/**
* Returns a list of descriptions corresponding to every item matching the search.
*
* @return a list of descriptions
* @throws SQLException thrown if an SQLException occurs
* @throws ClassNotFoundException thrown if a ClassNotFoundException occurs
* @throws IOException thrown if an IOException occurs
* @throws InterruptedException thrown if an InterruptedException occurs
*/
public ArrayList<String> getPossibilitiesDescriptions()
throws SQLException, ClassNotFoundException, IOException, InterruptedException {
Identification identification = peptideShakerGUI.getIdentification();
// Some necessary pre-caching
ArrayList<Type> typeList = types.get(jumpType);
ArrayList<String> keys = possibilities.get(jumpType),
proteinKeys = new ArrayList<String>(),
peptideKeys = new ArrayList<String>();
for (int i = 0; i < keys.size(); i++) {
String key = keys.get(i);
if (typeList.get(i) == Type.PROTEIN) {
proteinKeys.add(key);
} else if (typeList.get(i) == Type.PEPTIDE) {
peptideKeys.add(key);
}
}
if (!proteinKeys.isEmpty()) {
identification.loadProteinMatches(proteinKeys, null, false);
}
if (!peptideKeys.isEmpty()) {
identification.loadPeptideMatches(peptideKeys, null, false);
}
ArrayList<String> descriptions = new ArrayList<String>();
for (int i = 0; i < keys.size(); i++) {
String key = keys.get(i);
Type type = typeList.get(i);
String description = getItemDescription(key, type);
descriptions.add(description);
}
return descriptions;
}
/**
* Returns the description of an item.
*
* @param key the key of the item
* @param itemType the type of the item
* @return the description of an item
* @throws SQLException thrown if an SQLException occurs
* @throws ClassNotFoundException thrown if a ClassNotFoundException occurs
* @throws IOException thrown if an IOException occurs
* @throws InterruptedException thrown if an InterruptedException occurs
*/
private String getItemDescription(String key, Type itemType)
throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException,
InterruptedException {
Identification identification = peptideShakerGUI.getIdentification();
switch (itemType) {
case PROTEIN:
ProteinMatch proteinMatch = identification.getProteinMatch(key);
String mainMatch = proteinMatch.getMainMatch();
String description = sequenceFactory.getHeader(mainMatch).getSimpleProteinDescription();
String result = mainMatch;
for (String accession : ProteinMatch.getAccessions(key)) {
if (!accession.equals(mainMatch)) {
if (!result.equals(mainMatch)) {
result += ", ";
}
result += accession;
}
}
result += " - " + description;
return result;
case PEPTIDE:
PeptideMatch peptideMatch = identification.getPeptideMatch(key);
return peptideShakerGUI
.getDisplayFeaturesGenerator()
.getTaggedPeptideSequence(peptideMatch, true, true, true);
case SPECTRUM:
return Spectrum.getSpectrumTitle(key) + " (" + Spectrum.getSpectrumFile(key) + ")";
default:
return "Unknown";
}
}
/**
* 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
/**
* Sets the main match if the main match column is selected, or opens the protein web link if the
* accession number column is selected.
*
* @param evt
*/
private void proteinMatchTableMouseReleased(
java.awt.event.MouseEvent evt) { // GEN-FIRST:event_proteinMatchTableMouseReleased
int row = proteinMatchTable.rowAtPoint(evt.getPoint());
int column = proteinMatchTable.columnAtPoint(evt.getPoint());
if (row != -1) {
if (column == 1) {
try {
inspectedMatch.setMainMatch(accessions.get(row));
identification.updateProteinMatch(inspectedMatch);
peptideShakerGUI
.getIdentificationFeaturesGenerator()
.updateCoverableAA(inspectedMatch.getKey());
peptideShakerGUI
.getIdentificationFeaturesGenerator()
.updateSequenceCoverage(inspectedMatch.getKey());
peptideShakerGUI
.getIdentificationFeaturesGenerator()
.updateObservableCoverage(inspectedMatch.getKey());
} catch (Exception e) {
peptideShakerGUI.catchException(e);
}
proteinMatchTable.revalidate();
proteinMatchTable.repaint();
} else if (column == 2) {
// open protein link in web browser
if (evt.getButton() == MouseEvent.BUTTON1
&& ((String) proteinMatchTable.getValueAt(row, column)).lastIndexOf("<html>") != -1) {
String link = (String) proteinMatchTable.getValueAt(row, column);
link = link.substring(link.indexOf("\"") + 1);
link = link.substring(0, link.indexOf("\""));
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL(link);
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}
}
}
} // GEN-LAST:event_proteinMatchTableMouseReleased
/**
* Open the protein html links.
