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

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

3176
3177
3178
3179
3180
3181
3182
3183
3184
3185
3186
3187
3188
3189
3190
3191
3192
3193
3194
3195
3196
3197
3198
3199
3200
3201
3202
3203
3204
3205
3206
3207
3208
3209
3210
3211
3212
3213
3214
3215
3216
3217
3218
3219
3220
3221
3222
3223
3224
3225
3226
3227
3228
3229
3230
3231
3232
3233
3234
3235
3236
3237
                    case 1:
                        int idSoftwareAgreement;
                        if (!identification.matchExists(spectrumKey)) {
                            idSoftwareAgreement = NO_ID;
                        } else {
                            SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                            idSoftwareAgreement = isBestPsmEqualForAllIdSoftware(spectrumMatch, peptideShakerGUI.getSequenceMatchingPreferences());
                        }
                        return idSoftwareAgreement;
                    case 2:
                        return spectrumFactory.getSpectrumTitles(fileSelected).get(row);
                    case 3:
                        Precursor precursor = peptideShakerGUI.getPrecursor(spectrumKey, false);
                        if (precursor != null) {
                            return precursor.getMz();
                        } else {
                            return null;
                        }
                    case 4:
                        precursor = peptideShakerGUI.getPrecursor(spectrumKey, false);
                        Integer charge = null;
                        if (precursor != null && !precursor.getPossibleCharges().isEmpty()) {
                            charge = precursor.getPossibleCharges().get(0).value; // @TODO: find a way of displaying multiple charges!!!
                        }
                        return charge;
                    case 5:
                        precursor = peptideShakerGUI.getPrecursor(spectrumKey, false);
                        if (precursor != null) {
                            return precursor.getIntensity();
                        } else {
                            return null;
                        }
                    case 6:
                        precursor = peptideShakerGUI.getPrecursor(spectrumKey, false);
                        if (precursor != null) {
                            return precursor.getRt();
                        } else {
                            return null;
                        }
                    case 7:
                        if (identification.matchExists(spectrumKey)) {
                            SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                            DisplayFeaturesGenerator displayFeaturesGenerator = peptideShakerGUI.getDisplayFeaturesGenerator();
                            if (spectrumMatch.getBestPeptideAssumption() != null) {
                                return displayFeaturesGenerator.getTaggedPeptideSequence(spectrumMatch, true, true, true);
                            } else if (spectrumMatch.getBestTagAssumption() != null) {
                                //TODO: include fixed ptms
                                return spectrumMatch.getBestTagAssumption().getTag().getTaggedModifiedSequence(peptideShakerGUI.getSearchParameters().getModificationProfile(), true, true, true, false, false);
                            }
                        }
                        return null;
                    case 8:
                        if (identification.matchExists(spectrumKey)) {
                            SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                            DisplayFeaturesGenerator displayFeaturesGenerator = peptideShakerGUI.getDisplayFeaturesGenerator();
                            if (spectrumMatch.getBestPeptideAssumption() != null) {
                                return displayFeaturesGenerator.addDatabaseLinks(spectrumMatch.getBestPeptideAssumption().getPeptide().getParentProteins(
                                        peptideShakerGUI.getSequenceMatchingPreferences()));
                            }
                        }
                        return null;
                    case 9:
View Full Code Here
823
824
825
826
827
828
829
830
831
832
833
834
835
        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
2425
2426
2427
2428
2429
2430
2431
2432
2433
2434
2435
            if (column == selectedPsmsTable.getColumn("Sequence").getModelIndex()) {

                try {
                    String spectrumKey = identification.getPeptideMatch(getSelectedPeptide(false)).getSpectrumMatches().get(row);
                    SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                    selectedPsmsTable.setToolTipText(peptideShakerGUI.getDisplayFeaturesGenerator().getPeptideModificationTooltipAsHtml(spectrumMatch));
                } catch (Exception e) {
                    peptideShakerGUI.catchException(e);
                    e.printStackTrace();
                }
View Full Code Here
2506
2507
2508
2509
2510
2511
2512
2513
2514
2515
2516
        if (row != -1 && column != -1 && relatedPsmsTable.getValueAt(row, column) != null) {
            if (column == relatedPsmsTable.getColumn("Sequence").getModelIndex()) {
                try {
                    String spectrumKey = identification.getPeptideMatch(getSelectedPeptide(true)).getSpectrumMatches().get(row);
                    SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                    relatedPsmsTable.setToolTipText(peptideShakerGUI.getDisplayFeaturesGenerator().getPeptideModificationTooltipAsHtml(spectrumMatch));
                } catch (Exception e) {
                    peptideShakerGUI.catchException(e);
                    e.printStackTrace();
                }
View Full Code Here
3323
3324
3325
3326
3327
3328
3329
3330
3331
3332
3333
3334
3335
        if (selectedKey.equals(PeptideShakerGUI.NO_SELECTION)
                && !peptideShakerGUI.getSelectedPsmKey().equals(PeptideShakerGUI.NO_SELECTION)) {
            String psmKey = peptideShakerGUI.getSelectedPsmKey();
            if (peptideShakerGUI.getIdentification().matchExists(psmKey)) {
                try {
                    SpectrumMatch spectrumMatch = peptideShakerGUI.getIdentification().getSpectrumMatch(psmKey);
                    if (spectrumMatch.getBestPeptideAssumption() != null) {
                        Peptide peptide = spectrumMatch.getBestPeptideAssumption().getPeptide();
                        selectedKey = peptide.getMatchingKey(peptideShakerGUI.getSequenceMatchingPreferences());
                    }
                } catch (Exception e) {
                    peptideShakerGUI.catchException(e);
                    return;
View Full Code Here
3862
3863
3864
3865
3866
3867
3868
3869
3870
3871
3872
3873
3874
3875
3876
3877
3878
3879
3880
3881
3882
3883
3884
3885
3886
3887
3888
3889
3890
3891
3892
3893
3894
3895
3896
3897
            MSnSpectrum currentSpectrum = peptideShakerGUI.getSpectrum(spectrumKey);

