Examples with SequenceProvider com.compomics.util.experiment.io.biology.protein.SequenceProvider used on opensource projects

Example 1 with SequenceProvider

use of com.compomics.util.experiment.io.biology.protein.SequenceProvider in project peptide-shaker by compomics.

the class SpectrumIdentificationPanel method updateSpectrum.

/**
 * Update the spectrum based on the currently selected PSM.
 */
public void updateSpectrum() {
    if (spectrumTable.getSelectedRow() != -1) {
        spectrumChartPanel.removeAll();
        String spectrumTitle = getSelectedSpectrumTitle();
        Spectrum currentSpectrum = peptideShakerGUI.getSpectrumProvider().getSpectrum(fileSelected, spectrumTitle);
        AnnotationParameters annotationParameters = peptideShakerGUI.getIdentificationParameters().getAnnotationParameters();
        long spectrumMatchKey = SpectrumMatch.getKey(fileSelected, spectrumTitle);
        SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumMatchKey);
        // get the selected spectrum
        if (currentSpectrum != null && currentSpectrum.getNPeaks() > 0) {
            Precursor precursor = currentSpectrum.getPrecursor();
            String chargeAsString = "";
            if (spectrumMatch != null) {
                if (spectrumMatch.getBestPeptideAssumption() != null) {
                    chargeAsString = Charge.toString(spectrumMatch.getBestPeptideAssumption().getIdentificationCharge());
                } else if (spectrumMatch.getBestTagAssumption() != null) {
                    chargeAsString = Charge.toString(spectrumMatch.getBestTagAssumption().getIdentificationCharge());
                }
            } else {
                chargeAsString = precursor.getPossibleChargesAsString();
            }
            double[] intensitiesAsArray = searchResultsTable.getSelectedRowCount() == 1 ? currentSpectrum.intensity : ArrayUtil.scaleToMax(currentSpectrum.intensity);
            spectrumPanel = new SpectrumPanel(currentSpectrum.mz, intensitiesAsArray, precursor.mz, chargeAsString, "", 40, false, false, false, 2, false);
            spectrumPanel.setKnownMassDeltas(peptideShakerGUI.getCurrentMassDeltas());
            spectrumPanel.setDeltaMassWindow(annotationParameters.getFragmentIonAccuracy());
            spectrumPanel.setBorder(null);
            spectrumPanel.setDataPointAndLineColor(peptideShakerGUI.getUtilitiesUserParameters().getSpectrumAnnotatedPeakColor(), 0);
            spectrumPanel.setPeakWaterMarkColor(peptideShakerGUI.getUtilitiesUserParameters().getSpectrumBackgroundPeakColor());
            spectrumPanel.setPeakWidth(peptideShakerGUI.getUtilitiesUserParameters().getSpectrumAnnotatedPeakWidth());
            spectrumPanel.setBackgroundPeakWidth(peptideShakerGUI.getUtilitiesUserParameters().getSpectrumBackgroundPeakWidth());
            // add the mirrored spectrum
            if (searchResultsTable.getSelectedRowCount() == 2) {
                spectrumPanel.addMirroredSpectrum(currentSpectrum.mz, ArrayUtil.scaleToMax(currentSpectrum.intensity), precursor.mz, chargeAsString, "", false, peptideShakerGUI.getUtilitiesUserParameters().getSpectrumAnnotatedMirroredPeakColor(), peptideShakerGUI.getUtilitiesUserParameters().getSpectrumAnnotatedMirroredPeakColor());
            }
        }
        // add spectrum annotations
        if (spectrumMatch != null) {
            SequenceProvider sequenceProvider = peptideShakerGUI.getSequenceProvider();
            IdentificationParameters identificationParameters = peptideShakerGUI.getIdentificationParameters();
            ModificationParameters modificationParameters = identificationParameters.getSearchParameters().getModificationParameters();
            SequenceMatchingParameters modificationSequenceMatchingParameters = identificationParameters.getModificationLocalizationParameters().getSequenceMatchingParameters();
            SearchParameters searchParameters = identificationParameters.getSearchParameters();
            DisplayParameters displayParameters = peptideShakerGUI.getDisplayParameters();
            int forwardIon = searchParameters.getForwardIons().get(0);
            int rewindIon = searchParameters.getRewindIons().get(0);
            if (currentSpectrum != null && spectrumPanel != null) {
                if (currentSpectrum.getNPeaks() > 0) {
                    int maxPrecursorCharge = 1;
                    String modifiedSequence = "";
                    HashSet<String> allModifications = new HashSet<>();
                    ArrayList<IonMatch[]> allAnnotations = new ArrayList<>();
                    ArrayList<Spectrum> allSpectra = new ArrayList<>();
                    ArrayList<String> selectedIndexes = new ArrayList<>();
                    SpecificAnnotationParameters specificAnnotationParameters = null;
                    for (int i = 0; i < searchResultsTable.getSelectedRowCount(); i++) {
