List of usage examples for org.jdom2 Element setAttribute
public Element setAttribute(final String name, final String value)
This sets an attribute value for this element.
From source file:es.upm.dit.xsdinferencer.generation.generatorimpl.statisticsgeneration.StatisticResultsDocGeneratorImpl.java
License:Apache License
/** * This method generates an element with all the info contained on a {@link ComplexTypeStatisticsEntry} object * @param elementName the name of the generated element * @param complexType the complex type described by the entry * @param complexTypeStatisticsEntry the entry * @param elementInfoElementName the name of the element that describes the elements info * @param elementInfoSubElementName the name of the element that describes the info of each element * @param attributeInfoElementName the name of the element that describes the attributes info * @param attributeInfoSubElementName the name of the element that describes the info of each attributes * @param valuesInfoElementName the name of the element with the values info * @param valuesInfoSubElementName the name of the elements which contains all the info of each concrete value (on each node) * @param subpatternsInfoElementName the name of the element that describes the subpatterns info * @return An element with all the information described *//* ww w . j av a 2 s .c om*/ protected Element generateComplexTypeEntry(String elementName, ComplexType complexType, ComplexTypeStatisticsEntry complexTypeStatisticsEntry, String elementInfoElementName, String elementInfoSubElementName, String attributeInfoElementName, String attributeInfoSubElementName, String valuesInfoElementName, String valuesInfoSubElementName, String subpatternsInfoElementName) { Element complexTypeStatisticsEntryElement = new Element("complexType", STATISTICS_NAMESPACE); complexTypeStatisticsEntryElement.setAttribute("name", complexType.getName()); Element elementsAtComplexTypeElement = generateNodesOfComplexTypesInfoElements(elementInfoElementName, elementInfoSubElementName, complexTypeStatisticsEntry.getElementInfo(), valuesInfoElementName, valuesInfoSubElementName, complexTypeStatisticsEntry.getValuesInfo(), complexTypeStatisticsEntry.getStatisticsOfNumericValuesOfNodes(), "numericValuesStatistics"); complexTypeStatisticsEntryElement.addContent(elementsAtComplexTypeElement); Element attributesAtComplexTypeElement = generateNodesOfComplexTypesInfoElements(attributeInfoElementName, attributeInfoSubElementName, complexTypeStatisticsEntry.getAttributeOccurrencesInfo(), valuesInfoElementName, valuesInfoSubElementName, complexTypeStatisticsEntry.getValuesInfo(), complexTypeStatisticsEntry.getStatisticsOfNumericValuesOfNodes(), "numericValuesStatistics"); complexTypeStatisticsEntryElement.addContent(attributesAtComplexTypeElement); Element subpatternsInfoElement = generateSubpatternsInfoElement(subpatternsInfoElementName, complexTypeStatisticsEntry.getSubpatternsInfo()); complexTypeStatisticsEntryElement.addContent(subpatternsInfoElement); return complexTypeStatisticsEntryElement; }
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 ww w . ja va 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); }/*w ww.j a v a2 s . c o m*/ } Element plattform = new Element(PLATTFORM); plattform.addContent(this.getPlattform().getDisplayName()); configurationFile.getRootElement().addContent(plattform); if (!this.getCheckCasava().equals(checkCasava_DV)) { Element checkCasava = new Element(CHECKCASAVA); checkCasava.addContent(this.getCheckCasava().toString()); configurationFile.getRootElement().addContent(checkCasava); } Element dirOutBase = new Element(DIROUTBASE); dirOutBase.addContent(this.getDirOutBase().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(dirOutBase); Element projectId = new Element(PROJECTID); projectId.addContent(this.getProjectId()); configurationFile.getRootElement().addContent(projectId); if (!this.getUserName().equals(userName_DV)) { Element userName = new Element(USERNAME); userName.addContent(this.getUserName()); configurationFile.getRootElement().addContent(userName); } Element dataInDirpreProcess = new Element(INDIRPREPROCESS); dataInDirpreProcess.addContent(this.getDataInDirpreProcess().