Java Code Examples for com.opencsv.CSVWriter#close()

public static void writeOutput(Set<Set<Match<Document>>> result) throws IOException {
    CSVWriter writer = new CSVWriter(new FileWriter("src/test/resources/output.csv"));
    writer.writeNext(new String[]{"Key", "Matched Key", "Score", "Name", "Address", "Email", "Phone"});

    result.forEach(matches -> {
        String[] arr = {"Group"};
        writer.writeNext(arr);

        matches.stream().forEach(match -> {
                    Document md = match.getMatchedWith();
                    String[] matchArrs = Stream.concat(Stream.of("", md.getKey(), Double.toString(match.getResult())),
                            getOrderedElements(md.getElements()).map(e -> e.getValue())).toArray(String[]::new);
                    writer.writeNext(matchArrs);
                });
            });
    writer.close();
}
 

public static void csvWriter(
    String filePath, String fileName, char separator, String[] headers, List<String[]> dataList)
    throws IOException {
  CSVWriter reconWriter = setCsvFile(filePath, fileName, separator);
  if (headers != null) {
    reconWriter.writeNext(headers);
  }
  reconWriter.writeAll(dataList);
  reconWriter.flush();
  try {
    reconWriter.close();
  } catch (IOException e) {

    reconWriter = null;
  }
}
 

private MetaFile writeCSV(Map<String, List<String[]>> data) throws IOException {

    File zipFile = MetaFiles.createTempFile("Data", ".zip").toFile();
    try (ZipOutputStream zout = new ZipOutputStream(new FileOutputStream(zipFile))) {

      for (String model : data.keySet()) {
        File modelFile = MetaFiles.createTempFile(model, ".csv").toFile();
        CSVWriter writer = new CSVWriter(new FileWriter(modelFile), ';');
        writer.writeAll(data.get(model));
        writer.close();
        zout.putNextEntry(new ZipEntry(model + ".csv"));
        zout.write(IOUtils.toByteArray(new FileInputStream(modelFile)));
        zout.closeEntry();
      }
      zout.close();
    }
    return metaFiles.upload(zipFile);
  }
 

protected void writeCsvDocument(BandData rootBand, OutputStream outputStream) {
    try {
        List<BandData> actualData = getActualData(rootBand);
        CSVWriter writer = new CSVWriter(new OutputStreamWriter(outputStream), separator, CSVWriter.DEFAULT_QUOTE_CHARACTER);

        writer.writeNext(header);

        for (BandData row : actualData) {
            String[] entries = new String[parametersToInsert.size()];
            for (int i = 0; i < parametersToInsert.size(); i++) {
                String parameterName = parametersToInsert.get(i);
                String fullParameterName = row.getName() + "." + parameterName;
                entries[i] = formatValue(row.getData().get(parameterName), parameterName, fullParameterName);
            }
            writer.writeNext(entries);
        }

        writer.close();
    } catch (IOException e) {
        throw new ReportFormattingException("Error while writing a csv document", e);
    }
}
 

public static void csvWriter(
    String filePath,
    String fileName,
    char separator,
    char quoteChar,
    String[] headers,
    List<String[]> dataList)
    throws IOException {
  CSVWriter reconWriter = setCsvFile(filePath, fileName, separator, quoteChar);
  if (headers != null) {
    reconWriter.writeNext(headers);
  }
  reconWriter.writeAll(dataList);
  reconWriter.flush();
  try {
    reconWriter.close();
  } catch (IOException e) {

    reconWriter = null;
  }
}
 

private static void saveEigenValues(double[] eigenValues, File file) throws IOException {

		final CSVWriter eigenWriter = new CSVWriter(new FileWriter(file), '\t', '\0', '\0', "\n");
		final String[] outputLine = new String[2];
		int c = 0;
		outputLine[c++] = "Component";
		outputLine[c++] = "EigenValue";
		eigenWriter.writeNext(outputLine);

		for (int i = 0; i < eigenValues.length; ++i) {

			c = 0;
			outputLine[c++] = "PC" + (i + 1);
			outputLine[c++] = String.valueOf(eigenValues[i]);
			eigenWriter.writeNext(outputLine);

		}

		eigenWriter.close();

