Examples of com.compomics.util.experiment.identification.matches.SpectrumMatch

Package com.compomics.util.experiment.identification.matches

Examples of com.compomics.util.experiment.identification.matches.SpectrumMatch

com.compomics.util.experiment.identification.matches.SpectrumMatch


                // check if we ought to show a tooltip with mod details
                if (identification.matchExists(spectrumKey)) {
                    try {
                        DisplayFeaturesGenerator displayFeaturesGenerator = peptideShakerGUI.getDisplayFeaturesGenerator();
                        SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                        if (spectrumMatch.getBestPeptideAssumption() != null) {
                            String tooltip = displayFeaturesGenerator.getPeptideModificationTooltipAsHtml(spectrumMatch);
                            spectrumTable.setToolTipText(tooltip);
                        } else if (spectrumMatch.getBestTagAssumption() != null) {
                            TagAssumption tagAssumption = spectrumMatch.getBestTagAssumption();
                            spectrumTable.setToolTipText(peptideShakerGUI.getDisplayFeaturesGenerator().getTagModificationTooltipAsHtml(tagAssumption.getTag()));
                        } else {
                            throw new IllegalArgumentException("No best match found for spectrum " + spectrumMatch.getKey() + ".");
                        }
                    } catch (Exception e) {
                        peptideShakerGUI.catchException(e);
                    }
                }

View Full Code Here

            for (String spectrumKey : identification.getSpectrumIdentification(fileName)) {
                if (progressDialog.isRunCanceled()) {
                    break;
                }


                SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);


                if (spectrumMatch.getBestPeptideAssumption() != null) {
                    ArrayList<Integer> currentAdvocates = new ArrayList<Integer>();
                    probabilities = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, probabilities);


                    if (probabilities.getMatchValidationLevel().isValidated()) {


                        totalPeptideShakerIds++;
                        numberOfValidatedPsms++;


                        for (Integer tempAdvocate : advocatesUsed) {
                            if (spectrumMatch.getFirstHit(tempAdvocate) != null) {
                                SpectrumIdentificationAssumption firstHit = spectrumMatch.getFirstHit(tempAdvocate);
                                if ((firstHit instanceof PeptideAssumption) && ((PeptideAssumption) firstHit).getPeptide().isSameSequenceAndModificationStatus(spectrumMatch.getBestPeptideAssumption().getPeptide(),
                                        peptideShakerGUI.getSequenceMatchingPreferences())) {
                                    currentAdvocates.add(tempAdvocate);
                                }
                            }
                        }

View Full Code Here

                searchResultsTablePeptideTooltips = new ArrayList<String>();
                String key = getSelectedSpectrumKey();


                if (identification.matchExists(key)) {


                    SpectrumMatch spectrumMatch = identification.getSpectrumMatch(key);
                    PSParameter probabilities = new PSParameter();
                    probabilities = (PSParameter) identification.getSpectrumMatchParameter(key, probabilities);


                    // fill peptide shaker table
                    DisplayFeaturesGenerator displayFeaturesGenerator = peptideShakerGUI.getDisplayFeaturesGenerator();
                    String proteins = "";
                    String sequence;
                    if (spectrumMatch.getBestPeptideAssumption() != null) {
                        proteins = displayFeaturesGenerator.addDatabaseLinks(spectrumMatch.getBestPeptideAssumption().getPeptide().getParentProteins(peptideShakerGUI.getSequenceMatchingPreferences()));
                        sequence = displayFeaturesGenerator.getTaggedPeptideSequence(spectrumMatch, true, true, true);
                        peptideShakerJTablePeptideTooltip = displayFeaturesGenerator.getPeptideModificationTooltipAsHtml(spectrumMatch);
                    } else if (spectrumMatch.getBestTagAssumption() != null) {
                        sequence = spectrumMatch.getBestTagAssumption().getTag().getTaggedModifiedSequence(peptideShakerGUI.getSearchParameters().getModificationProfile(), true, true, true, false, false);
                        peptideShakerJTablePeptideTooltip = displayFeaturesGenerator.getTagModificationTooltipAsHtml(spectrumMatch.getBestTagAssumption().getTag());
                    } else {
                        throw new IllegalArgumentException("No best hit found for spectrum " + spectrumMatch.getKey());
                    }
                    ((DefaultTableModel) peptideShakerJTable.getModel()).addRow(new Object[]{
                        1,
                        isBestPsmEqualForAllIdSoftware(spectrumMatch, peptideShakerGUI.getSequenceMatchingPreferences()),
                        sequence,
                        proteins,
                        probabilities.getPsmConfidence(),
                        probabilities.getMatchValidationLevel().getIndex()
                    });


