Examples with PeptideMatchesIterator com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator used on opensource projects

Example 1 with PeptideMatchesIterator

use of com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator 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 2 with PeptideMatchesIterator

use of com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator 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 3 with PeptideMatchesIterator

use of com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator 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;
}

Example 4 with PeptideMatchesIterator

use of com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator in project peptide-shaker by compomics.

the class MatchesValidator method attachPeptideProbabilities.

/**
 * Attaches the peptide posterior error probabilities to the peptide
 * matches.
 *
 * @param identification the identification class containing the matches to
 * validate
 * @param fastaParameters the FASTA file parameters
 * @param waitingHandler the handler displaying feedback to the user
 */
public void attachPeptideProbabilities(Identification identification, FastaParameters fastaParameters, WaitingHandler waitingHandler) {
    waitingHandler.setWaitingText("Attaching Peptide Probabilities. Please Wait...");
    waitingHandler.setSecondaryProgressCounterIndeterminate(false);
    waitingHandler.setMaxSecondaryProgressCounter(identification.getPeptideIdentification().size());
    PSParameter psParameter = new PSParameter();
    PeptideMatchesIterator peptideMatchesIterator = identification.getPeptideMatchesIterator(waitingHandler);
    PeptideMatch peptideMatch;
    while ((peptideMatch = peptideMatchesIterator.next()) != null) {
        long peptideKey = peptideMatch.getKey();
        psParameter = (PSParameter) peptideMatch.getUrParam(psParameter);
        if (fastaParameters.isTargetDecoy()) {
            double probability = peptideMap.getProbability(psParameter.getScore());
            psParameter.setProbability(probability);
        } else {
            psParameter.setProbability(1.0);
        }
        Set<String> fractions = psParameter.getFractions();
        if (fractions == null) {
            throw new IllegalArgumentException("Fractions not found for peptide " + peptideKey + ".");
        }
        for (String fraction : fractions) {
            if (fastaParameters.isTargetDecoy()) {
                double probability = peptideMap.getProbability(psParameter.getFractionScore(fraction));
                psParameter.setFractionPEP(fraction, probability);
            } else {
                psParameter.setFractionPEP(fraction, 1.0);
            }
        }
        identification.updateObject(peptideKey, peptideMatch);
        waitingHandler.increaseSecondaryProgressCounter();
        if (waitingHandler.isRunCanceled()) {
            return;
        }
    }
    waitingHandler.setSecondaryProgressCounterIndeterminate(true);
}

Example 5 with PeptideMatchesIterator

use of com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator in project peptide-shaker by compomics.

the class PsPeptideSection method writeSection.

/**
 * Writes the desired section.
 *
 * @param identification The identification of the project.
 * @param identificationFeaturesGenerator The identification features
 * generator of the project.
 * @param sequenceProvider The sequence provider.
 * @param proteinDetailsProvider The protein details provider.
 * @param spectrumProvider The spectrum provider.
 * @param identificationParameters The identification parameters.
 * @param keys The keys of the PSM matches to output.
 * @param linePrefix The line prefix.
 * @param nSurroundingAA The number of surrounding amino acids to export.
 * @param validatedOnly Whether only validated matches should be exported.
 * @param decoys Whether decoy matches should be exported as well.
 * @param waitingHandler The waiting handler.
 *
 * @throws java.io.IOException exception thrown if an error occurred while
 * reading or writing a file
 */
public void writeSection(Identification identification, IdentificationFeaturesGenerator identificationFeaturesGenerator, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider, IdentificationParameters identificationParameters, long[] keys, int nSurroundingAA, String linePrefix, boolean validatedOnly, boolean decoys, WaitingHandler waitingHandler) throws IOException {
    if (waitingHandler != null) {
        waitingHandler.setSecondaryProgressCounterIndeterminate(true);
    }
    if (header) {
        writeHeader();
    }
    int lineNumber = 1;
    if (waitingHandler != null) {
        waitingHandler.setWaitingText("Exporting. Please Wait...");
        waitingHandler.resetSecondaryProgressCounter();
        waitingHandler.setMaxSecondaryProgressCounter(keys == null ? identification.getPeptideIdentification().size() : keys.length);
    }
    PeptideMatchesIterator peptideMatchesIterator = identification.getPeptideMatchesIterator(keys, waitingHandler);
    PeptideMatch peptideMatch;
    while ((peptideMatch = peptideMatchesIterator.next()) != null) {
        if (waitingHandler != null) {
            if (waitingHandler.isRunCanceled()) {
                return;
            }
            waitingHandler.increaseSecondaryProgressCounter();
        }
        PSParameter psParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
        if (!validatedOnly || psParameter.getMatchValidationLevel().isValidated()) {
            if (decoys || !PeptideUtils.isDecoy(peptideMatch.getPeptide(), sequenceProvider)) {
                boolean first = true;
                if (indexes) {
                    if (linePrefix != null) {
                        writer.write(linePrefix);
                    }
                    writer.write(Integer.toString(lineNumber));
                    first = false;
                }
                for (ExportFeature exportFeature : peptideFeatures) {
                    if (!first) {
                        writer.addSeparator();
                    } else {
                        first = false;
                    }
                    PsPeptideFeature peptideFeature = (PsPeptideFeature) exportFeature;
                    writer.write(getfeature(identification, identificationFeaturesGenerator, sequenceProvider, proteinDetailsProvider, identificationParameters, nSurroundingAA, linePrefix, peptideMatch, peptideFeature, validatedOnly, decoys, waitingHandler));
                }
                writer.newLine();
                if (psmSection != null) {
                    String psmSectionPrefix = "";
                    if (linePrefix != null) {
                        psmSectionPrefix += linePrefix;
                    }
                    psmSectionPrefix += lineNumber + ".";
                    writer.increaseDepth();
                    if (waitingHandler != null) {
                        waitingHandler.setDisplayProgress(false);
                    }
                    psmSection.writeSection(identification, identificationFeaturesGenerator, sequenceProvider, proteinDetailsProvider, spectrumProvider, identificationParameters, peptideMatch.getSpectrumMatchesKeys(), psmSectionPrefix, nSurroundingAA, validatedOnly, decoys, waitingHandler);
                    if (waitingHandler != null) {
                        waitingHandler.setDisplayProgress(true);
                    }
                    writer.decreseDepth();
                }
                lineNumber++;
            }
        }
    }
}