Example usage for org.jdom2.output Format getPrettyFormat

List of usage examples for org.jdom2.output Format getPrettyFormat

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Introduction

In this page you can find the example usage for org.jdom2.output Format getPrettyFormat.

Prototype

public static Format getPrettyFormat()

Source Link

Document

Returns a new Format object that performs whitespace beautification with 2-space indents, uses the UTF-8 encoding, doesn't expand empty elements, includes the declaration and encoding, and uses the default entity escape strategy.

Usage

From source file:es.upm.dit.xsdinferencer.Results.java

License:Apache License

/**
 * Converts a Map<String,Document> to a Map<String,String> with the same keys and String representations 
 * of the documents as values.<br/>
 * The XMLs are generated using the format returned by {@link Format#getPrettyFormat()} and the system line separator. 
 * For more information about this, see {@link Format}.
 * @param inputMap a map between Strings and Documents
 * @return a map between the Strings and the String representation of the documents (null if inputMap is null).
 *//*w  w  w  .  j  a  v a 2 s.  c  o m*/
private Map<String, String> getStringMapFromXMLMap(Map<String, Document> inputMap, TextMode textMode) {
    if (inputMap == null) {
        return null;
    }
    Map<String, String> results = new HashMap<>(inputMap.size());
    Format xmlFormat = Format.getPrettyFormat();
    xmlFormat.setLineSeparator(LineSeparator.SYSTEM);
    //xmlFormat.setTextMode(textMode);
    XMLOutputter outputter = new XMLOutputter(xmlFormat);
    for (String fileName : inputMap.keySet()) {
        Document currentDocument = inputMap.get(fileName);
        String xsdString = outputter.outputString(currentDocument);
        results.put(fileName, xsdString);
    }
    return ImmutableMap.copyOf(results);
}

From source file:es.uvigo.ei.sing.rubioseq.gui.view.models.configuration.ConfigProgramPathsChipSeq.java

License:Open Source License

public void exportToXML(File output) throws IOException {
    Document configurationFile = new Document();
    Comment comment = new Comment(COMMENT_CHIPSEQ);
    configurationFile.addContent(comment);

    Element configData = new Element(CONFIG_DATA);
    configurationFile.setRootElement(configData);

    Element bwaPath = new Element(BWA_PATH);
    bwaPath.addContent(this.getBwaPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(bwaPath);

    Element samtoolsPath = new Element(SAMTOOLS_PATH);
    samtoolsPath.addContent(this.getSamtoolsPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(samtoolsPath);

    Element picardPath = new Element(PICARD_PATH);
    picardPath.addContent(this.getPicardPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(picardPath);

    Element MACSPath = new Element(MACS_PATH);
    MACSPath.addContent(this.getMacsPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(MACSPath);

    Element PythonPath = new Element(PYTHON_PATH);
    PythonPath.addContent(this.getPythonPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(PythonPath);

    Element BEDToolsPath = new Element(BED_TOOLS_PATH);
    BEDToolsPath.addContent(this.getBedtoolsPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(BEDToolsPath);

    Element CCATPath = new Element(CCAT_PATH);
    CCATPath.addContent(this.getCcatPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(CCATPath);

    Element BedgraphtoWigPath = new Element(BGTW_PATH);
    BedgraphtoWigPath.addContent(this.getBedgraphtobigwigPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(BedgraphtoWigPath);

    Element IDRPath = new Element(IDR_PATH);
    IDRPath.addContent(this.getIdrPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(IDRPath);

    Element PeakAnnotatorPath = new Element(PEAKANNOTATOR_PATH);
    PeakAnnotatorPath.addContent(this.getPeakannotatorPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(PeakAnnotatorPath);

    Element fastqcPath = new Element(FASTQC_PATH);
    fastqcPath.addContent(this.getFastqcPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(fastqcPath);

    if (!this.getNthr().equals(nthr_DV)) {
        Element nthr = new Element(NTHR);
        nthr.addContent(String.valueOf(this.getNthr()));
        configurationFile.getRootElement().addContent(nthr);
    }/* w w  w. j a va2s. c om*/

    if (!this.getJavaRam().equals(javaRam_DV)) {
        Element javaRam = new Element(JAVA_RAM);
        javaRam.addContent(this.getJavaRam());
        configurationFile.getRootElement().addContent(javaRam);
    }

    Element queueSystem = new Element(QUEUE_SYSTEM);
    queueSystem.addContent(this.getQueueSystem().getDisplayName());
    configurationFile.getRootElement().addContent(queueSystem);

    if (!this.getQueueName().equals(queueName_DV)) {
        Element queueName = new Element(QUEUE_NAME);
        queueName.addContent(this.getQueueName());
        configurationFile.getRootElement().addContent(queueName);
    }

    if (!this.getMulticoreName().equals(multicoreName_DV)) {
        Element multicoreName = new Element(MULTICORE_NAME);
        multicoreName.addContent(this.getMulticoreName());
        configurationFile.getRootElement().addContent(multicoreName);
    }

    if (!this.getMulticoreNumber().equals(multicoreNumber_DV)) {
        Element multicoreNumber = new Element(MULTICORE_NUMBER);
        multicoreNumber.addContent(String.valueOf(this.getMulticoreNumber()));
        configurationFile.getRootElement().addContent(multicoreNumber);
    }

