From d96895970dee8a130b2a0664048d739e2ed80f59 Mon Sep 17 00:00:00 2001
From: Sebastian <dr.sebastian.koehler@gmail.com>
Date: Tue, 12 Dec 2017 13:48:13 +0100
Subject: [PATCH] intermediate save to continue work at home

---
 src/de/phenomics/Obo2Xls.java | 61 +++++++++++++++++------------------
 1 file changed, 30 insertions(+), 31 deletions(-)

diff --git a/src/de/phenomics/Obo2Xls.java b/src/de/phenomics/Obo2Xls.java
index fe3c5e0..7a39c33 100644
--- a/src/de/phenomics/Obo2Xls.java
+++ b/src/de/phenomics/Obo2Xls.java
@@ -3,9 +3,7 @@
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
-import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.HashSet;
 import java.util.stream.Collectors;
 
 import org.apache.commons.cli.CommandLine;
@@ -87,7 +85,7 @@ public static void main(String[] args) throws IOException, ParseException {
 		File oboFilePathFile = new File(oboFilePath);
 		Ontology ontology = OntologyUtil.parseOntology(oboFilePathFile.getAbsolutePath());
 
-		Term selectedRootTerm = null;
+		Term selectedRootTerm = ontology.getRootTerm();
 		if (classId != null) {
 			classId = classId.trim();
 			if (!classId.equals("")) {
@@ -131,47 +129,48 @@ private static void createXlsFromObo(Ontology ontology, Term selectedRootTerm, S
 
 		rowIndex = createHeaderRow(createHelper, style, rowIndex, sheet0, headersTermAdd);
 
-		ArrayList<Term> termsInTopologicalOrder = ontology.getTermsInTopologicalOrder();
-		HashSet<Term> termsToReport = new HashSet<>();
-		if (selectedRootTerm != null) {
-			termsToReport.addAll(ontologySlim.getDescendants(selectedRootTerm));
-		} else {
-			termsToReport.addAll(ontology.getAllTerms());
+		recursiveWriteTermsAndTheirChildren();
+
+		for (int i = 0; i < wb.getNumberOfSheets(); i++) {
+			wb.getSheetAt(i).setDefaultColumnWidth(defaultColumnWidth);
 		}
 
-		for (Term term : termsInTopologicalOrder) {
+		wb.write(fileOut);
+		fileOut.close();
+	}
 
-			if (term.isObsolete())
-				continue;
+	private static void recursiveWriteTermsAndTheirChildren() {
+		// if (term.isObsolete())
+		// continue;
+		//
+		// if (!termsToReport.contains(term))
+		// continue;
+		//
+		// createRowForTerm(term, rowIndex++, sheet0, createHelper, ontologySlim);
 
-			if (!termsToReport.contains(term))
-				continue;
+	}
 
-			Row row = sheet0.createRow((short) rowIndex++);
+	private static void createRowForTerm(Term term, int rowIndex, Sheet sheet0, XSSFCreationHelper createHelper,
+			SlimDirectedGraphView<Term> ontologySlim) {
 
-			int columnIndex = 0;
-			row.createCell(columnIndex++).setCellValue(createHelper.createRichTextString(term.getName()));
-			row.createCell(columnIndex++).setCellValue(createHelper.createRichTextString(term.getIDAsString()));
+		Row row = sheet0.createRow((short) rowIndex);
 
-			String altIds = Arrays.stream(term.getAlternatives()).map(Object::toString).collect(Collectors.joining("; "));
-			row.createCell(columnIndex++).setCellValue(createHelper.createRichTextString(altIds));
+		int columnIndex = 0;
 
-			String synonyms = String.join("; ", term.getSynonymsArrayList());
+		row.createCell(columnIndex++).setCellValue(createHelper.createRichTextString(term.getName()));
+		row.createCell(columnIndex++).setCellValue(createHelper.createRichTextString(term.getIDAsString()));
 
-			row.createCell(columnIndex++).setCellValue(createHelper.createRichTextString(synonyms));
-			row.createCell(columnIndex++).setCellValue(createHelper.createRichTextString(term.getDefinition()));
+		String altIds = Arrays.stream(term.getAlternatives()).map(Object::toString).collect(Collectors.joining("; "));
+		row.createCell(columnIndex++).setCellValue(createHelper.createRichTextString(altIds));
 
-			String parents = ontologySlim.getParents(term).stream().map(Object::toString).collect(Collectors.joining("; "));
-			row.createCell(columnIndex++).setCellValue(createHelper.createRichTextString(parents));
+		String synonyms = String.join("; ", term.getSynonymsArrayList());
 
-		}
+		row.createCell(columnIndex++).setCellValue(createHelper.createRichTextString(synonyms));
+		row.createCell(columnIndex++).setCellValue(createHelper.createRichTextString(term.getDefinition()));
 
-		for (int i = 0; i < wb.getNumberOfSheets(); i++) {
-			wb.getSheetAt(i).setDefaultColumnWidth(defaultColumnWidth);
-		}
+		String parents = ontologySlim.getParents(term).stream().map(Object::toString).collect(Collectors.joining("; "));
+		row.createCell(columnIndex++).setCellValue(createHelper.createRichTextString(parents));
 
-		wb.write(fileOut);
-		fileOut.close();
 	}
 
 	private static int createHeaderRow(XSSFCreationHelper createHelper, XSSFCellStyle style, int rowIndex, Sheet sheet, String[] strings) {