	}
 

public void exportFile(String dirName, int fileCount) throws SQLException, IOException {
    String sql = "SELECT stat.filename, sum(fileCount) AS allCount\n" +
            "FROM ((SELECT hfm.filename, count(*) AS fileCount FROM host_file_map hfm GROUP BY hfm.filename)\n" +
            "      UNION ALL\n" +
            "      (SELECT filename, count AS fileCount FROM file)) stat\n" +
            "GROUP BY stat.filename\n" +
            "HAVING allCount >= ?\n" +
            "ORDER BY allCount DESC";
    PreparedStatement preparedStatement = getPreparedStatement(sql);
    preparedStatement.setInt(1, fileCount);
    ResultSet resultSet = preparedStatement.executeQuery();

    File file = new File(dirName + FILE_FILE);
    File fileImportFile = new File(dirName + FILE_IMPORT_FILE);
    FileOutputStream fileOutputStream = new FileOutputStream(file);
    FileWriter fileWriter = new FileWriter(fileImportFile);
    CSVWriter csvWriter = new CSVWriter(fileWriter);
    String[] fileHead = new String[]{"file", "count"};
    csvWriter.writeNext(fileHead);
    while (resultSet.next()) {
        String fileName = resultSet.getString(1);
        String row = fileName + "\n";
        int count = resultSet.getInt(2);
        fileOutputStream.write(row.getBytes());
        csvWriter.writeNext(new String[]{fileName, String.valueOf(count)}, true);
    }
    fileOutputStream.close();
    csvWriter.close();
}
 

public void exportDir(String dirName, int dirCount) throws SQLException, IOException {
    String sql = "SELECT stat.dir, sum(dirCount) AS allCount\n" +
            "FROM ((SELECT hdm.dir, count(*) AS dirCount FROM host_dir_map hdm GROUP BY hdm.dir)\n" +
            "      UNION ALL\n" +
            "      (SELECT dir, count AS dirCount FROM dir)) stat\n" +
            "GROUP BY stat.dir\n" +
            "HAVING allCount >= ?\n" +
            "ORDER BY allCount DESC";
    PreparedStatement preparedStatement = getPreparedStatement(sql);
    preparedStatement.setInt(1, dirCount);
    ResultSet resultSet = preparedStatement.executeQuery();

    File dirFile = new File(dirName + DIR_FILE);
    File dirImportFile = new File(dirName + DIR_IMPORT_FILE);
    FileOutputStream dirFileOutputStream = new FileOutputStream(dirFile);
    FileWriter fileWriter = new FileWriter(dirImportFile);
    CSVWriter csvWriter = new CSVWriter(fileWriter);
    String[] fileHead = new String[]{"dir", "count"};
    csvWriter.writeNext(fileHead);
    while (resultSet.next()) {
        String dir = resultSet.getString(1);
        String row = dir + "\n";
        int count = resultSet.getInt(2);
        dirFileOutputStream.write(row.getBytes());
        csvWriter.writeNext(new String[]{dir, String.valueOf(count)}, true);

    }
    dirFileOutputStream.close();
    csvWriter.close();
}
 

public void exportPath(String dirName, int pathCount) throws SQLException, IOException {
    String sql = "SELECT stat.path, sum(pathCount) AS allCount\n" +
            "FROM ((SELECT hpm.path, count(*) AS pathCount FROM host_path_map hpm GROUP BY hpm.path)\n" +
            "      UNION ALL\n" +
            "      (SELECT path, count AS pathCount FROM path)) stat\n" +
            "GROUP BY stat.path\n" +
            "HAVING allCount >= ?\n" +
            "ORDER BY allCount DESC";
    PreparedStatement preparedStatement = getPreparedStatement(sql);
    preparedStatement.setInt(1, pathCount);
    ResultSet resultSet = preparedStatement.executeQuery();