                        SpectrumIdentificationAssumption currentAssumption = currentAssumptionsList.get(searchResultsTable.getSelectedRows()[i]);
                        if (currentAssumption != null) {
                            selectedIndexes.add((i + 1) + " " + Charge.toString(currentAssumption.getIdentificationCharge()));
                            if (currentAssumption instanceof PeptideAssumption) {
                                PeptideAssumption currentPeptideAssumption = (PeptideAssumption) currentAssumption;
                                Peptide peptide = currentPeptideAssumption.getPeptide();
                                PeptideSpectrumAnnotator peptideSpectrumAnnotator = new PeptideSpectrumAnnotator();
                                specificAnnotationParameters = peptideShakerGUI.getSpecificAnnotationParameters(fileSelected, spectrumTitle, currentPeptideAssumption);
                                IonMatch[] annotations = peptideSpectrumAnnotator.getSpectrumAnnotation(annotationParameters, specificAnnotationParameters, fileSelected, spectrumTitle, currentSpectrum, peptide, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters);
                                allAnnotations.add(annotations);
                                allSpectra.add(currentSpectrum);
                                // add the spectrum annotations
                                if (i == 0) {
                                    // @TODO: the selection of the peak to annotate should be done outside the spectrum panel
                                    spectrumPanel.setAnnotations(SpectrumAnnotator.getSpectrumAnnotation(annotations), annotationParameters.getTiesResolution() == SpectrumAnnotator.TiesResolution.mostIntense);
                                    // add de novo sequencing
                                    spectrumPanel.addAutomaticDeNovoSequencing(peptide, annotations, forwardIon, rewindIon, annotationParameters.getDeNovoCharge(), annotationParameters.showForwardIonDeNovoTags(), annotationParameters.showRewindIonDeNovoTags(), false, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters);
                                } else {
                                    spectrumPanel.setAnnotationsMirrored(SpectrumAnnotator.getSpectrumAnnotation(annotations));
                                    // add de novo sequencing
                                    spectrumPanel.addAutomaticDeNovoSequencing(peptide, annotations, forwardIon, rewindIon, annotationParameters.getDeNovoCharge(), annotationParameters.showForwardIonDeNovoTags(), annotationParameters.showRewindIonDeNovoTags(), true, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters);
                                }
                                if (currentPeptideAssumption.getIdentificationCharge() > maxPrecursorCharge) {
                                    maxPrecursorCharge = currentPeptideAssumption.getIdentificationCharge();
                                }
                                if (!modifiedSequence.isEmpty()) {
                                    modifiedSequence += " vs. ";
                                }
                                modifiedSequence += peptide.getTaggedModifiedSequence(modificationParameters, sequenceProvider, modificationSequenceMatchingParameters, false, false, true, displayParameters.getDisplayedModifications());
                                allModifications.addAll(ModificationUtils.getAllModifications(peptide, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters));
                            } else if (currentAssumption instanceof TagAssumption) {
                                TagAssumption tagAssumption = (TagAssumption) currentAssumption;
                                TagSpectrumAnnotator spectrumAnnotator = new TagSpectrumAnnotator();
                                specificAnnotationParameters = peptideShakerGUI.getSpecificAnnotationParameters(fileSelected, spectrumTitle, tagAssumption);
                                IonMatch[] annotations = spectrumAnnotator.getSpectrumAnnotation(annotationParameters, modificationParameters, modificationSequenceMatchingParameters, specificAnnotationParameters, fileSelected, spectrumTitle, currentSpectrum, tagAssumption.getTag());
                                // add the spectrum annotations
                                // @TODO: the selection of the peak to annotate should be done outside the spectrum panel
                                spectrumPanel.setAnnotations(SpectrumAnnotator.getSpectrumAnnotation(annotations), annotationParameters.getTiesResolution() == SpectrumAnnotator.TiesResolution.mostIntense);
                                // add de novo sequencing
