/*.................................................................................................................*/
public void actionPerformed(ActionEvent e) {
if (e.getActionCommand().equalsIgnoreCase("setToDefaults")) {
setDefaultTNTCommandsSearchOptions();
searchField.setText(searchArguments);
bootstrapSearchField.setText(bootstrapSearchArguments);
harvestOnlyStrictConsensusBox.setState(harvestOnlyStrictConsensus);
resamplingAllConsensusTreesBox.setState(!resamplingAllConsensusTrees);
bootStrapRepsField.setValue(bootstrapreps);
} else if (e.getActionCommand().equalsIgnoreCase("setToDefaultsOtherOptions")) {
setDefaultTNTCommandsOtherOptions();
otherOptionsField.setText(otherOptions);
convertGapsBox.setState(convertGapsToMissing);
} else if (e.getActionCommand().equalsIgnoreCase("browseSearchScript")
&& searchScriptPathField != null) {
MesquiteString directoryName = new MesquiteString();
MesquiteString fileName = new MesquiteString();
String path =
MesquiteFile.openFileDialog("Choose Search Script File", directoryName, fileName);
if (StringUtil.notEmpty(path)) searchScriptPathField.setText(path);
} else if (e.getActionCommand().equalsIgnoreCase("browseBootSearchScript")
&& bootSearchScriptPathField != null) {
MesquiteString directoryName = new MesquiteString();
MesquiteString fileName = new MesquiteString();
String path =
MesquiteFile.openFileDialog(
"Choose Resampling Search Script File", directoryName, fileName);
if (StringUtil.notEmpty(path)) bootSearchScriptPathField.setText(path);
}
}
/*.................................................................................................................*/
public void actionPerformed(ActionEvent e) {
if ("Equal".equals(e.getActionCommand())) {
double probEach = 1.0 / getNumStates();
for (int i = 0; i < getNumStates(); i++) stateFrequenciesTemp[i] = probEach;
setOptions();
// setStateFrequencies(stateFrequenciesTemp);
} else if ("Norm+-".equals(e.getActionCommand())) {
double total = 0;
for (int i = 0; i < getNumStates(); i++) total += stateFreqField[i].getValue();
double difference = (total - 1.0) / getNumStates();
for (int i = 0; i < getNumStates(); i++)
stateFrequenciesTemp[i] = stateFreqField[i].getValue() - difference;
setOptions();
} else if ("Norm*/".equals(e.getActionCommand())) {
double total = 0;
for (int i = 0; i < getNumStates(); i++) total += stateFreqField[i].getValue();
for (int i = 0; i < getNumStates(); i++)
stateFrequenciesTemp[i] = stateFreqField[i].getValue() / total;
setOptions();
}
}