Example usage for org.jdom2.input SAXBuilder build

List of usage examples for org.jdom2.input SAXBuilder build

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Introduction

In this page you can find the example usage for org.jdom2.input SAXBuilder build.

Prototype

@Override
public Document build(final String systemId) throws JDOMException, IOException

Source Link

Document

This builds a document from the supplied URI.

Usage

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);//from   w  w w . ja v a2s . 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.ConfigProgramPathsSNV.java

License:Open Source License

public void loadDataFromFile(File editFile) {

    loadDefaultParameters(editFile);//from w w  w .  jav a2 s.  co 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.experiments.ChipSeqExperiment.java

License:Open Source License

public static String getWorkingDirectory(File inputFile) {
    SAXBuilder saxBuilder = new SAXBuilder();
    try {/* www  . j a va 2 s  .c  om*/
        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  w  ww  . j  a  v  a 2 s.  c om
        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);
    }
}

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

License:Open Source License

public void loadDataFromFile(File editFile) throws InvalidRubioSeqParameterException {
    SAXBuilder saxBuilder = new SAXBuilder();
    try {//  w ww  .  j av 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 dbSnpAnnot = configData.getChild(DBSNPANNOT);
        if (validElement(dbSnpAnnot)) {
            this.setDbSnpAnnotPath(Utils.getRUbioSeqFile(dbSnpAnnot.getValue()));
        }

        Element indelAnnot = configData.getChild(INDELANNOT);
        if (validElement(indelAnnot)) {
            this.setIndelAnnotPath(Utils.getRUbioSeqFile(indelAnnot.getValue()));
        }

        Element intervals = configData.getChild(INTERVALS);
        if (validElement(intervals)) {
            this.setIntervalsPath(Utils.getRUbioSeqFile(intervals.getValue()));
        }

        for (Element knownIndels : configData.getChildren(KNOWNINDELS)) {
            if (validElement(knownIndels)) {
                KnownIndels kI = new KnownIndels();
                kI.setFile(Utils.getRUbioSeqFile(knownIndels.getValue()));
                this.knownIndels.add(kI);
            }
        }

        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 sampleElement : configData.getChildren(SAMPLE)) {
            Sample newSample = new Sample();

            Element sampleName = sampleElement.getChild(SAMPLE_NAME);
            if (validElement(sampleName)) {
                newSample.setSampleName(sampleName.getValue());
            }

            Element sampleFiles = sampleElement.getChild(SAMPLE_FILES);
            if (validElement(sampleFiles)) {
                newSample.setSampleFiles(sampleFiles.getValue());
            }

            Element sampleSuffix = sampleElement.getChild(SAMPLE_SUFFIX);
            if (validElement(sampleSuffix)) {
                newSample.setSampleSuffix(sampleSuffix.getValue());
            }

            Element sampleType = sampleElement.getChild(SAMPLE_TYPE);
            if (validElement(sampleType)) {
                newSample.setSampleType(
                        sampleType.getValue().equals("1") ? SampleType.SingleEnd : SampleType.PairedEnd);
            }

            this.getSamples().add(newSample);
        }

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

        Element extraContra = configData.getChild(EXTRACONTRA);
        if (validElement(extraContra)) {
            this.setExtraContra(extraContra.getValue());
        }

        Element baseline = configData.getChild(BASELINE);
        if (validElement(baseline)) {
            this.setBaseline(Utils.getRUbioSeqFile(baseline.getValue()));
        }

        Element mDFlag = configData.getChild(MDFLAG);
        if (validElement(mDFlag)) {
            this.setmDFlag(Integer.valueOf(mDFlag.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);
    }
}

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

License:Open Source License

public static ExperimentType getExperimentType(File inputFile) throws InvalidRubioSeqParameterException {
    if (inputFile.isDirectory() || !inputFile.canRead() || !inputFile.getName().endsWith(".xml")) {
        return null;
    }//from  w w w. jav a  2 s .  com
    SAXBuilder saxBuilder = new SAXBuilder();
    try {
        Document document = saxBuilder.build(inputFile);
        Element configData = document.getRootElement();
        String branch = configData.getAttributeValue(ExperimentUtils.BRANCH);
        if (branch == null) {
            throw new InvalidRubioSeqParameterException(ExperimentUtils.BRANCH_MISSING_MESSAGE);
        } else {
            if (branch.equals(BRANCH_METHYLATION)) {
                return ExperimentType.Methylation;
            } else if (branch.equals(BRANCH_SNV)) {
                return ExperimentType.SNV;
            } else if (branch.equals(BRANCH_CNV)) {
                return ExperimentType.CNV;
            } else if (branch.equals(BRANCH_CHIPSEQ)) {
                return ExperimentType.CHIPSeq;
            }
        }
    } catch (JDOMException e) {
        e.printStackTrace();
    } catch (IOException e) {
        e.printStackTrace();
    }
    return null;
}

