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);