/*...............................................................................................................*/
public void setTableAndTaxa(MesquiteTable table, Taxa taxa) {
// if (this.data !=null)
// this.data.removeListener(this);
if (taxa != this.taxa) observedStates = null;
this.taxa = taxa;
matrixSourceTask.initialize(taxa);
this.table = table;
doCalcs();
}
public void doCalcs() {
if (bits != null) bits.clearAllBits();
if (taxa == null) return;
if (bits == null) bits = new Bits(taxa.getNumTaxa());
else bits.resetSize(taxa.getNumTaxa());
if (observedStates == null) {
tInfo = null;
observedStates = matrixSourceTask.getCurrentMatrix(taxa);
if (observedStates != null) {
captureCharacterDataFromObservedStates();
if (data != null) tInfo = data.getTaxaInfo(true);
}
}
if (observedStates == null) return;
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if (hasData(it)) bits.setBit(it);
}
}
public void calculateNumber(Taxon taxon, MesquiteNumber result, MesquiteString resultString) {
if (result == null) return;
clearResultAndLastResult(result);
Taxa taxa = taxon.getTaxa();
int it = taxa.whichTaxonNumber(taxon);
if (taxa != currentTaxa || observedStates == null) {
observedStates = matrixSourceTask.getCurrentMatrix(taxa);
currentTaxa = taxa;
}
if (observedStates == null || !(observedStates.getParentData() instanceof DNAData)) return;
DNAData data = (DNAData) observedStates.getParentData();
int count = data.getAminoAcidNumbers(it, ProteinData.TER, countEvenIfOthers.getValue());
if (result != null) result.setValue(count);
if (resultString != null)
resultString.setValue(
"Number of stop codons in taxon " + observedStates.getName() + ": " + count);
saveLastResult(result);
saveLastResultString(resultString);
}
/**
* Called to provoke any necessary initialization. This helps prevent the module's intialization
* queries to the user from happening at inopportune times (e.g., while a long chart calculation
* is in mid-progress)
*/
public void initialize(Taxa taxa) {
currentTaxa = taxa;
matrixSourceTask.initialize(currentTaxa);
}
public String getParameters() {
return "Number of stops coded by nucleotides in taxon in matrix from: "
+ matrixSourceTask.getParameters();
}