    File pathFile = new File(dirName + PATH_FILE);
    File pathImportFile = new File(dirName + PATH_IMPORT_FILE);
    FileOutputStream pathOutputStream = new FileOutputStream(pathFile);
    FileWriter fileWriter = new FileWriter(pathImportFile);
    CSVWriter csvWriter = new CSVWriter(fileWriter);
    String[] fileHead = {"path", "count"};
    csvWriter.writeNext(fileHead);
    while (resultSet.next()) {
        String path = resultSet.getString(1);
        String row = path + "\n";
        int count = resultSet.getInt(2);
        pathOutputStream.write(row.getBytes());
        csvWriter.writeNext(new String[]{path, String.valueOf(count)}, true);
    }
    pathOutputStream.close();
    csvWriter.close();
}
 

public static String csvWriterAll(List<String[]> stringArray, Path path) {
    try {
        CSVWriter writer = new CSVWriter(new FileWriter(path.toString()));
        writer.writeAll(stringArray);
        writer.close();
    } catch (Exception ex) {
        Helpers.err(ex);
    }
    return Helpers.readFile(path);
}
 

protected void saveXlsxAsCsv(Document document, OutputStream outputStream) throws IOException, Docx4JException {
    CSVWriter writer = new CSVWriter(new OutputStreamWriter(outputStream), ';', CSVWriter.DEFAULT_QUOTE_CHARACTER);

    for (Document.SheetWrapper sheetWrapper : document.getWorksheets()) {
        Worksheet worksheet = sheetWrapper.getWorksheet().getContents();
        for (Row row : worksheet.getSheetData().getRow()) {
            String rows[] = new String[row.getC().size()];
            List<Cell> cells = row.getC();

            boolean emptyRow = true;
            for (int i = 0; i < cells.size(); i++) {
                checkThreadInterrupted();
                Cell cell = cells.get(i);
                String value = cell.getV();
                rows[i] = value;
                if (value != null && !value.isEmpty())
                    emptyRow = false;
            }

            if (!emptyRow)
                writer.writeNext(rows);
        }
    }
    writer.close();
}
 

public void exportFullPath(String dirName, int fullPathCount) throws SQLException, IOException {
    String sql = "SELECT stat.full_path, sum(fullPathCount) AS allCount\n" +
            "FROM ((SELECT hfpm.full_path, count(*) AS fullPathCount FROM host_full_path_map hfpm GROUP BY hfpm.full_path)\n" +
            "      UNION ALL\n" +
            "      (SELECT full_path, count AS fullPathCount FROM full_path)) stat\n" +
            "GROUP BY stat.full_path\n" +
            "HAVING allCount >= ?\n" +
            "ORDER BY allCount DESC";
    PreparedStatement preparedStatement = getPreparedStatement(sql);
    preparedStatement.setInt(1, fullPathCount);
    ResultSet resultSet = preparedStatement.executeQuery();

    File fullPathFile = new File(dirName + FULL_PATH_FILE);
    File fullPathImportFile = new File(dirName + FULL_PATH_IMPORT_FILE);
    FileOutputStream fullPathOutputStream = new FileOutputStream(fullPathFile);
    FileWriter fileWriter = new FileWriter(fullPathImportFile);
    CSVWriter csvWriter = new CSVWriter(fileWriter);
    String[] fileHead = new String[]{"full_path", "count"};
    csvWriter.writeNext(fileHead);
    while (resultSet.next()) {
        String fullPath = resultSet.getString(1);
        String row = fullPath + "\n";
        int count = resultSet.getInt(2);
        fullPathOutputStream.write(row.getBytes());
        csvWriter.writeNext(new String[]{fullPath, String.valueOf(count)}, true);
    }
    fullPathOutputStream.close();
    csvWriter.close();
}
 

private void csvSpreadsheet(OutputStream os, List<SignupMeetingWrapper> meetingWrappers) throws IOException {
	
	CSVExport export = new CSVExport(meetingWrappers, getSakaiFacade());

	
	CSVWriter writer = new CSVWriter(new OutputStreamWriter(os), ',', CSVWriter.DEFAULT_QUOTE_CHARACTER, CSVWriter.DEFAULT_ESCAPE_CHARACTER, downloadVersion);
	//header
	List<String> header = export.getHeaderRow();
	
	int cols = header.size(); //total number of columns is based on header row
	
	String[] headerRow = new String[cols];
	headerRow = header.toArray(headerRow);
	writer.writeNext(headerRow);
	
	//data rows
	List<List<String>> data = export.getDataRows();
	Iterator<List<String>> iter = data.iterator();
	while(iter.hasNext()) {
		List<String> row = iter.next();
		String[] dataRow = new String[cols];
		dataRow = row.toArray(dataRow);
		writer.writeNext(dataRow);
	}
	
	writer.close();
	