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

License:Open Source License

public static String getWorkingDirectory(File inputFile) {
    SAXBuilder saxBuilder = new SAXBuilder();
    try {//from   w  w  w.ja v  a  2 s . com
        Document document = saxBuilder.build(inputFile);
        Element configData = document.getRootElement();

        Element projectCompletePath = configData.getChild(PROJECT_COMPLETE_PATH);

        return projectCompletePath.getValue();

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

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

License:Open Source License

public void loadDataFromFile(File editFile) throws InvalidRubioSeqParameterException {
    SAXBuilder saxBuilder = new SAXBuilder();
    try {// w ww.jav  a2 s  .  co m
        Document document = saxBuilder.build(editFile);
        Element configData = document.getRootElement();

        Element referencePath = configData.getChild(REFERENCEPATH);
        if (validElement(referencePath)) {
            this.setReferencePath(Utils.getRUbioSeqFile(referencePath.getValue()));
        }

        Element intervals = configData.getChild(INTERVALS);
        if (validElement(intervals)) {
            this.setIntervalsPath(Utils.getRUbioSeqFile(intervals.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("fastq")) {
                this.setPlattform(PlattformTech.FASTQ);
            }
        }

        Element projectCompletePath = configData.getChild(PROJECT_COMPLETE_PATH);
        if (validElement(projectCompletePath)) {
            this.setProjectCompletePath(Utils.getRUbioSeqFile(projectCompletePath.getValue(), false));
        }

        Element readsPath = configData.getChild(READSPATH);
        if (validElement(readsPath)) {
            this.setReadsPath(Utils.getRUbioSeqFile(readsPath.getValue()));
        }

        Iterator<Element> sample1It = configData.getChildren(SAMPLE1).iterator();
        Iterator<Element> sample2It = configData.getChildren(SAMPLE2).iterator();
        this.samples = new LinkedList<MethylationSample>();

        while (sample1It.hasNext()) {

            MethylationSample newMS = new MethylationSample();

            Element sample1 = sample1It.next();
            if (validElement(sample1)) {
                newMS.setSample1(Utils.getRUbioSeqFile(
                        Utils.getDirectoryNameWithFinalSlash(this.getReadsPath().getFile().getAbsolutePath())
                                + sample1.getValue()));
            }

            if (sample2It.hasNext()) {
                Element sample2 = sample2It.next();
                if (validElement(sample2)) {
                    newMS.setSample2(Utils.getRUbioSeqFile(Utils.getDirectoryNameWithFinalSlash(
                            this.getReadsPath().getFile().getAbsolutePath()) + sample2.getValue()));
                }
            }

            this.getSamples().add(newMS);
        }

        Element seedLength = configData.getChild(SEED_LENGTH);
        if (validElement(seedLength)) {
            this.setSeedLength(Integer.valueOf(seedLength.getValue()));
        }

        Element numMiss = configData.getChild(NUM_MIS);
        if (validElement(numMiss)) {
            this.setNumMis(Integer.valueOf(numMiss.getValue()));
        }

        Element minQual = configData.getChild(MINQUAL);
        if (validElement(minQual)) {
            this.setNumMis(Integer.valueOf(minQual.getValue()));
        }

        Element depthFilter = configData.getChild(DEPTHFILTER);
        if (validElement(depthFilter)) {
            this.setDepthFilter(Double.valueOf(depthFilter.getValue()));
        }

        Element methylType = configData.getChild(METHYLTYPE);
        if (validElement(methylType)) {
            String methylTypeValue = methylType.getValue().toUpperCase();
            if (methylTypeValue.equals("LISTER")) {
                this.setMethylType(MethylType.LISTER);
            } else if (methylTypeValue.equals("COKUS")) {
                this.setMethylType(MethylType.COKUS);
            }
        }

        Element contextType = configData.getChild(CONTEXT);
        if (validElement(contextType)) {
            String contextTypeValue = contextType.getValue();
            if (contextTypeValue.equals("ALL")) {
                this.setContextType(ContextType.ALL);
            } else if (contextTypeValue.equals("CpG")) {
                this.setContextType(ContextType.CPG);
            } else if (contextTypeValue.equals("CHG")) {
                this.setContextType(ContextType.CHG);
            } else if (contextTypeValue.equals("CHH")) {
                this.setContextType(ContextType.CHH);
            }
        }

        Element multiExec = configData.getChild(MULTIEXEC);
        if (validElement(multiExec)) {
            this.setMultiExec(Integer.valueOf(multiExec.getValue()));
        }

        Element trimTagLenght = configData.getChild(TRIMTAGLENGTH);
        if (validElement(trimTagLenght)) {
            this.setTrimTagLength(trimTagLenght.getValue());
        }

