Example usage for org.jdom2 Document getRootElement

List of usage examples for org.jdom2 Document getRootElement

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Introduction

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

Prototype

public Element getRootElement()

Source Link

Document

This will return the root Element for this Document

Usage

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 v  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));
    //      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 loadDataFromFile(File editFile) {

    loadDefaultParameters(editFile);/*w  ww . j a  v a2  s.  com*/

    SAXBuilder saxBuilder = new SAXBuilder();
    try {
        Document document = saxBuilder.build(editFile);
        Element configData = document.getRootElement();

        Element bwaPath = configData.getChild(BWA_PATH);
        if (validElement(bwaPath)) {
            this.setBwaPath(Utils.getRUbioSeqFile(bwaPath.getValue()));
        }

        Element samtoolsPath = configData.getChild(SAMTOOLS_PATH);
        if (validElement(samtoolsPath)) {
            this.setSamtoolsPath(Utils.getRUbioSeqFile(samtoolsPath.getValue()));
        }

        Element gatkpath = configData.getChild(GATK_PATH);
        if (validElement(gatkpath)) {
            this.setGatkpath(Utils.getRUbioSeqFile(gatkpath.getValue()));
        }

        Element picardPath = configData.getChild(PICARD_PATH);
        if (validElement(picardPath)) {
            this.setPicardPath(Utils.getRUbioSeqFile(picardPath.getValue()));
        }

        Element BFASTPath = configData.getChild(BFAST_PATH);
        if (validElement(BFASTPath)) {
            this.setBfastPath(Utils.getRUbioSeqFile(BFASTPath.getValue()));
        }

        Element fastqcPath = configData.getChild(FASTQC_PATH);
        if (validElement(fastqcPath)) {
            this.setFastqcPath(Utils.getRUbioSeqFile(fastqcPath.getValue()));
        }

        Element BEDToolsPath = configData.getChild(BED_TOOLS_PATH);
        if (validElement(BEDToolsPath)) {
            this.setBedtoolsPath(Utils.getRUbioSeqFile(BEDToolsPath.getValue()));
        }

        Element CONTRAPath = configData.getChild(CONTRA_PATH);
        if (validElement(CONTRAPath)) {
            this.setContraPath(Utils.getRUbioSeqFile(CONTRAPath.getValue()));
        }

        Element nthr = configData.getChild(NTHR);
        if (validElement(nthr)) {
            try {
                this.setNthr(Integer.valueOf(nthr.getValue()));
            } catch (Exception e) {
            }
        }

        Element javaRam = configData.getChild(JAVA_RAM);
        if (validElement(javaRam)) {
            this.setJavaRam(javaRam.getValue());
        }

        Element queueSystem = configData.getChild(QUEUE_SYSTEM);
        if (validElement(queueSystem)) {
            String queueSystemValue = queueSystem.getValue().toUpperCase();
            if (queueSystemValue.equals("SGE")) {
                this.setQueueSystem(QueueSystem.SGE);
            } else if (queueSystemValue.equals("PBS")) {
                this.setQueueSystem(QueueSystem.PBS);
            } else if (queueSystemValue.equals("NONE")) {
                this.setQueueSystem(QueueSystem.NONE);
            }
        }

        Element queueName = configData.getChild(QUEUE_NAME);
        if (validElement(queueName)) {
            this.setQueueName(queueName.getValue());
        }

        Element multicoreName = configData.getChild(MULTICORE_NAME);
        if (validElement(multicoreName)) {
            this.setMulticoreName(multicoreName.getValue());
        }

        Element multicoreNumber = configData.getChild(MULTICORE_NUMBER);
        if (validElement(multicoreNumber)) {
            try {
                this.setMulticoreNumber(Integer.valueOf(multicoreNumber.getValue()));
            } catch (Exception e) {
            }
        }

    } catch (JDOMException e) {
        e.printStackTrace();
    } catch (IOException e) {
        e.printStackTrace();
    }
}

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);
    }//ww w . j  ava2s.  com

    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 loadDataFromFile(File editFile) {

    loadDefaultParameters(editFile);// ww w.ja va  2 s.  c  o  m

    SAXBuilder saxBuilder = new SAXBuilder();
    try {
        Document document = saxBuilder.build(editFile);
        Element configData = document.getRootElement();

        Element bismarkPath = configData.getChild(BISMARK_PATH);
        if (validElement(bismarkPath)) {
            this.setBismarkPath(Utils.getRUbioSeqFile(bismarkPath.getValue()));
        }

