/**
* Update the protein table according to the protein inference selection.
*
* @param evt
*/
private void okButtonActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_okButtonActionPerformed
PSParameter psParameter = new PSParameter();
try {
psParameter =
(PSParameter)
identification.getProteinMatchParameter(inspectedMatch.getKey(), psParameter);
} catch (Exception e) {
peptideShakerGUI.catchException(e);
this.dispose();
return;
}
if (!inspectedMatch.getMainMatch().equals(previousMainMatch)
|| groupClassJComboBox.getSelectedIndex() != psParameter.getGroupClass()) {
try {
psParameter.setGroupClass(groupClassJComboBox.getSelectedIndex());
identification.updateProteinMatchParameter(inspectedMatch.getKey(), psParameter);
peptideShakerGUI.updateMainMatch(
inspectedMatch.getMainMatch(), groupClassJComboBox.getSelectedIndex());
} catch (Exception e) {
peptideShakerGUI.catchException(e);
}
peptideShakerGUI.setDataSaved(false);
}
this.dispose();
} // GEN-LAST:event_okButtonActionPerformed
@Override
public Object getValueAt(int row, int column) {
PSParameter pSParameter = new PSParameter();
try {
pSParameter =
(PSParameter)
identification.getProteinMatchParameter(associatedMatches.get(row), pSParameter);
} catch (Exception e) {
peptideShakerGUI.catchException(e);
}
switch (column) {
case 0:
return (row + 1);
case 1:
return peptideShakerGUI
.getIdentificationFeaturesGenerator()
.addDatabaseLinks(
new ArrayList<String>(
Arrays.asList(ProteinMatch.getAccessions(associatedMatches.get(row)))));
case 2:
return pSParameter.getProteinScore();
case 3:
return pSParameter.getProteinConfidence();
case 4:
return pSParameter.isValidated();
default:
return "";
}
}
/**
* Creates new form ProteinInferenceDialog.
*
* @param peptideShakerGUI
* @param inspectedMatch
* @param identification
*/
public ProteinInferenceDialog(
PeptideShakerGUI peptideShakerGUI, String inspectedMatch, Identification identification) {
super(peptideShakerGUI, true);
this.identification = identification;
this.peptideShakerGUI = peptideShakerGUI;
try {
this.inspectedMatch = identification.getProteinMatch(inspectedMatch);
previousMainMatch = this.inspectedMatch.getMainMatch();
} catch (Exception e) {
peptideShakerGUI.catchException(e);
this.dispose();
}
accessions = new ArrayList(Arrays.asList(ProteinMatch.getAccessions(inspectedMatch)));
for (String proteinAccession : accessions) {
if (identification.getProteinIdentification().contains(proteinAccession)) {
uniqueMatches.add(proteinAccession);
}
}
for (String proteinKey : identification.getProteinIdentification()) {
if (ProteinMatch.getNProteins(proteinKey) > 1
&& !associatedMatches.contains(proteinKey)
&& !proteinKey.equals(inspectedMatch)) {
for (String proteinAccession : accessions) {
if (proteinKey.contains(proteinAccession)) {
associatedMatches.add(proteinKey);
break;
}
}
}
}
initComponents();
// make sure that the scroll panes are see-through
proteinMatchJScrollPane.getViewport().setOpaque(false);
uniqueHitsJScrollPane.getViewport().setOpaque(false);
relatedHitsJScrollPane.getViewport().setOpaque(false);
groupClassJComboBox.setRenderer(new AlignedListCellRenderer(SwingConstants.CENTER));
PSParameter psParameter = new PSParameter();
try {
psParameter =
(PSParameter) identification.getProteinMatchParameter(inspectedMatch, psParameter);
} catch (Exception e) {
peptideShakerGUI.catchException(e);
}
matchInfoLbl.setText(
"[Score: "
+ Util.roundDouble(psParameter.getProteinScore(), 2)
+ ", Confidence: "
+ Util.roundDouble(psParameter.getProteinConfidence(), 2)
+ "]");
// set up the table column properties
setColumnProperies();
// The index should be set in the design according to the PSParameter class static fields!
groupClassJComboBox.setSelectedIndex(psParameter.getGroupClass());
setLocationRelativeTo(peptideShakerGUI);
setVisible(true);
}