/*.................................................................................................................*/
public void modifyTree(Tree tree, MesquiteTree modified, RandomBetween rng) {
if (tree == null || modified == null) return;
if (tree.getTaxa().anySelected()) { // error fixed in 1. 12
int[] terminals = tree.getTerminalTaxa(tree.getRoot());
if (terminals == null) return;
int numTerminals = 0;
for (int i = 0; i < terminals.length; i++)
if (tree.getTaxa().getSelected(terminals[i])) numTerminals++;
if (numTerminals > numExcluded) {
int[] selTerminals = new int[numTerminals];
int icount = 0;
for (int i = 0; i < terminals.length; i++)
if (tree.getTaxa().getSelected(terminals[i])) {
selTerminals[icount] = terminals[i];
icount++;
}
terminals = selTerminals;
for (int it = 0; it < numExcluded; it++) {
int taxon = -1;
int count = 0;
int ntries = 100000;
while (terminals[taxon = rng.randomIntBetween(0, numTerminals - 1)] < 0
&& count < ntries) {
count++;
}
if (count >= ntries)
discreetAlert(
"ERROR: Rarefy tree failed to find taxon to delete in " + ntries + " tries.");
else {
int nT = modified.nodeOfTaxonNumber(terminals[taxon]);
modified.deleteClade(nT, false);
terminals[taxon] = -1;
}
}
} else
MesquiteMessage.warnUser(
"Sorry, the tree could not be rarefied because more taxa are to be excluded than those available");
} else {
int numTerminals = tree.numberOfTerminalsInClade(tree.getRoot());
if (numTerminals > numExcluded) {
for (int it = 0; it < numExcluded; it++) {
int taxon = rng.randomIntBetween(0, numTerminals - it - 1);
int nT = modified.getTerminalNode(modified.getRoot(), taxon);
modified.deleteClade(nT, false);
}
} else
MesquiteMessage.warnUser(
"Sorry, the tree could not be rarefied because more taxa are to be excluded than those available");
}
}
/*.................................................................................................................*/
public String getStringForTree(int ic) {
if (treesBlock == null) return "";
Tree tree = treesBlock.getTree(ic);
if (tree == null) return "";
if (tree.hasPolytomies(tree.getRoot())) return "Yes";
else return "No";
}
/**
* Returns a new object indicating the states at the tips (used whether or not History is
* reconstruction)
*/
public CharacterDistribution getStatesAtTips(Tree tree) {
if (observedStates != null) return (CharacterDistribution) observedStates.getAdjustableClone();
else {
ContinuousAdjustable d =
new ContinuousAdjustable(tree.getTaxa(), tree.getTaxa().getNumTaxa());
d.setItemsAs(this);
fillDistribution(tree, tree.getRoot(), d);
return d;
}
}