        Element bowtiePath = configData.getChild(BOWTIE_PATH);
        if (validElement(bowtiePath)) {
            this.setBowtiePath(Utils.getRUbioSeqFile(bowtiePath.getValue()));
        }

        Element picardPath = configData.getChild(PICARD_PATH);
        if (validElement(picardPath)) {
            this.setPicardPath(Utils.getRUbioSeqFile(picardPath.getValue()));
        }

        Element fastqcPath = configData.getChild(FASTQC_PATH);
        if (validElement(fastqcPath)) {
            this.setFastqcPath(Utils.getRUbioSeqFile(fastqcPath.getValue()));
        }

        Element BEDToolsPath = configData.getChild(BED_TOOLS_PATH);
        if (validElement(BEDToolsPath)) {
            this.setBedtoolsPath(Utils.getRUbioSeqFile(BEDToolsPath.getValue()));
        }

        Element fastxPath = configData.getChild(FASTX_PATH);
        if (validElement(fastxPath)) {
            this.setFastxPath(Utils.getRUbioSeqFile(fastxPath.getValue()));
        }

        Element filoPath = configData.getChild(FILO_PATH);
        if (validElement(filoPath)) {
            this.setFiloPath(Utils.getRUbioSeqFile(filoPath.getValue()));
        }

        Element nthr = configData.getChild(NTHR);
        if (validElement(nthr)) {
            try {
                this.setNthr(Integer.valueOf(nthr.getValue()));
            } catch (Exception e) {
            }
        }

        Element javaRam = configData.getChild(JAVA_RAM);
        if (validElement(javaRam)) {
            this.setJavaRam(javaRam.getValue());
        }

        Element queueSystem = configData.getChild(QUEUE_SYSTEM);
        if (validElement(queueSystem)) {
            String queueSystemValue = queueSystem.getValue().toUpperCase();
            if (queueSystemValue.equals("SGE")) {
                this.setQueueSystem(QueueSystem.SGE);
            } else if (queueSystemValue.equals("PBS")) {
                this.setQueueSystem(QueueSystem.PBS);
            } else if (queueSystemValue.equals("NONE")) {
                this.setQueueSystem(QueueSystem.NONE);
            }
        }

        Element queueName = configData.getChild(QUEUE_NAME);
        if (validElement(queueName)) {
            this.setQueueName(queueName.getValue());
        }

        Element multicoreName = configData.getChild(MULTICORE_NAME);
        if (validElement(multicoreName)) {
            this.setMulticoreName(multicoreName.getValue());
        }

        Element multicoreNumber = configData.getChild(MULTICORE_NUMBER);
        if (validElement(multicoreNumber)) {
            try {
                this.setMulticoreNumber(Integer.valueOf(multicoreNumber.getValue()));
            } catch (Exception e) {
            }
        }

    } catch (JDOMException e) {
        e.printStackTrace();
    } catch (IOException e) {
        e.printStackTrace();
    }
}

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 w  w.j a va2  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.ConfigProgramPathsSNV.java

License:Open Source License

public void loadDataFromFile(File editFile) {

    loadDefaultParameters(editFile);/*from w  w  w  .ja va  2 s  . c  o m*/

    SAXBuilder saxBuilder = new SAXBuilder();
    try {
        Document document = saxBuilder.build(editFile);
        Element configData = document.getRootElement();

        Element bwaPath = configData.getChild(BWA_PATH);
        if (validElement(bwaPath)) {
            this.setBwaPath(Utils.getRUbioSeqFile(bwaPath.getValue()));
        }

        Element samtoolsPath = configData.getChild(SAMTOOLS_PATH);
        if (validElement(samtoolsPath)) {
            this.setSamtoolsPath(Utils.getRUbioSeqFile(samtoolsPath.getValue()));
        }

        Element gatkpath = configData.getChild(GATK_PATH);
        if (validElement(gatkpath)) {
            this.setGatkpath(Utils.getRUbioSeqFile(gatkpath.getValue()));
        }

        Element picardPath = configData.getChild(PICARD_PATH);
        if (validElement(picardPath)) {
            this.setPicardPath(Utils.getRUbioSeqFile(picardPath.getValue()));
        }

        Element BFASTPath = configData.getChild(BFAST_PATH);
        if (validElement(BFASTPath)) {
            this.setBfastPath(Utils.getRUbioSeqFile(BFASTPath.getValue()));
        }

        Element fastqcPath = configData.getChild(FASTQC_PATH);
        if (validElement(fastqcPath)) {
            this.setFastqcPath(Utils.getRUbioSeqFile(fastqcPath.getValue()));
        }