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(dataInDirpreProcess); for (Sample s : this.getSamples()) { Element sample = new Element(SAMPLE); Element sampleName = new Element(SAMPLE_NAME); sampleName.addContent(s.getSampleName()); sample.addContent(sampleName); Element sampleFiles = new Element(SAMPLE_FILES); sampleFiles.addContent(s.getSampleFiles()); sample.addContent(sampleFiles); Element sampleSuffix = new Element(SAMPLE_SUFFIX); sampleSuffix.addContent(s.getSampleSuffix()); sample.addContent(sampleSuffix); Element sampleType = new Element(SAMPLE_TYPE); sampleType.addContent(s.getSampleType().getDisplayName()); sample.addContent(sampleType); configurationFile.getRootElement().addContent(sample); } if (!this.getFastqc().equals(fastqc_DV)) { Element fastqc = new Element(FASTQC); fastqc.addContent(this.getFastqc().toString()); configurationFile.getRootElement().addContent(fastqc); } if (!this.getExtraContra().equals(extraContra_DV)) { Element extraContra = new Element(EXTRACONTRA); extraContra.addContent(this.getExtraContra().toString()); configurationFile.getRootElement().addContent(extraContra); } if (this.getBaseline() != baseline_DV) { Element baseline = new Element(BASELINE); baseline.addContent(this.getBaseline().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(baseline); } if (!this.getmDFlag().equals(mDFlag_DV)) { Element mDFlag = new Element(MDFLAG); mDFlag.addContent(this.getmDFlag().toString()); configurationFile.getRootElement().addContent(mDFlag); } if (!this.getQueueSGEProject().equals(queueSGEProject_DV)) { Element queueSGEProject = new Element(QUEUESGEPROJECT); queueSGEProject.addContent(this.getQueueSGEProject().toString()); configurationFile.getRootElement().addContent(queueSGEProject); } XMLOutputter xmlOutput = new XMLOutputter(); xmlOutput.setFormat(Format.getPrettyFormat()); xmlOutput.output(configurationFile, new FileWriter(output)); }
From source file:es.uvigo.ei.sing.rubioseq.gui.view.models.experiments.MethylationExperiment.java
License:Open Source License
public void generateXMLConfigurationFile(File output) throws IOException { Document configurationFile = new Document(); Element configData = new Element(CONFIG_DATA); configurationFile.setRootElement(configData); configData.setAttribute(ExperimentUtils.BRANCH, ExperimentUtils.BRANCH_METHYLATION); Element referencePath = new Element(REFERENCEPATH); referencePath.addContent(this.getReferencePath().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(referencePath); Element readsPath = new Element(READSPATH); readsPath.addContent(this.getReadsPath().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(readsPath); Element projectCompletePath = new Element(PROJECT_COMPLETE_PATH); projectCompletePath.addContent(this.getProjectCompletePath().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(projectCompletePath); Element plattform = new Element(PLATTFORM); plattform.addContent(this.getPlattform().getDisplayName()); configurationFile.getRootElement().addContent(plattform); Element methylType = new Element(METHYLTYPE); methylType.addContent(this.getMethylType().toString()); configurationFile.getRootElement().addContent(methylType); for (MethylationSample ms : this.getSamples()) { Element sample1 = new Element(SAMPLE1); sample1.addContent(ms.getSample1().getFile().getName()); configurationFile.getRootElement().addContent(sample1); }//ww w. ja va 2s. c om for (MethylationSample ms : this.getSamples()) { if (ms.getSample2() != null) { Element sample2 = new Element(SAMPLE2); sample2.addContent(ms.getSample2().getFile().getName()); configurationFile.getRootElement().addContent(sample2); } } if (!this.getSeedLength().equals(seedLength_DV)) { Element seedLength = new Element(SEED_LENGTH); seedLength.addContent(this.getSeedLength().toString()); configurationFile.getRootElement().addContent(seedLength); } if (!this.getNumMis().equals(numMis_DV)) { Element numMiss = new Element(NUM_MIS); numMiss.addContent(this.getNumMis().toString()); configurationFile.getRootElement().addContent(numMiss); } if (this.getIntervalsPath() != intervalsPath_DV) { Element intervalsPath = new Element(INTERVALS); intervalsPath.addContent(this.getIntervalsPath().