boolean hasData(int it) {
CharacterState cs = null;
try {
for (int ic = 0; ic < observedStates.getNumChars(); ic++) {
cs = observedStates.getCharacterState(cs, ic, it);
if (cs == null) return false;
if (!cs.isInapplicable() && !cs.isUnassigned()) return true;
}
} catch (NullPointerException e) {
}
return false;
}
/*...............................................................................................................*/
int numSites(int it) {
CharacterState cs = null;
if (observedStates == null) return 0;
int count = 0;
for (int ic = 0; ic < observedStates.getNumChars(); ic++) {
cs = observedStates.getCharacterState(cs, ic, it);
if (cs == null) return 0;
if (!cs.isInapplicable() && !cs.isUnassigned()) count++;
}
return count;
} /*...............................................................................................................*/
/*...............................................................................................................*/
int sequenceLength(int it) {
CharacterState cs = null;
if (observedStates == null) return 0;
int count = 0;
for (int ic = 0; ic < observedStates.getNumChars(); ic++) {
cs = observedStates.getCharacterState(cs, ic, it);
if (cs == null) return 0;
if (cs instanceof MolecularState) {
if (!cs.isInapplicable()) // if Molecular, then count missing & with state
count++;
} else if (!cs.isInapplicable()
&& !cs.isUnassigned()) // if Molecular, then count missing & with state
count++;
}
return count;
}
/** returns the state of character ic in taxon it */
public CharacterState getCharacterState(CharacterState cs, int ic, int it) {
if (cs == null || cs.getClass() != GeographicState.class) {
cs = new GeographicState();
}
((GeographicState) cs).setItemsAs(this);
for (int i = 0; i < getNumItems(); i++) {
((GeographicState) cs).setValue(i, getState(ic, it, i));
}
return cs;
}