/**
* Method that makes the necessary JComponents for the SettingsPanel. The used JComponents are: a
* textfield for the cluster name, a TextOrGraphPanel for choosing between text and graph input,
* two comboboxes for the distributions and the corrections, a textfield for the alpha, two
* comboboxes for the option against what cluster should be tested and one for the option how many
* categories must be displayed int the graph, two SettingsOpenPanels for choosing the annotation
* and ontology file, a SettingsSavePanel for the data-file and a button to start the
* calculations.
*/
public void makeJComponents() {
helpButton = new JButton("Help");
helpButton.setMnemonic(KeyEvent.VK_H);
helpButton.addActionListener(new HelpButtonActionListener(this, openBrowserService));
saveSettingsButton = new JButton("Save settings as default");
saveSettingsButton.setMnemonic(KeyEvent.VK_S);
saveSettingsButton.addActionListener(new SaveSettingsButtonActionListener(this));
// JComboboxes.
testBox = new JComboBox(testsArray);
testBox.setSelectedItem(bingo_props.getProperty("tests_def"));
correctionBox = new JComboBox(correctionArray);
correctionBox.setSelectedItem(bingo_props.getProperty("correction_def"));
categoriesBox = new JComboBox(categoriesArray);
categoriesBox.setSelectedItem(bingo_props.getProperty("categories_def"));
clusterVsPanel =
new ChooseRefSetPanel(
this, bingoDir, clusterVsArray, bingo_props.getProperty("refset_def"));
// JTextField.
alphaField = new JTextField(bingo_props.getProperty("signif_def"));
nameField = new JTextField("");
// OverUnderPanel
overUnderPanel = new OverUnderPanel();
// OverUnderPanel
vizPanel = new VizPanel();
// TextOrGraphPanel
textOrGraphPanel = new TextOrGraphPanel();
// JLabels.
overUnderLabel = new JLabel(overunder_label);
nameLabel = new JLabel(clustername_label);
testLabel = new JLabel(test_label);
correctionLabel = new JLabel(correction_label);
alphaLabel = new JLabel(sig_label);
categoriesLabel = new JLabel(category_label);
clusterVsLabel = new JLabel(ref_label);
testLabel.setForeground(Color.black);
correctionLabel.setForeground(Color.black);
alphaLabel.setForeground(Color.black);
categoriesLabel.setForeground(Color.black);
clusterVsLabel.setForeground(Color.black);
ecLabel = new JLabel(ec_label);
// annotationPanel.
annotationLabel = new JLabel(annotation_label);
annotationPanel =
new ChooseAnnotationPanel(
this, bingoDir, params.getSpeciesLabels(), bingo_props.getProperty("species_def"));
// evidence code Field
ecField = new JTextField();
// ontologyPanel.
namespaceLabel = new JLabel(namespace_label);
namespacePanel =
new ChooseNamespacePanel(
this, bingoDir, params.getNamespaceLabels(), bingo_props.getProperty("namespace_def"));
ontologyLabel = new JLabel(ontology_label);
ontologyPanel =
new ChooseOntologyPanel(
this,
bingoDir,
params.getOntologyLabels(),
bingo_props.getProperty("ontology_file_def"));
// Creating SettingsSavePanels.
dataPanel = new SaveResultsPanel("Data", this, bingoDir);
// the bingo-button to start the calculations.
bingoButton = new JButton("Start bingo");
bingoButton.setMnemonic(KeyEvent.VK_B);
bingoButton.addActionListener(new SettingsPanelActionListener(params, this, adapter));
}
/** This constructor creates the panel with its swing-components. */
public SettingsPanel(
final String bingoDir, final CySwingAppAdapter adapter, OpenBrowser openBrowserService) {
super();
this.bingoDir = bingoDir;
this.adapter = adapter;
this.openBrowserService = openBrowserService;
// Create a new bingo parameter set
try {
params = new BingoParameters(bingoDir);
} catch (IOException e) {
JOptionPane.showMessageDialog(
this,
"Error opening the properties file."
