Examples of mesquite.lib.Tree

      setCurrentTaxaList(treeTaxonLabels);
      setCurrentTreeTaxa(treeTaxa);


      Enumeration e = treeVector.elements();
      while (e.hasMoreElements()) {
        Tree mesqTree = (Tree) e.nextElement();
        String newick = mesqTree.writeTreeByNames(true);


        if (LOGGER.isDebugEnabled()) {
          LOGGER.debug(" tree=" + newick); //$NON-NLS-1$
        }


        // System.out.println(" tree: " + mesqTree.getName() + " " + newick);


        PhyloTree phyloTree = new PhyloTree();
        phyloTree.setLabel(mesqTree.getName());
        phyloTree.setNexusFileName(pFile.getName());
        phyloTree.setPublished(false);
        phyloTree.setRootedTree(mesqTree.getRooted());
        phyloTree.setNewickString(newick);
        phyloTree.setStudy(pStudy);
        // phyloTree.setBigTree(false); //TODO
        // 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);

    if (LOGGER.isDebugEnabled()) {
      LOGGER.debug("replace newick=" + newick); //$NON-NLS-1$
    }


    // TODO: handle NPE in readClade()
    Tree mesqTree = new MesquiteTree(taxa, newick.toString());


    // used by tree traversal
    setCurrentTaxaList(pTaxonLabels);
    setCurrentTreeTaxa(taxa);


    // String newick = mesqTree.writeTreeByNames(true);


    // if (LOGGER.isDebugEnabled()) {
    // LOGGER.debug(" tree=" + newick); //$NON-NLS-1$
    // }


    // phyloTree.setLabel(mesqTree.getName());
    // phyloTree.setNexusFileName(pFile.getName());
    // phyloTree.setPublished(false);
    // phyloTree.setRootedTree(mesqTree.getRooted());
    // phyloTree.setNewickString(newick);
    // phyloTree.setBigTree(false); //
    // 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);

Examples of mesquite.lib.Tree

Related Classes of mesquite.lib.Tree