Package org.cipres.treebase.domain.nexus.nexml

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

106
107
108
109
110
111
112
113
114
115
    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());
  }
View Full Code Here
180
181
182
183
184
185
186
187
188
189
190
191
      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();
View Full Code Here
86
87
88
89
90
91
92
93
    } catch (URISyntaxException e) {
      e.printStackTrace();
    } catch (ParserConfigurationException e) {
      e.printStackTrace();
    }
    NexmlDocumentWriter ndc = new NexmlDocumentWriter(study,getTaxonLabelHome(),document,baseURI);
    return ndc;
  }
View Full Code Here
91
92
93
94
95
96
97
98
    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();
  }
View Full Code Here
96
97
98
99
100
101
102
103
    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();
  } 
View Full Code Here
101
102
103
104
105
106
107
108
    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();
  }
View Full Code Here
25
26
27
28
29
30
31
32
33
34
35
36
37
38
 
  /**
   *
   */
  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
View Full Code Here
43
44
45
46
47
48
49
50
51
52
53
54
55
56
 
  /**
   *
   */
  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
View Full Code Here
61
62
63
64
65
66
67
68
69
70
71
72
73
74
 
  /**
   *
   */
  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
View Full Code Here
79
80
81
82
83
84
85
86
87
88
89
90
91
92
  /**
   *
   */
  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
View Full Code Here
TOP

Related Classes of org.cipres.treebase.domain.nexus.nexml.NexmlDocumentWriter

  • 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.domain.search.SearchResultsType
  • org.cipres.treebase.service.nexus.NexusServiceNexml
  • org.cipres.treebase.service.nexus.NexusServiceRDFa
  • org.cipres.treebase.web.controllers.SearchController
  • org.nexml.model.OTUs
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.