TreesManager treeManager = (TreesManager) project.ownerModule
.findElementManager(TreeVector.class);
ListableVector treeVectors = treeManager.getTreeBlockVector();
for (int i = 0; i < treeVectors.size(); i++) {
// One treeVector represents one tree block
TreeVector treeVector = (TreeVector) treeVectors.elementAt(i);
// System.out.println(" treeVector: " + i + " - " + treeVector.getName());
TreeBlock treeblock = new TreeBlock();
treeblock.setTitle(treeVector.getName());
// first get the taxon list for the trees:
Taxa treeTaxa = treeVector.getTaxa();
// String taxaName = treeTaxa.getName();
TaxonLabelSet tlSet = pDataSet.getTaxonLabelSet(treeTaxa);
treeblock.setTaxonLabelSet(tlSet);
List<TaxonLabel> treeTaxonLabels = null;
if (tlSet != null) {
treeTaxonLabels = tlSet.getTaxonLabelsReadOnly();
}
// To be used by the tree traversal methods.
setCurrentTaxaList(treeTaxonLabels);
setCurrentTreeTaxa(treeTaxa);
Enumeration e = treeVector.elements();
while (e.hasMoreElements()) {
Tree mesqTree = (Tree) e.nextElement();
String newick = mesqTree.writeTreeByNames(true);
if (LOGGER.isDebugEnabled()) {