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

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

License:Open Source License

public void loadDataFromFile(File editFile) throws InvalidRubioSeqParameterException {
    SAXBuilder saxBuilder = new SAXBuilder();
    try {//from w  ww  . java 2 s . c om
        Document document = saxBuilder.build(editFile);
        Element configData = document.getRootElement();

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

        Element dbSnpAnnot = configData.getChild(DBSNPANNOT);
        if (validElement(dbSnpAnnot)) {
            this.setDbSnpAnnotPath(Utils.getRUbioSeqFile(dbSnpAnnot.getValue()));
        }

        Element genomes1000Annot = configData.getChild(GENOMES1000ANNOT);
        if (validElement(genomes1000Annot)) {
            this.setGenomes1000AnnotPath(Utils.getRUbioSeqFile(genomes1000Annot.getValue()));
        }

        Element indelAnnot = configData.getChild(INDELANNOT);
        if (validElement(indelAnnot)) {
            this.setIndelAnnotPath(Utils.getRUbioSeqFile(indelAnnot.getValue()));
        }

        Element intervals = configData.getChild(INTERVALS);
        if (validElement(intervals)) {
            this.setIntervalsPath(Utils.getRUbioSeqFile(intervals.getValue()));
        }

        for (Element knownIndels : configData.getChildren(KNOWNINDELS)) {
            if (validElement(knownIndels)) {
                KnownIndels kI = new KnownIndels();
                kI.setFile(Utils.getRUbioSeqFile(knownIndels.getValue()));
                this.knownIndels.add(kI);
            }
        }

        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 sampleElement : configData.getChildren(SAMPLE)) {
            Sample newSample = new Sample();

            Element sampleName = sampleElement.getChild(SAMPLE_NAME);
            if (validElement(sampleName)) {
                newSample.setSampleName(sampleName.getValue());
            }

            Element sampleFiles = sampleElement.getChild(SAMPLE_FILES);
            if (validElement(sampleFiles)) {
                newSample.setSampleFiles(sampleFiles.getValue());
            }

            Element sampleSuffix = sampleElement.getChild(SAMPLE_SUFFIX);
            if (validElement(sampleSuffix)) {
                newSample.setSampleSuffix(sampleSuffix.getValue());
            }

            Element sampleType = sampleElement.getChild(SAMPLE_TYPE);
            if (validElement(sampleType)) {
                newSample.setSampleType(
                        sampleType.getValue().equals("1") ? SampleType.SingleEnd : SampleType.PairedEnd);
            }

            this.getSamples().add(newSample);
        }

        Element callingType = configData.getChild(CALLYING_TYPE);
        if (validElement(callingType)) {
            String callingTypeValue = callingType.getValue().toUpperCase();
            if (callingTypeValue.equals("SNP")) {
                this.setCallingType(CallingType.SNP);
            } else if (callingTypeValue.equals("INDEL")) {
                this.setCallingType(CallingType.INDEL);
            } else if (callingTypeValue.equals("BOTH")) {
                this.setCallingType(CallingType.BOTH);
            }
        }

        Element gATKoutputModeoutputMode = configData.getChild(GATKOUTPUTMODE);
        if (validElement(gATKoutputModeoutputMode)) {
            String gatkOutputModeValue = gATKoutputModeoutputMode.getValue().toUpperCase();
            if (gatkOutputModeValue.equals("EMIT_VARIANTS_ONLY")) {
                this.setgATKoutputMode(GATKoutputMode.EMIT_VARIANTS_ONLY);
            } else if (gatkOutputModeValue.equals("EMIT_ALL_SITES")) {
                this.setgATKoutputMode(GATKoutputMode.EMIT_ALL_SITES);
            } else if (gatkOutputModeValue.equals("EMIT_ALL_CONFIDENT_SITES")) {
                this.setgATKoutputMode(GATKoutputMode.EMIT_ALL_CONFIDENT_SITES);
            }
        }

        Element rsFilter = configData.getChild(RSFILTER);
        if (validElement(rsFilter)) {
            this.setRsFilter(Integer.valueOf(rsFilter.getValue()));
        }

        Element rUbioSeq_Mode = configData.getChild(RUBIOSEQMODE);
        if (validElement(rUbioSeq_Mode)) {
            this.setrUbioSeqMode(Integer.valueOf(rUbioSeq_Mode.getValue()));
        }

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

        Element vEPFlag = configData.getChild(VEPFLAG);
        if (validElement(vEPFlag)) {
            this.setvEPFlag(Integer.valueOf(vEPFlag.getValue()));
        }

        Element tCFlag = configData.getChild(TCFLAG);
        if (validElement(tCFlag)) {
            this.settCFlag(Integer.valueOf(tCFlag.getValue()));
        }

