Examples with ModificationLocalizationScorer eu.isas.peptideshaker.ptm.ModificationLocalizationScorer used on opensource projects

Example 1 with ModificationLocalizationScorer

use of eu.isas.peptideshaker.ptm.ModificationLocalizationScorer in project peptide-shaker by compomics.

the class ProteinProcessor method processProteins.

/**
 * Scores the PTMs of all protein matches contained in an identification
 * object, estimates spectrum counting and summary statistics.
 *
 * @param modificationLocalizationScorer The modification localization
 * scorer to use.
 * @param metrics If provided, metrics on proteins will be saved while
 * iterating the matches.
 * @param modificationProvider The modification provider to use.
 * @param waitingHandler The handler displaying feedback to the user.
 * @param exceptionHandler The exception handler to use.
 * @param processingParameters The processing parameters.
 *
 * @throws java.lang.InterruptedException exception thrown if a thread gets
 * interrupted
 * @throws java.util.concurrent.TimeoutException exception thrown if the
 * operation times out
 */
public void processProteins(ModificationLocalizationScorer modificationLocalizationScorer, Metrics metrics, ModificationProvider modificationProvider, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler, ProcessingParameters processingParameters) throws InterruptedException, TimeoutException {
    waitingHandler.setWaitingText("Scoring Protein Modification Localization. Please Wait...");
    int max = identification.getProteinIdentification().size();
    waitingHandler.setSecondaryProgressCounterIndeterminate(false);
    waitingHandler.setMaxSecondaryProgressCounter(max);
    // validate the proteins
    ExecutorService pool = Executors.newFixedThreadPool(processingParameters.getnThreads());
    ProteinMatchesIterator proteinMatchesIterator = identification.getProteinMatchesIterator(waitingHandler);
    ArrayList<ProteinRunnable> runnables = new ArrayList<>(processingParameters.getnThreads());
    for (int i = 1; i <= processingParameters.getnThreads(); i++) {
        ProteinRunnable runnable = new ProteinRunnable(proteinMatchesIterator, modificationLocalizationScorer, modificationProvider, waitingHandler, exceptionHandler);
        pool.submit(runnable);
        runnables.add(runnable);
    }
    if (waitingHandler.isRunCanceled()) {
        pool.shutdownNow();
    }
    pool.shutdown();
    if (!pool.awaitTermination(identification.getProteinIdentification().size(), TimeUnit.MINUTES)) {
        throw new InterruptedException("Protein matches validation timed out. Please contact the developers.");
    }
    waitingHandler.setSecondaryProgressCounterIndeterminate(true);
    if (metrics != null) {
        metrics.setMaxSpectrumCounting(runnables.stream().mapToDouble(ProteinRunnable::getMaxSpectrumCounting).sum());
        metrics.setnValidatedProteins(runnables.stream().mapToInt(ProteinRunnable::getnValidatedProteins).sum());
        metrics.setnConfidentProteins(runnables.stream().mapToInt(ProteinRunnable::getnConfidentProteins).sum());
        metrics.setMaxNPeptides(runnables.stream().mapToInt(ProteinRunnable::getMaxPeptides).max().orElse(0));
        metrics.setMaxNPsms(runnables.stream().mapToInt(ProteinRunnable::getMaxPsms).max().orElse(0));
        metrics.setMaxMW(runnables.stream().mapToDouble(ProteinRunnable::getMaxMW).max().orElse(0.0));
        metrics.setMaxProteinAccessionLength(runnables.stream().mapToInt(ProteinRunnable::getMaxProteinAccessionLength).max().orElse(0));
        TreeMap<Double, TreeMap<Integer, TreeMap<Integer, TreeSet<Long>>>> orderMap1 = new TreeMap<>();
        for (int i = 0; i < runnables.size(); i++) {
            HashMap<Double, HashMap<Integer, HashMap<Integer, HashSet<Long>>>> threadMap1 = runnables.get(i).getOrderMap();
            for (Entry<Double, HashMap<Integer, HashMap<Integer, HashSet<Long>>>> entry1 : threadMap1.entrySet()) {
                double key1 = entry1.getKey();
                HashMap<Integer, HashMap<Integer, HashSet<Long>>> threadMap2 = entry1.getValue();
                TreeMap<Integer, TreeMap<Integer, TreeSet<Long>>> orderMap2 = orderMap1.get(key1);
                if (orderMap2 == null) {
                    orderMap2 = new TreeMap<>();
                    orderMap1.put(key1, orderMap2);
                }
                for (Entry<Integer, HashMap<Integer, HashSet<Long>>> entry2 : threadMap2.entrySet()) {
                    int key2 = entry2.getKey();
                    HashMap<Integer, HashSet<Long>> threadMap3 = entry2.getValue();
                    TreeMap<Integer, TreeSet<Long>> orderMap3 = orderMap2.get(key2);
                    if (orderMap3 == null) {
                        orderMap3 = new TreeMap<>();
                        orderMap2.put(key2, orderMap3);
                    }
                    for (Entry<Integer, HashSet<Long>> entry3 : threadMap3.entrySet()) {
                        int key3 = entry3.getKey();
                        HashSet<Long> threadSet = entry3.getValue();
                        TreeSet<Long> orderedSet = orderMap3.get(key3);
                        if (orderedSet == null) {
                            orderedSet = new TreeSet<>();
                            orderMap3.put(key3, orderedSet);
                        }
                        orderedSet.addAll(threadSet);
                    }
                }
            }
        }
        long[] proteinKeys = orderMap1.values().stream().flatMap(map -> map.values().stream()).flatMap(map -> map.values().stream()).flatMap(set -> set.stream()).mapToLong(a -> a).toArray();
        metrics.setProteinKeys(proteinKeys);
    }
}

