Package org.cipres.treebase.domain.tree

Examples of org.cipres.treebase.domain.tree.PhyloTreeNode

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    }
    t = getTreeService().resurrect(t);
   
    getErrorStream().println("Got tree " + t.getId() + " '" + t.getTitle() + "'");

      PhyloTreeNode root = t.getRootNode();
      long left = root.getLeftNode(), right = 0;
      if (left != 0) { right = root.getRightNode(); }
     
      if (left == 0 || right == 0) {
        t.updateSubtreeBounds();
        getErrorStream().println("Finished with tree " + treeId + ".");
      } else {
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   * @param xmlTree
   * @param tbPhyloTree
   */
  private void copyXmlTree(Tree<?> xmlTree, PhyloTree tbPhyloTree) {
    StringBuilder sb = new StringBuilder();
    PhyloTreeNode tbRoot = new PhyloTreeNode();   
    traverseXmlTree(xmlTree,sb,xmlTree.getRoot(), tbRoot, tbPhyloTree);
    tbPhyloTree.setRootNode(tbRoot);
    sb.append(';');
    tbPhyloTree.setNewickString(sb.toString());
  }
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    if ( ! xmlChildren.isEmpty() ) {// xmlNode is internal
      sb.append('(');
    }
    int currentChild = 1;
    for ( Node child : xmlChildren ) {
      PhyloTreeNode tbChild = new PhyloTreeNode();
      tbNode.addChildNode(tbChild);
      traverseXmlTree(xmlTree,sb,child,tbChild,tbTree);
      if ( currentChild < xmlChildren.size() ) {
        sb.append(',');
      }
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Related Classes of org.cipres.treebase.domain.tree.PhyloTreeNode

  • org.cipres.treebase.dao.tree.PhyloTreeDAOTest
  • org.cipres.treebase.domain.nexus.mesquite.MesquiteConverter
  • org.cipres.treebase.domain.nexus.nexml.NexmlTreeBlockReader
  • org.cipres.treebase.service.tree.PhyloTreeServiceImplTest
  • org.cipres.treebase.util.AnnotateTree
  • org.cipres.treebase.web.controllers.TreeParserResultController
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