/*.................................................................................................................*/ public boolean transformTree(AdjustableTree tree, MesquiteString resultString, boolean notify) { if (!(tree instanceof MesquiteTree)) return false; reinterpret((MesquiteTree) tree, tree.getRoot()); if (notify && tree instanceof Listened) ((Listened) tree).notifyListeners(this, new Notification(MesquiteListener.NAMES_CHANGED)); return true; }
/*.................................................................................................................*/ public boolean transformTree(AdjustableTree tree, MesquiteString resultString, boolean notify) { Taxa taxa = tree.getTaxa(); // counting how many excluded int count = 0; for (int i = 0; i < taxa.getNumTaxa(); i++) { if (!tree.taxonInTree(i)) count++; } if (count == 0) { discreetAlert( "The tree contains all of the taxa available in the block of taxa. There are none available to be added"); return true; } // getting list of excluded ListableVector excluded = new ListableVector(count); count = 0; for (int i = 0; i < taxa.getNumTaxa(); i++) { if (!tree.taxonInTree(i)) { excluded.addElement(taxa.getTaxon(i), false); } } // presenting choice Listable[] toInclude = ListDialog.queryListMultiple( containerOfModule(), "Add taxa to tree", "Select taxa to be added to the tree", MesquiteString.helpString, "Add", false, excluded, null); if (toInclude == null || toInclude.length == 0) return true; for (int i = 0; i < toInclude.length; i++) { int taxon = taxa.whichTaxonNumber((Taxon) toInclude[i]); tree.graftTaxon(taxon, tree.getRoot(), false); } if (notify && tree instanceof Listened) ((Listened) tree) .notifyListeners(this, new Notification(MesquiteListener.BRANCHES_REARRANGED)); return true; }