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(intervalsPath); } if (!this.getContextType().equals(contextType_DV)) { Element contextType = new Element(CONTEXT); contextType.addContent(this.getContextType().toString()); configurationFile.getRootElement().addContent(contextType); } if (!this.getTrimTagLength().equals(trimTagLength_DV)) { Element trimTagLength = new Element(TRIMTAGLENGTH); trimTagLength.addContent(this.getTrimTagLength()); configurationFile.getRootElement().addContent(trimTagLength); } if (!this.getMinQual().equals(minQual_DV)) { Element minQual = new Element(MINQUAL); minQual.addContent(this.getMinQual().toString()); configurationFile.getRootElement().addContent(minQual); } if (!this.getFastqc().equals(fastqc_DV)) { Element fastqc = new Element(FASTQC); fastqc.addContent(this.getFastqc().toString()); configurationFile.getRootElement().addContent(fastqc); } if (!this.getDepthFilter().equals(depthFilter_DV)) { Element depthFilter = new Element(DEPTHFILTER); depthFilter.addContent(this.getDepthFilter().toString()); configurationFile.getRootElement().addContent(depthFilter); } if (!this.getQueueSGEProject().equals(queueSGEProject_DV)) { Element queueProject = new Element(QUEUESGEPROJECT); queueProject.addContent(this.getQueueSGEProject().toString()); configurationFile.getRootElement().addContent(queueProject); } if (!this.getMultiExec().equals(multiExec_DV)) { Element multiExec = new Element(MULTIEXEC); multiExec.addContent(this.getMultiExec().toString()); configurationFile.getRootElement().addContent(multiExec); } XMLOutputter xmlOutput = new XMLOutputter(); xmlOutput.setFormat(Format.getPrettyFormat()); xmlOutput.output(configurationFile, new FileWriter(output)); }
From source file:es.uvigo.ei.sing.rubioseq.gui.view.models.experiments.SingleNucleotideVariantExperiment.java
License:Open Source License
public void generateXMLConfigurationFile(File output) throws IOException { Document configurationFile = new Document(); Element configData = new Element(CONFIG_DATA); configurationFile.setRootElement(configData); configData.setAttribute(ExperimentUtils.BRANCH, ExperimentUtils.BRANCH_SNV); Element genRef = new Element(GENREF); genRef.addContent(this.getGenRefPath().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(genRef); Element dbSnpAnnot = new Element(DBSNPANNOT); dbSnpAnnot.addContent(this.getDbSnpAnnotPath().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(dbSnpAnnot); Element genomes1000Annot = new Element(GENOMES1000ANNOT); genomes1000Annot.addContent(this.getGenomes1000AnnotPath().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(genomes1000Annot); Element indelAnnot = new Element(INDELANNOT); indelAnnot.addContent(this.getIndelAnnotPath().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(indelAnnot); if (this.getIntervalsPath() != getIntervalsPath_DV()) { Element intervals = new Element(INTERVALS); intervals.addContent(this.getIntervalsPath().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(intervals); }//from w w w . j a va2s . c o m if (this.getKnownIndels().size() > 0) { for (KnownIndels kI : this.getKnownIndels()) { Element knownIndels = new Element(KNOWNINDELS); knownIndels.addContent(kI.getFile().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(knownIndels); } } Element plattform = new Element(PLATTFORM); plattform.addContent(this.getPlattform().getDisplayName()); configurationFile.getRootElement().addContent(plattform); if (!this.getCheckCasava().equals(checkCasava_DV)) { Element checkCasava = new Element(CHECKCASAVA); checkCasava.addContent(this.getCheckCasava().toString()); configurationFile.getRootElement().addContent(checkCasava); } Element dirOutBase = new Element(DIROUTBASE); dirOutBase.addContent(this.getDirOutBase().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(dirOutBase); Element projectId = new Element(PROJECTID); projectId.addContent(this.getProjectId()); configurationFile.getRootElement().addContent(projectId); if (!this.getUserName().equals(userName_DV)) { Element userName = new Element(USERNAME); userName.addContent(this.getUserName()); configurationFile.getRootElement().addContent(userName); } Element dataInDirpreProcess = new Element(INDIRPREPROCESS); dataInDirpreProcess.addContent(this.getDataInDirpreProcess().