/** get CharacterState at node N */
public CharacterState getCharacterState(CharacterState cs, int ic, int it) {
ContinuousState c;
if (cs != null && cs instanceof ContinuousState) c = (ContinuousState) cs;
else c = new ContinuousState();
c.setItemsAs(this);
for (int item = 0; item < getNumberOfItems(); item++) c.setValue(item, getState(ic, it, item));
return c;
}
/**
* places into the already instantiated ColorDistribution the colors corresponding to the
* CharacterState, and returns the number of colors. Uses default colors. Mode is
* MesquiteColorTable.GRAYSCALE, COLORS, COLORS_NO_BW, or DEFAULT (default depends on subclass)
*/
public int getColorsOfState(
CharacterState state, ColorDistribution colors, MesquiteColorTable colorTable) {
if (colors == null || state == null || !(state instanceof ContinuousState)) return 0;
int numBinBoundaries = 10;
double[] binBoundaries = colorTable.getPreferredBinBoundaries();
if (binBoundaries != null) numBinBoundaries = binBoundaries.length;
colors.initialize();
ContinuousState cState = (ContinuousState) state;
if (cState.getNumItems() == 1) {
double s = cState.getValue(0);
colors.setWeight(0, 1.0);
if (!MesquiteDouble.isCombinable(s)) colors.setColor(0, Color.white);
else {
int place =
getPlace(s, colorTable); // (int)(((s-minState)/(maxState-minState))*numBinBoundaries);
colors.setColor(
0,
colorTable.getColor(
numBinBoundaries, place)); // bug fixed in 1. 12 that had been introduced in 1. 10
// colors.setColor(0, colorTable.getColor(s, minState, maxState)); 1.10 to 1.11
}
} else {
for (int i = 0; i < cState.getNumItems(); i++) {
double s = cState.getValue(i);
colors.setWeight(i, 1.0 / cState.getNumItems());
if (!MesquiteDouble.isCombinable(s)) colors.setColor(0, Color.white);
else {
int place =
getPlace(
s, colorTable); // (int)(((s-minState)/(maxState-minState))*numBinBoundaries);
colors.setColor(
i,
colorTable.getColor(
numBinBoundaries, place)); // bug fixed in 1. 12 that had been introduced in 1. 10
// colors.setColor(i, colorTable.getColor(s, minState, maxState)); 1.10 to 1.11
}
}
}
return cState.getNumItems();
}