}
 

@Override
public int export(String path) throws IOException {
  List<Address> addresses = addressRepo.all().filter("self.certifiedOk IS FALSE").fetch();

  CSVWriter csv =
      new CSVWriter(new java.io.FileWriter(path), "|".charAt(0), CSVWriter.NO_QUOTE_CHARACTER);
  List<String> header = new ArrayList<>();
  header.add("Id");
  header.add("AddressL1");
  header.add("AddressL2");
  header.add("AddressL3");
  header.add("AddressL4");
  header.add("AddressL5");
  header.add("AddressL6");
  header.add("CodeINSEE");

  csv.writeNext(header.toArray(new String[header.size()]));
  List<String> items = new ArrayList<>();
  for (Address a : addresses) {

    items.add(a.getId() != null ? a.getId().toString() : "");
    items.add(a.getAddressL2() != null ? a.getAddressL2() : "");
    items.add(a.getAddressL3() != null ? a.getAddressL3() : "");
    items.add(a.getAddressL4() != null ? a.getAddressL4() : "");
    items.add(a.getAddressL5() != null ? a.getAddressL5() : "");
    items.add(a.getAddressL6() != null ? a.getAddressL6() : "");
    items.add(a.getInseeCode() != null ? a.getInseeCode() : "");

    csv.writeNext(items.toArray(new String[items.size()]));
    items.clear();
  }
  csv.close();
  LOG.info("{} exported", path);

  return addresses.size();
}
 

public void exportParameter(String dirName, int parameterCount) throws SQLException, IOException {
    String sql = "SELECT stat.parameter, sum(parameterPathCount) AS allCount\n" +
            "FROM ((SELECT hpm.parameter, count(*) AS parameterPathCount FROM host_parameter_map hpm GROUP BY hpm.parameter)\n" +
            "      UNION ALL\n" +
            "      (SELECT parameter, count AS parameterPathCount FROM parameter)) stat\n" +
            "GROUP BY stat.parameter\n" +
            "HAVING allCount >= ?\n" +
            "ORDER BY allCount DESC";
    PreparedStatement preparedStatement = getPreparedStatement(sql);
    preparedStatement.setInt(1, parameterCount);
    ResultSet resultSet = preparedStatement.executeQuery();

    File parameterFile = new File(dirName + PARAMETER_FILE);
    File parameterImportFile = new File(dirName + PARAMETER_IMPORT_FILE);
    FileOutputStream parameterOutputStream = new FileOutputStream(parameterFile);
    FileWriter fileWriter = new FileWriter(parameterImportFile);
    CSVWriter csvWriter = new CSVWriter(fileWriter);
    String[] fileHead = new String[]{"parameter", "count"};
    csvWriter.writeNext(fileHead);
    while (resultSet.next()) {
        String parameter = resultSet.getString(1);
        String row = parameter + "\n";
        int count = resultSet.getInt(2);
        parameterOutputStream.write(row.getBytes());
        csvWriter.writeNext(new String[]{parameter, String.valueOf(count)}, true);
    }
    parameterOutputStream.close();
    csvWriter.close();
}
 

/**
	 * @param args the command line arguments
	 */
	public static void main(String[] args) throws FileNotFoundException, IOException {
//
//		final File sampleFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\Prioritisations\\samplesWithGeno.txt");
//		final File genoFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\Prioritisations\\gavinRes\\");
//		final File prioFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\Prioritisations");
//		final File resultFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\Prioritisations\\rankingCandidateGenes");

//		final File sampleFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\Prioritisations3\\samplesWithGeno.txt");
//		final File genoFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\Prioritisations\\gavinRes\\");
//		final File prioFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\Prioritisations3");
//		final File resultFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\Prioritisations3\\rankingCandidateGenes");
		
		final File sampleFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\extraUnsolved\\samplesWithGeno.txt");
		final File genoFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\extraUnsolved\\gavinRes\\");
		final File prioFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\extraUnsolved\\Prioritisations");
		final File resultFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\extraUnsolved\\rankingCandidateGenes");