    XMLOutputter xmlOutput = new XMLOutputter();
    xmlOutput.setFormat(Format.getPrettyFormat());
    xmlOutput.output(configurationFile, new FileWriter(output));
    //      xmlOutput.output(configurationFile, new FileWriter(new File(output.getAbsolutePath()+".test")));
}

From source file:es.uvigo.ei.sing.rubioseq.gui.view.models.configuration.ConfigProgramPathsCNV.java

License:Open Source License

public void exportToXML(File output) throws IOException {
    Document configurationFile = new Document();
    Comment comment = new Comment(COMMENT_VARIANT_CALLER);
    configurationFile.addContent(comment);

    Element configData = new Element(CONFIG_DATA);
    configurationFile.setRootElement(configData);

    Element bwaPath = new Element(BWA_PATH);
    bwaPath.addContent(this.getBwaPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(bwaPath);

    Element samtoolsPath = new Element(SAMTOOLS_PATH);
    samtoolsPath.addContent(this.getSamtoolsPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(samtoolsPath);

    Element gatkpath = new Element(GATK_PATH);
    gatkpath.addContent(this.getGatkpath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(gatkpath);

    Element picardPath = new Element(PICARD_PATH);
    picardPath.addContent(this.getPicardPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(picardPath);

    Element BFASTPath = new Element(BFAST_PATH);
    BFASTPath.addContent(this.getBfastPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(BFASTPath);

    Element BEDToolsPath = new Element(BED_TOOLS_PATH);
    BEDToolsPath.addContent(this.getBedtoolsPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(BEDToolsPath);

    Element CONTRAPath = new Element(CONTRA_PATH);
    CONTRAPath.addContent(this.getContraPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(CONTRAPath);

    Element fastqcPath = new Element(FASTQC_PATH);
    fastqcPath.addContent(this.getFastqcPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(fastqcPath);

    if (!this.getNthr().equals(nthr_DV)) {
        Element nthr = new Element(NTHR);
        nthr.addContent(String.valueOf(this.getNthr()));
        configurationFile.getRootElement().addContent(nthr);
    }/*from w w w .  j a  v a  2  s.  c o  m*/

    if (!this.getJavaRam().equals(javaRam_DV)) {
        Element javaRam = new Element(JAVA_RAM);
        javaRam.addContent(this.getJavaRam());
        configurationFile.getRootElement().addContent(javaRam);
    }

    Element queueSystem = new Element(QUEUE_SYSTEM);
    queueSystem.addContent(this.getQueueSystem().getDisplayName());
    configurationFile.getRootElement().addContent(queueSystem);

    if (!this.getQueueName().equals(queueName_DV)) {
        Element queueName = new Element(QUEUE_NAME);
        queueName.addContent(this.getQueueName());
        configurationFile.getRootElement().addContent(queueName);
    }

    if (!this.getMulticoreName().equals(multicoreName_DV)) {
        Element multicoreName = new Element(MULTICORE_NAME);
        multicoreName.addContent(this.getMulticoreName());
        configurationFile.getRootElement().addContent(multicoreName);
    }

    if (!this.getMulticoreNumber().equals(multicoreNumber_DV)) {
        Element multicoreNumber = new Element(MULTICORE_NUMBER);
        multicoreNumber.addContent(String.valueOf(this.getMulticoreNumber()));
        configurationFile.getRootElement().addContent(multicoreNumber);
    }

    XMLOutputter xmlOutput = new XMLOutputter();
    xmlOutput.setFormat(Format.getPrettyFormat());
    xmlOutput.output(configurationFile, new FileWriter(output));
}

From source file:es.uvigo.ei.sing.rubioseq.gui.view.models.configuration.ConfigProgramPathsMethylation.java

License:Open Source License

public void exportToXML(File output) throws IOException {
    Document configurationFile = new Document();
    Comment comment = new Comment(COMMENT_METHYLATION);
    configurationFile.addContent(comment);

    Element configData = new Element(CONFIG_DATA);
    configurationFile.setRootElement(configData);

    Element bismarkPath = new Element(BISMARK_PATH);
    bismarkPath.addContent(this.getBismarkPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(bismarkPath);

    Element bowtiePath = new Element(BOWTIE_PATH);
    bowtiePath.addContent(this.getBowtiePath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(bowtiePath);

    Element picardPath = new Element(PICARD_PATH);
    picardPath.addContent(this.getPicardPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(picardPath);

    Element BEDToolsPath = new Element(BED_TOOLS_PATH);
    BEDToolsPath.addContent(this.getBedtoolsPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(BEDToolsPath);

    Element fastxPath = new Element(FASTX_PATH);
    fastxPath.addContent(this.getFastxPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(fastxPath);

    Element filoPath = new Element(FILO_PATH);
    filoPath.addContent(this.getFiloPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(filoPath);

