Package com.compomics.util.experiment.massspectrometry

Examples of com.compomics.util.experiment.massspectrometry.Precursor

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
                        }
                        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)) {
View Full Code Here
4320
4321
4322
4323
4324
4325
4326
4327
4328
4329
4330
4331
4332
4333
                        spectrumKey = identification.getPeptideMatch(getSelectedPeptide(relatedTable)).getSpectrumMatches().get(row);
                        return identification.getSpectrumMatch(spectrumKey).getBestPeptideAssumption().getIdentificationCharge().value;
                    case 5:
                        spectrumKey = identification.getPeptideMatch(getSelectedPeptide(relatedTable)).getSpectrumMatches().get(row);
                        try {
                            Precursor precursor = peptideShakerGUI.getPrecursor(spectrumKey); // @TODO: there is sometimes an IOException when closing the tool...

                            if (precursor != null) {
                                return precursor.getRt();
                            } else {
                                return null;
                            }
                        } catch (Exception e) {
                            e.printStackTrace();
View Full Code Here
3779
3780
3781
3782
3783
3784
3785
3786
3787
3788
3789
3790
3791
3792
3793
            for (int i = 0; i < relatedPsmsTable.getRowCount(); i++) {

                progressDialog.increasePrimaryProgressCounter();

                String spectrumKey = identification.getPeptideMatch(getSelectedPeptide(true)).getSpectrumMatches().get(i);
                Precursor precursor = peptideShakerGUI.getPrecursor(spectrumKey, false);

                if (precursor != null) {

                    double retentionTime = precursor.getRt();

                    if (!retentionTimeValues && retentionTime != -1) {
                        retentionTimeValues = true;
                    }
View Full Code Here
3861
3862
3863
3864
3865
3866
3867
3868
3869
3870
3871
3872
3873
3874
3875
            AnnotationPreferences annotationPreferences = peptideShakerGUI.getAnnotationPreferences();
            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);
View Full Code Here
1901
1902
1903
1904
1905
1906
1907
1908
1909
1910
1911
1912
1913
                        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;
                            }
View Full Code Here
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
                    return "0";
                }
            case identification_charge:
                return peptideAssumption.getIdentificationCharge().toString();
            case isotope:
                Precursor precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
                return peptideAssumption.getIsotopeNumber(precursor.getMz()) + "";
            case mz:
                precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
                return precursor.getMz() + "";
            case total_spectrum_intensity:
                Spectrum spectrum = SpectrumFactory.getInstance().getSpectrum(spectrumKey);
                return spectrum.getTotalIntensity() + "";
            case max_intensity:
                spectrum = SpectrumFactory.getInstance().getSpectrum(spectrumKey);
                return spectrum.getMaxIntensity() + "";
            case intensity_coverage:
                spectrum = SpectrumFactory.getInstance().getSpectrum(spectrumKey);
                double coveredIntensity = 0;
                Peptide peptide = peptideAssumption.getPeptide();
                ArrayList<IonMatch> matches = peptideSpectrumAnnotator.getSpectrumAnnotation(
                        annotationPreferences.getIonTypes(), annotationPreferences.getNeutralLosses(), annotationPreferences.getValidatedCharges(),
                        peptideAssumption.getIdentificationCharge().value,
                        (MSnSpectrum) spectrum, peptide, 0, searchParameters.getFragmentIonAccuracy(), false, true);
                for (IonMatch ionMatch : matches) {
                    coveredIntensity += ionMatch.peak.intensity;
                }
                double coverage = 100 * coveredIntensity / spectrum.getTotalIntensity();
                return coverage + "";
            case mz_error:
                precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
                return peptideAssumption.getDeltaMass(precursor.getMz(), true) + "";
            case rt:
                precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
                return precursor.getRt() + "";
            case algorithm_score:
                int id = peptideAssumption.getAdvocate();
                double score = peptideAssumption.getScore();
                return Advocate.getAdvocate(id).getName() + " (" + score + ")";
            case sequence:
                return peptideAssumption.getPeptide().getSequence();
            case missed_cleavages:
                String sequence = peptideAssumption.getPeptide().getSequence();
                return Peptide.getNMissedCleavages(sequence, searchParameters.getEnzyme()) + "";
            case modified_sequence:
                return peptideAssumption.getPeptide().getTaggedModifiedSequence(searchParameters.getModificationProfile(), false, false, true) + "";
            case spectrum_charge:
                precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
                return precursor.getPossibleChargesAsString() + "";
            case spectrum_file:
                String spectrumFile = Spectrum.getSpectrumFile(spectrumKey);
                return spectrumFile;
            case spectrum_scan_number:
                return SpectrumFactory.getInstance().getSpectrum(spectrumKey).getScanNumber();
View Full Code Here
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
                    return "0";
                }
            case identification_charge:
                return tagAssumption.getIdentificationCharge().toString();
            case isotope:
                Precursor precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
                return tagAssumption.getIsotopeNumber(precursor.getMz()) + "";
            case mz:
                precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
                return precursor.getMz() + "";
            case total_spectrum_intensity:
                Spectrum spectrum = SpectrumFactory.getInstance().getSpectrum(spectrumKey);
                return spectrum.getTotalIntensity() + "";
            case max_intensity:
                spectrum = SpectrumFactory.getInstance().getSpectrum(spectrumKey);
                return spectrum.getMaxIntensity() + "";
            case mz_error:
                precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
                return tagAssumption.getDeltaMass(precursor.getMz(), true) + "";
            case rt:
                precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
                return precursor.getRt() + "";
            case algorithm_score:
                int id = tagAssumption.getAdvocate();
                double score = tagAssumption.getScore();
                return Advocate.getAdvocate(id).getName() + " (" + score + ")";
            case sequence:
                return tagAssumption.getTag().asSequence();
            case missed_cleavages:
                return "";
            case modified_sequence:
                return tagAssumption.getTag().getTaggedModifiedSequence(searchParameters.getModificationProfile(), false, false, true, false);
            case spectrum_charge:
                precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
                return precursor.getPossibleChargesAsString() + "";
            case spectrum_file:
                String spectrumFile = Spectrum.getSpectrumFile(spectrumKey);
                return spectrumFile;
            case spectrum_scan_number:
                return SpectrumFactory.getInstance().getSpectrum(spectrumKey).getScanNumber();
View Full Code Here
2668
2669
2670
2671
2672
2673
2674
2675
2676
2677
2678
2679
2680
2681
2682
2683
2684
2685
2686
2687
2688
2689
2690
2691
2692
2693
2694
2695
                MSnSpectrum currentSpectrum = peptideShakerGUI.getSpectrum(key);
                SpectrumPanel tempSpectrumPanel = null;
                AnnotationPreferences annotationPreferences = peptideShakerGUI.getAnnotationPreferences();

