@Override
public void actionPerformed(ActionEvent e) {
if (e.getSource().equals(decoyStrategy_pattern)
|| e.getSource().equals(decoyStrategy_searchengine)) {
// decoy pattern can only be edited, if decoy strategy is pattern
decoyPattern_pattern.setEnabled(decoyStrategy_pattern.isSelected());
} else if (e.getSource().equals(addToPreferred_button)
&& (availableScoresList.getSelectedIndex() > -1)) {
preferredScoresModel.addElement(availableScoresList.getSelectedValue());
availableScoresModel.remove(availableScoresList.getSelectedIndex());
} else if (e.getSource().equals(removeFromPreferred_button)
&& (preferredScoresList.getSelectedIndex() > -1)) {
availableScoresModel.addElement(preferredScoresList.getSelectedValue());
preferredScoresModel.remove(preferredScoresList.getSelectedIndex());
} else if (e.getSource().equals(calculatePSMFDR)) {
// execute PSM level operations
if (piaViewModel != null) {
for (Map.Entry<String, Object> setIt : getSettings().entrySet()) {
piaViewModel.addSetting(setIt.getKey(), setIt.getValue());
}
piaViewModel.executePSMOperations();
}
updateFDRPanel();
}
}
/** Paints the FDR information on the panel, if it is calculated */
public void updateFDRPanel() {
if (piaViewModel == null) {
psmFDRPanel.removeAll();
psmFDRPanel.add(new JLabel("No file loaded yet."));
} else {
psmFDRPanel.removeAll();
GridBagConstraints cFDRPanel = new GridBagConstraints();
cFDRPanel.fill = GridBagConstraints.HORIZONTAL;
cFDRPanel.insets = new Insets(5, 5, 5, 5);
JPanel overviewPanel = new JPanel(new GridBagLayout());
overviewPanel.setBorder(BorderFactory.createTitledBorder("FDR for PSM sets / all files"));
GridBagConstraints c = new GridBagConstraints();
c.fill = GridBagConstraints.HORIZONTAL;
c.insets = new Insets(5, 5, 5, 5);
// >> the information data --------------------
JPanel fdrDataPanel = new JPanel(new GridBagLayout());
if (piaViewModel.getPSMModeller().isCombinedFDRScoreCalculated()) {
c.insets = new Insets(0, 5, 5, 5);
c.gridx = 0;
c.gridy = 0;
fdrDataPanel.add(new JLabel("#PSM sets:"), c);
c.gridx = 1;
c.gridy = 0;
fdrDataPanel.add(new JLabel("" + piaViewModel.getPSMModeller().getNrReportPSMs(0L)), c);
FDRData fdrData = piaViewModel.getPSMModeller().getFilesFDRData(0L);
c.gridx = 0;
c.gridy = 1;
fdrDataPanel.add(new JLabel("#PSM sets with FDR:"), c);
c.gridx = 1;
c.gridy = 1;
fdrDataPanel.add(new JLabel("" + fdrData.getNrItems()), c);
c.gridx = 0;
c.gridy = 2;
fdrDataPanel.add(new JLabel("#targets:"), c);
c.gridx = 1;
c.gridy = 2;
fdrDataPanel.add(new JLabel("" + fdrData.getNrTargets()), c);
c.gridx = 0;
c.gridy = 3;
fdrDataPanel.add(new JLabel("#decoys:"), c);
c.gridx = 1;
c.gridy = 3;
fdrDataPanel.add(new JLabel("" + fdrData.getNrDecoys()), c);
c.gridx = 0;
c.gridy = 4;
fdrDataPanel.add(new JLabel("#targets below threshold:"), c);
c.gridx = 1;
c.gridy = 4;
fdrDataPanel.add(new JLabel("" + fdrData.getNrFDRGoodTargets()), c);
c.gridx = 0;
c.gridy = 5;
fdrDataPanel.add(new JLabel("#decoys below threshold:"), c);
c.gridx = 1;
c.gridy = 5;
fdrDataPanel.add(new JLabel("" + fdrData.getNrFDRGoodDecoys()), c);
c.insets = new Insets(5, 5, 5, 5);
} else {
fdrDataPanel.add(new JLabel("<html>Combined FDR score<br/>was not calculated.</html>"), c);
}
c.gridx = 0;
c.gridy = 0;
overviewPanel.add(fdrDataPanel, c);
// >> the information data --------------------
// >> draw PPM deviation ----------------------
/*
VisualizePSM vPSM = new VisualizePSM(piaViewModel.getPSMModeller());