    Element fastqcPath = new Element(FASTQC_PATH);
    fastqcPath.addContent(this.getFastqcPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(fastqcPath);

    if (!this.getNthr().equals(nthr_DV)) {
        Element nthr = new Element(NTHR);
        nthr.addContent(String.valueOf(this.getNthr()));
        configurationFile.getRootElement().addContent(nthr);
    }/*  w  ww  .ja va 2  s . c o m*/

    if (!this.getJavaRam().equals(javaRam_DV)) {
        Element javaRam = new Element(JAVA_RAM);
        javaRam.addContent(this.getJavaRam());
        configurationFile.getRootElement().addContent(javaRam);
    }

    Element queueSystem = new Element(QUEUE_SYSTEM);
    queueSystem.addContent(this.getQueueSystem().getDisplayName());
    configurationFile.getRootElement().addContent(queueSystem);

    if (!this.getQueueName().equals(queueName_DV)) {
        Element queueName = new Element(QUEUE_NAME);
        queueName.addContent(this.getQueueName());
        configurationFile.getRootElement().addContent(queueName);
    }

    if (!this.getMulticoreName().equals(multicoreName_DV)) {
        Element multicoreName = new Element(MULTICORE_NAME);
        multicoreName.addContent(this.getMulticoreName());
        configurationFile.getRootElement().addContent(multicoreName);
    }

    if (!this.getMulticoreNumber().equals(multicoreNumber_DV)) {
        Element multicoreNumber = new Element(MULTICORE_NUMBER);
        multicoreNumber.addContent(String.valueOf(this.getMulticoreNumber()));
        configurationFile.getRootElement().addContent(multicoreNumber);
    }

    XMLOutputter xmlOutput = new XMLOutputter();
    xmlOutput.setFormat(Format.getPrettyFormat());
    xmlOutput.output(configurationFile, new FileWriter(output));
}

From source file:es.uvigo.ei.sing.rubioseq.gui.view.models.configuration.ConfigProgramPathsSNV.java

License:Open Source License

public void exportToXML(File output) throws IOException {
    Document configurationFile = new Document();
    Comment comment = new Comment(COMMENT_VARIANT_CALLER);
    configurationFile.addContent(comment);

    Element configData = new Element(CONFIG_DATA);
    configurationFile.setRootElement(configData);

    Element bwaPath = new Element(BWA_PATH);
    bwaPath.addContent(this.getBwaPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(bwaPath);

    Element samtoolsPath = new Element(SAMTOOLS_PATH);
    samtoolsPath.addContent(this.getSamtoolsPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(samtoolsPath);

    Element gatkpath = new Element(GATK_PATH);
    gatkpath.addContent(this.getGatkpath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(gatkpath);

    Element picardPath = new Element(PICARD_PATH);
    picardPath.addContent(this.getPicardPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(picardPath);

    Element BFASTPath = new Element(BFAST_PATH);
    BFASTPath.addContent(this.getBfastPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(BFASTPath);

    Element fastqcPath = new Element(FASTQC_PATH);
    fastqcPath.addContent(this.getFastqcPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(fastqcPath);

    if (!this.getNthr().equals(nthr_DV)) {
        Element nthr = new Element(NTHR);
        nthr.addContent(String.valueOf(this.getNthr()));
        configurationFile.getRootElement().addContent(nthr);
    }/*from   w  w w . j a va 2 s. c o m*/

    if (!this.getJavaRam().equals(javaRam_DV)) {
        Element javaRam = new Element(JAVA_RAM);
        javaRam.addContent(this.getJavaRam());
        configurationFile.getRootElement().addContent(javaRam);
    }

    Element queueSystem = new Element(QUEUE_SYSTEM);
    queueSystem.addContent(this.getQueueSystem().getDisplayName());
    configurationFile.getRootElement().addContent(queueSystem);

    if (!this.getQueueName().equals(queueName_DV)) {
        Element queueName = new Element(QUEUE_NAME);
        queueName.addContent(this.getQueueName());
        configurationFile.getRootElement().addContent(queueName);
    }

    if (!this.getMulticoreName().equals(multicoreName_DV)) {
        Element multicoreName = new Element(MULTICORE_NAME);
        multicoreName.addContent(this.getMulticoreName());
        configurationFile.getRootElement().addContent(multicoreName);
    }

    if (!this.getMulticoreNumber().equals(multicoreNumber_DV)) {
        Element multicoreNumber = new Element(MULTICORE_NUMBER);
        multicoreNumber.addContent(String.valueOf(this.getMulticoreNumber()));
        configurationFile.getRootElement().addContent(multicoreNumber);
    }

    XMLOutputter xmlOutput = new XMLOutputter();
    xmlOutput.setFormat(Format.getPrettyFormat());
    xmlOutput.output(configurationFile, new FileWriter(output));
}

From source file:es.uvigo.ei.sing.rubioseq.gui.view.models.experiments.ChipSeqExperiment.java