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(dataInDirpreProcess); for (Sample s : this.getSamples()) { Element sample = new Element(SAMPLE); Element sampleName = new Element(SAMPLE_NAME); sampleName.addContent(s.getSampleName()); sample.addContent(sampleName); Element sampleFiles = new Element(SAMPLE_FILES); sampleFiles.addContent(s.getSampleFiles()); sample.addContent(sampleFiles); Element sampleSuffix = new Element(SAMPLE_SUFFIX); sampleSuffix.addContent(s.getSampleSuffix()); sample.addContent(sampleSuffix); Element sampleType = new Element(SAMPLE_TYPE); sampleType.addContent(s.getSampleType().getDisplayName()); sample.addContent(sampleType); configurationFile.getRootElement().addContent(sample); } if (!this.getCallingType().equals(callingType_DV)) { Element callingType = new Element(CALLYING_TYPE); callingType.addContent(this.getCallingType().toString()); configurationFile.getRootElement().addContent(callingType); } if (!this.getgATKoutputMode().equals(gATKoutputMode_DV)) { Element gATKoutputModeoutputMode = new Element(GATKOUTPUTMODE); gATKoutputModeoutputMode.addContent(this.getgATKoutputMode().toString()); configurationFile.getRootElement().addContent(gATKoutputModeoutputMode); } if (!this.getRsFilter().equals(rsFilter_DV)) { Element rsFilter = new Element(RSFILTER); rsFilter.addContent(this.getRsFilter().toString()); configurationFile.getRootElement().addContent(rsFilter); } if (!this.getrUbioSeqMode().equals(rUbioSeqMode_DV)) { Element rUbioSeq_Mode = new Element(RUBIOSEQMODE); rUbioSeq_Mode.addContent(this.getrUbioSeqMode().toString()); configurationFile.getRootElement().addContent(rUbioSeq_Mode); } if (!this.getFastqc().equals(fastqc_DV)) { Element fastqc = new Element(FASTQC); fastqc.addContent(this.getFastqc().toString()); configurationFile.getRootElement().addContent(fastqc); } if (!this.getvEPFlag().equals(vEPFlag_DV)) { Element vEPFlag = new Element(VEPFLAG); vEPFlag.addContent(this.getvEPFlag().toString()); configurationFile.getRootElement().addContent(vEPFlag); } if (!this.gettCFlag().equals(tCFlag_DV)) { Element tCFlag = new Element(TCFLAG); tCFlag.addContent(this.gettCFlag().toString()); configurationFile.getRootElement().addContent(tCFlag); } if (!this.getmDFlag().equals(mDFlag_DV)) { Element mDFlag = new Element(MDFLAG); mDFlag.addContent(this.getmDFlag().toString()); configurationFile.getRootElement().addContent(mDFlag); } if (!this.getStandCallConf().equals(standCallConf_DV)) { Element standCallConf = new Element(STANDCALLCONF); standCallConf.addContent(this.getStandCallConf().toString()); configurationFile.getRootElement().addContent(standCallConf); } if (!this.getStandEmitConf().equals(standEmitConf_DV)) { Element standEmitConf = new Element(STANDEMITCONF); standEmitConf.addContent(this.getStandEmitConf().toString()); configurationFile.getRootElement().addContent(standEmitConf); } if (!this.getQueueSGEProject().equals(queueSGEProject_DV)) { Element queueSGEProject = new Element(QUEUESGEPROJECT); queueSGEProject.addContent(this.getQueueSGEProject().toString()); configurationFile.getRootElement().addContent(queueSGEProject); } if (this.getChoiceVqrsHardFilters().equals(VQRSHardFiltersChoice.VQRS) && this.getvQSRblockMills() != VQSRblockMills_DV && this.getvQSRblockHapMAp() != VQSRblockHapMAp_DV && this.getvQSRblockThousandG() != VQSRblockThousandG_DV) { Element vQSR_block = new Element(VQSRBLOCK); Element mills = new Element(MILLS); mills.addContent(this.getvQSRblockMills().getFile().getAbsolutePath()); vQSR_block.addContent(mills); Element hapmap = new Element(HAPMAP); hapmap.addContent(this.getvQSRblockHapMAp().getFile().getAbsolutePath()); vQSR_block.addContent(hapmap); Element thousandg = new Element(THOUSANDG); thousandg.addContent(this.getvQSRblockThousandG().getFile().getAbsolutePath()); vQSR_block.addContent(thousandg); configurationFile.getRootElement().addContent(vQSR_block); } if (this.getChoiceVqrsHardFilters().equals(VQRSHardFiltersChoice.HARDFILTERS) && (!this.getminQual().equals(minQual_DV) || !this.getdPmin().equals(DPmin_DV) || this.getHardFilters().size() > 0)) { Element hardFiltersBlock = new Element(HFILTERS); if (!this.getdPmin().equals(DPmin_DV)) { Element dpMin = new Element(DPMIN); dpMin.addContent(this.getdPmin().toString()); hardFiltersBlock.addContent(dpMin); } if (!this.getminQual().equals(minQual_DV)) { Element minQual = new Element(MINQUAL); minQual.addContent(this.getminQual().toString()); hardFiltersBlock.addContent(minQual); } for (HardFilter hF : this.getHardFilters()) { Element name = hF.getType().equals(HardFilter.HFilterType.SNP) ? new Element(HFILTER_NAME_SNP) : new Element(HFILTER_NAME_INDEL); name.addContent(hF.getName()); Element rule = hF.getType().equals(HardFilter.HFilterType.SNP) ? new Element(HFILTER_RULE_SNP) : new Element(HFILTER_RULE_INDEL); rule.addContent(hF.getRule()); hardFiltersBlock.addContent(name); hardFiltersBlock.addContent(rule); } configurationFile.getRootElement().addContent(hardFiltersBlock); } XMLOutputter xmlOutput = new XMLOutputter(); xmlOutput.setFormat(Format.getPrettyFormat()); xmlOutput.output(configurationFile, new FileWriter(output)); }