//		final File sampleFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\PrioritisationsDcm\\samplesWithGeno.txt");
//		final File genoFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\PrioritisationsDcm\\gavinRes\\");
//		final File prioFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\PrioritisationsDcm");
//		final File resultFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\PrioritisationsDcm\\rankingCandidateGenes");
//
//		final File sampleFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\Prioritisations3\\samplesWithGeno.txt");
//		final File genoFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\Prioritisations\\gavinRes\\");
//		final File prioFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\PrioritisationsSpiked");
//		final File resultFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\PrioritisationsSpiked\\rankingCandidateGenes");
//		final File sampleFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\PrioritisationsCardioMieke\\samplesWithGeno.txt");
//		final File genoFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\PrioritisationsCardioMieke\\Gavin\\");
//		final File prioFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\PrioritisationsCardioMieke\\Prioritisations");
//		final File resultFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\PrioritisationsCardioMieke\\");
//		
//		final File sampleFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\PrioritisationsCardioEdgar\\Prioritisations\\samples.txt");
//		final File genoFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\PrioritisationsCardioEdgar\\CandidateGenes\\");
//		final File prioFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\PrioritisationsCardioEdgar\\Prioritisations");
//		final File resultFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\PrioritisationsCardioEdgar\\");
//
//		
		resultFolder.mkdirs();

		final CSVParser parser = new CSVParserBuilder().withSeparator('\t').withIgnoreQuotations(true).build();
		final CSVReader sampleFileReader = new CSVReaderBuilder(new BufferedReader(new FileReader(sampleFile))).withSkipLines(0).withCSVParser(parser).build();

		String[] nextLine;
		while ((nextLine = sampleFileReader.readNext()) != null) {

			String sample = nextLine[0];

			String genoSampleName = new File(nextLine[1]).getName();
			if (!genoSampleName.endsWith(".txt")) {
				genoSampleName += ".txt";
			}

			File genoFile = new File(genoFolder, genoSampleName);
			File prioFile = new File(prioFolder, sample + ".txt");
			File rankingFile = new File(resultFolder, sample + ".txt");

			System.out.println("------------------------------------------------------------------");
			System.out.println("Sample: " + sample);
			System.out.println("Geno: " + genoFile.getAbsolutePath());
			System.out.println("Prio: " + prioFile.getAbsolutePath());
			System.out.println("Ranking: " + rankingFile.getAbsolutePath());

			HashSet<String> genesWithMutation = getMutatedGenes(genoFile);

			final CSVReader prioFileReader = new CSVReaderBuilder(new BufferedReader(new FileReader(prioFile))).withSkipLines(0).withCSVParser(parser).build();

			CSVWriter writer = new CSVWriter(new FileWriter(rankingFile), '\t', '\0', '\0', "\n");

			String[] outputLine = prioFileReader.readNext();
			writer.writeNext(outputLine);

			while ((outputLine = prioFileReader.readNext()) != null) {

				if (genesWithMutation.contains(outputLine[1])) {
					writer.writeNext(outputLine);
				}

			}

			writer.close();
			prioFileReader.close();

		}

	}
 

/**
	 * @param args the command line arguments
	 * @throws java.lang.Exception
	 */
	public static void main(String[] args) throws Exception {

		final File predictionMatrixFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\Data31995Genes05-12-2017\\PCA_01_02_2018\\predictions\\hpo_predictions.txt.gz");
		final File annotationMatrixFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\Data31995Genes05-12-2017\\PCA_01_02_2018\\PathwayMatrix\\ALL_SOURCES_ALL_FREQUENCIES_phenotype_to_genes.txt_matrix.txt.gz");
		final File predictedHpoTermFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\Data31995Genes05-12-2017\\PCA_01_02_2018\\predictions\\hpo_predictions_auc_bonferroni.txt");
//		final File predictionMatrixFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\Data31995Genes05-12-2017\\PCA_01_02_2018\\predictions\\hpo_predictions_testSet.txt");
//		final File annotationMatrixFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\Data31995Genes05-12-2017\\PCA_01_02_2018\\PathwayMatrix\\hpo_annotation_testSet.txt");
//		final File predictedHpoTermFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\Data31995Genes05-12-2017\\PCA_01_02_2018\\predictions\\hpo_predictions_testSet_auc_bonferroni.txt");
		final File hpoOboFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\HPO\\135\\hp.obo");
		final File ouputLogFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\Data31995Genes05-12-2017\\PCA_01_02_2018\\predictions\\hpo_predictions_improved.log");
		final File updatedPredictionMatrixFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\Data31995Genes05-12-2017\\PCA_01_02_2018\\predictions\\hpo_predictions_improved.txt.gz");