License:Open Source License

public void generateXMLConfigurationFile(File output) throws IOException {
    Document configurationFile = new Document();
    Element configData = new Element(CONFIG_DATA);
    configurationFile.setRootElement(configData);
    configData.setAttribute(ExperimentUtils.BRANCH, ExperimentUtils.BRANCH_CHIPSEQ);

    Element genRef = new Element(GENREF);
    genRef.addContent(this.getGenRefPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(genRef);

    Element plattform = new Element(PLATTFORM);
    plattform.addContent(this.getPlattform().getDisplayName());
    configurationFile.getRootElement().addContent(plattform);

    if (!this.checkCasava.equals(checkCasava_DV)) {
        Element checkCasava = new Element(CHECKCASAVA);
        checkCasava.addContent(this.getCheckCasava().toString());
        configurationFile.getRootElement().addContent(checkCasava);
    }/*  w w w . j ava  2s.  c  o m*/

    Element dirOutBase = new Element(DIROUTBASE);
    dirOutBase.addContent(this.getDirOutBase().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(dirOutBase);

    Element projectId = new Element(PROJECTID);
    projectId.addContent(this.getProjectId());
    configurationFile.getRootElement().addContent(projectId);

    if (!this.getUserName().equals(userName_DV)) {
        Element userName = new Element(USERNAME);
        userName.addContent(this.getUserName());
        configurationFile.getRootElement().addContent(userName);
    }

    Element inDirPreProcess = new Element(INDIRPREPROCESS);
    inDirPreProcess.addContent(this.getDataInDirpreProcess().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(inDirPreProcess);

    for (CSExperiment experiment : this.getExperiments()) {
        Element chipSeqExperiment = new Element(EXPERIMENT);

        for (ChipSeqUnit csUnit : experiment.getChipSeqUnits()) {
            Element csUnitElement = new Element(CHIPSEQUNIT);

            Sample sampleTreatment = csUnit.getSampleTreatment();

            Element sampleTreatmentElement = new Element(SAMPLE_TREATMENT);

            Element sampleName = new Element(SAMPLE_NAME);
            sampleName.addContent(sampleTreatment.getSampleName());
            sampleTreatmentElement.addContent(sampleName);

            Element sampleFiles = new Element(SAMPLE_FILES);
            sampleFiles.addContent(sampleTreatment.getSampleFiles());
            sampleTreatmentElement.addContent(sampleFiles);

            Element sampleSuffix = new Element(SAMPLE_SUFFIX);
            sampleSuffix.addContent(sampleTreatment.getSampleSuffix());
            sampleTreatmentElement.addContent(sampleSuffix);

            Element sampleType = new Element(SAMPLE_TYPE);
            sampleType.addContent(sampleTreatment.getSampleType().getDisplayName());
            sampleTreatmentElement.addContent(sampleType);

            csUnitElement.addContent(sampleTreatmentElement);

            Sample sampleInput = csUnit.getSampleInput();
            if (sampleInput.checkSample()) {

                Element sampleInputElement = new Element(SAMPLE_INPUT);

                Element sampleInputName = new Element(SAMPLE_NAME);
                sampleInputName.addContent(sampleInput.getSampleName());
                sampleInputElement.addContent(sampleInputName);

                Element sampleInputFiles = new Element(SAMPLE_FILES);
                sampleInputFiles.addContent(sampleInput.getSampleFiles());
                sampleInputElement.addContent(sampleInputFiles);

                Element sampleInputSuffix = new Element(SAMPLE_SUFFIX);
                sampleInputSuffix.addContent(sampleInput.getSampleSuffix());
                sampleInputElement.addContent(sampleInputSuffix);

                Element sampleInputType = new Element(SAMPLE_TYPE);
                sampleInputType.addContent(sampleInput.getSampleType().getDisplayName());
                sampleInputElement.addContent(sampleInputType);

                csUnitElement.addContent(sampleInputElement);
            }

            chipSeqExperiment.addContent(csUnitElement);
        }

        Element replicatesFlag = new Element(REPLICATES_FLAG);
        replicatesFlag.addContent(experiment.isReplicatesFlag() ? "1" : "0");
        chipSeqExperiment.addContent(replicatesFlag);

        configurationFile.getRootElement().addContent(chipSeqExperiment);
    }

    Element chromSize = new Element(CHROMSIZE);
    chromSize.addContent(this.getChromSize().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(chromSize);

    if (!this.getPeakAnalysisType().equals(peakAnalysisType_DV)) {
        Element peakAnalysis = new Element(PEAKANALYSIS);
        peakAnalysis.addContent(this.getPeakAnalysisType().getDisplayName());
        configurationFile.getRootElement().addContent(peakAnalysis);
    }

    if (this.getCcatConfigFile() != ccatConfigFile_DV) {
        Element ccaConfigFile = new Element(CCAT_CONFIG_FILE);
        ccaConfigFile.addContent(this.getCcatConfigFile().getFile().getAbsolutePath());
        configurationFile.getRootElement().addContent(ccaConfigFile);
    }

    if (!this.getMacsExtraArgs().equals(macsExtraArgs_DV)) {
        Element macsExtraArgs = new Element(MACS_EXTRAARGS);
        macsExtraArgs.addContent(this.getMacsExtraArgs());
        configurationFile.getRootElement().addContent(macsExtraArgs);
    }