From source file:eu.himeros.cophi.ocr.proofreader.controller.pojo.HocrDocumentBuilder.java
License:Open Source License
/** * Builds the hocr document, extracting the header from the old hocr document. * @param the old hocrDocument//from w w w . j a v a 2 s .co m * @return the new ohocrDocument */ public Document build(Document hocrDocument) { Element root = hocrDocument.getRootElement(); xmlns = root.getNamespace(); Element bodyEl = root.getChildren().get(1); Element ocrPageEl = bodyEl.getChildren().get(0).detach(); String pageId = ocrPageEl.getAttributeValue("id"); ocrPageEl = new Element("div", xmlns); ocrPageEl.setAttribute("class", "ocr_page"); ocrPageEl.setAttribute("id", pageId); for (OcrLine ocrLine : ocrPage.getOcrLines()) { ocrPageEl.addContent(makeOcrLineEl(ocrLine)); ocrPageEl.addContent(new Element("br", xmlns)); } bodyEl.addContent(ocrPageEl); return hocrDocument; }
From source file:eu.himeros.cophi.ocr.proofreader.controller.pojo.HocrDocumentBuilder.java
License:Open Source License
/** * Makes the line.//from w w w . ja v a 2 s .co m * @param ocrLine * @return the related element. */ private Element makeOcrLineEl(OcrLine ocrLine) { Element ocrLineEl = new Element("span", xmlns); ocrLineEl.setAttribute("class", "ocr_line"); ocrLineEl.setAttribute("title", ocrLine.getScan().getCoords().getBbox()); for (OcrWord ocrWord : ocrLine.getOcrWords()) { ocrLineEl.addContent(makeOcrWordEl(ocrWord)); } return ocrLineEl; }
From source file:eu.himeros.cophi.ocr.proofreader.controller.pojo.HocrDocumentBuilder.java
License:Open Source License
/** * Makes the token.// ww w . j a va2s .co m * @param ocrWord * @return the related element. */ private Element makeOcrWordEl(OcrWord ocrWord) { Element ocrWordEl = new Element("span", xmlns); String wordId = ocrWord.getId(); ocrWordEl.setAttribute("id", wordId); ocrWordEl.setAttribute("class", "ocr_word"); ocrWordEl.setAttribute("title", ocrWord.getScan().getCoords().getBbox()); Element alternativeEl = new Element("span", xmlns); alternativeEl.setAttribute("class", "alternatives"); Element alternativeInsertionEl = new Element("ins", xmlns); alternativeInsertionEl.setAttribute("class", "alt"); alternativeInsertionEl.setAttribute("title", ocrWord.getInsertion().getNlp()); alternativeInsertionEl.setText(ocrWord.getInsertion().getText()); alternativeEl.addContent(alternativeInsertionEl); for (Deletion alternativeDeletion : ocrWord.getDeletions()) { alternativeEl.addContent(makeAlternativeDeletionEl(alternativeDeletion)); } ocrWordEl.addContent(alternativeEl); return ocrWordEl; }
From source file:eu.himeros.cophi.ocr.proofreader.controller.pojo.HocrDocumentBuilder.java
License:Open Source License
/** * Makes the alternative deletion.//w w w.j a va2s . c o m * @param alternativeDeletion * @return an alternative deletion. */ private Element makeAlternativeDeletionEl(Deletion alternativeDeletion) { Element alternativeDeletionEl = new Element("del", xmlns); //alternativeDeletionEl.setAttribute("class", "alt"); alternativeDeletionEl.setAttribute("title", alternativeDeletion.getNlp()); alternativeDeletionEl.setText(alternativeDeletion.getText()); return alternativeDeletionEl; }
From source file:eu.himeros.digitaledition.AlignedQuotationParser.java
License:Open Source License
private Element appendToAnchor(Element root) throws Exception { Element anchorRoot = new Element("text"); List<Element> words = root.getChildren(); Element currAnchor = new Element("w"); currAnchor.setAttribute("id", "0"); anchorRoot.addContent(currAnchor);//from w w w . j a va 2 s . c o m Element currNode; for (Element word : words) { currNode = word.clone(); if ("1".equals(word.getAttributeValue("occ"))) { currAnchor = currNode; anchorRoot.addContent(currAnchor); } else { currAnchor.addContent(currNode); } } return anchorRoot; }