                                spectrumPanel.addAutomaticDeNovoSequencing(tagAssumption.getTag(), annotations, forwardIon, rewindIon, annotationParameters.getDeNovoCharge(), annotationParameters.showForwardIonDeNovoTags(), annotationParameters.showRewindIonDeNovoTags(), false);
                                // get the modifications for the tag
                                allModifications.addAll(ModificationUtils.getAllModifications(tagAssumption.getTag(), modificationParameters, modificationSequenceMatchingParameters));
                                if (tagAssumption.getIdentificationCharge() > maxPrecursorCharge) {
                                    maxPrecursorCharge = tagAssumption.getIdentificationCharge();
                                }
                                if (!modifiedSequence.isEmpty()) {
                                    modifiedSequence += " vs. ";
                                }
                                modifiedSequence += tagAssumption.getTag().getTaggedModifiedSequence(modificationParameters, false, false, true, false, modificationSequenceMatchingParameters, displayParameters.getDisplayedModifications());
                            } else {
                                throw new UnsupportedOperationException("Spectrum annotation not implemented for identification assumption of type " + currentAssumption.getClass() + ".");
                            }
                        }
                    }
                    spectrumPanel.showAnnotatedPeaksOnly(!annotationParameters.showAllPeaks());
                    spectrumPanel.setYAxisZoomExcludesBackgroundPeaks(annotationParameters.yAxisZoomExcludesBackgroundPeaks());
                    peptideShakerGUI.updateAnnotationMenus(specificAnnotationParameters, maxPrecursorCharge, allModifications);
                    // update the spectrum title
                    if (searchResultsTable.getSelectedRowCount() == 1) {
                        ((TitledBorder) spectrumPanelPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Spectrum & Fragment Ions (" + modifiedSequence + "   " + maxPrecursorCharge + "   " + Util.roundDouble(currentSpectrum.getPrecursor().mz, 2) + " m/z)" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
                    } else if (searchResultsTable.getSelectedRowCount() == 2) {
                        ((TitledBorder) spectrumPanelPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Spectrum & Fragment Ions (" + modifiedSequence + ")" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
                    } else if (searchResultsTable.getSelectedRowCount() > 2) {
                        ((TitledBorder) spectrumPanelPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Spectrum & Fragment Ions (" + searchResultsTable.getSelectedRowCount() + " PSMs)" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
                    }
                    spectrumPanelPanel.repaint();
                    if (searchResultsTable.getSelectedRowCount() > 2) {
                        SearchParameters.MassAccuracyType fragmentAccuracyType = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getFragmentAccuracyType();
                        double bubbleScale = annotationParameters.getFragmentIonAccuracy() * 10 * peptideShakerGUI.getBubbleScale();
                        DisplayParameters displayPreferences = peptideShakerGUI.getDisplayParameters();
                        MassErrorBubblePlot massErrorBubblePlot = new MassErrorBubblePlot(selectedIndexes, allAnnotations, allSpectra, annotationParameters.getFragmentIonAccuracy(), bubbleScale, selectedIndexes.size() == 1, displayPreferences.showBars(), fragmentAccuracyType == SearchParameters.MassAccuracyType.PPM);
                        // hide the legend if selecting more than 20 spectra // @TODO: 20 should not be hardcoded here..
                        if (selectedIndexes.size() > 20) {
                            massErrorBubblePlot.getChartPanel().getChart().getLegend().setVisible(false);
                        }
                        // hide the outline
                        massErrorBubblePlot.getChartPanel().getChart().getPlot().setOutlineVisible(false);
                        spectrumChartPanel.add(massErrorBubblePlot);
                    }
                }
            }
            if (searchResultsTable.getSelectedRowCount() <= 2) {
                spectrumChartPanel.add(spectrumPanel);
            }
        } else {
            // update the spectrum title
            ((TitledBorder) spectrumPanelPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Spectrum & Fragment Ions (" + Util.roundDouble(currentSpectrum.getPrecursor().mz, 2) + " m/z)" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
            if (currentSpectrum.getNPeaks() > 0) {
                spectrumChartPanel.add(spectrumPanel);
            }
            spectrumPanelPanel.repaint();
        }
    }
    spectrumChartPanel.revalidate();
    spectrumChartPanel.repaint();
}

