Examples of NexmlDocumentWriter

Examples of org.cipres.treebase.domain.nexus.nexml.NexmlDocumentWriter

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    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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Examples of org.cipres.treebase.domain.nexus.nexml.NexmlDocumentWriter

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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();
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Examples of org.cipres.treebase.domain.nexus.nexml.NexmlDocumentWriter

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    } catch (URISyntaxException e) {
      e.printStackTrace();
    } catch (ParserConfigurationException e) {
      e.printStackTrace();
    }
    NexmlDocumentWriter ndc = new NexmlDocumentWriter(study,getTaxonLabelHome(),document,baseURI);
    return ndc;
  }
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Examples of org.cipres.treebase.domain.nexus.nexml.NexmlDocumentWriter

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    NexmlDocumentWriter ndc = new NexmlDocumentWriter(study,getTaxonLabelHome(),document,baseURI);
    return ndc;
  }

  public String serialize(NexusDataSet nexusDataSet, Properties properties) {
    NexmlDocumentWriter ndc = getNexmlDocumentConverter(null, properties);
    return ndc.fromTreeBaseToXml(nexusDataSet).getXmlString();
  }
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Examples of org.cipres.treebase.domain.nexus.nexml.NexmlDocumentWriter

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    NexmlDocumentWriter ndc = getNexmlDocumentConverter(null, properties);
    return ndc.fromTreeBaseToXml(nexusDataSet).getXmlString();
  }
 
  public String serialize(NexusDataSet nexusDataSet, Properties properties,Study study) {
    NexmlDocumentWriter ndc = getNexmlDocumentConverter(study, properties);
    return ndc.fromTreeBaseToXml(nexusDataSet).getXmlString();
  } 
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Examples of org.cipres.treebase.domain.nexus.nexml.NexmlDocumentWriter

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    NexmlDocumentWriter ndc = getNexmlDocumentConverter(study, properties);
    return ndc.fromTreeBaseToXml(nexusDataSet).getXmlString();
  } 

  public String serialize(Study study, Properties properties) {
    NexmlDocumentWriter ndc = getNexmlDocumentConverter(study, properties);
    return ndc.fromTreeBaseToXml(study).getXmlString();
  }
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Examples of org.cipres.treebase.domain.nexus.nexml.NexmlDocumentWriter

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  /**
   *
   */
  public String serialize(NexusDataSet nexusDataSet,Properties properties) {
    NexmlDocumentWriter ndc = getNexmlDocumentConverter(null, properties);
    String result = null;
    try {
      result = transform(ndc.fromTreeBaseToXml(nexusDataSet).getXmlString());
    } catch (DocumentException e) {
      // TODO Auto-generated catch block
      e.printStackTrace();
    } catch (TransformerException e) {
      // TODO Auto-generated catch block
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Examples of org.cipres.treebase.domain.nexus.nexml.NexmlDocumentWriter

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  /**
   *
   */
  public String serialize(NexusDataSet nexusDataSet,Properties properties,Study study) {
    NexmlDocumentWriter ndc = getNexmlDocumentConverter(study, properties);
    String result = null;
    try {
      result = transform(ndc.fromTreeBaseToXml(nexusDataSet).getXmlString());
    } catch (DocumentException e) {
      // TODO Auto-generated catch block
      e.printStackTrace();
    } catch (TransformerException e) {
      // TODO Auto-generated catch block
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Examples of org.cipres.treebase.domain.nexus.nexml.NexmlDocumentWriter

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  /**
   *
   */
  public String serialize(NexusDataSet nexusDataSet) {
    NexmlDocumentWriter ndc = getNexmlDocumentConverter(null, null);
    String result = null;
    try {
      result = transform(ndc.fromTreeBaseToXml(nexusDataSet).getXmlString());
    } catch (DocumentException e) {
      // TODO Auto-generated catch block
      e.printStackTrace();
    } catch (TransformerException e) {
      // TODO Auto-generated catch block
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Examples of org.cipres.treebase.domain.nexus.nexml.NexmlDocumentWriter

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  /**
   *
   */
  public String serialize(Study study,Properties properties) {
    NexmlDocumentWriter ndc = getNexmlDocumentConverter(study, properties);
    String result = null;
    try {
      result = transform(ndc.fromTreeBaseToXml(study).getXmlString());
    } catch (DocumentException e) {
      // TODO Auto-generated catch block
      e.printStackTrace();
    } catch (TransformerException e) {
      // TODO Auto-generated catch block
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