        Element nthr = configData.getChild(NTHR);
        if (validElement(nthr)) {
            try {
                this.setNthr(Integer.valueOf(nthr.getValue()));
            } catch (Exception e) {
            }
        }

        Element javaRam = configData.getChild(JAVA_RAM);
        if (validElement(javaRam)) {
            this.setJavaRam(javaRam.getValue());
        }

        Element queueSystem = configData.getChild(QUEUE_SYSTEM);
        if (validElement(queueSystem)) {
            String queueSystemValue = queueSystem.getValue().toUpperCase();
            if (queueSystemValue.equals("SGE")) {
                this.setQueueSystem(QueueSystem.SGE);
            } else if (queueSystemValue.equals("PBS")) {
                this.setQueueSystem(QueueSystem.PBS);
            } else if (queueSystemValue.equals("NONE")) {
                this.setQueueSystem(QueueSystem.NONE);
            }
        }

        Element queueName = configData.getChild(QUEUE_NAME);
        if (validElement(queueName)) {
            this.setQueueName(queueName.getValue());
        }

        Element multicoreName = configData.getChild(MULTICORE_NAME);
        if (validElement(multicoreName)) {
            this.setMulticoreName(multicoreName.getValue());
        }

        Element multicoreNumber = configData.getChild(MULTICORE_NUMBER);
        if (validElement(multicoreNumber)) {
            try {
                this.setMulticoreNumber(Integer.valueOf(multicoreNumber.getValue()));
            } catch (Exception e) {
            }
        }

    } catch (JDOMException e) {
        e.printStackTrace();
    } catch (IOException e) {
        e.printStackTrace();
    }
}

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);
    }/*  w  ww  .ja  va  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);
    }/*from  w  ww  . jav  a 2s.co  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.ChipSeqExperiment.java

License:Open Source License

public static String getWorkingDirectory(File inputFile) {
    SAXBuilder saxBuilder = new SAXBuilder();
    try {//from w ww .  jav a2s .  co  m
        Document document = saxBuilder.build(inputFile);
        Element configData = document.getRootElement();

        Element dirOutBase = configData.getChild(DIROUTBASE);
        Element projectId = configData.getChild(PROJECTID);
        if (dirOutBase.getValue().endsWith("/")) {
            return dirOutBase.getValue() + projectId.getValue();
        } else {
            return dirOutBase.getValue() + "/" + projectId.getValue();
        }

    } catch (JDOMException e) {
        e.printStackTrace();
    } catch (IOException e) {
        e.printStackTrace();
    }
    return "";
}

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

License:Open Source License

public void loadDataFromFile(File editFile) throws InvalidRubioSeqParameterException {
    SAXBuilder saxBuilder = new SAXBuilder();
    try {/*from ww  w.  j  a  v a  2s. c  o  m*/
        Document document = saxBuilder.build(editFile);
        Element configData = document.getRootElement();

        Element genRef = configData.getChild(GENREF);
        if (validElement(genRef)) {
            this.setGenRefPath(Utils.getRUbioSeqFile(genRef.getValue()));
        }

        Element plattform = configData.getChild(PLATTFORM);
        if (validElement(plattform)) {
            String plattformValue = plattform.getValue().toLowerCase();
            if (plattformValue.equals("illumina")) {
                this.setPlattform(PlattformTech.ILLUMINA);
            } else if (plattformValue.equals("ion")) {
                this.setPlattform(PlattformTech.ION);
            } else if (plattformValue.equals("solid")) {
                this.setPlattform(PlattformTech.SOLID);
            }
        }

        Element checkCasava = configData.getChild(CHECKCASAVA);
        if (validElement(checkCasava)) {
            this.setCheckCasava(Integer.valueOf(checkCasava.getValue()));
        }

        Element dirOutBase = configData.getChild(DIROUTBASE);
        if (validElement(dirOutBase)) {
            this.setDirOutBase(Utils.getRUbioSeqFile(dirOutBase.getValue()));
        }

        Element projectId = configData.getChild(PROJECTID);
        if (validElement(projectId)) {
            this.setProjectId(projectId.getValue());
        }

        Element userName = configData.getChild(USERNAME);
        if (validElement(userName)) {
            this.setUserName(userName.getValue());
        }

        Element dataInDirpreProcess = configData.getChild(INDIRPREPROCESS);
        if (validElement(dataInDirpreProcess)) {
            this.setDataInDirpreProcess(Utils.getRUbioSeqFile(dataInDirpreProcess.getValue()));
        }

        for (Element experimentElement : configData.getChildren(EXPERIMENT)) {
            CSExperiment newExperiment = new CSExperiment();

            for (Element csUnitElement : experimentElement.getChildren(CHIPSEQUNIT)) {
                ChipSeqUnit newCSUnit = new ChipSeqUnit();

