Package org.nexml.model

Examples of org.nexml.model.Document

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    ndw.fromTreeBaseToXml(msr);
    assertNotNull(doc.getXmlString());
  }
 
  public void testTreeSearchSerialization() {
    Document doc = DocumentFactory.safeCreateDocument();
    NexmlDocumentWriter ndw = new NexmlDocumentWriter(null, mTaxonLabelHome, doc);   
    TreeSearchResults tsr = ssr.convertToTrees();
    ndw.fromTreeBaseToXml(tsr);
    assertNotNull(doc.getXmlString());
  }
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   * @param pFile
   * @param pStudy
   * @param pDataSet
   */
  public void parseOneFile(File pFile, Study pStudy, NexusDataSet pDataSet) {
    Document document = null;
    try {
      document = DocumentFactory.parse(pFile);
    } catch (Exception e) {
      e.printStackTrace();
    }
   
    // Taxa
    NexmlOTUReader noc = new NexmlOTUReader(pStudy,getTaxonLabelHome(),document);
    for ( OTUs xmlOTUs : document.getOTUsList() ) {
      pDataSet.addTaxonLabelSet(xmlOTUs, noc.fromXmlToTreeBase(xmlOTUs));
    }
 
    // Matrices
    NexmlMatrixReader nmc = new NexmlMatrixReader(pStudy,getTaxonLabelHome(),document);
    for ( org.nexml.model.Matrix<?> xmlMatrix : document.getMatrices() ) {
      Matrix tbMatrix = nmc.fromXmlToTreeBase(xmlMatrix);
      tbMatrix.setNexusFileName(pFile.getName());
      pDataSet.getMatrices().add(tbMatrix);
    }   
   
    // Trees
    NexmlTreeBlockReader ntbc = new NexmlTreeBlockReader(pStudy,getTaxonLabelHome(),document);
    for ( org.nexml.model.TreeBlock xmlTreeBlock : document.getTreeBlockList() ) {
      TreeBlock tbTreeBlock = ntbc.fromXmlToTreeBase(xmlTreeBlock);
      for ( PhyloTree phyloTree : tbTreeBlock.getTreeList() ) {
        phyloTree.setNexusFileName(pFile.getName());
      }
      pDataSet.getTreeBlocks().add(tbTreeBlock);
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  protected NexmlDocumentWriter getNexmlDocumentConverter(Study study,Properties properties) {
    String baseURI = null;
    if ( null != properties ) {
      baseURI = properties.getProperty("nexml.uri.base");
    }
    Document document = null;
    try {
      document = DocumentFactory.createDocument();
      document.setBaseURI(new URI(baseURI));//NPE
    } catch (URISyntaxException e) {
      e.printStackTrace();
    } catch (ParserConfigurationException e) {
      e.printStackTrace();
    }
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      String fileName = "TB" + date.getTime();
      StringBuilder builder = new StringBuilder();
     
      if ( getFormat(request) == FORMAT_NEXML ) {
        Document doc = DocumentFactory.safeCreateDocument();
        NexmlDocumentWriter ndw = new NexmlDocumentWriter(null,getTaxonLabelHome(), doc);   
        ndw.fromTreeBaseToXml(treeResults);
        builder.append(doc.getXmlString());
      }
      else {
        Set<PhyloTree> trees =  treeResults.getResults();
        TreeBlock treeBlock = new TreeBlock();
        TaxonLabelSet taxonLabelSet = new TaxonLabelSet();
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Related Classes of org.nexml.model.Document

  • org.cipres.treebase.domain.nexus.nexml.NexmlConverter
  • org.cipres.treebase.domain.nexus.NexmlAnalysisConverterTest
  • org.cipres.treebase.domain.nexus.NexmlMatrixConverterTest
  • org.cipres.treebase.domain.nexus.NexmlSearchResultConverterTest
  • org.cipres.treebase.domain.nexus.NexmlSerializationTest
  • org.cipres.treebase.domain.nexus.NexmlTreeConverterTest
  • org.cipres.treebase.service.nexus.NexusServiceNexml
  • org.cipres.treebase.web.controllers.SearchController
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