/** 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;
}
}
/**
* Must be called before a tree is shaded. Goes through all nodes to find states present, to set
* minima and maxima.
*/
public void prepareColors(Tree tree, int drawnRoot) {
minState = MesquiteDouble.unassigned;
maxState = MesquiteDouble.unassigned;
calcMinMaxStates(tree, drawnRoot);
if (getParentData() != null && getParentCharacter() >= 0) {
int ic = getParentCharacter();
ContinuousData data = ((ContinuousData) getParentData());
for (int it = 0; it < data.getNumTaxa(); it++) {
double s = data.getState(ic, it, 0);
maxState = MesquiteDouble.maximum(maxState, s);
minState = MesquiteDouble.minimum(minState, s);
}
} else if (getObservedStates() != null) {
int ic = getParentCharacter();
ContinuousDistribution data = (ContinuousDistribution) getObservedStates();
for (int it = 0; it < data.getNumNodes(); it++) {
double s = data.getState(it);
maxState = MesquiteDouble.maximum(maxState, s);
minState = MesquiteDouble.minimum(minState, s);
}
}
}
// TODO: here should use super.setToClone(data) to handle specssets etc.???
public CharacterData cloneDataBlock(int icStart, int icEnd, int itStart, int itEnd) {
int blockChars = icEnd - icStart + 1;
int blockTaxa = itEnd - itStart + 1;
boolean[] taxaToClone = new boolean[getNumTaxa()];
for (int it = 0; it < getNumTaxa(); it++) {
taxaToClone[it] = it >= itStart && it <= itEnd;
}
Taxa taxa = getTaxa().cloneTaxa(taxaToClone);
ContinuousData cD = new GeographicData(getMatrixManager(), blockTaxa, blockChars, taxa);
int nItems = getNumItems();
cD.setItemsAs(this);
for (int i = 0; i < nItems; i++) {
Double2DArray imatrix = null;
imatrix = cD.getItem(i);
Double2DArray oldMatrix = getItem(i);
for (int ic = icStart; ic <= icEnd; ic++)
for (int it = itStart; it <= itEnd; it++)
imatrix.setValue(ic - icStart, it - itStart, oldMatrix.getValue(ic, it));
}
for (int ic = 0; ic < numChars; ic++) if (getSelected(ic)) cD.setSelected(ic - icStart, true);
return cD;
}
/*.......................................... ..................................................*/
public void setState(int ic, int it, int item, double states) {
if (!legalValue(ic, states)) {
return;
}
super.setState(ic, it, item, states);
}