/**
* Updates the available settings according to the opened file. This should be called e.g. after
* loading a PIA intermediate file
*/
public void applyLoadedSettings(NodeSettingsRO settings) {
checkCreatePSMSets.setSelected(
settings.getBoolean(
PIASettings.CREATE_PSMSETS.getKey(), PIASettings.CREATE_PSMSETS.getDefaultBoolean()));
fdrThreshold.setValue(
settings.getDouble(
PIASettings.FDR_THRESHOLD.getKey(), PIASettings.FDR_THRESHOLD.getDefaultDouble()));
if (settings
.getString(
PIASettings.ALL_DECOY_STRATEGY.getKey(),
PIASettings.ALL_DECOY_STRATEGY.getDefaultString())
.equals(FDRData.DecoyStrategy.ACCESSIONPATTERN.toString())) {
decoyStrategy_pattern.setSelected(true);
} else {
decoyStrategy_searchengine.setSelected(true);
}
decoyPattern_pattern.setText(
settings.getString(
PIASettings.ALL_DECOY_PATTERN.getKey(),
PIASettings.ALL_DECOY_PATTERN.getDefaultString()));
if (settings.getInt(
PIASettings.ALL_USED_IDENTIFICATIONS.getKey(),
PIASettings.ALL_USED_IDENTIFICATIONS.getDefaultInteger())
== 0) {
usedIdentifications_all.setSelected(true);
} else {
usedIdentifications_top.setSelected(true);
}
preferredScoresModel.removeAllElements();
for (String scoreShort :
settings.getStringArray(
PIASettings.FDR_PREFERRED_SCORES.getKey(),
PIASettings.FDR_PREFERRED_SCORES.getDefaultStringArray())) {
ScoreModelEnum modelType = ScoreModelEnum.getModelByDescription(scoreShort);
ScoreModel model;
if (modelType.equals(ScoreModelEnum.UNKNOWN_SCORE)) {
model = new ScoreModel(0.0, scoreShort, scoreShort);
} else {
model = new ScoreModel(0.0, modelType);
}
preferredScoresModel.addElement(model);
}
}
/**
* Creates a panel, which contains the settings for the wizard on PSM level
*
* @return
*/
private JPanel initializeSettingsPanel() {
JPanel psmPanel = new JPanel(new GridBagLayout());
GridBagConstraints c = new GridBagConstraints();
c.fill = GridBagConstraints.HORIZONTAL;
c.insets = new Insets(5, 5, 5, 5);
// >> create PSM sets and general FDR threshold ---
c.gridx = 0;
c.gridy = 0;
checkCreatePSMSets = new JCheckBox("Create PSM sets");
checkCreatePSMSets.setSelected(true);
psmPanel.add(checkCreatePSMSets, c);
c.gridx = 0;
c.gridy = 1;
psmPanel.add(new JLabel("FDR threshold:"), c);
NumberFormat nf = NumberFormat.getNumberInstance();
nf.setMaximumFractionDigits(32);
fdrThreshold = new JFormattedTextField(nf);
fdrThreshold.setValue(0.01);
c.gridx = 1;
c.gridy = 1;
psmPanel.add(fdrThreshold, c);
// << create PSM sets and general FDR threshold ---
// >> how to define decoys ------------------------
c.gridx = 0;
c.gridy = 2;
psmPanel.add(new JLabel("How to define decoys:"), c);
decoyStrategy_pattern = new JRadioButton("accession pattern");
decoyStrategy_pattern.setActionCommand(FDRData.DecoyStrategy.ACCESSIONPATTERN.toString());
decoyStrategy_pattern.addActionListener(this);
decoyStrategy_searchengine = new JRadioButton("by searchengine");
decoyStrategy_searchengine.setActionCommand(FDRData.DecoyStrategy.SEARCHENGINE.toString());
decoyStrategy_searchengine.addActionListener(this);
decoyStrategyGroup = new ButtonGroup();
decoyStrategyGroup.add(decoyStrategy_pattern);
decoyStrategyGroup.add(decoyStrategy_searchengine);
c.insets = new Insets(0, 5, 0, 5);
c.gridx = 1;
c.gridy = 2;
psmPanel.add(decoyStrategy_pattern, c);
c.gridx = 1;
c.gridy = 3;
psmPanel.add(decoyStrategy_searchengine, c);
c.insets = new Insets(5, 5, 5, 5);
// << how to define decoys ------------------------
// >> decoy pattern -------------------------------
c.gridx = 0;
c.gridy = 4;
psmPanel.add(new JLabel("Decoy pattern:"), c);
decoyPattern_pattern = new JTextField("rev_.*", 10);
c.gridx = 1;
c.gridy = 4;
psmPanel.add(decoyPattern_pattern, c);
// << decoy pattern -------------------------------
// >> used identifications ------------------------
c.gridx = 0;
c.gridy = 5;