    if (!this.getFastqc().equals(fastqc_DV)) {
        Element fastqc = new Element(FASTQC);
        fastqc.addContent(this.getFastqc().toString());
        configurationFile.getRootElement().addContent(fastqc);
    }

    if (this.getAnnotFile() != annotFile_DV) {
        Element annotFile = new Element(ANNOTFILE);
        annotFile.addContent(this.getAnnotFile().getFile().getAbsolutePath());
        configurationFile.getRootElement().addContent(annotFile);
    }

    if (!this.getQueueSGEProject().equals(queueSGEProject_DV)) {
        Element queueProject = new Element(QUEUESGEPROJECT);
        queueProject.addContent(this.getQueueSGEProject().toString());
        configurationFile.getRootElement().addContent(queueProject);
    }

    XMLOutputter xmlOutput = new XMLOutputter();
    xmlOutput.setFormat(Format.getPrettyFormat());
    xmlOutput.output(configurationFile, new FileWriter(output));
}

From source file:es.uvigo.ei.sing.rubioseq.gui.view.models.experiments.CopyNumberVariationExperiment.java

License:Open Source License

public void generateXMLConfigurationFile(File output) throws IOException {
    Document configurationFile = new Document();
    Element configData = new Element(CONFIG_DATA);
    configurationFile.setRootElement(configData);
    configData.setAttribute(ExperimentUtils.BRANCH, ExperimentUtils.BRANCH_CNV);

    Element genRef = new Element(GENREF);
    genRef.addContent(this.getGenRefPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(genRef);

    Element dbSnpAnnot = new Element(DBSNPANNOT);
    dbSnpAnnot.addContent(this.getDbSnpAnnotPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(dbSnpAnnot);

    Element indelAnnot = new Element(INDELANNOT);
    indelAnnot.addContent(this.getIndelAnnotPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(indelAnnot);

    Element intervals = new Element(INTERVALS);
    intervals.addContent(this.getIntervalsPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(intervals);

    if (this.getKnownIndels().size() > 0) {
        for (KnownIndels kI : this.getKnownIndels()) {
            Element knownIndels = new Element(KNOWNINDELS);
            knownIndels.addContent(kI.getFile().getFile().getAbsolutePath());
            configurationFile.getRootElement().addContent(knownIndels);
        }/*from  w  w w.j  a va 2 s .  co  m*/
    }

    Element plattform = new Element(PLATTFORM);
    plattform.addContent(this.getPlattform().getDisplayName());
    configurationFile.getRootElement().addContent(plattform);

    if (!this.getCheckCasava().equals(checkCasava_DV)) {
        Element checkCasava = new Element(CHECKCASAVA);
        checkCasava.addContent(this.getCheckCasava().toString());
        configurationFile.getRootElement().addContent(checkCasava);
    }

    Element dirOutBase = new Element(DIROUTBASE);
    dirOutBase.addContent(this.getDirOutBase().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(dirOutBase);

    Element projectId = new Element(PROJECTID);
    projectId.addContent(this.getProjectId());
    configurationFile.getRootElement().addContent(projectId);

    if (!this.getUserName().equals(userName_DV)) {
        Element userName = new Element(USERNAME);
        userName.addContent(this.getUserName());
        configurationFile.getRootElement().addContent(userName);
    }

    Element dataInDirpreProcess = new Element(INDIRPREPROCESS);
    dataInDirpreProcess.addContent(this.getDataInDirpreProcess().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(dataInDirpreProcess);

    for (Sample s : this.getSamples()) {
        Element sample = new Element(SAMPLE);

        Element sampleName = new Element(SAMPLE_NAME);
        sampleName.addContent(s.getSampleName());
        sample.addContent(sampleName);

        Element sampleFiles = new Element(SAMPLE_FILES);
        sampleFiles.addContent(s.getSampleFiles());
        sample.addContent(sampleFiles);

        Element sampleSuffix = new Element(SAMPLE_SUFFIX);
        sampleSuffix.addContent(s.getSampleSuffix());
        sample.addContent(sampleSuffix);

        Element sampleType = new Element(SAMPLE_TYPE);
        sampleType.addContent(s.getSampleType().getDisplayName());
        sample.addContent(sampleType);

        configurationFile.getRootElement().addContent(sample);
    }

    if (!this.getFastqc().equals(fastqc_DV)) {
        Element fastqc = new Element(FASTQC);
        fastqc.addContent(this.getFastqc().toString());
        configurationFile.getRootElement().addContent(fastqc);
    }

    if (!this.getExtraContra().equals(extraContra_DV)) {
        Element extraContra = new Element(EXTRACONTRA);
        extraContra.addContent(this.getExtraContra().toString());
        configurationFile.getRootElement().addContent(extraContra);
    }

    if (this.getBaseline() != baseline_DV) {
        Element baseline = new Element(BASELINE);
        baseline.addContent(this.getBaseline().getFile().getAbsolutePath());
        configurationFile.getRootElement().addContent(baseline);
    }

    if (!this.getmDFlag().equals(mDFlag_DV)) {
        Element mDFlag = new Element(MDFLAG);
        mDFlag.addContent(this.getmDFlag().toString());
        configurationFile.getRootElement().addContent(mDFlag);
    }

    if (!this.getQueueSGEProject().equals(queueSGEProject_DV)) {
        Element queueSGEProject = new Element(QUEUESGEPROJECT);
        queueSGEProject.addContent(this.getQueueSGEProject().toString());
        configurationFile.getRootElement().addContent(queueSGEProject);
    }

