/** * 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"; } }
/** * 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 = reporterGUI.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; default: return "Unknown"; } }
/** * 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); }