/** * 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
/** * 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); }
/** * Returns the component of the section corresponding to the given feature. * * @param identification the identification of the project * @param identificationFeaturesGenerator the identification features generator of the project * @param identificationParameters the identification parameters * @param keys the keys of the protein matches to output * @param nSurroundingAA the number of surrounding amino acids to export * @param linePrefix the line prefix to use. * @param peptideMatch the peptide match * @param psParameter the PeptideShaker parameters of the match * @param peptideFeature the peptide feature to export * @param validatedOnly whether only validated matches should be exported * @param decoys whether decoy matches should be exported as well * @param waitingHandler the waiting handler * @return the component of the section corresponding to the given feature * @throws IOException exception thrown whenever an error occurred while interacting with a file * while mapping potential modification sites * @throws InterruptedException exception thrown whenever a threading issue occurred while mapping * potential modification sites * @throws ClassNotFoundException exception thrown whenever an error occurred while deserializing * an object from the ProteinTree * @throws SQLException exception thrown whenever an error occurred while interacting with the * ProteinTree * @throws uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException exception thrown whenever an error * occurred while reading an mzML file */ public static String getfeature( Identification identification, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, ArrayList<String> keys, int nSurroundingAA, String linePrefix, PeptideMatch peptideMatch, PSParameter psParameter, PsPeptideFeature peptideFeature, boolean validatedOnly, boolean decoys, WaitingHandler waitingHandler) throws IOException, IllegalArgumentException, SQLException, ClassNotFoundException, InterruptedException, MzMLUnmarshallerException { switch (peptideFeature) { case accessions: StringBuilder proteins = new StringBuilder(); ArrayList<String> accessions = peptideMatch .getTheoreticPeptide() .getParentProteins(identificationParameters.getSequenceMatchingPreferences()); Collections.sort(accessions); for (String accession : accessions) { if (proteins.length() > 0) { proteins.append("; "); } proteins.append(accession); } return proteins.toString(); case protein_description: SequenceFactory sequenceFactory = SequenceFactory.getInstance(); StringBuilder descriptions = new StringBuilder(); accessions = peptideMatch .getTheoreticPeptide() .getParentProteins(identificationParameters.getSequenceMatchingPreferences()); Collections.sort(accessions); for (String accession : accessions) { if (descriptions.length() > 0) { descriptions.append("; "); } descriptions.append(sequenceFactory.getHeader(accession).getDescription()); } return descriptions.toString(); case protein_groups: HashSet<String> proteinGroups = identification.getProteinMatches(peptideMatch.getTheoreticPeptide()); proteins = new StringBuilder(); ArrayList<String> proteinGroupsList = new ArrayList<String>(proteinGroups); Collections.sort(proteinGroupsList); if (proteinGroupsList.size() > 1) { identification.loadProteinMatchParameters( proteinGroupsList, psParameter, waitingHandler, false); } psParameter = new PSParameter(); for (String proteinGroup : proteinGroupsList) { if (identification.getProteinIdentification().contains(proteinGroup)) { psParameter = (PSParameter) identification.getProteinMatchParameter(proteinGroup, psParameter); if (proteins.length() > 0) { proteins.append("; "); } List<String> groupAccessions = Arrays.asList(ProteinMatch.getAccessions(proteinGroup)); Collections.sort(groupAccessions); boolean first = true; for (String accession : groupAccessions) { if (first) { first = false; } else { proteins.append(", "); } proteins.append(accession); } proteins.append(" ("); proteins.append(psParameter.getMatchValidationLevel().getName()); proteins.append(")"); } } return proteins.toString(); case best_protein_group_validation: MatchValidationLevel bestProteinValidationLevel = MatchValidationLevel.none; proteinGroups = identification.getProteinMatches(peptideMatch.getTheoreticPeptide()); proteinGroupsList = new