            if (currentSpectrum != null && currentSpectrum.getMzValuesAsArray().length > 0) {

                Precursor precursor = currentSpectrum.getPrecursor();
                SpectrumMatch spectrumMatch = peptideShakerGUI.getIdentification().getSpectrumMatch(spectrumKey);
                spectrum = new SpectrumPanel(
                        currentSpectrum.getMzValuesAsArray(), currentSpectrum.getIntensityValuesAsArray(),
                        precursor.getMz(), spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().toString(),
                        "", 40, false, false, false, 2, false);
                spectrum.setKnownMassDeltas(peptideShakerGUI.getCurrentMassDeltas());
                spectrum.setDeltaMassWindow(peptideShakerGUI.getAnnotationPreferences().getFragmentIonAccuracy());
                spectrum.setBorder(null);
                spectrum.setDataPointAndLineColor(peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumAnnotatedPeakColor(), 0);
                spectrum.setPeakWaterMarkColor(peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumBackgroundPeakColor());
                spectrum.setPeakWidth(peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumAnnotatedPeakWidth());
                spectrum.setBackgroundPeakWidth(peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumBackgroundPeakWidth());

                // get the spectrum annotations
                PeptideAssumption peptideAssumption = spectrumMatch.getBestPeptideAssumption();
                Peptide peptide = peptideAssumption.getPeptide();
                int identificationCharge = spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().value;
                annotationPreferences.setCurrentSettings(peptideAssumption, !currentSpectrumKey.equalsIgnoreCase(spectrumMatch.getKey()), peptideShakerGUI.getSequenceMatchingPreferences());
                ArrayList<IonMatch> annotations = annotator.getSpectrumAnnotation(annotationPreferences.getIonTypes(),
                        annotationPreferences.getNeutralLosses(),
                        annotationPreferences.getValidatedCharges(),
                        identificationCharge,
                        currentSpectrum, peptide,
                        currentSpectrum.getIntensityLimit(annotationPreferences.getAnnotationIntensityLimit()),
                        annotationPreferences.getFragmentIonAccuracy(), false, annotationPreferences.isHighResolutionAnnotation());
                currentSpectrumKey = spectrumMatch.getKey();

                // add the spectrum annotations
                spectrum.setAnnotations(SpectrumAnnotator.getSpectrumAnnotation(annotations));
                spectrum.showAnnotatedPeaksOnly(!annotationPreferences.showAllPeaks());
                spectrum.setYAxisZoomExcludesBackgroundPeaks(annotationPreferences.yAxisZoomExcludesBackgroundPeaks());
View Full Code Here
1896
1897
1898
1899
1900
1901
1902
1903
1904
1905
1906
1907
1908
1909
1910
1911
1912
1913
1914
1915
1916
1917
1918
1919
1920
1921
1922
1923
1924
1925
1926
1927
1928
1929
1930
1931
1932
1933
1934
1935
1936
1937
1938
1939
1940
1941
1942
1943
1944
1945
1946
1947
1948
1949
1950
1951
1952
1953
1954
1955
1956
1957
1958
1959
1960
1961
1962
1963
1964
1965
1966
1967
1968
                        if (progressDialog.isRunCanceled()) {
                            break;
                        }

                        SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                        psmParameter = (PSParameter) identification.getSpectrumMatchParameter(spectrumKey, psmParameter);

                        if (!psmParameter.isHidden() && spectrumMatch.getBestPeptideAssumption() != null) {

                            Precursor precursor = peptideShakerGUI.getPrecursor(spectrumKey);
                            double value = spectrumMatch.getBestPeptideAssumption().getDeltaMass(
                                    precursor.getMz(),
                                    peptideShakerGUI.getSearchParameters().isPrecursorAccuracyTypePpm());
                            if (value > maxValue) {
                                maxValue = value;
                            }

