public AddAssociationDialog(
Component parentComponent,
boolean modal,
AlgorithmView view,
boolean createSelected,
String project,
String traits,
String markers) {
super();
parentComponentReference = parentComponent;
currentComponentReference = this;
this.view = view;
labelFactory();
textFieldFactory();
comboBoxFactory();
radioButtonFactory();
buttonFactory();
panelFactory();
dialogSettings();
componentSettings();
for (int i = 0; i < Algorithms.AssociationAlgorithms.algonames().size(); i++) {
this.algorithmComboBox.addItem(Algorithms.AssociationAlgorithms.getalgorithms().get(i));
}
ArrayList<Project> temp = Model.getInstance().getProjects();
for (int i = 0; i < temp.size(); i++) {
this.projectComboBox.addItem(temp.get(i).getName());
}
if (project != null) {
this.projectComboBox.setSelectedItem(project);
}
if (traits != null) {
this.traitSetComboBox.setSelectedItem(traits);
}
if (markers != null) {
this.markerSetComboBox.setSelectedItem(markers);
}
if (project != null && traits == null) {
if (this.traitSetComboBox.getItemCount() > 1) {
this.traitSetComboBox.setSelectedIndex(1);
if (this.markerSetComboBox.getItemCount() > 1) {
this.markerSetComboBox.setSelectedIndex(1);
}
}
}
}
private void algorithmComboBoxActionPerformed(java.awt.event.ActionEvent evt) {
int structtype =
algorithmComboBox.getSelectedIndex() < 0
? -1
: Algorithms.AssociationAlgorithms.inputStructure()
.get(algorithmComboBox.getSelectedIndex());
if (structtype == 2) {
networkLabel.setText("Population");
numberLabel.setVisible(true);
numberComboBox.setVisible(true);
} else if (structtype == 1) {
networkLabel.setText("Network");
numberLabel.setVisible(false);
numberComboBox.setVisible(false);
}
this.traitComboBoxActionPerformed(evt);
}
private void traitComboBoxActionPerformed(java.awt.event.ActionEvent evt) {
if (this.traitSetComboBox.getSelectedObjects().length == 0
|| this.traitSetComboBox.getSelectedIndex() < 0) {
return;
}
String s = this.markerSetComboBox.getSelectedItem().toString();
markerSetComboBox.removeAllItems();
Project project =
Model.getInstance().getProject(this.projectComboBox.getSelectedItem().toString());
TraitSet ts = project.getTrait(this.traitSetComboBox.getSelectedItem().toString());
MarkerSet ms = null;
if (!s.equals("")) ;
{
ms = project.getMarker(s);
}
if ((ts.getHasData() && ms == null) || (ts.getHasData() && ms != null && ms.hasData())) {
algorithmComboBox.setEnabled(true);
this.createAssociationRadioButton.setEnabled(true);
this.createAssociationRadioButton.setSelected(true);
} else {
this.algorithmComboBox.setEnabled(false);
this.createAssociationRadioButton.setEnabled(false);
this.loadAssociationRadioButton.setSelected(true);
}
for (MarkerSet m : project.getMarkers()) {
if (isSameSampleSet(
m, project.getTrait(this.traitSetComboBox.getSelectedItem().toString()))) {
markerSetComboBox.addItem(m.getName());
}
}
for (int i = 0; i < markerSetComboBox.getItemCount(); i++) {
if (markerSetComboBox.getItemAt(i).equals(s)) {
markerSetComboBox.setSelectedIndex(i);
}
}
int structtype =
algorithmComboBox.getSelectedIndex() < 0
? -1
: Algorithms.AssociationAlgorithms.inputStructure()
.get(algorithmComboBox.getSelectedIndex());
if (algorithmComboBox.getSelectedIndex() < 0
|| !(structtype > 0)
|| structtype == 3
|| !this.algorithmComboBox.isEnabled()) {
this.networkComboBox.setEnabled(false);
return;
} else {
this.networkComboBox.setEnabled(true);
}
this.networkComboBox.removeAllItems();
if (structtype == 1) {
TraitSet t = project.getTrait(this.traitSetComboBox.getSelectedItem().toString());
for (int i = 0; i < t.getNetworkIdentifiers().size(); i++) {
this.networkComboBox.addItem(t.getNetworkIdentifiers().get(i));
}
} else if (structtype == 2) {
MarkerSet m = project.getMarker(this.markerSetComboBox.getSelectedItem().toString());
if (m == null) {
return;
}
for (int i = 0; i < m.getPopulations().size(); i++) {
this.networkComboBox.addItem(m.getPopulations().get(i));
}
}
}
/**
* Checks conditions and starts the algorithm.