                    currentAssumptionsList = new ArrayList<SpectrumIdentificationAssumption>();


                    // add the search results
                    for (Integer tempAdvocate : advocatesUsed) {
                        if (spectrumMatch.getAllAssumptions(tempAdvocate) != null) {
                            ArrayList<Double> eValues = new ArrayList<Double>(spectrumMatch.getAllAssumptions(tempAdvocate).keySet());
                            Collections.sort(eValues);
                            for (double eValue : eValues) {
                                for (SpectrumIdentificationAssumption currentAssumption : spectrumMatch.getAllAssumptions(tempAdvocate).get(eValue)) {
                                    addIdResultsToTable(currentAssumption, probabilities, tempAdvocate);
                                }
                            }
                        }
                    }

View Full Code Here


                if (currentSpectrum != null) {
                    Precursor precursor = currentSpectrum.getPrecursor();
                    String charge;
                    if (identification.matchExists(currentSpectrumKey)) {
                        SpectrumMatch spectrumMatch = identification.getSpectrumMatch(currentSpectrumKey);
                        if (spectrumMatch.getBestPeptideAssumption() != null) {
                            charge = spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().toString();
                        } else if (spectrumMatch.getBestTagAssumption() != null) {
                            charge = spectrumMatch.getBestTagAssumption().getIdentificationCharge().toString();
                        } else {
                            throw new IllegalArgumentException("Best hit not found for spectrum " + key + ".");
                        }
                    } else {
                        charge = precursor.getPossibleChargesAsString();
                    }
                    if (currentSpectrum.getMzValuesAsArray().length > 0 && currentSpectrum.getIntensityValuesAsArray().length > 0) {
                        tempSpectrumPanel = new SpectrumPanel(
                                currentSpectrum.getMzValuesAsArray(), currentSpectrum.getIntensityValuesAsArray(),
                                precursor.getMz(), charge,
                                "", 40, false, false, false, 2, false);
                        tempSpectrumPanel.setKnownMassDeltas(peptideShakerGUI.getCurrentMassDeltas());
                        tempSpectrumPanel.setDeltaMassWindow(annotationPreferences.getFragmentIonAccuracy());
                        tempSpectrumPanel.setBorder(null);
                        tempSpectrumPanel.setDataPointAndLineColor(peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumAnnotatedPeakColor(), 0);
                        tempSpectrumPanel.setPeakWaterMarkColor(peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumBackgroundPeakColor());
                        tempSpectrumPanel.setPeakWidth(peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumAnnotatedPeakWidth());
                        tempSpectrumPanel.setBackgroundPeakWidth(peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumBackgroundPeakWidth());
                    }
                }


                if (identification.matchExists(key)) {


                    SpectrumMatch spectrumMatch = identification.getSpectrumMatch(key);


                    SearchParameters searchParameters = peptideShakerGUI.getSearchParameters();
                    int forwardIon = searchParameters.getIonSearched1();
                    int rewindIon = searchParameters.getIonSearched2();
                    ModificationProfile modificationProfile = searchParameters.getModificationProfile();


                    if (currentSpectrum != null && tempSpectrumPanel != null) {


                        if (currentSpectrum.getMzValuesAsArray().length > 0 && currentSpectrum.getIntensityValuesAsArray().length > 0) {


