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formating improved
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@drseb
drseb committed Dec 13, 2017
1 parent d968959 commit 24bac9c
Showing 1 changed file with 63 additions and 33 deletions.
96 changes: 63 additions & 33 deletions src/de/phenomics/Obo2Xls.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,13 @@
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
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;
Expand All @@ -14,15 +18,15 @@
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.CellStyle;
import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.ss.usermodel.Sheet;
import org.apache.poi.xssf.usermodel.XSSFCellStyle;
import org.apache.poi.xssf.usermodel.XSSFColor;
import org.apache.poi.xssf.usermodel.XSSFCreationHelper;
import org.apache.poi.xssf.usermodel.XSSFFont;
import org.apache.poi.xssf.usermodel.XSSFWorkbook;

import ontologizer.go.Ontology;
import ontologizer.go.Term;
import sonumina.math.graph.SlimDirectedGraphView;
import util.OntologyUtil;

Expand All @@ -35,6 +39,8 @@
*/
public class Obo2Xls {

private static int rowIndexNextRow;

public static void main(String[] args) throws IOException, ParseException {

// configure command line parser
Expand Down Expand Up @@ -62,15 +68,14 @@ 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();
}
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();
Expand All @@ -93,8 +98,8 @@ public static void main(String[] args) throws IOException, ParseException {
if (t != null) {
selectedRootTerm = t;
} else {
System.err.println(
"Warning! You selected " + classId + " as class to be investigated, but this ID couldn't be found in the ontology.");
System.err.println("Warning! You selected " + classId
+ " as class to be investigated, but this ID couldn't be found in the ontology.");
}
}
}
Expand Down Expand Up @@ -123,13 +128,14 @@ private static void createXlsFromObo(Ontology ontology, Term selectedRootTerm, S
style.setFont(bold);

Sheet sheet0 = wb.createSheet("Excel version of " + fileNameParsedOboFrom + " version: " + date);
int rowIndex = 0;
String[] headersTermAdd = new String[] { "Class Label", "Class ID", "Alternative IDs", "Synonyms (separated by semicolon)", "Definition",
"Subclass-of (label+id)" };

rowIndex = createHeaderRow(createHelper, style, rowIndex, sheet0, headersTermAdd);
rowIndexNextRow = 1;

createHeaderRow(createHelper, style, sheet0, headersTermAdd);

recursiveWriteTermsAndTheirChildren();
recursiveWriteTermsAndTheirChildren(selectedRootTerm, wb, sheet0, createHelper, ontologySlim, false, false);

for (int i = 0; i < wb.getNumberOfSheets(); i++) {
wb.getSheetAt(i).setDefaultColumnWidth(defaultColumnWidth);
Expand All @@ -139,42 +145,66 @@ private static void createXlsFromObo(Ontology ontology, Term selectedRootTerm, S
fileOut.close();
}

private static void recursiveWriteTermsAndTheirChildren() {
// if (term.isObsolete())
// continue;
//
// if (!termsToReport.contains(term))
// continue;
//
// createRowForTerm(term, rowIndex++, sheet0, createHelper, ontologySlim);
private static void recursiveWriteTermsAndTheirChildren(Term currentTerm, XSSFWorkbook wb, Sheet sheet0, XSSFCreationHelper createHelper,
SlimDirectedGraphView<Term> ontologySlim, boolean style, boolean isLast) {

}
if (currentTerm.isObsolete())
return;

private static void createRowForTerm(Term term, int rowIndex, Sheet sheet0, XSSFCreationHelper createHelper,
SlimDirectedGraphView<Term> ontologySlim) {
createRowForTerm(currentTerm, sheet0, createHelper, ontologySlim, wb, style);

Row row = sheet0.createRow((short) rowIndex);
ArrayList<Term> children = ontologySlim.getChildren(currentTerm);
for (int i = 0; i < children.size(); i++) {
Term child = children.get(i);
boolean isLastChild = (i == children.size() - 1);
recursiveWriteTermsAndTheirChildren(child, wb, sheet0, createHelper, ontologySlim, !style, isLastChild);
}
if (children.size() < 1 && isLast)
++rowIndexNextRow;
}

private static void createRowForTerm(Term term, Sheet sheet0, XSSFCreationHelper createHelper, SlimDirectedGraphView<Term> ontologySlim,
XSSFWorkbook wb, boolean style) {

Row row = sheet0.createRow(rowIndexNextRow);
rowIndexNextRow++;
int columnIndex = 0;

row.createCell(columnIndex++).setCellValue(createHelper.createRichTextString(term.getName()));
row.createCell(columnIndex++).setCellValue(createHelper.createRichTextString(term.getIDAsString()));
XSSFCellStyle style1 = null;
if (style) {
style1 = wb.createCellStyle();
style1.setFillForegroundColor(new XSSFColor(new java.awt.Color(220, 220, 220)));
style1.setFillPattern(CellStyle.SOLID_FOREGROUND);
}
addCellWithStyle(term.getName(), createHelper, row, columnIndex++, style1);

addCellWithStyle(term.getIDAsString(), createHelper, row, columnIndex++, style1);

String altIds = Arrays.stream(term.getAlternatives()).map(Object::toString).collect(Collectors.joining("; "));
row.createCell(columnIndex++).setCellValue(createHelper.createRichTextString(altIds));
addCellWithStyle(altIds, createHelper, row, columnIndex++, style1);

String synonyms = String.join("; ", term.getSynonymsArrayList());
addCellWithStyle(synonyms, createHelper, row, columnIndex++, style1);

row.createCell(columnIndex++).setCellValue(createHelper.createRichTextString(synonyms));
row.createCell(columnIndex++).setCellValue(createHelper.createRichTextString(term.getDefinition()));
addCellWithStyle(term.getDefinition(), createHelper, row, columnIndex++, style1);

String parents = ontologySlim.getParents(term).stream().map(Object::toString).collect(Collectors.joining("; "));
row.createCell(columnIndex++).setCellValue(createHelper.createRichTextString(parents));
addCellWithStyle(parents, createHelper, row, columnIndex++, style1);

}

private static int createHeaderRow(XSSFCreationHelper createHelper, XSSFCellStyle style, int rowIndex, Sheet sheet, String[] strings) {
Row headerrow = sheet.createRow((short) rowIndex++);
private static void addCellWithStyle(String content, XSSFCreationHelper createHelper, Row row, int columnIndex, XSSFCellStyle style1) {
Cell c = row.createCell(columnIndex);
c.setCellValue(createHelper.createRichTextString(content));

if (style1 != null) {
c.setCellStyle(style1);
}
}

private static void createHeaderRow(XSSFCreationHelper createHelper, XSSFCellStyle style, Sheet sheet, String[] strings) {
Row headerrow = sheet.createRow((short) rowIndexNextRow);
rowIndexNextRow++;
int colIndex = 0;
for (String s : strings) {
headerrow.createCell(colIndex++).setCellValue(createHelper.createRichTextString(s));
Expand All @@ -183,7 +213,6 @@ private static int createHeaderRow(XSSFCreationHelper createHelper, XSSFCellStyl
Cell cell = headerrow.getCell(i);
cell.setCellStyle(style);
}
return rowIndex;
}

public static String getOption(Option opt, final CommandLine commandLine) {
Expand All @@ -196,4 +225,5 @@ public static String getOption(Option opt, final CommandLine commandLine) {
}
return null;
}

}

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