Example 2 with SequenceProvider

use of com.compomics.util.experiment.io.biology.protein.SequenceProvider in project peptide-shaker by compomics.

the class ModificationLocalizationScorer method attachProbabilisticScore.

/**
 * Attaches the selected probabilistic modification score.
 *
 * @param spectrumMatch The spectrum match studied, the score will be
 * calculated for the best assumption only.
 * @param sequenceProvider The protein sequence provider to use.
 * @param spectrumProvider The spectrum provider to use.
 * @param modificationProvider The modification provider to use.
 * @param identificationParameters The identification parameters.
 * @param peptideSpectrumAnnotator The peptide spectrum annotator to use.
 * @param identification The identification object containing the matches.
 */
private void attachProbabilisticScore(SpectrumMatch spectrumMatch, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, ModificationProvider modificationProvider, IdentificationParameters identificationParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, Identification identification) {
    SearchParameters searchParameters = identificationParameters.getSearchParameters();
    AnnotationParameters annotationParameters = identificationParameters.getAnnotationParameters();
    ModificationLocalizationParameters scoringParameters = identificationParameters.getModificationLocalizationParameters();
    SequenceMatchingParameters sequenceMatchingParameters = identificationParameters.getSequenceMatchingParameters();
    SequenceMatchingParameters modificationSequenceMatchingParameters = scoringParameters.getSequenceMatchingParameters();
    ModificationParameters modificationParameters = searchParameters.getModificationParameters();
    PSModificationScores modificationScores = (PSModificationScores) spectrumMatch.getUrParam(PSModificationScores.dummy);
    if (modificationScores != null) {
        modificationScores = new PSModificationScores();
        spectrumMatch.addUrParam(modificationScores);
    }
    HashMap<Double, ArrayList<Modification>> modificationsMap = new HashMap<>(1);
    HashMap<Double, Integer> nMod = new HashMap<>(1);
    PeptideAssumption bestPeptideAssumption = spectrumMatch.getBestPeptideAssumption();
    Peptide peptide = bestPeptideAssumption.getPeptide();
    for (ModificationMatch modificationMatch : peptide.getVariableModifications()) {
        Modification refMod = modificationProvider.getModification(modificationMatch.getModification());
        double modMass = refMod.getMass();
        if (!modificationsMap.containsKey(modMass)) {
            ArrayList<Modification> modifications = modificationFactory.getSameMassNotFixedModifications(modMass, searchParameters).stream().map(modification -> modificationProvider.getModification(modification)).collect(Collectors.toCollection(ArrayList::new));
            modificationsMap.put(modMass, modifications);
            nMod.put(modMass, 1);
        } else {
            nMod.put(modMass, nMod.get(modMass) + 1);
        }
    }
    if (!modificationsMap.isEmpty()) {
        String spectrumFile = spectrumMatch.getSpectrumFile();
        String spectrumTitle = spectrumMatch.getSpectrumTitle();
        Spectrum spectrum = spectrumProvider.getSpectrum(spectrumFile, spectrumTitle);
        SpecificAnnotationParameters specificAnnotationParameters = annotationParameters.getSpecificAnnotationParameters(spectrumFile, spectrumTitle, bestPeptideAssumption, modificationParameters, sequenceProvider, modificationSequenceMatchingParameters, peptideSpectrumAnnotator);
        for (double modMass : modificationsMap.keySet()) {
            HashMap<Integer, Double> scores = null;
            if (scoringParameters.getSelectedProbabilisticScore() == ModificationLocalizationScore.PhosphoRS) {
                scores = PhosphoRS.getSequenceProbabilities(peptide, modificationsMap.get(modMass), modificationParameters, spectrum, sequenceProvider, annotationParameters, specificAnnotationParameters, scoringParameters.isProbabilisticScoreNeutralLosses(), sequenceMatchingParameters, modificationSequenceMatchingParameters, peptideSpectrumAnnotator);
                if (scores == null) {
                    throw new IllegalArgumentException("An error occurred while scoring spectrum " + spectrumTitle + " of file " + spectrumFile + " with PhosphoRS.");
                // Most likely a compatibility issue with utilities
                }
            }
            if (scores != null) {
                // remap to searched modifications
                Modification mappedModification = null;
                String peptideSequence = peptide.getSequence();
                for (int site : scores.keySet()) {
                    if (site == 0) {
                        // N-term mod
                        for (Modification modification : modificationsMap.get(modMass)) {
                            if (modification.getModificationType().isNTerm()) {
                                mappedModification = modification;
                                break;
                            }
                        }
                        if (mappedModification == null) {
                            throw new IllegalArgumentException("Could not map the PTM of mass " + modMass + " on the N-terminus of the peptide " + peptideSequence + ".");
                        }
                    } else if (site == peptideSequence.length() + 1) {
                        // C-term mod
                        for (Modification modification : modificationsMap.get(modMass)) {
                            if (modification.getModificationType().isCTerm()) {
                                mappedModification = modification;
                                break;
                            }
                        }
                        if (mappedModification == null) {
                            throw new IllegalArgumentException("Could not map the PTM of mass " + modMass + " on the C-terminus of the peptide " + peptideSequence + ".");
                        }
                    } else {
                        for (Modification modification : modificationsMap.get(modMass)) {
                            mappedModification = modification;
                            break;
                        }
                        if (mappedModification == null) {
                            throw new IllegalArgumentException("Could not map the PTM of mass " + modMass + " at site " + site + " in peptide " + peptide.getSequence() + ".");
                        }
                    }
                    String modName = mappedModification.getName();
                    ModificationScoring modificationScoring = modificationScores.getModificationScoring(modName);
                    if (modificationScoring == null) {
                        modificationScoring = new ModificationScoring(modName);
                        modificationScores.addModificationScoring(modName, modificationScoring);
                    }
                    modificationScoring.setProbabilisticScore(site, scores.get(site));
                }
            }
        }
        identification.updateObject(spectrumMatch.getKey(), spectrumMatch);
    }
}