HistogramDataset hd = vPSM.getPPMHistogramData(0l, piaViewModel.getPSMModeller().isCombinedFDRScoreCalculated());
JFreeChart chart = ChartFactory.createHistogram("mass shift (PPM)",
null,
"nrPSMs",
hd,
PlotOrientation.VERTICAL,
false,
false,
false);
chart.getTitle().setFont(new Font("Dialog", Font.BOLD, 14));
XYPlot plot = chart.getXYPlot();
plot.getDomainAxis().setStandardTickUnits(NumberAxis.createIntegerTickUnits());
plot.getRangeAxis().setStandardTickUnits(NumberAxis.createIntegerTickUnits());
plot.getDomainAxis().setTickLabelFont(new Font("Dialog", Font.PLAIN, 10));
plot.getRangeAxis().setTickLabelFont(new Font("Dialog", Font.PLAIN, 10));
plot.getRangeAxis().setLabelFont(new Font("Dialog", Font.BOLD, 12));
XYBarRenderer renderer = (XYBarRenderer) plot.getRenderer();
renderer.setBarPainter(new StandardXYBarPainter());
renderer.setDrawBarOutline(false);
renderer.setShadowVisible(false);
renderer.setSeriesPaint(0, new Color(47, 105, 191));
JPanel ppmPanel = new ChartPanel(chart,
240, 140,
240, 140,
800, 600,
true, true, false, false, true, true);
ppmPanel.setMinimumSize(new Dimension(240, 140));
c.insets = new Insets(0, 0, 0, 0);
c.gridx = 1;
c.gridy = 0;
overviewPanel.add(ppmPanel, c);
*/
// << draw PPM deviation ----------------------
cFDRPanel.gridx = 0;
cFDRPanel.gridy = 0;
psmFDRPanel.add(overviewPanel, cFDRPanel);
}
psmFDRPanel.validate();
psmFDRPanel.repaint();
}
/** Sets recommended settings, based on the loaded PIA interemdiate data. */
public void applyRecommendedSettings() {
if (piaViewModel != null) {
checkCreatePSMSets.setSelected(piaViewModel.getPSMModeller().getFiles().size() > 2);
boolean allAllowStrategySearchengine = true;
for (Long fileID : piaViewModel.getPSMModeller().getFiles().keySet()) {
if (!piaViewModel.getPSMModeller().getFileHasInternalDecoy(fileID)) {
allAllowStrategySearchengine = false;
break;
}
}
if (allAllowStrategySearchengine) {
decoyStrategy_searchengine.setSelected(true);
} else {
decoyStrategy_searchengine.setText("by searchengine (files without internal decoys)");
decoyStrategy_searchengine.setEnabled(false);
decoyStrategy_pattern.setSelected(true);
}
preferredScoresModel.removeAllElements();
availableScoresModel.removeAllElements();
for (Long fileID : piaViewModel.getPSMModeller().getFiles().keySet()) {
for (String scoreShort :
piaViewModel.getPSMModeller().getFilesAvailableScoreShortsForFDR(fileID)) {
ScoreModelEnum modelType = ScoreModelEnum.getModelByDescription(scoreShort);
ScoreModel model;
if (modelType.equals(ScoreModelEnum.UNKNOWN_SCORE)) {
model =
new ScoreModel(
0.0, scoreShort, piaViewModel.getPSMModeller().getScoreName(scoreShort));
} else {
model = new ScoreModel(0.0, modelType);
}
if (!ScoreModelEnum.getNotForPSMFdrScore().contains(model)) {
if (modelType.isSearchengineMainScore()) {
if (!preferredScoresModel.contains(model)) {
preferredScoresModel.addElement(model);
}
} else {
if (!availableScoresModel.contains(model)) {
availableScoresModel.addElement(model);
}
}
}
}
}
calculatePSMFDR.setEnabled(true);
} else {
// the default settings
checkCreatePSMSets.setSelected(true);
decoyStrategy_pattern.setSelected(true);
for (ScoreModelEnum model : ScoreModelEnum.values()) {
if (!ScoreModelEnum.getNotForPSMFdrScore().contains(model)
&& !model.equals(ScoreModelEnum.UNKNOWN_SCORE)) {
availableScoresModel.addElement(
new ScoreModel(0.0, model.getShortName(), model.getName()));
}
}
calculatePSMFDR.setEnabled(false);
}
}