                            if (searchResultsTable.getSelectedRow() != -1) {
                                SpectrumIdentificationAssumption currentAssumption = currentAssumptionsList.get(searchResultsTable.getSelectedRow());


                                if (currentAssumption != null) {
                                    currentSpectrumKey = spectrumMatch.getKey();
                                    if (currentAssumption instanceof PeptideAssumption) {
                                        PeptideAssumption currentPeptideAssumption = (PeptideAssumption) currentAssumption;
                                        Peptide peptide = currentPeptideAssumption.getPeptide();
                                        annotationPreferences.setCurrentSettings(currentPeptideAssumption, !currentSpectrumKey.equalsIgnoreCase(spectrumMatch.getKey()),
                                                peptideShakerGUI.getSequenceMatchingPreferences());
                                        ArrayList<IonMatch> annotations = specificAnnotator.getSpectrumAnnotation(annotationPreferences.getIonTypes(),
                                                annotationPreferences.getNeutralLosses(),
                                                annotationPreferences.getValidatedCharges(),
                                                currentPeptideAssumption.getIdentificationCharge().value,
                                                currentSpectrum, peptide,
                                                currentSpectrum.getIntensityLimit(annotationPreferences.getAnnotationIntensityLimit()),
                                                annotationPreferences.getFragmentIonAccuracy(), false, annotationPreferences.isHighResolutionAnnotation());


                                        // add the spectrum annotations
                                        tempSpectrumPanel.setAnnotations(SpectrumAnnotator.getSpectrumAnnotation(annotations));
                                        tempSpectrumPanel.showAnnotatedPeaksOnly(!annotationPreferences.showAllPeaks());
                                        tempSpectrumPanel.setYAxisZoomExcludesBackgroundPeaks(annotationPreferences.yAxisZoomExcludesBackgroundPeaks());


                                        // add de novo sequencing
                                        tempSpectrumPanel.addAutomaticDeNovoSequencing(peptide, annotations,
                                                forwardIon, rewindIon, annotationPreferences.getDeNovoCharge(),
                                                annotationPreferences.showForwardIonDeNovoTags(),
                                                annotationPreferences.showRewindIonDeNovoTags());


                                        peptideShakerGUI.updateAnnotationMenus(currentPeptideAssumption.getIdentificationCharge().value, peptide.getModificationMatches());


                                        // update the spectrum title
                                        String modifiedSequence = peptide.getTaggedModifiedSequence(modificationProfile, false, false, true);
                                        ((TitledBorder) spectrumPanel.getBorder()).setTitle(
                                                PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING
                                                + "Spectrum & Fragment Ions (" + modifiedSequence
                                                + "   " + currentPeptideAssumption.getIdentificationCharge().toString() + "   "
                                                + Util.roundDouble(currentSpectrum.getPrecursor().getMz(), 2) + " m/z)"
                                                + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
                                    } else if (currentAssumption instanceof TagAssumption) {
                                        TagAssumption tagAssumption = (TagAssumption) currentAssumption;


                                        // add the annotations
                                        annotationPreferences.setCurrentSettings(tagAssumption, !currentSpectrumKey.equalsIgnoreCase(spectrumMatch.getKey()),
                                                peptideShakerGUI.getSequenceMatchingPreferences());


                                        TagSpectrumAnnotator spectrumAnnotator = new TagSpectrumAnnotator();


                                        ArrayList<IonMatch> annotations = spectrumAnnotator.getSpectrumAnnotation(annotationPreferences.getIonTypes(),