psmPanel.add(new JLabel("Used identifications:"), c);
usedIdentifications_top = new JRadioButton("only top identification");
usedIdentifications_top.setActionCommand("1");
usedIdentifications_top.setSelected(true);
usedIdentifications_all = new JRadioButton("all identifications");
usedIdentifications_all.setActionCommand("0");
usedIdentificationsGroup = new ButtonGroup();
usedIdentificationsGroup.add(usedIdentifications_top);
usedIdentificationsGroup.add(usedIdentifications_all);
c.insets = new Insets(0, 5, 0, 5);
c.gridx = 1;
c.gridy = 5;
psmPanel.add(usedIdentifications_top, c);
c.gridx = 1;
c.gridy = 6;
psmPanel.add(usedIdentifications_all, c);
c.insets = new Insets(5, 5, 5, 5);
// << used identifications ------------------------
// >> Preferred score(s) --------------------------
c.gridx = 0;
c.gridy = 7;
psmPanel.add(new JLabel("Preferred score(s):"), c);
JPanel fdrScorePanel = new JPanel(new GridBagLayout());
GridBagConstraints layoutFdrScorePanel = new GridBagConstraints();
layoutFdrScorePanel.fill = GridBagConstraints.HORIZONTAL;
layoutFdrScorePanel.gridx = 0;
layoutFdrScorePanel.gridy = 0;
fdrScorePanel.add(new JLabel("Available PSM scores"), layoutFdrScorePanel);
availableScoresModel = new DefaultListModel<ScoreModel>();
availableScoresList = new JList<ScoreModel>(availableScoresModel);
availableScoresList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
availableScoresList.setLayoutOrientation(JList.VERTICAL);
availableScoresList.setVisibleRowCount(-1);
availableScoresList.setCellRenderer(new ScoreNameListCellRenderer());
JScrollPane listScroller = new JScrollPane(availableScoresList);
listScroller.setPreferredSize(new Dimension(200, 100));
layoutFdrScorePanel.gridx = 0;
layoutFdrScorePanel.gridy = 1;
fdrScorePanel.add(listScroller, layoutFdrScorePanel);
layoutFdrScorePanel.gridx = 2;
layoutFdrScorePanel.gridy = 0;
fdrScorePanel.add(new JLabel("Preferred PSM scores"), layoutFdrScorePanel);
preferredScoresModel = new DefaultListModel<ScoreModel>();
preferredScoresList = new JList<ScoreModel>(preferredScoresModel);
preferredScoresList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
preferredScoresList.setLayoutOrientation(JList.VERTICAL);
preferredScoresList.setVisibleRowCount(-1);
preferredScoresList.setCellRenderer(new ScoreNameListCellRenderer());
listScroller = new JScrollPane(preferredScoresList);
listScroller.setPreferredSize(new Dimension(200, 100));
layoutFdrScorePanel.gridx = 2;
layoutFdrScorePanel.gridy = 1;
fdrScorePanel.add(listScroller, layoutFdrScorePanel);
JPanel psmScoreButtonsPanel = new JPanel();
psmScoreButtonsPanel.setLayout(new BoxLayout(psmScoreButtonsPanel, BoxLayout.Y_AXIS));
psmScoreButtonsPanel.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
addToPreferred_button = new JButton("Add >>");
addToPreferred_button.setAlignmentX(Component.CENTER_ALIGNMENT);
addToPreferred_button.addActionListener(this);
psmScoreButtonsPanel.add(addToPreferred_button);
psmScoreButtonsPanel.add(Box.createRigidArea(new Dimension(0, 5)));
removeFromPreferred_button = new JButton("Remove <<");
removeFromPreferred_button.setAlignmentX(Component.CENTER_ALIGNMENT);
removeFromPreferred_button.addActionListener(this);
psmScoreButtonsPanel.add(removeFromPreferred_button);
layoutFdrScorePanel.gridx = 1;
layoutFdrScorePanel.gridy = 1;
fdrScorePanel.add(psmScoreButtonsPanel, layoutFdrScorePanel);
c.gridx = 1;
c.gridy = 7;
psmPanel.add(fdrScorePanel, c);
// << Preferred score(s) --------------------------
// >> calculate the FDR ---------------------------
calculatePSMFDR = new JButton("Calculate FDR");
calculatePSMFDR.addActionListener(this);
c.gridx = 0;
c.gridy = 8;
c.fill = GridBagConstraints.CENTER;
c.gridwidth = 2;
psmPanel.add(calculatePSMFDR, c);
// >> calculate the FDR ---------------------------
updateAvailableSettings();
return psmPanel;
}