		LinkedHashSet<String> predictedHpoTerms = readPredictedHpoTermFile(predictedHpoTermFile);

		DoubleMatrixDataset<String, String> predictionMatrixFull = DoubleMatrixDataset.loadDoubleData(predictionMatrixFile.getAbsolutePath());
		DoubleMatrixDataset<String, String> annotationMatrixFull = DoubleMatrixDataset.loadDoubleData(annotationMatrixFile.getAbsolutePath());

		DoubleMatrixDataset<String, String> predictionMatrixPredicted = predictionMatrixFull.viewColSelection(predictedHpoTerms);
		DoubleMatrixDataset<String, String> annotationMatrixPredicted = annotationMatrixFull.viewColSelection(predictedHpoTerms);

		Ontology hpoOntology = HpoFinder.loadHpoOntology(hpoOboFile);

		ImproveHpoPredictionBasedOnChildTerms improver = new ImproveHpoPredictionBasedOnChildTerms(predictionMatrixPredicted, annotationMatrixPredicted, hpoOntology);

		HashMap<String, UpdatedPredictionInfo> checkedHpoInfo = improver.run();

		System.out.println("Done with improving");

		CSVWriter writer = new CSVWriter(new FileWriter(ouputLogFile), '\t', '\0', '\0', "\n");

		String[] outputLine = new String[11];
		int c = 0;
		outputLine[c++] = "HPO";
		outputLine[c++] = "Gene_count";
		outputLine[c++] = "Origanl_AUC";
		outputLine[c++] = "Orignal_Pvalue";
		outputLine[c++] = "Updated_AUC";
		outputLine[c++] = "Updated_Pvalue";
		outputLine[c++] = "Is_significant";
		outputLine[c++] = "Distance_to_top";
		outputLine[c++] = "Number_of_child_terms";
		outputLine[c++] = "Number_of_child_terms_used";
		outputLine[c++] = "Child_terms_used";
		writer.writeNext(outputLine);

		for (UpdatedPredictionInfo pi : checkedHpoInfo.values()) {
			c = 0;
			outputLine[c++] = pi.getHpo();
			outputLine[c++] = String.valueOf(pi.getGeneCount());
			outputLine[c++] = String.valueOf(pi.getOriginalAuc());
			outputLine[c++] = String.valueOf(pi.getOriginalPvalue());
			outputLine[c++] = String.valueOf(pi.getUpdatedAuc());
			outputLine[c++] = String.valueOf(pi.getUpdatedPvalue());
			outputLine[c++] = String.valueOf(pi.isIsSignificant());
			outputLine[c++] = "-";
			outputLine[c++] = String.valueOf(pi.getChildTermCount());
			outputLine[c++] = String.valueOf(pi.getUsedChildTerms().size());
			outputLine[c++] = String.join(";", pi.getUsedChildTerms());
			writer.writeNext(outputLine);
		}
		writer.close();

		improver.writeUpdatedMatrix(updatedPredictionMatrixFile);
	}
 

/**
 * @param args the command line arguments
 */
public static void main(String[] args) throws IOException, ParseException {

	final File hpoOboFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\HPO\\135\\hp.obo");
	final File hpoPredictionInfoFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\Data31995Genes05-12-2017\\PCA_01_02_2018\\predictions\\hpo_predictions_auc_bonferroni.txt");
	final File queryFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\originalHpo.txt");
	final File outputFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\selectedHpo.txt");
	final double correctedPCutoff = 0.05;

	Map<String, PredictionInfo> predictionInfo = HpoFinder.loadPredictionInfo(hpoPredictionInfoFile);

	Ontology hpoOntology = HpoFinder.loadHpoOntology(hpoOboFile);

	HpoFinder hpoFinder = new HpoFinder(hpoOntology, predictionInfo);