View Full Code Here

                String spectrumKey = getSpectrumKey(row);
                if (spectrumKey == null) {
                    return "";
                }
                PSParameter psParameter;
                SpectrumMatch spectrumMatch;
                Precursor precursor;
                switch (column) {
                    case 0:
                        return row + 1;
                    case 1:
                        psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, new PSParameter());
                        return psParameter.isStarred();
                    case 2:
                        psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, new PSParameter());
                        return psParameter.isHidden();
                    case 3:
                        return Spectrum.getSpectrumFile(spectrumKey);
                    case 4:
                        return Spectrum.getSpectrumTitle(spectrumKey);
                    case 5:
                        precursor = peptideShakerGUI.getPrecursor(spectrumKey);
                        return precursor.getRt();
                    case 6:
                        precursor = peptideShakerGUI.getPrecursor(spectrumKey);
                        return precursor.getMz();
                    case 7:
                        spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                        if (spectrumMatch.getBestPeptideAssumption() != null) {
                            return spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().value;
                        } else if (spectrumMatch.getBestTagAssumption() != null) {
                            return spectrumMatch.getBestTagAssumption().getIdentificationCharge().value;
                        } else {
                            throw new IllegalArgumentException("No best assumption found for spectrum " + spectrumKey + ".");
                        }
                    case 8:
                        spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                        precursor = peptideShakerGUI.getPrecursor(spectrumKey);
                        if (spectrumMatch.getBestPeptideAssumption() != null) {
                            return Math.abs(spectrumMatch.getBestPeptideAssumption().getDeltaMass(precursor.getMz(), peptideShakerGUI.getSearchParameters().isPrecursorAccuracyTypePpm()));
                        } else if (spectrumMatch.getBestTagAssumption() != null) {
                            return Math.abs(spectrumMatch.getBestTagAssumption().getDeltaMass(precursor.getMz(), peptideShakerGUI.getSearchParameters().isPrecursorAccuracyTypePpm()));
                        } else {
                            throw new IllegalArgumentException("No best assumption found for spectrum " + spectrumKey + ".");
                        }
                    case 9:
                        psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, new PSParameter());

View Full Code Here

        if (proteinKey.equals(PeptideShakerGUI.NO_SELECTION)
                && peptideKey.equals(PeptideShakerGUI.NO_SELECTION)
                && !psmKey.equals(PeptideShakerGUI.NO_SELECTION)) {
            if (peptideShakerGUI.getIdentification().matchExists(psmKey)) {
                try {
                    SpectrumMatch spectrumMatch = peptideShakerGUI.getIdentification().getSpectrumMatch(psmKey);
                    if (spectrumMatch.getBestPeptideAssumption() != null) {
                        Peptide peptide = spectrumMatch.getBestPeptideAssumption().getPeptide();
                        peptideKey = peptide.getMatchingKey(peptideShakerGUI.getSequenceMatchingPreferences());
                    }
                } catch (Exception e) {
                    peptideShakerGUI.catchException(e);
                    return;

View Full Code Here

        this.annotationPreferences = annotationPreferences;
        this.sequenceMatchingPreferences = sequenceMatchingPreferences;
        type = Type.PSM;


        String fileName = Spectrum.getSpectrumFile(psmMatchKey);
        SpectrumMatch spectrumMatch = identification.getSpectrumMatch(psmMatchKey);
        Integer charge;
        if (spectrumMatch.getBestPeptideAssumption() != null) {
            charge = spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().value;
        } else if (spectrumMatch.getBestTagAssumption() != null) {
            charge = spectrumMatch.getBestTagAssumption().getIdentificationCharge().value;
        } else {
            throw new IllegalArgumentException("No best match found for spectrum " + psmMatchKey + ".");
        }
        ArrayList<MatchFilter> filters = new ArrayList<MatchFilter>();
        for (PsmFilter psmFilter : psmSpecificMap.getDoubtfulMatchesFilters(charge, fileName)) {