                Sample sampleTreatment = new Sample();
                newCSUnit.setSampleTreatment(sampleTreatment);

                Element sampleTreatmentElement = csUnitElement.getChild(SAMPLE_TREATMENT);
                Element sampleName = sampleTreatmentElement.getChild(SAMPLE_NAME);
                sampleTreatment.setSampleName(sampleName.getValue());
                Element sampleFiles = sampleTreatmentElement.getChild(SAMPLE_FILES);
                sampleTreatment.setSampleFiles(sampleFiles.getValue());
                Element sampleSuffix = sampleTreatmentElement.getChild(SAMPLE_SUFFIX);
                sampleTreatment.setSampleSuffix(sampleSuffix.getValue());
                Element sampleType = sampleTreatmentElement.getChild(SAMPLE_TYPE);
                sampleTreatment.setSampleType(
                        sampleType.getValue().equals("1") ? SampleType.SingleEnd : SampleType.PairedEnd);

                Element sampleInputElement = csUnitElement.getChild(SAMPLE_INPUT);
                if (sampleInputElement != null) {
                    Sample sampleInput = new Sample();
                    newCSUnit.setSampleInput(sampleInput);

                    Element sampleInputName = sampleInputElement.getChild(SAMPLE_NAME);
                    sampleInput.setSampleName(sampleInputName.getValue());
                    Element sampleInputFiles = sampleInputElement.getChild(SAMPLE_FILES);
                    sampleInput.setSampleFiles(sampleInputFiles.getValue());
                    Element sampleInputSuffix = sampleInputElement.getChild(SAMPLE_SUFFIX);
                    sampleInput.setSampleSuffix(sampleInputSuffix.getValue());
                    Element sampleInputType = sampleInputElement.getChild(SAMPLE_TYPE);
                    sampleInput.setSampleType(sampleInputType.getValue().equals("1") ? SampleType.SingleEnd
                            : SampleType.PairedEnd);
                }

                newExperiment.getChipSeqUnits().add(newCSUnit);
            }

            Element replicatesFlag = experimentElement.getChild(REPLICATES_FLAG);
            newExperiment.setReplicatesFlag(replicatesFlag.getValue().equals("1") ? true : false);

            this.getExperiments().add(newExperiment);
        }

        Element chromSize = configData.getChild(CHROMSIZE);
        if (validElement(chromSize)) {
            this.setChromSize(Utils.getRUbioSeqFile(chromSize.getValue()));
        }

        Element peakAnalysis = configData.getChild(PEAKANALYSIS);
        if (validElement(peakAnalysis)) {
            String peakAnalysisValue = peakAnalysis.getValue().toLowerCase();
            if (peakAnalysisValue.equals("sharp")) {
                this.setPeakAnalysisType(PeakAnalysisType.SHARP);
            } else if (peakAnalysisValue.equals("broad")) {
                this.setPeakAnalysisType(PeakAnalysisType.BROAD);
            } else if (peakAnalysisValue.equals("both")) {
                this.setPeakAnalysisType(PeakAnalysisType.BOTH);
            }
        }

        Element ccaConfigFile = configData.getChild(CCAT_CONFIG_FILE);
        if (validElement(ccaConfigFile)) {
            this.setCcatConfigFile(Utils.getRUbioSeqFile(ccaConfigFile.getValue()));
        }

        Element macsExtraArgs = configData.getChild(MACS_EXTRAARGS);
        if (validElement(macsExtraArgs)) {
            this.setMacsExtraArgs(macsExtraArgs.getValue());
        }

        Element fastqc = configData.getChild(FASTQC);
        if (validElement(fastqc)) {
            this.setFastqc(Integer.valueOf(fastqc.getValue()));
        }

        Element annotFile = configData.getChild(ANNOTFILE);
        if (validElement(annotFile)) {
            this.setAnnotFile(Utils.getRUbioSeqFile(annotFile.getValue()));
        }

        Element queueSGEProject = configData.getChild(QUEUESGEPROJECT);
        if (validElement(queueSGEProject)) {
            this.setQueueSGEProject(queueSGEProject.getValue());
        }

    } catch (JDOMException e) {
        e.printStackTrace();
    } catch (IOException e) {
        e.printStackTrace();
    } catch (Exception e) {
        throw new InvalidRubioSeqParameterException(InvalidRubioSeqParameterException.DEFAULT_MESSAGE);
    }
}