Example 3 with SequenceProvider

use of com.compomics.util.experiment.io.biology.protein.SequenceProvider in project peptide-shaker by compomics.

the class QCPanel method getPeptideDataset.

/**
 * Returns the dataset to use for the peptide QC plot.
 */
private void getPeptideDataset() {
    maxValue = Double.MIN_VALUE;
    SequenceProvider sequenceProvider = peptideShakerGUI.getSequenceProvider();
    if (peptideValidatedPsmsJRadioButton.isSelected()) {
        progressDialog.setPrimaryProgressCounterIndeterminate(false);
        progressDialog.setMaxPrimaryProgressCounter(peptideShakerGUI.getIdentification().getPeptideIdentification().size());
        progressDialog.setValue(0);
        // values for the number of validated PSMs
        validatedValues = new ArrayList<>();
        validatedDoubtfulValues = new ArrayList<>();
        nonValidatedValues = new ArrayList<>();
        validatedDecoyValues = new ArrayList<>();
        nonValidatedDecoyValues = new ArrayList<>();
        PeptideMatchesIterator peptideMatchesIterator = peptideShakerGUI.getIdentification().getPeptideMatchesIterator(progressDialog);
        PeptideMatch peptideMatch;
        while ((peptideMatch = peptideMatchesIterator.next()) != null) {
            if (progressDialog.isRunCanceled()) {
                break;
            }
            double value = 0;
            for (long spectrumMatchKey : peptideMatch.getSpectrumMatchesKeys()) {
                if (progressDialog.isRunCanceled()) {
                    break;
                }
                SpectrumMatch spectrumMatch = peptideShakerGUI.getIdentification().getSpectrumMatch(spectrumMatchKey);
                PSParameter spectrumParameter = (PSParameter) spectrumMatch.getUrParam(PSParameter.dummy);
                if (spectrumParameter.getMatchValidationLevel().isValidated() && !spectrumParameter.getHidden()) {
                    value = value + 1;
                }
            }
            if (value > maxValue) {
                maxValue = value;
            }
            PSParameter peptideParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
            if (!peptideParameter.getHidden()) {
                if (!PeptideUtils.isDecoy(peptideMatch.getPeptide(), sequenceProvider)) {
                    if (peptideParameter.getMatchValidationLevel().isValidated()) {
                        if (peptideParameter.getMatchValidationLevel() == MatchValidationLevel.confident) {
                            validatedValues.add(value);
                        } else {
                            validatedDoubtfulValues.add(value);
                        }
                    } else {
                        nonValidatedValues.add(value);
                    }
                } else if (peptideParameter.getMatchValidationLevel().isValidated()) {
                    validatedDecoyValues.add(value);
                } else {
                    nonValidatedDecoyValues.add(value);
                }
            }
            progressDialog.increasePrimaryProgressCounter();
        }
    } else if (peptideMissedCleavagesJRadioButton.isSelected()) {
        progressDialog.setPrimaryProgressCounterIndeterminate(false);
        progressDialog.setMaxPrimaryProgressCounter(peptideShakerGUI.getIdentification().getPeptideIdentification().size());
        progressDialog.setValue(0);
        // Values for the missed cleavages
        validatedValues = new ArrayList<>();
        validatedDoubtfulValues = new ArrayList<>();
        nonValidatedValues = new ArrayList<>();
        validatedDecoyValues = new ArrayList<>();
        nonValidatedDecoyValues = new ArrayList<>();
        PeptideMatchesIterator peptideMatchesIterator = peptideShakerGUI.getIdentification().getPeptideMatchesIterator(progressDialog);
        PeptideMatch peptideMatch;
        while ((peptideMatch = peptideMatchesIterator.next()) != null) {
            if (progressDialog.isRunCanceled()) {
                break;
            }
            PSParameter peptideParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
            if (!peptideParameter.getHidden()) {
                Double value = null;