View Full Code Here


                    PSMaps pSMaps = new PSMaps();
                    pSMaps = (PSMaps) identification.getUrParam(pSMaps);
                    PeptideSpecificMap peptideMap = pSMaps.getPeptideSpecificMap();
                    ProteinMap proteinMap = pSMaps.getProteinMap();
                    SpectrumMatch spectrumMatch = identification.getSpectrumMatch(matchKey);
                    if (spectrumMatch.getBestPeptideAssumption() != null) {
                        Peptide peptide = spectrumMatch.getBestPeptideAssumption().getPeptide();
                        String peptideKey = peptide.getMatchingKey(sequenceMatchingPreferences);
                        identificationFeaturesGenerator.updateNConfidentSpectraForPeptide(peptideKey);
                        PSParameter peptidePSParameter = (PSParameter) identification.getPeptideMatchParameter(peptideKey, psParameter);


                        if (peptidePSParameter.getMatchValidationLevel().isValidated()) {

View Full Code Here

                psmMap.get(fileName).add(key);
            }
        }


        PSParameter psParameter = new PSParameter();
        SpectrumMatch spectrumMatch = null;
        int line = 1;


        int totalSize = 0;


        for (String spectrumFile : psmMap.keySet()) {
            totalSize += psmMap.get(spectrumFile).size();
        }


        // get the spectrum keys
        ArrayList<String> spectrumKeys = new ArrayList<String>();


        for (String spectrumFile : psmMap.keySet()) {
            for (String spectrumKey : psmMap.get(spectrumFile)) {
                if (!spectrumKeys.contains(spectrumKey)) {
                    spectrumKeys.add(spectrumKey);
                }
            }
        }


        if (waitingHandler != null) {
            waitingHandler.setWaitingText("Loading Spectra. Please Wait...");
            waitingHandler.resetSecondaryProgressCounter();
        }
        identification.loadSpectrumMatches(spectrumKeys, waitingHandler);


        if (waitingHandler != null) {
            waitingHandler.setWaitingText("Loading Spectrum Details. Please Wait...");
            waitingHandler.resetSecondaryProgressCounter();
        }
        identification.loadSpectrumMatchParameters(spectrumKeys, psParameter, waitingHandler);


        if (waitingHandler != null) {
            waitingHandler.setWaitingText("Exporting. Please Wait...");
            waitingHandler.resetSecondaryProgressCounter();
            waitingHandler.setMaxSecondaryProgressCounter(totalSize);
        }


        for (String spectrumFile : psmMap.keySet()) {


            for (String spectrumKey : psmMap.get(spectrumFile)) {


                if (waitingHandler != null) {
                    if (waitingHandler.isRunCanceled()) {
                        return;
                    }
                    waitingHandler.increaseSecondaryProgressCounter();
                }


                psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, psParameter);


                if (!validatedOnly || psParameter.getMatchValidationLevel().isValidated()) {


                    spectrumMatch = identification.getSpectrumMatch(spectrumKey);


                    PeptideAssumption peptideAssumption = spectrumMatch.getBestPeptideAssumption();


                    if (decoys || peptideAssumption == null || !peptideAssumption.getPeptide().isDecoy(sequenceMatchingPreferences)) {


                        boolean first = true;


                        if (indexes) {
                            if (linePrefix != null) {
                                writer.write(linePrefix);
                            }
                            writer.write(line + "");
                            first = false;
                        }
                        for (PsIdentificationAlgorithmMatchesFeature identificationAlgorithmMatchesFeature : identificationAlgorithmMatchesFeatures) {
                            if (!first) {
                                writer.addSeparator();
                            } else {
                                first = false;
                            }
                            String feature;
                            if (peptideAssumption != null) {
                                peptideAssumption = spectrumMatch.getBestPeptideAssumption();
                                feature = PsIdentificationAlgorithmMatchesSection.getPeptideAssumptionFeature(identification, identificationFeaturesGenerator, searchParameters, annotationPreferences, sequenceMatchingPreferences, keys, linePrefix, peptideAssumption, spectrumMatch.getKey(), psParameter, identificationAlgorithmMatchesFeature, waitingHandler);
                            } else if (spectrumMatch.getBestTagAssumption() != null) {
                                TagAssumption tagAssumption = spectrumMatch.getBestTagAssumption();
                                feature = PsIdentificationAlgorithmMatchesSection.getTagAssumptionFeature(identification, identificationFeaturesGenerator, searchParameters, annotationPreferences, keys, linePrefix, tagAssumption, spectrumMatch.getKey(), psParameter, identificationAlgorithmMatchesFeature, waitingHandler);
                            } else {
                                throw new IllegalArgumentException("No best match found for spectrum " + spectrumMatch.getKey() + ".");
                            }
                            writer.write(feature);
                        }
                        for (PsPsmFeature psmFeature : psmFeatures) {
                            if (!first) {