    XMLOutputter xmlOutput = new XMLOutputter();
    xmlOutput.setFormat(Format.getPrettyFormat());
    xmlOutput.output(configurationFile, new FileWriter(output));
}

From source file:es.uvigo.ei.sing.rubioseq.gui.view.models.experiments.MethylationExperiment.java

License:Open Source License

public void generateXMLConfigurationFile(File output) throws IOException {
    Document configurationFile = new Document();
    Element configData = new Element(CONFIG_DATA);
    configurationFile.setRootElement(configData);
    configData.setAttribute(ExperimentUtils.BRANCH, ExperimentUtils.BRANCH_METHYLATION);

    Element referencePath = new Element(REFERENCEPATH);
    referencePath.addContent(this.getReferencePath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(referencePath);

    Element readsPath = new Element(READSPATH);
    readsPath.addContent(this.getReadsPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(readsPath);

    Element projectCompletePath = new Element(PROJECT_COMPLETE_PATH);
    projectCompletePath.addContent(this.getProjectCompletePath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(projectCompletePath);

    Element plattform = new Element(PLATTFORM);
    plattform.addContent(this.getPlattform().getDisplayName());
    configurationFile.getRootElement().addContent(plattform);

    Element methylType = new Element(METHYLTYPE);
    methylType.addContent(this.getMethylType().toString());
    configurationFile.getRootElement().addContent(methylType);

    for (MethylationSample ms : this.getSamples()) {
        Element sample1 = new Element(SAMPLE1);
        sample1.addContent(ms.getSample1().getFile().getName());
        configurationFile.getRootElement().addContent(sample1);
    }//from  w w w.jav a 2 s .  c om

    for (MethylationSample ms : this.getSamples()) {
        if (ms.getSample2() != null) {
            Element sample2 = new Element(SAMPLE2);
            sample2.addContent(ms.getSample2().getFile().getName());
            configurationFile.getRootElement().addContent(sample2);
        }
    }

    if (!this.getSeedLength().equals(seedLength_DV)) {
        Element seedLength = new Element(SEED_LENGTH);
        seedLength.addContent(this.getSeedLength().toString());
        configurationFile.getRootElement().addContent(seedLength);
    }

    if (!this.getNumMis().equals(numMis_DV)) {
        Element numMiss = new Element(NUM_MIS);
        numMiss.addContent(this.getNumMis().toString());
        configurationFile.getRootElement().addContent(numMiss);
    }

    if (this.getIntervalsPath() != intervalsPath_DV) {
        Element intervalsPath = new Element(INTERVALS);
        intervalsPath.addContent(this.getIntervalsPath().getFile().getAbsolutePath());
        configurationFile.getRootElement().addContent(intervalsPath);
    }

    if (!this.getContextType().equals(contextType_DV)) {
        Element contextType = new Element(CONTEXT);
        contextType.addContent(this.getContextType().toString());
        configurationFile.getRootElement().addContent(contextType);
    }

    if (!this.getTrimTagLength().equals(trimTagLength_DV)) {
        Element trimTagLength = new Element(TRIMTAGLENGTH);
        trimTagLength.addContent(this.getTrimTagLength());
        configurationFile.getRootElement().addContent(trimTagLength);
    }

    if (!this.getMinQual().equals(minQual_DV)) {
        Element minQual = new Element(MINQUAL);
        minQual.addContent(this.getMinQual().toString());
        configurationFile.getRootElement().addContent(minQual);
    }

    if (!this.getFastqc().equals(fastqc_DV)) {
        Element fastqc = new Element(FASTQC);
        fastqc.addContent(this.getFastqc().toString());
        configurationFile.getRootElement().addContent(fastqc);
    }

    if (!this.getDepthFilter().equals(depthFilter_DV)) {
        Element depthFilter = new Element(DEPTHFILTER);
        depthFilter.addContent(this.getDepthFilter().toString());
        configurationFile.getRootElement().addContent(depthFilter);
    }

    if (!this.getQueueSGEProject().equals(queueSGEProject_DV)) {
        Element queueProject = new Element(QUEUESGEPROJECT);
        queueProject.addContent(this.getQueueSGEProject().toString());
        configurationFile.getRootElement().addContent(queueProject);
    }

    if (!this.getMultiExec().equals(multiExec_DV)) {
        Element multiExec = new Element(MULTIEXEC);
        multiExec.addContent(this.getMultiExec().toString());
        configurationFile.getRootElement().addContent(multiExec);
    }