                            if (!spectrumMatch.getBestPeptideAssumption().getPeptide().isDecoy(peptideShakerGUI.getSequenceMatchingPreferences())) {
                                if (psmParameter.getMatchValidationLevel().isValidated()) {
                                    if (psmParameter.getMatchValidationLevel() == MatchValidationLevel.confident) {
                                        validatedValues.add(value);
                                    } else {
                                        validatedDoubtfulValues.add(value);
                                    }
                                } else {
                                    nonValidatedValues.add(value);
                                }
                            } else {
                                if (psmParameter.getMatchValidationLevel().isValidated()) {
                                    validatedDecoyValues.add(value);
                                } else {
                                    nonValidatedDecoyValues.add(value);
                                }
                            }
                        }

                        progressDialog.increasePrimaryProgressCounter();
                    }
                }
            } else if (psmPrecursorChargeJRadioButton.isSelected()) {

                // Values for the precursor charge
                validatedValues = new ArrayList<Double>();
                validatedDoubtfulValues = new ArrayList<Double>();
                nonValidatedValues = new ArrayList<Double>();
                validatedDecoyValues = new ArrayList<Double>();
                nonValidatedDecoyValues = new ArrayList<Double>();

                for (String spectrumFileName : identification.getSpectrumFiles()) {
                    identification.loadSpectrumMatches(spectrumFileName, progressDialog);
                    identification.loadSpectrumMatchParameters(spectrumFileName, psmParameter, progressDialog);
                    for (String spectrumKey : identification.getSpectrumIdentification(spectrumFileName)) {
                        if (progressDialog.isRunCanceled()) {
                            break;
                        }

                        SpectrumMatch spectrumMatch = peptideShakerGUI.getIdentification().getSpectrumMatch(spectrumKey);
                        psmParameter = (PSParameter) peptideShakerGUI.getIdentification().getSpectrumMatchParameter(spectrumKey, psmParameter);

                        if (!psmParameter.isHidden() && spectrumMatch.getBestPeptideAssumption() != null) {

                            double value = spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().value;
                            if (value > maxValue) {
                                maxValue = value;
                            }

                            if (!spectrumMatch.getBestPeptideAssumption().getPeptide().isDecoy(peptideShakerGUI.getSequenceMatchingPreferences())) {
                                if (psmParameter.getMatchValidationLevel().isValidated()) {
                                    if (psmParameter.getMatchValidationLevel() == MatchValidationLevel.confident) {
                                        validatedValues.add(value);
                                    } else {
                                        validatedDoubtfulValues.add(value);
View Full Code Here
188
189
190
191
192
193
194
195
196
197
198
199
200
201
                        return;
                    }
                    waitingHandler.increaseSecondaryProgressCounter();
                }

                SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);

                for (int advocateId : spectrumMatch.getAdvocates()) {
                    HashMap<Double, ArrayList<SpectrumIdentificationAssumption>> assumptions = spectrumMatch.getAllAssumptions(advocateId);
                    ArrayList<Double> scores = new ArrayList<Double>(assumptions.keySet());
                    Collections.sort(scores);
                    for (double score : scores) {
                        for (SpectrumIdentificationAssumption assumption : assumptions.get(score)) {
View Full Code Here
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
            identification.loadSpectrumMatches(spectrumFileName, null);

            for (String spectrumKey : identification.getSpectrumIdentification(spectrumFileName)) {

                waitingHandler.increaseSecondaryProgressCounter();
                SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);

                for (int advocateIndex : spectrumMatch.getAdvocates()) {
                    for (double eValue : spectrumMatch.getAllAssumptions(advocateIndex).keySet()) {
                        for (SpectrumIdentificationAssumption assumption : spectrumMatch.getAllAssumptions(advocateIndex).get(eValue)) {

                            if (assumption instanceof PeptideAssumption) {

                                PeptideAssumption peptideAssumption = (PeptideAssumption) assumption;
                                annotationPreferences.setCurrentSettings(peptideAssumption, true, sequenceMatchingPreferences);
View Full Code Here
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
            for (String spectrumKey : identification.getSpectrumIdentification(spectrumFileName)) {

                waitingHandler.increaseSecondaryProgressCounter();

                SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);

                for (int advocateIndex : spectrumMatch.getAdvocates()) {

                    for (double eValue : spectrumMatch.getAllAssumptions(advocateIndex).keySet()) {

                        for (SpectrumIdentificationAssumption assumption : spectrumMatch.getAllAssumptions(advocateIndex).get(eValue)) {

                            if (assumption instanceof PeptideAssumption) {

                                psParameter = (PSParameter) assumption.getUrParam(psParameter);
View Full Code Here
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
    • Copyright © 2018 www.massapicom. All rights reserved.
    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.