View Full Code Here

            case non_validated_psms:
            case validated_psms:
                if (identification.matchExists(spectrumKey)) {
                    psParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, psParameter);
                    if (psParameter.getMatchValidationLevel().isValidated()) {
                        SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                        if (spectrumMatch.getBestPeptideAssumption() != null) {
                            boolean decoy = false;
                            for (String accession : spectrumMatch.getBestPeptideAssumption().getPeptide().getParentProteins(sequenceMatchingPreferences)) {
                                if (sequenceFactory.isDecoyAccession(accession)) {
                                    decoy = true;
                                    break;
                                }
                            }
                            return !decoy && exportType == ExportType.validated_psms;
                        } else {
                            return false;
                        }
                    }
                }
                return exportType == ExportType.non_validated_psms;
            case non_validated_peptides:
            case validated_psms_peptides:
                if (identification.matchExists(spectrumKey)) {
                    SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                    if (spectrumMatch.getBestPeptideAssumption() != null) {
                        Peptide peptide = spectrumMatch.getBestPeptideAssumption().getPeptide();
                        boolean decoy = false;
                        for (String accession : peptide.getParentProteins(sequenceMatchingPreferences)) {
                            if (sequenceFactory.isDecoyAccession(accession)) {
                                decoy = true;
                                break;
                            }
                        }
                        if (!decoy) {
                            String peptideKey = peptide.getMatchingKey(sequenceMatchingPreferences);
                            psParameter = (PSParameter) identification.getPeptideMatchParameter(peptideKey, psParameter);
                            if (exportType == ExportType.non_validated_peptides || ((PSParameter) identification.getSpectrumMatchParameter(spectrumKey, psParameter)).getMatchValidationLevel().isValidated()) {
                                if (psParameter.getMatchValidationLevel().isValidated()) {
                                    return exportType == ExportType.validated_psms_peptides;
                                }
                            }
                        }
                    }
                    return exportType == ExportType.non_validated_peptides;
                } else {
                    return false;
                }
            case non_validated_proteins:
            case validated_psms_peptides_proteins:
                if (identification.matchExists(spectrumKey)) {
                    SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                    if (spectrumMatch.getBestPeptideAssumption() != null) {
                        Peptide peptide = spectrumMatch.getBestPeptideAssumption().getPeptide();
                        boolean decoy = false;
                        for (String accession : peptide.getParentProteins(sequenceMatchingPreferences)) {
                            if (sequenceFactory.isDecoyAccession(accession)) {
                                decoy = true;
                                break;

View Full Code Here

0 1 2 3 4

TOP

Related Classes of com.compomics.util.experiment.identification.matches.SpectrumMatch

eu.isas.peptideshaker.export.OutputGenerator

eu.isas.peptideshaker.export.sections.PsIdentificationAlgorithmMatchesSection

eu.isas.peptideshaker.export.sections.PsPsmSection

eu.isas.peptideshaker.fileimport.PsmImporter

eu.isas.peptideshaker.filtering.PsmFilter

eu.isas.peptideshaker.followup.InclusionListExport

eu.isas.peptideshaker.followup.ProgenesisExcelExport

eu.isas.peptideshaker.followup.ProgenesisExport

eu.isas.peptideshaker.followup.SpectrumExporter

eu.isas.peptideshaker.followup.SwathExport

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.