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

org.cipres.treebase.domain.tree.PhyloTreeNode
PhyloTreeNode.java The treebase implementation of a general tree node. Created on Mar 13, 2006 @author Jin Ruan

   * 
   * @param PhyloTree
   */


  public void treeAnalyzer(PhyloTree mytree, StringBuilder xmlPlaceHolder) {
    PhyloTreeNode rootNode = mytree.getRootNode();
    printNodeProperties(rootNode, xmlPlaceHolder);
    List<PhyloTreeNode> firstlevelnodes = rootNode.getChildNodes();


    nodesListParser(firstlevelnodes, xmlPlaceHolder);


  }

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   */
  public void nodesListParser(List<PhyloTreeNode> nodesList, StringBuilder xmlPlaceHolder) {


    for (int i = 0; i < nodesList.size(); i++) {


      PhyloTreeNode tmpnode = nodesList.get(i);


      nodeAnalyzer(tmpnode, xmlPlaceHolder);


      if (!tmpnode.isLeaf()) {
        printEndTag("Node", xmlPlaceHolder);
      }


    }

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    PhyloTree t = (PhyloTree) loadObject(PhyloTree.class);
    RandomList<PhyloTreeNode> nodes = new RandomList<PhyloTreeNode> ();
    nodes.addAll(t.getTreeNodesReadOnly());
    
    while (searchResult == null) {
      PhyloTreeNode a;
      do{ a = nodes.someElement();}
      while (a.getTaxonLabel()==null);
      PhyloTreeNode b;
      do{ b = nodes.someElement();}
      while (b.getTaxonLabel()==null);
      PhyloTreeNode c;
      do{ c = nodes.someElement();}
      while (c.getTaxonLabel()==null);      
      
      searchResult = false;
      if (c.haveABCTopology(a, b)) {
        TaxonVariant as = a.getTaxonLabel().getTaxonVariant();
        TaxonVariant bs = b.getTaxonLabel().getTaxonVariant();
        TaxonVariant cs = c.getTaxonLabel().getTaxonVariant();


        logger.debug("Searching for trees with a=" + as + ", b=" + bs + ", c=" + cs);


        Collection<PhyloTree> trees = 
          getFixture().findByTopology3(as, bs, cs);

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          return null;
      }
      return root.getTaxonLabel() == null ? null : root;  // If it's labelled, return it
    } else { // Otherwise, search downwards 
      for (PhyloTreeNode child : children) {
        PhyloTreeNode result = findLabeledLeaf(child);
        if (result != null) return result;
      }
      return null;
    }
  }

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        // phyloTree.setTreeType(treeType);
        // phyloTree.setTreeAttribute(pNewTreeAttribute);
        // phyloTree.setTreeQuality(pNewTreeQuality);


        int rootIndex = mesqTree.getRoot();
        PhyloTreeNode rootNode = createNode(mesqTree, null, rootIndex);
        phyloTree.addTreeNode(rootNode);
        phyloTree.setRootNode(rootNode);


        treeTraversal(mesqTree, rootIndex, rootNode);

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    // phyloTree.setTreeType(treeType);
    // phyloTree.setTreeAttribute(pNewTreeAttribute);
    // phyloTree.setTreeQuality(pNewTreeQuality);


    int rootIndex = mesqTree.getRoot();
    PhyloTreeNode rootNode = createNode(mesqTree, null, rootIndex);
    pTree.addTreeNode(rootNode);
    pTree.setRootNode(rootNode);


    treeTraversal(mesqTree, rootIndex, rootNode);

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    int index = pMesquiteTree.firstDaughterOfNode(pParentNodeIndex);
    if (!pMesquiteTree.nodeExists(index)) {
      return;
    }


    PhyloTreeNode aNode = createNode(pMesquiteTree, pParentNode, index);


    // for sibling nodes:
    int siblingNodeIndex = pMesquiteTree.nextSisterOfNode(index);
    while (siblingNodeIndex > 0) {
      PhyloTreeNode siblingNode = createNode(pMesquiteTree, pParentNode, siblingNodeIndex);


      treeTraversal(pMesquiteTree, siblingNodeIndex, siblingNode);


      siblingNodeIndex = pMesquiteTree.nextSisterOfNode(siblingNodeIndex);
    }

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   * @param pParentNode
   * @param pNodeIndex
   * @return
   */
  private PhyloTreeNode createNode(Tree pMesquiteTree, PhyloTreeNode pParentNode, int pNodeIndex) {
    PhyloTreeNode aNode = new PhyloTreeNode();
    // PhyloTree tree = pParentNode.getTree();
    // aNode.setTree(tree);


    double branchLength = pMesquiteTree.getBranchLength(pNodeIndex);
    if (MesquiteDouble.unassigned != branchLength) {
      aNode.setBranchLength(branchLength);
    }


    String nodeLabel = pMesquiteTree.getNodeLabel(pNodeIndex);
    if (!TreebaseUtil.isEmpty(nodeLabel)) {


      // Note: the node label is the same as the taxon label name
      // for qualified leave nodes.
      aNode.setName(nodeLabel);


      // TODO: need verify
      List<TaxonLabel> currentTaxa = getCurrentTaxaList();
      Taxa currentTreeTaxa = getCurrentTreeTaxa();


      String taxonLabelName = currentTreeTaxa.getTaxonName(pMesquiteTree
        .taxonNumberOfNode(pNodeIndex));
      aNode.setTaxonLabel(getTaxaLabel(currentTaxa, taxonLabelName));


    }


    // TODO aNode.setNodeDepth();

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    PhyloTree tree = new PhyloTree();
    tree.setTitle(newName);
    tree.setLabel(newName);
    tree.setNexusFileName(null);


    PhyloTreeNode rootNode = new PhyloTreeNode();
    tree.addTreeNode(rootNode);
    tree.setRootNode(rootNode);


    PhyloTreeNode node1 = new PhyloTreeNode();
    rootNode.addChildNode(node1);


    PhyloTreeNode node2 = new PhyloTreeNode();
    rootNode.addChildNode(node2);


    PhyloTreeNode node3 = new PhyloTreeNode();
    node1.addChildNode(node3);


    PhyloTreeNode node4 = new PhyloTreeNode();
    node3.addChildNode(node4);


    getFixture().store(tree);


    // force commit immediately, important:

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    PhyloTree tree = new PhyloTree();
    tree.setTitle(newName);
    tree.setLabel(newName);
    tree.setNexusFileName(null);


    PhyloTreeNode rootNode = new PhyloTreeNode();
    tree.addTreeNode(rootNode);
    tree.setRootNode(rootNode);


    PhyloTreeNode node1 = new PhyloTreeNode();
    rootNode.addChildNode(node1);


    PhyloTreeNode node2 = new PhyloTreeNode();
    rootNode.addChildNode(node2);


    PhyloTreeNode node3 = new PhyloTreeNode();
    node1.addChildNode(node3);


    PhyloTreeNode node4 = new PhyloTreeNode();
    node3.addChildNode(node4);


    // tree2:
    PhyloTree tree2 = new PhyloTree();
    tree2.setLabel(newName + "2");
    PhyloTreeNode node21 = new PhyloTreeNode();
    tree2.addTreeNode(node21);
    tree2.setRootNode(node21);


    // treeblock:
    TreeBlock block = new TreeBlock();

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