	CSVWriter writer = new CSVWriter(new FileWriter(outputFile), '\t', '\0', '\0', "\n");

	int c = 0;
	String[] outputLine = new String[7];
	outputLine[c++] = "originalHPO";
	outputLine[c++] = "originalDescription";
	outputLine[c++] = "matchHPO";
	outputLine[c++] = "matchDescription";
	outputLine[c++] = "matchPvalue";
	outputLine[c++] = "matchauc";
	outputLine[c++] = "multiMatch";

	writer.writeNext(outputLine);

	BufferedReader queryReader = new BufferedReader(new FileReader(queryFile));
	String queryHpo;

	while ((queryHpo = queryReader.readLine()) != null) {

		if (hpoOntology.containsTerm(queryHpo)) {
			Term queryHpoTerm = hpoOntology.getTerm(queryHpo);

			List<Term> alternativeTerms = hpoFinder.getPredictableTerms(queryHpoTerm, correctedPCutoff);

			for (Term alternativeTerm : alternativeTerms) {

				PredictionInfo info = predictionInfo.get(alternativeTerm.getName());

				c = 0;
				outputLine[c++] = queryHpo;
				outputLine[c++] = queryHpoTerm.getDescription();
				outputLine[c++] = alternativeTerm.getName();
				outputLine[c++] = alternativeTerm.getDescription();
				outputLine[c++] = String.valueOf(info.getpValue());
				outputLine[c++] = String.valueOf(info.getAuc());
				outputLine[c++] = alternativeTerms.size() > 1 ? "x" : "-";
				writer.writeNext(outputLine);

				//System.out.println(alternativeTerm.getName() + " P-value: " + info.getpValue() + " AUC: " + info.getAuc() + " " + alternativeTerm.getDescription());
			}

			if (alternativeTerms.isEmpty()) {
				c = 0;
				outputLine[c++] = queryHpo;
				outputLine[c++] = queryHpoTerm.getDescription();
				outputLine[c++] = "NA";
				outputLine[c++] = "NA";
				outputLine[c++] = "NA";
				outputLine[c++] = "NA";
				outputLine[c++] = "NA";
				writer.writeNext(outputLine);
			}

		} else {
			c = 0;
			outputLine[c++] = queryHpo;
			outputLine[c++] = "NA";
			outputLine[c++] = "NA";
			outputLine[c++] = "NA";
			outputLine[c++] = "NA";
			outputLine[c++] = "NA";
			outputLine[c++] = "NA";
			writer.writeNext(outputLine);
		}

	}

	writer.close();

}
 

/**
	 * @param args the command line arguments
	 */
	public static void main(String[] args) throws FileNotFoundException, IOException {

//		final File sampleFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\Prioritisations\\samplesWithGeno.txt");
//		final File genoFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\Prioritisations\\gavinRes\\");
//		final File prioFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\Prioritisations");
//		final File resultFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\Prioritisations\\rankingCandidateGenes");


//		final File sampleFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\PrioritizeRequests\\Prioritisations\\samples.txt");
//		final File genoFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\PrioritizeRequests\\CandidateGenes\\");
//		final File prioFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\PrioritizeRequests\\Prioritisations");
//		final File resultFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\PrioritizeRequests\\rankingCandidateGenes");

		final File sampleFile = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\New5gpm\\hpo5gpm.txt");
		final File genoFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\New5gpm\\Genes\\");
		final File prioFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\New5gpm\\Prioritisations\\");
		final File resultFolder = new File("C:\\UMCG\\Genetica\\Projects\\GeneNetwork\\BenchmarkSamples\\New5gpm\\RankingCandidateGenes\\");

		final CSVParser parser = new CSVParserBuilder().withSeparator('\t').withIgnoreQuotations(true).build();
		final CSVReader sampleFileReader = new CSVReaderBuilder(new BufferedReader(new FileReader(sampleFile))).withSkipLines(0).withCSVParser(parser).build();

		String[] nextLine;
		while ((nextLine = sampleFileReader.readNext()) != null) {

			String sample = nextLine[0];

			String genoSampleName = sample + ".txt";

			File genoFile = new File(genoFolder, genoSampleName);
			File prioFile = new File(prioFolder, sample + ".txt");
			File rankingFile = new File(resultFolder, sample + ".txt");

			System.out.println("------------------------------------------------------------------");
			System.out.println("Sample: " + sample);
			System.out.println("Geno: " + genoFile.getAbsolutePath());
			System.out.println("Prio: " + prioFile.getAbsolutePath());
			System.out.println("Ranking: " + rankingFile.getAbsolutePath());

