public void actionPerformed(final ActionEvent e) {
// browse alignmentfile button
if (e.getSource() == _alignment_button) {
showChooseAlignmentFile();
}
// alignmenttype dna radio button
else if (e.getSource() == _dna_radio) {
showDnaTypeOptions();
hideAaTypeOptions();
hidePartitionedTypeOptions();
}
// alignmenttype aa radio buttion
else if (e.getSource() == _aa_radio) {
hideDnaTypeOptions();
showAaTypeOptions();
hidePartitionedTypeOptions();
}
// alignmenttype partitioned radio button
else if (e.getSource() == _partitioned_radio) {
hideDnaTypeOptions();
hideAaTypeOptions();
showPartitionedTypeOptions();
}
// partitionfile browse button
else if (e.getSource() == _partitionfile_button && _partitioned_radio.isSelected()) {
showChoosePartitionFile();
}
// bootstrapping checkbox etc
else if (e.getSource() == _use_bootstrapping_checkbox) {
if (_use_bootstrapping_checkbox.isSelected()) {
showBootstrapOptions();
} else {
hideBootstrapOptions();
}
}
// Save Results Destination browse button
else if (e.getSource() == _jobfolder_button) {
showChooseJobDir();
}
// submit button
else if (e.getSource() == _submit_button) {
collectRemainingParameters();
validateInput();
if (_input_errors.size() < 1) {
_job.getMainFrame().getWorkflowPanel().setUsableSubmissionPanel(null);
submitJob(false);
} else {
showErrors();
}
}
// reset button
else if (e.getSource() == _reset_button) {
resetForm();
} else if (e.getSource() == _confirmation_button) {
_job.getMainFrame().setEnabled(true);
_confirmation_frame.setVisible(false);
}
}
public void submitJob(boolean testing) {
_configuration.setWorkspace(_parameters.get(_jobfolder));
_jobpath = _configuration.getWorkspace() + _parameters.get(_jobname);
_configuration.setWorkspace(_jobpath);
String[] submission_parameters = parametersCommand();
boolean status = new File(_jobpath).mkdir();
// execute shellfile
if (_job.getMainFrame().isVisible()) { // don't show confirmation dialogue when testing
_job.switchToWaitingPanel();
// _job.getMainFrame().setEnabled(false);
}
Submission sub = new Submission(submission_parameters, _job, Submission.Jobtype.SGA, testing);
_job.setSubmissionThread(sub);
Thread t = new Thread(sub);
t.start();
if (testing) {
try {
t.join();
} catch (InterruptedException e) {
// TODO Auto-generated catch block
Util.printErrors(e);
}
}
}
public TreeBuilderFormPanel(LayoutManager mgr, Job parent) {
_job = parent;
_configuration = _job.getMainFrame().getConfiguration();
_jobpath = _job.getMainFrame().getConfiguration().getWorkspace() + _parameters.get(_jobname);
this.setLayout(mgr);
_parameters.put(_alignmentfile, null);
_parameters.put(_alignmenttype, null);
_parameters.put(_het_model, null);
_parameters.put(_partitionfile, null);
_parameters.put(_cores, null);
_parameters.put(_use_bootstrap, null);
_parameters.put(_random_seed, null);
_parameters.put(_samples, null);
_parameters.put(_jobname, null);
_parameters.put(_jobfolder, null);
_parameters.put(_treebuilder, "true");
_parameters.put(_parsimony_rnd_seed, null);
_filechooser = _job.getMainFrame().getFilechooser();
buildForm();
resetForm();
}
private void showErrors() {
Set<String> errors = _input_errors.keySet();
for (String error : errors) {
System.out.println(error + " : " + _input_errors.get(error));
if (error.equals(_alignmentfile)) {
highlightError(_alignment_label, _input_errors.get(error));
} else if (error.equals(_partitionfile)) {
highlightError(_partitionfile_label, _input_errors.get(error));
} else if (error.equals(_cores)) {
highlightError(_cores_label, _input_errors.get(error));
} else if (error.equals(_samples)) {
highlightError(_bootstrap_samples_label, _input_errors.get(error));
} else if (error.equals(_random_seed)) {
highlightError(_bootstrap_rnd_seed_label, _input_errors.get(error));
} else if (error.equals(_jobname)) {
highlightError(_jobname_label, _input_errors.get(error));
} else if (error.equals(_jobfolder)) {
highlightError(_jobfolder_label, _input_errors.get(error));
}
}
if (_input_errors.get(_alignmentfile) == null) {
_alignment_label.setForeground(null);
} else if (_input_errors.get(_partitionfile) == null) {
_partitionfile_label.setForeground(null);
} else if (_input_errors.get(_cores) == null) {
_cores_label.setForeground(null);
} else if (_input_errors.get(_samples) == null) {
_bootstrap_samples_label.setForeground(null);
} else if (_input_errors.get(_random_seed) == null) {
_bootstrap_rnd_seed_label.setForeground(null);
} else if (_input_errors.get(_jobfolder) == null) {
_jobfolder_label.setForeground(null);
} else if (_input_errors.get(_jobname) == null) {
_jobname_label.setForeground(null);
}
if (_job.getMainFrame().isVisible()) { // don't show confirmation dialogue when testing
JOptionPane.showMessageDialog(
this, errorsToString(), "There some errors in your input!", JOptionPane.ERROR_MESSAGE);
}
}