                DigestionParameters digestionParameters = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getDigestionParameters();
                if (digestionParameters.getCleavageParameter() == DigestionParameters.CleavageParameter.enzyme) {
                    for (Enzyme enzyme : digestionParameters.getEnzymes()) {
                        int enzymeMissedCelavages = enzyme.getNmissedCleavages(peptideMatch.getPeptide().getSequence());
                        if (value == null || enzymeMissedCelavages < value) {
                            value = Double.valueOf(enzymeMissedCelavages);
                        }
                    }
                }
                if (value == null) {
                    value = 0.0;
                }
                if (value > 0) {
                    if (value > maxValue) {
                        maxValue = value;
                    }
                }
                if (!PeptideUtils.isDecoy(peptideMatch.getPeptide(), sequenceProvider)) {
                    if (peptideParameter.getMatchValidationLevel().isValidated()) {
                        if (peptideParameter.getMatchValidationLevel() == MatchValidationLevel.confident) {
                            validatedValues.add(value);
                        } else {
                            validatedDoubtfulValues.add(value);
                        }
                    } else {
                        nonValidatedValues.add(value);
                    }
                } else if (peptideParameter.getMatchValidationLevel().isValidated()) {
                    validatedDecoyValues.add(value);
                } else {
                    nonValidatedDecoyValues.add(value);
                }
            }
            progressDialog.increasePrimaryProgressCounter();
        }
    } else if (peptideLengthJRadioButton.isSelected()) {
        progressDialog.setPrimaryProgressCounterIndeterminate(false);
        progressDialog.setMaxPrimaryProgressCounter(peptideShakerGUI.getIdentification().getPeptideIdentification().size());
        progressDialog.setValue(0);
        // values for the peptide length
        validatedValues = new ArrayList<>();
        validatedDoubtfulValues = new ArrayList<>();
        nonValidatedValues = new ArrayList<>();
        validatedDecoyValues = new ArrayList<>();
        nonValidatedDecoyValues = new ArrayList<>();
        PeptideMatchesIterator peptideMatchesIterator = peptideShakerGUI.getIdentification().getPeptideMatchesIterator(progressDialog);
        PeptideMatch peptideMatch;
        while ((peptideMatch = peptideMatchesIterator.next()) != null) {
            if (progressDialog.isRunCanceled()) {
                break;
            }
            PSParameter peptideParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
            if (!peptideParameter.getHidden()) {
                double length = peptideMatch.getPeptide().getSequence().length();
                if (length > 0) {
                    if (length > maxValue) {
                        maxValue = length;
                    }
                }
                if (!PeptideUtils.isDecoy(peptideMatch.getPeptide(), sequenceProvider)) {
                    if (peptideParameter.getMatchValidationLevel().isValidated()) {
                        if (peptideParameter.getMatchValidationLevel() == MatchValidationLevel.confident) {
                            validatedValues.add(length);
                        } else {
                            validatedDoubtfulValues.add(length);
                        }
                    } else {
                        nonValidatedValues.add(length);
                    }
                } else if (peptideParameter.getMatchValidationLevel().isValidated()) {
                    validatedDecoyValues.add(length);
                } else {
                    nonValidatedDecoyValues.add(length);
                }
            }
            progressDialog.increasePrimaryProgressCounter();
        }
    }
}

Example 4 with SequenceProvider

use of com.compomics.util.experiment.io.biology.protein.SequenceProvider in project peptide-shaker by compomics.

the class QCPanel method getPeptideModificationEnrichmentSpecificityDataset.