    XMLOutputter xmlOutput = new XMLOutputter();
    xmlOutput.setFormat(Format.getPrettyFormat());
    xmlOutput.output(configurationFile, new FileWriter(output));
}

From source file:es.uvigo.ei.sing.rubioseq.gui.view.models.experiments.SingleNucleotideVariantExperiment.java

License:Open Source License

public void generateXMLConfigurationFile(File output) throws IOException {
    Document configurationFile = new Document();
    Element configData = new Element(CONFIG_DATA);
    configurationFile.setRootElement(configData);
    configData.setAttribute(ExperimentUtils.BRANCH, ExperimentUtils.BRANCH_SNV);

    Element genRef = new Element(GENREF);
    genRef.addContent(this.getGenRefPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(genRef);

    Element dbSnpAnnot = new Element(DBSNPANNOT);
    dbSnpAnnot.addContent(this.getDbSnpAnnotPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(dbSnpAnnot);

    Element genomes1000Annot = new Element(GENOMES1000ANNOT);
    genomes1000Annot.addContent(this.getGenomes1000AnnotPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(genomes1000Annot);

    Element indelAnnot = new Element(INDELANNOT);
    indelAnnot.addContent(this.getIndelAnnotPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(indelAnnot);

    if (this.getIntervalsPath() != getIntervalsPath_DV()) {
        Element intervals = new Element(INTERVALS);
        intervals.addContent(this.getIntervalsPath().getFile().getAbsolutePath());
        configurationFile.getRootElement().addContent(intervals);
    }//  w  ww.  j a  v a  2 s . com

    if (this.getKnownIndels().size() > 0) {
        for (KnownIndels kI : this.getKnownIndels()) {
            Element knownIndels = new Element(KNOWNINDELS);
            knownIndels.addContent(kI.getFile().getFile().getAbsolutePath());
            configurationFile.getRootElement().addContent(knownIndels);
        }
    }

    Element plattform = new Element(PLATTFORM);
    plattform.addContent(this.getPlattform().getDisplayName());
    configurationFile.getRootElement().addContent(plattform);

    if (!this.getCheckCasava().equals(checkCasava_DV)) {
        Element checkCasava = new Element(CHECKCASAVA);
        checkCasava.addContent(this.getCheckCasava().toString());
        configurationFile.getRootElement().addContent(checkCasava);
    }

    Element dirOutBase = new Element(DIROUTBASE);
    dirOutBase.addContent(this.getDirOutBase().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(dirOutBase);

    Element projectId = new Element(PROJECTID);
    projectId.addContent(this.getProjectId());
    configurationFile.getRootElement().addContent(projectId);

    if (!this.getUserName().equals(userName_DV)) {
        Element userName = new Element(USERNAME);
        userName.addContent(this.getUserName());
        configurationFile.getRootElement().addContent(userName);
    }

    Element dataInDirpreProcess = new Element(INDIRPREPROCESS);
    dataInDirpreProcess.addContent(this.getDataInDirpreProcess().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(dataInDirpreProcess);

    for (Sample s : this.getSamples()) {
        Element sample = new Element(SAMPLE);

        Element sampleName = new Element(SAMPLE_NAME);
        sampleName.addContent(s.getSampleName());
        sample.addContent(sampleName);

        Element sampleFiles = new Element(SAMPLE_FILES);
        sampleFiles.addContent(s.getSampleFiles());
        sample.addContent(sampleFiles);

        Element sampleSuffix = new Element(SAMPLE_SUFFIX);
        sampleSuffix.addContent(s.getSampleSuffix());
        sample.addContent(sampleSuffix);

        Element sampleType = new Element(SAMPLE_TYPE);
        sampleType.addContent(s.getSampleType().getDisplayName());
        sample.addContent(sampleType);

        configurationFile.getRootElement().addContent(sample);
    }

    if (!this.getCallingType().equals(callingType_DV)) {
        Element callingType = new Element(CALLYING_TYPE);
        callingType.addContent(this.getCallingType().toString());
        configurationFile.getRootElement().addContent(callingType);
    }

    if (!this.getgATKoutputMode().equals(gATKoutputMode_DV)) {
        Element gATKoutputModeoutputMode = new Element(GATKOUTPUTMODE);
        gATKoutputModeoutputMode.addContent(this.getgATKoutputMode().toString());
        configurationFile.getRootElement().addContent(gATKoutputModeoutputMode);
    }

    if (!this.getRsFilter().equals(rsFilter_DV)) {
        Element rsFilter = new Element(RSFILTER);
        rsFilter.addContent(this.getRsFilter().toString());
        configurationFile.getRootElement().addContent(rsFilter);
    }

    if (!this.getrUbioSeqMode().equals(rUbioSeqMode_DV)) {
        Element rUbioSeq_Mode = new Element(RUBIOSEQMODE);
        rUbioSeq_Mode.addContent(this.getrUbioSeqMode().toString());
        configurationFile.getRootElement().addContent(rUbioSeq_Mode);
    }