ArrayList<String>(proteinGroups); Collections.sort(proteinGroupsList); if (proteinGroupsList.size() > 1) { identification.loadProteinMatchParameters( proteinGroupsList, psParameter, waitingHandler, false); } psParameter = new PSParameter(); for (String proteinGroup : proteinGroupsList) { if (identification.getProteinIdentification().contains(proteinGroup)) { psParameter = (PSParameter) identification.getProteinMatchParameter(proteinGroup, psParameter); if (psParameter.getMatchValidationLevel().getIndex() > bestProteinValidationLevel.getIndex()) { bestProteinValidationLevel = psParameter.getMatchValidationLevel(); } } } return bestProteinValidationLevel.getName(); case confidence: return psParameter.getPeptideConfidence() + ""; case decoy: if (peptideMatch .getTheoreticPeptide() .isDecoy(identificationParameters.getSequenceMatchingPreferences())) { return "1"; } else { return "0"; } case hidden: if (psParameter.isHidden()) { return "1"; } else { return "0"; } case localization_confidence: return getPeptideModificationLocations( peptideMatch, identificationParameters.getSearchParameters().getPtmSettings()) + ""; case pi: return psParameter.getProteinInferenceClassAsString(); case position: accessions = peptideMatch .getTheoreticPeptide() .getParentProteins(identificationParameters.getSequenceMatchingPreferences()); Collections.sort(accessions); Peptide peptide = peptideMatch.getTheoreticPeptide(); String start = ""; for (String proteinAccession : accessions) { if (!start.equals("")) { start += "; "; } Protein protein = SequenceFactory.getInstance().getProtein(proteinAccession); ArrayList<Integer> starts = protein.getPeptideStart( peptide.getSequence(), identificationParameters.getSequenceMatchingPreferences()); Collections.sort(starts); boolean first = true; for (int startAa : starts) { if (first) { first = false; } else { start += ", "; } start += startAa; } } return start; case psms: return peptideMatch.getSpectrumCount() + ""; case variable_ptms: return Peptide.getPeptideModificationsAsString(peptideMatch.getTheoreticPeptide(), true); case fixed_ptms: return Peptide.getPeptideModificationsAsString(peptideMatch.getTheoreticPeptide(), false); case score: return psParameter.getPeptideScore() + ""; case raw_score: return psParameter.getPeptideProbabilityScore() + ""; case sequence: return peptideMatch.getTheoreticPeptide().getSequence(); case missed_cleavages: peptide = peptideMatch.getTheoreticPeptide(); Integer nMissedCleavages = peptide.getNMissedCleavages( identificationParameters.getSearchParameters().getDigestionPreferences()); if (nMissedCleavages == null) { nMissedCleavages = 0; } return nMissedCleavages + ""; case modified_sequence: return peptideMatch .getTheoreticPeptide() .getTaggedModifiedSequence( identificationParameters.getSearchParameters().getPtmSettings(), false, false, true); case starred: if (psParameter.isStarred()) { return "1"; } else { return "0"; } case aaBefore: peptide = peptideMatch.getTheoreticPeptide(); accessions = peptide.getParentProteins(identificationParameters.getSequenceMatchingPreferences()); Collections.sort(accessions); String subSequence = ""; for (String proteinAccession : accessions) { if (!subSequence.equals("")) { subSequence += "; "; } HashMap<Integer, String[]> surroundingAAs = SequenceFactory.getInstance() .getProtein(proteinAccession) .getSurroundingAA( peptide.getSequence(), nSurroundingAA, identificationParameters.getSequenceMatchingPreferences()); ArrayList<Integer> starts = new ArrayList<Integer>(surroundingAAs.keySet()); Collections.sort(starts); boolean first = true; for (int startAa : starts) { if (first) { first = false; } else { subSequence += ", "; } subSequence += surroundingAAs.get(startAa)[0]; } } return subSequence; case aaAfter: peptide = peptideMatch.getTheoreticPeptide(); accessions = peptide.getParentProteins(identificationParameters.getSequenceMatchingPreferences()); Collections.sort(accessions); subSequence = ""; for (String proteinAccession : accessions) { if (!subSequence.equals("")) { subSequence += "; "; } HashMap<Integer, String[]> surroundingAAs = SequenceFactory.getInstance() .getProtein(proteinAccession) .getSurroundingAA( peptide.getSequence(), nSurroundingAA, identificationParameters.getSequenceMatchingPreferences()); ArrayList<Integer> starts = new ArrayList<Integer>(surroundingAAs.keySet()); Collections.sort(starts); boolean first = true; for (int startAa : starts) { if (first) { first = false; } else { subSequence += ", "; } subSequence += surroundingAAs.get(startAa)[1]; } } return subSequence; case nValidatedProteinGroups: peptide = peptideMatch.getTheoreticPeptide(); return identificationFeaturesGenerator.getNValidatedProteinGroups(peptide, waitingHandler) + ""; case unique_database: peptide = peptideMatch.getTheoreticPeptide(); if (identification.isUniqueInDatabase(peptide)) { return "1"; } else { return "0"; } case validated: return psParameter.getMatchValidationLevel().toString(); case validated_psms: return identificationFeaturesGenerator.getNValidatedSpectraForPeptide(peptideMatch.getKey()) + ""; case probabilistic_score: PSPtmScores ptmScores = new PSPtmScores(); ptmScores = (PSPtmScores) peptideMatch.getUrParam(ptmScores); if (ptmScores != null) { StringBuilder result = new StringBuilder(); ArrayList<String> modList = new ArrayList<String>(ptmScores.getScoredPTMs()); Collections.sort(modList); for (String mod : modList) { PtmScoring ptmScoring = ptmScores.getPtmScoring(mod); ArrayList<Integer> sites = new ArrayList<Integer>(ptmScoring.getProbabilisticSites()); if (!sites.isEmpty()) { Collections.sort(sites); if (result.length() > 0) { result.append(", "); } result.append(mod).append(" ("); boolean firstSite = true; for (int site : sites) { if (firstSite) { firstSite = false; } else { result.append(", "); } result.append(site).append(": ").append(ptmScoring.getProbabilisticScore(site)); } result.append(")"); } } return result.toString(); } return ""; case d_score: StringBuilder result = new StringBuilder(); ptmScores = new PSPtmScores(); ptmScores = (PSPtmScores) peptideMatch.getUrParam(ptmScores); if (ptmScores != null) { ArrayList<String> modList = new ArrayList<String>(ptmScores.getScoredPTMs()); Collections.sort(modList); for (String mod : modList) { PtmScoring ptmScoring = ptmScores.getPtmScoring(mod); ArrayList<Integer> sites = new ArrayList<Integer>(ptmScoring.getDSites()); if (!sites.isEmpty()) { Collections.sort(sites); if (result.length() > 0) { result.append(", "); } result.append(mod).append(" ("); boolean firstSite = true; for (int site : sites) { if (firstSite) { firstSite = false; } else { result.append(", "); } result.append(site).append(": ").append(ptmScoring.getDeltaScore(site)); } result.append(")"); } } return result.toString(); } return ""; case confident_modification_sites: String sequence = peptideMatch.getTheoreticPeptide().getSequence(); return identificationFeaturesGenerator.getConfidentPtmSites(peptideMatch, sequence); case confident_modification_sites_number: return identificationFeaturesGenerator.getConfidentPtmSitesNumber(peptideMatch); case ambiguous_modification_sites: sequence = peptideMatch.getTheoreticPeptide().getSequence(); return identificationFeaturesGenerator.getAmbiguousPtmSites(peptideMatch, sequence); case ambiguous_modification_sites_number: return identificationFeaturesGenerator.getAmbiguousPtmSiteNumber(peptideMatch); case confident_phosphosites: ArrayList<String> modifications = new ArrayList<String>(); for (String ptm : identificationParameters .getSearchParameters() .getPtmSettings() .getAllNotFixedModifications()) { if (ptm.contains("Phospho")) { modifications.add(ptm); } } return identificationFeaturesGenerator.getConfidentPtmSites( peptideMatch, peptideMatch.getTheoreticPeptide().getSequence(), modifications); case confident_phosphosites_number: modifications = new ArrayList<String>(); for (String ptm : identificationParameters .getSearchParameters() .getPtmSettings() .getAllNotFixedModifications()) { if (ptm.contains("Phospho")) { modifications.add(ptm); } } return identificationFeaturesGenerator.getConfidentPtmSitesNumber( peptideMatch, modifications); case ambiguous_phosphosites: modifications = new ArrayList<String>(); for (String ptm : identificationParameters .getSearchParameters() .getPtmSettings() .getAllNotFixedModifications()) { if (ptm.contains("Phospho")) { modifications.add(ptm); } } return identificationFeaturesGenerator.getAmbiguousPtmSites( peptideMatch, peptideMatch.getTheoreticPeptide().getSequence(), modifications); case ambiguous_phosphosites_number: modifications = new ArrayList<String>(); for (String ptm : identificationParameters .getSearchParameters() .getPtmSettings() .getAllNotFixedModifications()) { if (ptm.contains("Phospho")) { modifications.add(ptm); } } return identificationFeaturesGenerator.getAmbiguousPtmSiteNumber( peptideMatch, modifications); default: return "Not implemented"; } }