List of addPhyloTree() Examples

Examples of addPhyloTree()

org.cipres.treebase.domain.tree.TreeBlock.addPhyloTree()
Append a new Tree to the end of the list. Creation date: Mar 14, 2006 @param pTree PhyloTree

Examples of org.cipres.treebase.domain.tree.TreeBlock.addPhyloTree()

    if ( getFormat(request) == FORMAT_NEXML || getFormat(request) == FORMAT_RDF ) {
      NexusDataSet nds = new NexusDataSet();
      nds.getTaxonLabelSets().add(tls);
      TreeBlock treeBlock = new TreeBlock();
      treeBlock.setTaxonLabelSet(tls);
      treeBlock.addPhyloTree(tree);
      nds.getTreeBlocks().add(treeBlock);
      return getNexmlService().serialize(nds,getDefaultProperties(request),tree.getStudy());
    }
    /*else if ( getFormat(request) == FORMAT_RDF ) {
      NexusDataSet nds = new NexusDataSet();

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Examples of org.cipres.treebase.domain.tree.TreeBlock.addPhyloTree()


            treeData.setStudy(theStudy);
            ContextManager.getTaxonLabelService().updateStudyForAllLabels(treeData, theStudy);
            treeData.setTB1TreeID(treeID);
            ContextManager.getPhyloTreeService().save(treeData);
            theTreeBlock.addPhyloTree(treeData);
            theSubmission.addPhyloTreeBlockIfNecessary(theTreeBlock);
            ContextManager.getSubmissionService().save(theSubmission);
            theTree.setTree(treeData);
            theData = theTree;
          } else {

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Examples of org.cipres.treebase.domain.tree.TreeBlock.addPhyloTree()

    TaxonLabelSet tls = tree.getTreeBlock().getTaxonLabelSet();
    NexusDataSet nds = new NexusDataSet();
    nds.getTaxonLabelSets().add(tls);
    TreeBlock treeBlock = new TreeBlock();
    treeBlock.setTaxonLabelSet(tls);
    treeBlock.addPhyloTree(tree);
    nds.getTreeBlocks().add(treeBlock);
    NexmlDocumentWriter conv = new NexmlDocumentWriter(tree.getStudy(),getTaxonLabelHome(),doc);
    String xml = conv.fromTreeBaseToXml(nds).getXmlString();
    System.out.println(xml);
    Assert.assertNotNull(xml);

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Examples of org.cipres.treebase.domain.tree.TreeBlock.addPhyloTree()


        treeTraversal(mesqTree, rootIndex, rootNode);


        phyloTree.updateSubtreeBounds();


        treeblock.addPhyloTree(phyloTree);
        // pDataSet.getPhyloTrees().add(phyloTree);


        // verification
        if (LOGGER.isDebugEnabled()) {
          Set<PhyloTreeNode> nodes = phyloTree.getTreeNodesReadOnly();

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Examples of org.cipres.treebase.domain.tree.TreeBlock.addPhyloTree()


    // treeblock:
    TreeBlock block = new TreeBlock();
    block.setTitle(newName);


    block.addPhyloTree(tree);
    block.addPhyloTree(tree2);


    // Create an analysis step and associate w/ tree.
    Study s = getTestStudy();
    Analysis a1 = new Analysis();

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Examples of org.cipres.treebase.domain.tree.TreeBlock.addPhyloTree()

    // treeblock:
    TreeBlock block = new TreeBlock();
    block.setTitle(newName);


    block.addPhyloTree(tree);
    block.addPhyloTree(tree2);


    // Create an analysis step and associate w/ tree.
    Study s = getTestStudy();
    Analysis a1 = new Analysis();
    a1.setName("1 " + newName);

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Examples of org.cipres.treebase.domain.tree.TreeBlock.addPhyloTree()

    while ( xmlNetworkIterator.hasNext() ) {
      Network<?> xmlNetwork = xmlNetworkIterator.next();
      if ( xmlNetwork instanceof Tree ) {
        PhyloTree tbPhyloTree = fromXmlToTreeBase((Tree<?>) xmlNetwork); 
        tbPhyloTree.setStudy(getStudy());
        tbTreeBlock.addPhyloTree(tbPhyloTree);
      }        
    }    
    return tbTreeBlock;
  }

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Examples of org.cipres.treebase.domain.tree.TreeBlock.addPhyloTree()

            if (! taxonLabels.contains(pTaxLabel.getTaxonLabel())) {
              taxonLabelSet.addPhyloTaxonLabel(pTaxLabel);
              taxonLabels.add(pTaxLabel.getTaxonLabel());        
            }
          }
          treeBlock.addPhyloTree(pTree);  
        }
        
        treeBlock.setTaxonLabelSet(taxonLabelSet);
        taxonLabelSet.setTitle("TB" + date.getTime());

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