			HashSet<String> genesWithMutation = getMutatedGenes(genoFile, 0, 0);

			final CSVReader prioFileReader = new CSVReaderBuilder(new BufferedReader(new FileReader(prioFile))).withSkipLines(0).withCSVParser(parser).build();

			CSVWriter writer = new CSVWriter(new FileWriter(rankingFile), '\t', '\0', '\0', "\n");

			String[] outputLine = prioFileReader.readNext();
			writer.writeNext(outputLine);

			while ((outputLine = prioFileReader.readNext()) != null) {

				if (genesWithMutation.contains(outputLine[1])) {
					writer.writeNext(outputLine);
				}

			}

			writer.close();
			prioFileReader.close();

		}

	}
 

public static void main(String[] args) throws IOException{
        Constituent cs1 = new Constituent("CS1", 120);
        Constituent cs2 = new Constituent("CS2", 120);
        Constituent cs3 = new Constituent("CS3", 120);

        Action a1 = new Action("Action1", 2, 1);
        a1.setActionType(Action.TYPE.NORMAL);
        Action a2 = new Action("Action2", 2, 2);
        a2.setActionType(Action.TYPE.NORMAL);
        Action a3 = new Action("Action3", 3, 3);
        a3.setActionType(Action.TYPE.NORMAL);

        cs1.addCapability(a1, 1);
        cs1.addCapability(a2, 2);

        cs2.addCapability(a2, 2);
        cs2.addCapability(a3, 3);

        cs3.addCapability(a1, 1);
        cs3.addCapability(a3, 3);

        Constituent[] CSs = {cs1, cs2, cs3};
        Action[] actions = {a1, a2, a3};
        SoS sos = new SoS("SoS Manager", CSs, actions);
        Environment env = new Environment(CSs, actions);

        Simulator sim = new Simulator(CSs, sos, env);
        sim.setEndTick(300);

        int[] boundArr = {120, 125, 130, 135, 140, 145, 150};
        for(int bound: boundArr){

            String outputName = "SIM_" + bound + ".csv";
            CSVWriter cw = new CSVWriter(new OutputStreamWriter(new FileOutputStream(outputName), "UTF-8"), ',', '"');
            cw.writeNext(new String[] {"prob", "num_of_samples", "execution_time", "min_tick", "max_tick", "result"});
            ArrayList<SMCResult> resList = new ArrayList<SMCResult>();

            System.out.println("----------------------------------------------------");
            System.out.println("SoS-level benefit is greater than "+bound + ".");
            BaseChecker checker = new BaseChecker();
            checker.init(10000, bound, BaseChecker.comparisonType.GREATER_THAN_AND_EQUAL_TO);
            SPRTMethod sprt = new SPRTMethod(0.01, 0.01, 0.005);

            for(int i=1; i<100; i++){
                double theta = 0.01 * i; // theta
                long start = System.currentTimeMillis();
                sprt.setExpression(theta);

                while(!sprt.checkStopCondition())
                {
                    sim.execute();
                    SIMResult res = sim.getResult();
                    int checkResult = checker.evaluateSample(res);
                    sprt.updateResult(checkResult);
                }


                boolean h0 = sprt.getResult(); // Result
                int numSamples = sprt.getNumSamples();
//                System.out.print("SMC decides that your hypothesis is ");
//                if(h0)
//                {
//                    System.out.println("accepted at " + theta + " / number of samples: " + numSamples);
//                }
//                else
//                {
//                    System.out.println("not accepted at " + theta + " / number of samples: " + numSamples);
//                }

                long exec_time = System.currentTimeMillis() - start; //exec time
                int minTick = checker.getMinTick();
                int maxTick = checker.getMaxTick();
                sprt.reset();
                resList.add(new SMCResult(theta, numSamples, exec_time, minTick, maxTick, h0));
                if(h0) System.out.print("T");
                else System.out.print("F");
            }
            System.out.println();
            System.out.print("w");
            for(SMCResult r : resList){
                System.out.print(".");
                cw.writeNext(r.getArr());
            }
            cw.close();
            resList.clear();
            System.out.println();
        }
        System.out.println("Finished");

    }