*
* @param evt
*/
private void runButtonActionPerformed(java.awt.event.ActionEvent evt) {
if (this.projectComboBox.getSelectedItem().equals("")) {
UIMessages.showErrorMessage("Please select a project", "Error");
return;
}
if (this.traitSetComboBox.getSelectedIndex() < 0) {
UIMessages.showErrorMessage("Please select a trait option", "Error");
return;
}
String projectName = projectComboBox.getSelectedItem().toString();
String traitName = traitSetComboBox.getSelectedItem().toString();
String markerName = markerSetComboBox.getSelectedItem().toString();
Project ap = Model.getInstance().getProject(projectName);
TraitSet ts = ap.getTrait(traitName);
MarkerSet ms = ap.getMarker(markerName);
if (this.algorithmComboBox.getSelectedIndex() < 0
&& !this.loadAssociationRadioButton.isSelected()) {
UIMessages.showErrorMessage("Please select an algorithm", "Error");
return;
}
if (this.algorithmComboBox.getSelectedItem().equals("Adaptive Multi-Task Lasso")) {
ArrayList<String> where = new ArrayList<String>();
where.add("markersetid = " + ms.getId());
if (Integer.parseInt(
DataManager.runSelectQuery("count(*)", "feature", true, where, null).get(0))
< 1) {
UIMessages.showErrorMessage("Selected marker set does not have features", "Error");
return;
}
}
if (this.markerSetComboBox.getSelectedIndex() < 0) {
UIMessages.showErrorMessage("Please select a marker", "Error");
return;
}
if (this.networkComboBox.getSelectedIndex() < 0 && this.networkComboBox.isEnabled()) {
UIMessages.showErrorMessage(
"Please select a valid network option for selected algorithm", "Error");
return;
}
if (this.networkComboBox.getSelectedIndex() < 0 && this.networkComboBox.isEnabled()) {
UIMessages.showErrorMessage(
"Please select a valid Population option for selected algorithm", "Error");
return;
}
if (this.numberComboBox.isEnabled() && this.numberComboBox.getSelectedIndex() < 0) {
UIMessages.showErrorMessage(
"Please select a valid Population option for this algorithm", "Error");
return;
}
if (this.nameTextField.getText().equals("")) {
UIMessages.showErrorMessage("Please specify a valid name", "Error");
return;
}
if (Model.getInstance()
.getProject(projectComboBox.getSelectedItem().toString())
.isAssocNamePresentInProject(this.nameTextField.getText())) {
UIMessages.showErrorMessage("Specified name already exists for this project", "Error");
return;
}
String networkName = this.networkComboBox.getSelectedItem().toString();
String algoName = this.algorithmComboBox.getSelectedItem().toString();
String popno = this.numberComboBox.getSelectedItem().toString();
if (!this.numberComboBox.isEnabled()) {
popno = "1";
}
algoName = (algoName.equals("")) ? null : algoName;
Network net = (Network) ts.getTraitStructure(networkName);
if (ts.getNetworks().size() == 0) // without a network, we will be unable
// to view this visualization, so we add it here.
{
try {
view.addAlgorithm(
Algorithms.NetworkAlgorithms.algonames().get(0),
Algorithms.NetworkAlgorithms.jobTypeID().get(0),
ap.getId(),
ts.getId(),
ms.getId());
} catch (Exception e) {
}
}
if (this.createAssociationRadioButton.isSelected()) {
int structtype =
algorithmComboBox.getSelectedIndex() < 0
? -1
: Algorithms.AssociationAlgorithms.inputStructure()
.get(algorithmComboBox.getSelectedIndex());
IOFilesForIOLasso ioffio = null;
if (structtype == 3) {
ioffio = new IOFilesForIOLasso(currentComponentReference);
ioffio.setVisible(true);
if (ioffio.getInputFilePath() == null
|| ioffio.getInputFilePath().length() < 5
|| ioffio.getOutputFilePath() == null
|| ioffio.getOutputFilePath().length() < 5) {
UIMessages.showErrorMessage("I/O Lasso needs valid group files", "Error");
return;
}
}
AssociationParameterObject apo =
new AssociationParameterObject(
(Network) ts.getTraitStructure(networkName),
this.nameTextField.getText(),
ms.getPopulation(networkName),
popno,
ioffio);
int idx = this.algorithmComboBox.getSelectedIndex() - 1;
view.addAlgorithm(
Algorithms.AssociationAlgorithms.algonames().get(idx),
Algorithms.AssociationAlgorithms.jobTypeID().get(idx),
ap.getId(),
ts.getId(),
ms.getId(),
apo);
} else {
DataAddRemoveHandler.getInstance()
.addAssociation(
ap.getId(),
ts,
ms,
this.nameTextField.getText(),
this.associationFilePathTextField.getText(),
null);
}
this.dispose();
}