/**
 * Returns the dataset for the peptide modification rate QC plot.
 *
 * @return the dataset for the peptide modification rate QC plot
 */
private DefaultCategoryDataset getPeptideModificationEnrichmentSpecificityDataset() {
    ModificationFactory modificationFactory = ModificationFactory.getInstance();
    Identification identification = peptideShakerGUI.getIdentification();
    SequenceProvider sequenceProvider = peptideShakerGUI.getSequenceProvider();
    IdentificationParameters identificationParameters = peptideShakerGUI.getIdentificationParameters();
    ModificationParameters modificationParameters = identificationParameters.getSearchParameters().getModificationParameters();
    SequenceMatchingParameters modificationSequenceMatchingParameters = identificationParameters.getModificationLocalizationParameters().getSequenceMatchingParameters();
    ArrayList<String> modNames = modificationParameters.getAllNotFixedModifications();
    HashMap<String, Integer> modifiedPeptidesMap = new HashMap<>(modNames.size());
    HashMap<String, Integer> possiblyModifiedPeptidesMap = new HashMap<>(modNames.size());
    progressDialog.setPrimaryProgressCounterIndeterminate(false);
    progressDialog.setMaxPrimaryProgressCounter(identification.getPeptideIdentification().size());
    progressDialog.setValue(0);
    PeptideMatchesIterator peptideMatchesIterator = identification.getPeptideMatchesIterator(progressDialog);
    PeptideMatch peptideMatch;
    while ((peptideMatch = peptideMatchesIterator.next()) != null) {
        PSParameter psParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
        if (psParameter.getMatchValidationLevel().isValidated()) {
            Peptide peptide = peptideMatch.getPeptide();
            for (String modName : modificationParameters.getAllNotFixedModifications()) {
                Modification modification = modificationFactory.getModification(modName);
                int[] possibleSites = ModificationUtils.getPossibleModificationSites(peptide, modification, sequenceProvider, modificationSequenceMatchingParameters);
                if (possibleSites.length != 0) {
                    Integer nPossiblePeptides = possiblyModifiedPeptidesMap.get(modName);
                    if (nPossiblePeptides == null) {
                        possiblyModifiedPeptidesMap.put(modName, 1);
                    } else {
                        possiblyModifiedPeptidesMap.put(modName, nPossiblePeptides + 1);
                    }
                    boolean modified = false;
                    for (ModificationMatch modificationMatch : peptide.getVariableModifications()) {
                        if (modificationMatch.getModification().equals(modName)) {
                            modified = true;
                            break;
                        }
                    }
                    if (modified) {
                        Integer nModifiedPeptides = modifiedPeptidesMap.get(modName);
                        if (nModifiedPeptides == null) {
                            modifiedPeptidesMap.put(modName, 1);
                        } else {
                            modifiedPeptidesMap.put(modName, nModifiedPeptides + 1);
                        }
                    }
                }
            }
        }
        if (progressDialog.isRunCanceled()) {
            break;
        }
        progressDialog.increaseSecondaryProgressCounter();
    }
    DefaultCategoryDataset dataset = new DefaultCategoryDataset();
    for (String modName : modificationParameters.getAllNotFixedModifications()) {
        Integer nFound = modifiedPeptidesMap.get(modName);
        if (nFound == null) {
            nFound = 0;
        }
        Integer nPossible = possiblyModifiedPeptidesMap.get(modName);
        Double rate = 0.0;
        if (nPossible != null) {
            rate = (100.0 * nFound) / nPossible;
        }
        dataset.addValue(rate, "Modified", modName);
        double rest = 0.0;
        if (nPossible != null) {
            rest = 100 - rate;
        }
        dataset.addValue(rest, "Not Modified", modName);
    }
    return dataset;
}

Example 5 with SequenceProvider

use of com.compomics.util.experiment.io.biology.protein.SequenceProvider in project peptide-shaker by compomics.

the class QCPanel method getPeptideModificationEfficiencyDataset.