*
* @param evt
*/
private void relatedHitsTableMouseReleased(
java.awt.event.MouseEvent evt) { // GEN-FIRST:event_relatedHitsTableMouseReleased
int row = relatedHitsTable.getSelectedRow();
int column = relatedHitsTable.getSelectedColumn();
if (row != -1) {
if (column == 1) {
// open protein links in web browser
if (evt != null
&& evt.getButton() == MouseEvent.BUTTON1
&& ((String) relatedHitsTable.getValueAt(row, column)).lastIndexOf("a href=") != -1) {
peptideShakerGUI.openProteinLinks((String) relatedHitsTable.getValueAt(row, column));
}
}
}
} // GEN-LAST:event_relatedHitsTableMouseReleased
/** Updates the item selection in the selected tab. */
public void updateSelectionInTab() {
indexLabel.setForeground(Color.BLACK);
if (types.get(jumpType).get(currentSelection.get(jumpType)) == Type.PROTEIN) {
peptideShakerGUI.setSelectedItems(
possibilities.get(jumpType).get(currentSelection.get(jumpType)),
PeptideShakerGUI.NO_SELECTION,
PeptideShakerGUI.NO_SELECTION);
peptideShakerGUI.updateSelectionInCurrentTab();
} else if (types.get(jumpType).get(currentSelection.get(jumpType)) == Type.PEPTIDE) {
peptideShakerGUI.setSelectedItems(
PeptideShakerGUI.NO_SELECTION,
possibilities.get(jumpType).get(currentSelection.get(jumpType)),
PeptideShakerGUI.NO_SELECTION);
if (peptideShakerGUI.getSelectedTab() == PeptideShakerGUI.MODIFICATIONS_TAB_INDEX
&& !peptideShakerGUI
.getDisplayedPeptides()
.contains(possibilities.get(jumpType).get(currentSelection.get(jumpType)))) {
// warn the user that the current selection is not in the tab
indexLabel.setForeground(Color.RED);
} else {
peptideShakerGUI.updateSelectionInCurrentTab();
}
} else {
peptideShakerGUI.setSelectedItems(
PeptideShakerGUI.NO_SELECTION,
PeptideShakerGUI.NO_SELECTION,
possibilities.get(jumpType).get(currentSelection.get(jumpType)));
peptideShakerGUI.updateSelectionInCurrentTab();
}
String label =
"("
+ (currentSelection.get(jumpType) + 1)
+ " of "
+ possibilities.get(jumpType).size()
+ ")";
indexLabel.setText(label);
lastLabel.put(jumpType, label);
}
/**
* 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);
}
/** Set the properties for the columns in the results tables. */
private void setColumnProperies() {
proteinMatchTable.getTableHeader().setReorderingAllowed(false);
uniqueHitsTable.getTableHeader().setReorderingAllowed(false);
relatedHitsTable.getTableHeader().setReorderingAllowed(false);
proteinMatchTable.getColumn(" ").setMinWidth(30);
proteinMatchTable.getColumn(" ").setMaxWidth(30);
// set the preferred size of the accession column
Integer width =
peptideShakerGUI.getPreferredAccessionColumnWidth(
proteinMatchTable, proteinMatchTable.getColumn("Accession").getModelIndex(), 2);
if (width != null) {
proteinMatchTable.getColumn("Accession").setMinWidth(width);
proteinMatchTable.getColumn("Accession").setMaxWidth(width);
} else {
proteinMatchTable.getColumn("Accession").setMinWidth(15);
proteinMatchTable.getColumn("Accession").setMaxWidth(Integer.MAX_VALUE);
}
// the validated column
uniqueHitsTable.getColumn(" ").setMaxWidth(30);
relatedHitsTable.getColumn(" ").setMaxWidth(30);
uniqueHitsTable.getColumn(" ").setMinWidth(30);
relatedHitsTable.getColumn(" ").setMinWidth(30);
proteinMatchTable.getColumn("").setMaxWidth(30);
uniqueHitsTable.getColumn("").setMaxWidth(30);
relatedHitsTable.getColumn("").setMaxWidth(30);
proteinMatchTable.getColumn("").setMinWidth(30);
uniqueHitsTable.getColumn("").setMinWidth(30);
relatedHitsTable.getColumn("").setMinWidth(30);
// the score and confidence columns
uniqueHitsTable.getColumn("Confidence").setMaxWidth(90);
uniqueHitsTable.getColumn("Confidence").setMinWidth(90);
uniqueHitsTable.getColumn("Score").setMaxWidth(90);