+ "\n"
+ "Please make sure that there is bingo_gui.properties file"
+ "\n"
+ "in the bingo.jar or in your cytoscape plugins directory.");
}
bingo_props = params.getbingo_props();
// create the JComponents.
makeJComponents();
setPreferredSize(new Dimension(DIM_WIDTH, DIM_HEIGHT));
setOpaque(false);
// create border.
setBorder(
BorderFactory.createTitledBorder(
BorderFactory.createLineBorder(Color.black),
"bingo settings",
0,
0,
new Font("bingo settings", Font.BOLD, 16),
Color.black));
// Layout with GridBagLayout.
GridBagLayout gridbag = new GridBagLayout();
GridBagConstraints c = new GridBagConstraints();
setLayout(gridbag);
c.weighty = 1;
c.weightx = 1;
c.fill = GridBagConstraints.HORIZONTAL;
JPanel dummyPanel = new JPanel();
dummyPanel.setOpaque(false);
dummyPanel.setPreferredSize(new Dimension(50, 20));
c.gridx = 0;
gridbag.setConstraints(dummyPanel, c);
add(dummyPanel);
c.gridx = 1;
c.fill = GridBagConstraints.NONE;
c.anchor = GridBagConstraints.WEST;
gridbag.setConstraints(saveSettingsButton, c);
add(saveSettingsButton);
c.gridx = 2;
c.anchor = GridBagConstraints.EAST;
gridbag.setConstraints(helpButton, c);
add(helpButton);
JPanel dummyPanel2 = new JPanel();
dummyPanel2.setOpaque(false);
dummyPanel2.setPreferredSize(new Dimension(50, 20));
c.gridx = 3;
c.fill = GridBagConstraints.HORIZONTAL;
c.anchor = GridBagConstraints.CENTER;
c.gridwidth = GridBagConstraints.REMAINDER;
gridbag.setConstraints(dummyPanel2, c);
add(dummyPanel2);
c.weighty = 1;
c.weightx = 100;
c.gridx = 1;
c.gridwidth = 2;
c.gridwidth = GridBagConstraints.RELATIVE;
c.fill = GridBagConstraints.HORIZONTAL;
gridbag.setConstraints(nameLabel, c);
add(nameLabel);
gridbag.setConstraints(nameField, c);
add(nameField);
c.fill = GridBagConstraints.BOTH;
c.gridheight = 1;
c.weighty = 100;
gridbag.setConstraints(textOrGraphPanel, c);
add(textOrGraphPanel);
c.fill = GridBagConstraints.HORIZONTAL;
c.gridheight = 1;
c.weighty = 1;
gridbag.setConstraints(overUnderLabel, c);
add(overUnderLabel);
gridbag.setConstraints(overUnderPanel, c);
add(overUnderPanel);
gridbag.setConstraints(vizPanel, c);
add(vizPanel);
gridbag.setConstraints(testLabel, c);
add(testLabel);
gridbag.setConstraints(testBox, c);
add(testBox);
gridbag.setConstraints(correctionLabel, c);
add(correctionLabel);
gridbag.setConstraints(correctionBox, c);
add(correctionBox);
gridbag.setConstraints(alphaLabel, c);
add(alphaLabel);
gridbag.setConstraints(alphaField, c);
add(alphaField);
gridbag.setConstraints(categoriesLabel, c);
add(categoriesLabel);
gridbag.setConstraints(categoriesBox, c);
add(categoriesBox);
gridbag.setConstraints(clusterVsLabel, c);
add(clusterVsLabel);
// include custom ref set option
gridbag.setConstraints(clusterVsPanel, c);
add(clusterVsPanel);
gridbag.setConstraints(ontologyLabel, c);
add(ontologyLabel);
gridbag.setConstraints(ontologyPanel, c);
add(ontologyPanel);
gridbag.setConstraints(namespaceLabel, c);
add(namespaceLabel);
gridbag.setConstraints(namespacePanel, c);
add(namespacePanel);
gridbag.setConstraints(annotationLabel, c);
add(annotationLabel);
gridbag.setConstraints(annotationPanel, c);
add(annotationPanel);
gridbag.setConstraints(ecLabel, c);
add(ecLabel);
gridbag.setConstraints(ecField, c);
add(ecField);
gridbag.setConstraints(dataPanel, c);
add(dataPanel);
gridbag.setConstraints(bingoButton, c);
add(bingoButton);
validate();
}