        Element mDFlag = configData.getChild(MDFLAG);
        if (validElement(mDFlag)) {
            this.setmDFlag(Integer.valueOf(mDFlag.getValue()));
        }

        Element standCallConf = configData.getChild(STANDCALLCONF);
        if (validElement(standCallConf)) {
            this.setStandCallConf(Double.valueOf(standCallConf.getValue()));
        }

        Element standEmitConf = configData.getChild(STANDEMITCONF);
        if (validElement(standEmitConf)) {
            this.setStandEmitConf(Double.valueOf(standEmitConf.getValue()));
        }

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

        Element vqsrBlock = configData.getChild(VQSRBLOCK);
        if (vqsrBlock != null) {

            this.setChoiceVqrsHardFilters(VQRSHardFiltersChoice.VQRS);

            Element mills = vqsrBlock.getChild(MILLS);
            if (validElement(mills)) {
                this.setvQSRblockMills(Utils.getRUbioSeqFile(mills.getValue()));
            }

            Element hapmap = vqsrBlock.getChild(HAPMAP);
            if (validElement(hapmap)) {
                this.setvQSRblockHapMAp(Utils.getRUbioSeqFile(hapmap.getValue()));
            }

            Element thousandg = vqsrBlock.getChild(THOUSANDG);
            if (validElement(thousandg)) {
                this.setvQSRblockThousandG(Utils.getRUbioSeqFile(thousandg.getValue()));
            }

        }

        Element hardFiltersBlock = configData.getChild(HFILTERS);
        if (hardFiltersBlock != null) {

            this.setChoiceVqrsHardFilters(VQRSHardFiltersChoice.HARDFILTERS);

            Element dpMin = hardFiltersBlock.getChild(DPMIN);
            if (validElement(dpMin)) {
                this.setdPmin(Integer.valueOf(dpMin.getValue()));
            }

            Element minQual = hardFiltersBlock.getChild(MINQUAL);
            if (validElement(minQual)) {
                this.setminQual(Integer.valueOf(minQual.getValue()));
            }

            Iterator<Element> hFilterNameSNP = hardFiltersBlock.getChildren(HFILTER_NAME_SNP).iterator();
            Iterator<Element> hFilterRuleSNP = hardFiltersBlock.getChildren(HFILTER_RULE_SNP).iterator();
            while (hFilterNameSNP.hasNext() && hFilterRuleSNP.hasNext()) {
                Element hFilterNameSNPElement = hFilterNameSNP.next();
                Element hFilterRuleSNPElement = hFilterRuleSNP.next();
                HardFilter newHardFilter = new HardFilter();
                newHardFilter.setName(hFilterNameSNPElement.getValue());
                newHardFilter.setRule(hFilterRuleSNPElement.getValue());
                newHardFilter.setType(HFilterType.SNP);
                this.getHardFilters().add(newHardFilter);
            }

            Iterator<Element> hFilterNameINDEL = hardFiltersBlock.getChildren(HFILTER_NAME_INDEL).iterator();
            Iterator<Element> hFilterRuleINDEL = hardFiltersBlock.getChildren(HFILTER_RULE_INDEL).iterator();
            while (hFilterNameINDEL.hasNext() && hFilterRuleINDEL.hasNext()) {
                Element hFilterNameINDELElement = hFilterNameINDEL.next();
                Element hFilterRuleINDELElement = hFilterRuleINDEL.next();
                HardFilter newHardFilter = new HardFilter();
                newHardFilter.setName(hFilterNameINDELElement.getValue());
                newHardFilter.setRule(hFilterRuleINDELElement.getValue());
                newHardFilter.setType(HFilterType.INDEL);
                this.getHardFilters().add(newHardFilter);
            }

        }

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

From source file:esiptestbed.mudrod.main.MudrodEngine.java

License:Apache License

/**
 * Load the configuration provided at <a href=
 * "https://github.com/mudrod/mudrod/blob/master/core/src/main/resources/config.xml">config.xml</a>.
 * /*  ww  w  . j a va  2 s. c o  m*/
 * @return a populated {@link java.util.Properties} object.
 */
public Properties loadConfig() {
    SAXBuilder saxBuilder = new SAXBuilder();
    InputStream configStream = MudrodEngine.class.getClassLoader().getResourceAsStream("config.xml");

    Document document;
    try {
        document = saxBuilder.build(configStream);
        Element rootNode = document.getRootElement();
        List<Element> paraList = rootNode.getChildren("para");

        for (int i = 0; i < paraList.size(); i++) {
            Element paraNode = paraList.get(i);
            props.put(paraNode.getAttributeValue("name"), paraNode.getTextTrim());
        }
    } catch (JDOMException | IOException e) {
        LOG.error("Exception whilst retreiving or processing XML contained within 'config.xml'!", e);
    }
    return getConfig();

}