                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);
View Full Code Here
1682
1683
1684
1685
1686
1687
1688
1689
1690
1691
1692
1693
1694
1695
1696
1697
1698
1699
1700
1701
1702
1703
1704
1705
1706
1707
1708
1709
1710
1711
1712
1713
1714
1715
1716
1717
1718
1719
1720
1721
1722
1723
1724
1725
1726
1727
                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
4347
4348
4349
4350
4351
4352
4353
4354
4355
4356
4357
4358
4359
4360
4361
                                lowerMzZoomRange = spectrumPanel.getXAxisZoomRangeLowerValue();
                                upperMzZoomRange = spectrumPanel.getXAxisZoomRangeUpperValue();
                            }

                            // add the data to the spectrum panel
                            Precursor precursor = currentSpectrum.getPrecursor();
                            SpectrumMatch spectrumMatch = peptideShakerGUI.getIdentification().getSpectrumMatch(spectrumKey);
                            spectrumPanel = new SpectrumPanel(
                                    currentSpectrum.getMzValuesAsArray(), currentSpectrum.getIntensityValuesAsArray(),
                                    precursor.getMz(), spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().toString(),
                                    "", 40, false, false, false, 2, false);
                            spectrumPanel.setKnownMassDeltas(peptideShakerGUI.getCurrentMassDeltas());
                            spectrumPanel.setDeltaMassWindow(peptideShakerGUI.getAnnotationPreferences().getFragmentIonAccuracy());
                            spectrumPanel.setBorder(null);
                            spectrumPanel.setDataPointAndLineColor(peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumAnnotatedPeakColor(), 0);
View Full Code Here
TOP

Related Classes of com.compomics.util.experiment.massspectrometry.Precursor

  • eu.isas.peptideshaker.export.OutputGenerator
  • eu.isas.peptideshaker.export.sections.PsIdentificationAlgorithmMatchesSection
  • eu.isas.peptideshaker.filtering.AssumptionFilter
  • eu.isas.peptideshaker.filtering.PsmFilter
  • eu.isas.peptideshaker.followup.InclusionListExport
  • eu.isas.peptideshaker.followup.ProgenesisExcelExport
  • eu.isas.peptideshaker.gui.FindDialog$PsmTable
  • eu.isas.peptideshaker.gui.JumpToPanel
  • eu.isas.peptideshaker.gui.tablemodels.PsmTableModel
  • eu.isas.peptideshaker.gui.tabpanels.OverviewPanel
    • 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.