/** Called to alter data in all cells */
public boolean operateOnData(CharacterData data) {
if (!(data instanceof ContinuousData)) return false;
ContinuousData cData = (ContinuousData) data;
int numItems = cData.getNumItems();
String[] items = new String[numItems];
for (int i = 0; i < items.length; i++) {
if (StringUtil.blank(cData.getItemName(i))) items[i] = "(unnamed)";
else items[i] = cData.getItemName(i);
}
int d =
ListDialog.queryList(
containerOfModule(),
"Rename item",
"Rename item:",
MesquiteString.helpString,
items,
0);
if (!MesquiteInteger.isCombinable(d) || d < 0 || d >= numItems) return false;
else {
String s =
MesquiteString.queryString(
containerOfModule(), "Rename Item", "New name for " + items[d], items[d]);
if (StringUtil.blank(s)) return false;
cData.setItemReference(d, NameReference.getNameReference(s));
return true;
}
}
/*..........................................MContinuousStates................*/
public int userQueryItem(String message, MesquiteModule module) {
int numItems = getNumItems();
String[] items = new String[numItems];
for (int i = 0; i < items.length; i++) {
if (StringUtil.blank(getItemName(i))) items[i] = "(unnamed)";
else items[i] = getItemName(i);
}
return ListDialog.queryList(
module.containerOfModule(), "Select item", message, MesquiteString.helpString, items, 0);
}
/*.................................................................................................................*/
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;
}
/** queryies the user to choose a tree and returns an integer of the tree chosen */
public int queryUserChoose(Taxa taxa, String forMessage) {
int ic = MesquiteInteger.unassigned;
int numBlocks = getNumberOfTreeBlocks(taxa);
if (MesquiteInteger.isCombinable(numBlocks)) {
String[] s = new String[numBlocks];
for (int i = 0; i < numBlocks; i++) {
s[i] = getTreeBlockNameString(taxa, i);
}
if (forMessage == null) {
forMessage = "Choose tree block";
}
return ListDialog.queryList(
containerOfModule(), "Choose tree block", forMessage, MesquiteString.helpString, s, 0);
} else {
if (forMessage == null) {
forMessage = "Number of tree block to be used";
}
int r = MesquiteInteger.queryInteger(containerOfModule(), "Choose tree block", forMessage, 1);
if (MesquiteInteger.isCombinable(r)) return MesquiteTree.toInternal(r);
else return r;
}
}