null) {
- parameterError = "Please provide the obo file using -" + ontologyOpt.getOpt() + " or --" + ontologyOpt.getLongOpt();
- } else if (!(new File(oboFilePath).exists())) {
+ parameterError = "Please provide the obo file using -" + ontologyOpt.getOpt() + " or --"
+ + ontologyOpt.getLongOpt();
+ }
+ else if (!(new File(oboFilePath).exists())) {
parameterError = "obo file does not exist!";
}
/*
- * Maybe something was wrong with the parameter. Print help for the user
- * and die here...
+ * Maybe something was wrong with the parameter. Print help for the user and die
+ * here...
*/
if (parameterError != null) {
String className = Obo2Xls.class.getSimpleName();
@@ -97,7 +99,8 @@ public static void main(String[] args) throws IOException, ParseException {
Term t = ontology.getTermIncludingAlternatives(classId);
if (t != null) {
selectedRootTerm = t;
- } else {
+ }
+ else {
System.err.println("Warning! You selected " + classId
+ " as class to be investigated, but this ID couldn't be found in the ontology.");
}
@@ -111,7 +114,8 @@ public static void main(String[] args) throws IOException, ParseException {
}
- private static void createXlsFromObo(Ontology ontology, Term selectedRootTerm, String fileNameParsedOboFrom, String outfile) throws IOException {
+ private static void createXlsFromObo(Ontology ontology, Term selectedRootTerm, String fileNameParsedOboFrom,
+ String outfile) throws IOException {
SlimDirectedGraphView ontologySlim = ontology.getSlimGraphView();
@@ -128,8 +132,8 @@ private static void createXlsFromObo(Ontology ontology, Term selectedRootTerm, S
style.setFont(bold);
Sheet sheet0 = wb.createSheet("Excel version of " + fileNameParsedOboFrom + " version: " + date);
- String[] headersTermAdd = new String[] { "Class Label", "Class ID", "Alternative IDs", "Synonyms (separated by semicolon)", "Definition",
- "Subclass-of (label+id)" };
+ String[] headersTermAdd = new String[] { "Class Label", "Class ID", "Alternative IDs",
+ "Synonyms (separated by semicolon)", "Definition", "Subclass-of (label+id)" };
rowIndexNextRow = 1;
@@ -145,8 +149,8 @@ private static void createXlsFromObo(Ontology ontology, Term selectedRootTerm, S
fileOut.close();
}
- private static void recursiveWriteTermsAndTheirChildren(Term currentTerm, XSSFWorkbook wb, Sheet sheet0, XSSFCreationHelper createHelper,
- SlimDirectedGraphView ontologySlim, boolean style, boolean isLast) {
+ private static void recursiveWriteTermsAndTheirChildren(Term currentTerm, XSSFWorkbook wb, Sheet sheet0,
+ XSSFCreationHelper createHelper, SlimDirectedGraphView ontologySlim, boolean style, boolean isLast) {
if (currentTerm.isObsolete())
return;
@@ -163,8 +167,8 @@ private static void recursiveWriteTermsAndTheirChildren(Term currentTerm, XSSFWo
++rowIndexNextRow;
}
- private static void createRowForTerm(Term term, Sheet sheet0, XSSFCreationHelper createHelper, SlimDirectedGraphView ontologySlim,
- XSSFWorkbook wb, boolean style) {
+ private static void createRowForTerm(Term term, Sheet sheet0, XSSFCreationHelper createHelper,
+ SlimDirectedGraphView ontologySlim, XSSFWorkbook wb, boolean style) {
Row row = sheet0.createRow(rowIndexNextRow);
rowIndexNextRow++;
@@ -193,7 +197,8 @@ private static void createRowForTerm(Term term, Sheet sheet0, XSSFCreationHelper
}
- private static void addCellWithStyle(String content, XSSFCreationHelper createHelper, Row row, int columnIndex, XSSFCellStyle style1) {
+ private static void addCellWithStyle(String content, XSSFCreationHelper createHelper, Row row, int columnIndex,
+ XSSFCellStyle style1) {
Cell c = row.createCell(columnIndex);
c.setCellValue(createHelper.createRichTextString(content));
@@ -202,7 +207,8 @@ private static void addCellWithStyle(String content, XSSFCreationHelper createHe
}
}
- private static void createHeaderRow(XSSFCreationHelper createHelper, XSSFCellStyle style, Sheet sheet, String[] strings) {
+ private static void createHeaderRow(XSSFCreationHelper createHelper, XSSFCellStyle style, Sheet sheet,
+ String[] strings) {
Row headerrow = sheet.createRow((short) rowIndexNextRow);
rowIndexNextRow++;
int colIndex = 0;