uniqueHitsTable.getColumn("Score").setMinWidth(90);
relatedHitsTable.getColumn("Confidence").setMaxWidth(90);
relatedHitsTable.getColumn("Confidence").setMinWidth(90);
relatedHitsTable.getColumn("Score").setMaxWidth(90);
relatedHitsTable.getColumn("Score").setMinWidth(90);
// change the cell renderer to fix a problem in Nimbus and alternating row colors
proteinMatchTable.getColumn(" ").setCellRenderer(new NimbusCheckBoxRenderer());
proteinMatchTable
.getColumn("Accession")
.setCellRenderer(
new HtmlLinksRenderer(
peptideShakerGUI.getSelectedRowHtmlTagFontColor(),
peptideShakerGUI.getNotSelectedRowHtmlTagFontColor()));
uniqueHitsTable
.getColumn("Protein(s)")
.setCellRenderer(
new HtmlLinksRenderer(
peptideShakerGUI.getSelectedRowHtmlTagFontColor(),
peptideShakerGUI.getNotSelectedRowHtmlTagFontColor()));
uniqueHitsTable
.getColumn(" ")
.setCellRenderer(
new TrueFalseIconRenderer(
new ImageIcon(this.getClass().getResource("/icons/accept.png")),
new ImageIcon(this.getClass().getResource("/icons/Error_3.png")),
"Validated",
"Not Validated"));
uniqueHitsTable
.getColumn("Score")
.setCellRenderer(
new JSparklinesBarChartTableCellRenderer(
PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
uniqueHitsTable
.getColumn("Confidence")
.setCellRenderer(
new JSparklinesBarChartTableCellRenderer(
PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
((JSparklinesBarChartTableCellRenderer) uniqueHitsTable.getColumn("Score").getCellRenderer())
.showNumberAndChart(true, peptideShakerGUI.getLabelWidth() + 5);
((JSparklinesBarChartTableCellRenderer)
uniqueHitsTable.getColumn("Confidence").getCellRenderer())
.showNumberAndChart(true, peptideShakerGUI.getLabelWidth() + 5);
relatedHitsTable
.getColumn("Protein(s)")
.setCellRenderer(
new HtmlLinksRenderer(
peptideShakerGUI.getSelectedRowHtmlTagFontColor(),
peptideShakerGUI.getNotSelectedRowHtmlTagFontColor()));
relatedHitsTable
.getColumn(" ")
.setCellRenderer(
new TrueFalseIconRenderer(
new ImageIcon(this.getClass().getResource("/icons/accept.png")),
new ImageIcon(this.getClass().getResource("/icons/Error_3.png")),
"Validated",
"Not Validated"));
relatedHitsTable
.getColumn("Score")
.setCellRenderer(
new JSparklinesBarChartTableCellRenderer(
PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
relatedHitsTable
.getColumn("Confidence")
.setCellRenderer(
new JSparklinesBarChartTableCellRenderer(
PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
((JSparklinesBarChartTableCellRenderer) relatedHitsTable.getColumn("Score").getCellRenderer())
.showNumberAndChart(true, peptideShakerGUI.getLabelWidth() + 5);
((JSparklinesBarChartTableCellRenderer)
relatedHitsTable.getColumn("Confidence").getCellRenderer())
.showNumberAndChart(true, peptideShakerGUI.getLabelWidth() + 5);
// set up the table header tooltips
candidateProteinsTableToolTips = new ArrayList<String>();
candidateProteinsTableToolTips.add(null);
candidateProteinsTableToolTips.add("Currently Selected Protein Match");
candidateProteinsTableToolTips.add("Protein Accession");
candidateProteinsTableToolTips.add("Protein Description");
uniqueHitsTableToolTips = new ArrayList<String>();
uniqueHitsTableToolTips.add(null);
uniqueHitsTableToolTips.add("Protein Accession(s)");
uniqueHitsTableToolTips.add("Protein Score");
uniqueHitsTableToolTips.add("Protein Confidence");
uniqueHitsTableToolTips.add("Validated");
relatedHitsTableToolTips = new ArrayList<String>();
relatedHitsTableToolTips.add(null);
relatedHitsTableToolTips.add("Protein Accession(s)");
relatedHitsTableToolTips.add("Protein Score");
relatedHitsTableToolTips.add("Protein Confidence");
relatedHitsTableToolTips.add("Validated");
}