/**
 * Returns the dataset for the peptide modification efficiency QC plot.
 *
 * @return the dataset for the peptide modification efficiency QC plot
 */
private DefaultCategoryDataset getPeptideModificationEfficiencyDataset() {
    ModificationFactory modificationFactory = ModificationFactory.getInstance();
    Identification identification = peptideShakerGUI.getIdentification();
    SequenceProvider sequenceProvider = peptideShakerGUI.getSequenceProvider();
    IdentificationParameters identificationParameters = peptideShakerGUI.getIdentificationParameters();
    ModificationParameters modificationParameters = identificationParameters.getSearchParameters().getModificationParameters();
    SequenceMatchingParameters modificationSequenceMatchingPreferences = identificationParameters.getModificationLocalizationParameters().getSequenceMatchingParameters();
    ArrayList<String> modNames = modificationParameters.getAllNotFixedModifications();
    HashMap<String, Integer> modifiedSitesMap = new HashMap<>(modNames.size());
    HashMap<String, Integer> possibleSitesMap = new HashMap<>(modNames.size());
    PSParameter psParameter = new PSParameter();
    progressDialog.setPrimaryProgressCounterIndeterminate(false);
    progressDialog.setMaxPrimaryProgressCounter(identification.getPeptideIdentification().size());
    progressDialog.setValue(0);
    PeptideMatchesIterator peptideMatchesIterator = identification.getPeptideMatchesIterator(progressDialog);
    PeptideMatch peptideMatch;
    while ((peptideMatch = peptideMatchesIterator.next()) != null) {
        psParameter = (PSParameter) peptideMatch.getUrParam(psParameter);
        if (psParameter.getMatchValidationLevel().isValidated()) {
            Peptide peptide = peptideMatch.getPeptide();
            HashMap<String, Integer> peptideModificationsMap = new HashMap<>(peptide.getVariableModifications().length);
            for (ModificationMatch modificationMatch : peptide.getVariableModifications()) {
                String modName = modificationMatch.getModification();
                Integer occurrence = peptideModificationsMap.get(modName);
                if (occurrence == null) {
                    peptideModificationsMap.put(modName, 1);
                } else {
                    peptideModificationsMap.put(modName, occurrence + 1);
                }
            }
            for (String modName : modificationParameters.getAllNotFixedModifications()) {
                Modification modification = modificationFactory.getModification(modName);
                int[] possibleSites = ModificationUtils.getPossibleModificationSites(peptide, modification, sequenceProvider, modificationSequenceMatchingPreferences);
                if (possibleSites.length != 0) {
                    Integer occurrencePeptide = peptideModificationsMap.get(modName);
                    if (occurrencePeptide != null) {
                        Integer occurrenceDataset = modifiedSitesMap.get(modName);
                        if (occurrenceDataset == null) {
                            modifiedSitesMap.put(modName, occurrencePeptide);
                        } else {
                            modifiedSitesMap.put(modName, occurrenceDataset + occurrencePeptide);
                        }
                    }
                    Integer possibleSitesDataset = possibleSitesMap.get(modName);
                    if (possibleSitesDataset == null) {
                        possibleSitesMap.put(modName, possibleSites.length);
                    } else {
                        possibleSitesMap.put(modName, possibleSitesDataset + possibleSites.length);
                    }
                }
            }
        }
        if (progressDialog.isRunCanceled()) {
            break;
        }
        progressDialog.increaseSecondaryProgressCounter();
    }
    DefaultCategoryDataset dataset = new DefaultCategoryDataset();
    for (String modName : modificationParameters.getAllNotFixedModifications()) {
        Integer nFound = modifiedSitesMap.get(modName);
        if (nFound == null) {
            nFound = 0;
        }
        Integer nPossible = possibleSitesMap.get(modName);
        Double rate = 0.0;
        if (nPossible != null) {
            rate = (100.0 * nFound) / nPossible;
        }
        dataset.addValue(rate, "Modified", modName);
        double rest = 100 - rate;
        dataset.addValue(rest, "Not Modified", modName);
    }
    return dataset;
}