    if (!this.getFastqc().equals(fastqc_DV)) {
        Element fastqc = new Element(FASTQC);
        fastqc.addContent(this.getFastqc().toString());
        configurationFile.getRootElement().addContent(fastqc);
    }

    if (!this.getvEPFlag().equals(vEPFlag_DV)) {
        Element vEPFlag = new Element(VEPFLAG);
        vEPFlag.addContent(this.getvEPFlag().toString());
        configurationFile.getRootElement().addContent(vEPFlag);
    }

    if (!this.gettCFlag().equals(tCFlag_DV)) {
        Element tCFlag = new Element(TCFLAG);
        tCFlag.addContent(this.gettCFlag().toString());
        configurationFile.getRootElement().addContent(tCFlag);
    }

    if (!this.getmDFlag().equals(mDFlag_DV)) {
        Element mDFlag = new Element(MDFLAG);
        mDFlag.addContent(this.getmDFlag().toString());
        configurationFile.getRootElement().addContent(mDFlag);
    }

    if (!this.getStandCallConf().equals(standCallConf_DV)) {
        Element standCallConf = new Element(STANDCALLCONF);
        standCallConf.addContent(this.getStandCallConf().toString());
        configurationFile.getRootElement().addContent(standCallConf);
    }

    if (!this.getStandEmitConf().equals(standEmitConf_DV)) {
        Element standEmitConf = new Element(STANDEMITCONF);
        standEmitConf.addContent(this.getStandEmitConf().toString());
        configurationFile.getRootElement().addContent(standEmitConf);
    }

    if (!this.getQueueSGEProject().equals(queueSGEProject_DV)) {
        Element queueSGEProject = new Element(QUEUESGEPROJECT);
        queueSGEProject.addContent(this.getQueueSGEProject().toString());
        configurationFile.getRootElement().addContent(queueSGEProject);
    }

    if (this.getChoiceVqrsHardFilters().equals(VQRSHardFiltersChoice.VQRS)
            && this.getvQSRblockMills() != VQSRblockMills_DV && this.getvQSRblockHapMAp() != VQSRblockHapMAp_DV
            && this.getvQSRblockThousandG() != VQSRblockThousandG_DV) {

        Element vQSR_block = new Element(VQSRBLOCK);

        Element mills = new Element(MILLS);
        mills.addContent(this.getvQSRblockMills().getFile().getAbsolutePath());
        vQSR_block.addContent(mills);

        Element hapmap = new Element(HAPMAP);
        hapmap.addContent(this.getvQSRblockHapMAp().getFile().getAbsolutePath());
        vQSR_block.addContent(hapmap);

        Element thousandg = new Element(THOUSANDG);
        thousandg.addContent(this.getvQSRblockThousandG().getFile().getAbsolutePath());
        vQSR_block.addContent(thousandg);

        configurationFile.getRootElement().addContent(vQSR_block);
    }

    if (this.getChoiceVqrsHardFilters().equals(VQRSHardFiltersChoice.HARDFILTERS)
            && (!this.getminQual().equals(minQual_DV) || !this.getdPmin().equals(DPmin_DV)
                    || this.getHardFilters().size() > 0)) {

        Element hardFiltersBlock = new Element(HFILTERS);

        if (!this.getdPmin().equals(DPmin_DV)) {
            Element dpMin = new Element(DPMIN);
            dpMin.addContent(this.getdPmin().toString());
            hardFiltersBlock.addContent(dpMin);
        }

        if (!this.getminQual().equals(minQual_DV)) {
            Element minQual = new Element(MINQUAL);
            minQual.addContent(this.getminQual().toString());
            hardFiltersBlock.addContent(minQual);
        }

        for (HardFilter hF : this.getHardFilters()) {
            Element name = hF.getType().equals(HardFilter.HFilterType.SNP) ? new Element(HFILTER_NAME_SNP)
                    : new Element(HFILTER_NAME_INDEL);
            name.addContent(hF.getName());
            Element rule = hF.getType().equals(HardFilter.HFilterType.SNP) ? new Element(HFILTER_RULE_SNP)
                    : new Element(HFILTER_RULE_INDEL);
            rule.addContent(hF.getRule());
            hardFiltersBlock.addContent(name);
            hardFiltersBlock.addContent(rule);
        }

        configurationFile.getRootElement().addContent(hardFiltersBlock);
    }

    XMLOutputter xmlOutput = new XMLOutputter();
    xmlOutput.setFormat(Format.getPrettyFormat());
    xmlOutput.output(configurationFile, new FileWriter(output));
}

From source file:eu.himeros.cophi.ocr.proofreader.controller.pojo.HocrDocumentBufferedWriter.java

License:Open Source License

/**
 * Saves the hocrDocument/* w w w  .java  2  s . c om*/
 * @param hocrDocument the hocr document.
 * @param bw the buffered writer.
 */
@Override
public void save(Document hocrDocument, BufferedWriter bw) {
    try {
        XMLOutputter xop = new XMLOutputter(Format.getPrettyFormat().setLineSeparator("\n"));
        xop.output(hocrDocument, bw);
    } catch (Exception ex) {
        ex.printStackTrace(System.err);
    }
}