Example usage for org.jdom2 Document Document

List of usage examples for org.jdom2 Document Document

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Introduction

In this page you can find the example usage for org.jdom2 Document Document.

Prototype

public Document()

Source Link

Document

Creates a new empty document.

Usage

From source file:delfos.io.xml.casestudy.CaseStudyXML.java

License:Open Source License

private static void caseStudyToXMLFile_onlyAggregate(CaseStudy caseStudy, String descriptivePrefix, File file) {
    if (!caseStudy.isFinished()) {
        throw new UnsupportedOperationException("No se ha ejecutado el caso de uso todava");
    }/*from  w ww .jav  a  2s .  co  m*/

    Document doc = new Document();
    Element casoDeUso = new Element("Case");

    casoDeUso.setAttribute("seed", Long.toString(caseStudy.getSeedValue()));
    casoDeUso.setAttribute("numExec", Integer.toString(caseStudy.getNumExecutions()));

    casoDeUso.addContent(RecommenderSystemXML.getElement(caseStudy.getRecommenderSystem()));
    casoDeUso.addContent(ValidationTechniqueXML.getElement(caseStudy.getValidationTechnique()));

    casoDeUso.addContent(PredictionProtocolXML.getElement(caseStudy.getPredictionProtocol()));

    casoDeUso.addContent(RelevanceCriteriaXML.getElement(caseStudy.getRelevanceCriteria()));
    casoDeUso.addContent(DatasetLoaderXML.getElement(caseStudy.getDatasetLoader()));

    //casoDeUso.addContent(getResultsElement(caseStudy));
    casoDeUso.addContent(getAggregatedResultsElement(caseStudy));

    doc.addContent(casoDeUso);

    XMLOutputter outputter = new XMLOutputter(Constants.getXMLFormat());
    try (FileWriter fileWriter = new FileWriter(file)) {
        outputter.output(doc, fileWriter);
    } catch (IOException ex) {
        ERROR_CODES.CANNOT_WRITE_RESULTS_FILE.exit(ex);
    }
}

From source file:devicerestmodel.services.ResourceBase.java

private void addGetResourceXML(final String path, final DevicePropertyNode element) {

    final Resource.Builder resourceBuilder = Resource.builder();
    resourceBuilder.path(path);/*from w  w  w. j a va  2s .com*/

    final ResourceMethod.Builder methodBuilder = resourceBuilder.addMethod("GET");
    methodBuilder.produces(MediaType.APPLICATION_XML)
            .handledBy(new Inflector<ContainerRequestContext, Response>() {

                @Override
                public Response apply(ContainerRequestContext containerRequestContext) {
                    try {
                        if (containerRequestContext.getMethod().equals("GET")) {
                            System.out.println("Got a GET for " + path);
                            LoggerOut.println("Get a GET for " + path);
                            Document myDocument = new Document();
                            myDocument.setRootElement(element.getXml(containerRequestContext));
                            return Response.ok().type(MediaType.APPLICATION_XML)
                                    .entity(MdUtil.document2XmlString(myDocument)).build();
                        } else {
                            return Response.status(Response.Status.NOT_FOUND).build();
                        }
                    } catch (Exception ex) {
                        return Response.status(Response.Status.INTERNAL_SERVER_ERROR).build();
                    }

                }
            });

    final Resource resource = resourceBuilder.build();
    registerResources(resource);
}

From source file:edu.ucla.loni.server.ServerUtils.java

License:Open Source License

/**
 * Writes the access file for the root directory
 * Side Effect: Updates accessFileModified in the database
 *//*w w  w.  j av  a 2s .co  m*/
public static void writeAccessFile(Directory root) throws Exception {
    File accessFile = getAccessFile(root);
    if (!accessFile.exists()) {
        boolean success = accessFile.createNewFile();
        if (!success) {
            throw new Exception("Could not create access file");
        }
    }

    // <files>
    Element filesRoot = new Element("files");

    // For each pipe, add a <file> child to <files>
    Pipefile[] pipes = Database.selectPipefiles(root.dirId);

    if (pipes != null) {
        for (Pipefile p : pipes) {
            // Only add the pipefile if access is not empty
            if (!p.access.equals("")) {
                Element file = new Element("file");
                file.setAttribute("type", p.type);
                file.setAttribute("name", p.name);
                file.setAttribute("package", p.packageName);

                // Add agents
                String[] agents = p.access.split(",");
                for (String agent : agents) {
                    if (!agent.equals("")) {
                        file.addContent(agentElement(agent));
                    }
                }

                filesRoot.addContent(file);
            }
        }
    }

    // <groups>
    Element groupsRoot = new Element("groups");

    // For each group, add a <group> child to <groups>
    Group[] groups = Database.selectGroups(root.dirId);

    if (groups != null) {
        for (Group g : groups) {
            Element group = new Element("group");
            group.setAttribute("name", g.name);

            // Add agents
            String[] agents = g.users.split(",");
            for (String agent : agents) {
                if (!agent.equals("")) {
                    group.addContent(agentElement(agent));
                }
            }

            groupsRoot.addContent(group);
        }
    }

    // Root Element
    Element access = new Element("access");
    access.addContent(filesRoot);
    access.addContent(groupsRoot);

    // Document
    Document doc = new Document();
    doc.addContent(access);

    // Write document
    writeXML(accessFile, doc);

    // Update when the access file was written
    root.accessModified = new Timestamp(accessFile.lastModified());
    Database.updateDirectory(root);
}

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);
    }//from w ww  .  ja 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));
    //      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);
    }//  w  w  w.  j ava  2 s  .  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));
}

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  . java  2 s  .  co  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.jav a 2s . 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  av a  2  s  . 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  ww  .j a va  2  s.c om*/
    }

    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   ww  w  .ja v a 2  s . co m

    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));
}