Example 2 with ModificationLocalizationScorer

use of eu.isas.peptideshaker.ptm.ModificationLocalizationScorer in project peptide-shaker by compomics.

the class PeptideShakerGUI method updateMainMatch.

/**
 * Update the protein match in the different tabs.
 *
 * @param mainMatch the protein match to use
 * @param proteinInferenceType the protein inference group type
 */
public void updateMainMatch(String mainMatch, int proteinInferenceType) {
    try {
        ModificationLocalizationScorer ptmScorer = new ModificationLocalizationScorer();
        Identification identification = getIdentification();
        ProteinMatch proteinMatch = identification.getProteinMatch(selectedProteinKey);
        ptmScorer.scorePTMs(identification, proteinMatch, getIdentificationParameters(), false, modificationFactory, null);
    } catch (Exception e) {
        catchException(e);
    }
    overviewPanel.updateProteinTable();
    proteinStructurePanel.updateMainMatch(mainMatch, proteinInferenceType);
}

Example 3 with ModificationLocalizationScorer

use of eu.isas.peptideshaker.ptm.ModificationLocalizationScorer in project peptide-shaker by compomics.

the class ModificationSiteInferenceDialog method okButtonActionPerformed.

// GEN-LAST:event_cancelButtonActionPerformed
/**
 * Updates the data and then closes the dialog.
 *
 * @param evt
 */
private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {
    // GEN-FIRST:event_okButtonActionPerformed
    boolean changed = false;
    if (changed) {
        try {
            // save changes in the peptide match
            Identification identification = peptideShakerGUI.getIdentification();
            // update protein level PTM scoring
            ModificationLocalizationScorer ptmScorer = new ModificationLocalizationScorer();
            IdentificationParameters identificationParameters = peptideShakerGUI.getIdentificationParameters();
            identification.getProteinMatches(peptideMatch.getKey()).stream().map(key -> identification.getProteinMatch(key)).forEach(proteinMatch -> ptmScorer.scorePTMs(identification, proteinMatch, identificationParameters, false, modificationFactory, null));
        } catch (Exception e) {
            peptideShakerGUI.catchException(e);
        }
    }
    dispose();
}

Example 4 with ModificationLocalizationScorer

use of eu.isas.peptideshaker.ptm.ModificationLocalizationScorer in project peptide-shaker by compomics.

the class PeptideShakerGUI method validationQcMenuItemActionPerformed.

// GEN-LAST:event_configurationFilesSettingsActionPerformed
/**
 * Open the ValidationQCPreferencesDialog.
 *
 * @param evt
 */
private void validationQcMenuItemActionPerformed(java.awt.event.ActionEvent evt) {
    // GEN-FIRST:event_validationQcMenuItemActionPerformed
    final IdMatchValidationParameters idValidationParameters = getIdentificationParameters().getIdValidationParameters();
    final ValidationQcParameters validationQCParameters = idValidationParameters.getValidationQCParameters();
    ValidationQCParametersDialog validationQCParametersDialog = new ValidationQCParametersDialog(this, validationQCParameters, getIdentificationParameters().getSearchParameters().getModificationParameters().getAllModifications(), true);
    if (!validationQCParametersDialog.isCanceled()) {
        ValidationQcParameters newParameters = validationQCParametersDialog.getValidationQCParameters();
        if (!newParameters.isSameAs(validationQCParameters)) {
            idValidationParameters.setValidationQCParameters(newParameters);
            // Update the assumptions QC filters
            for (Filter filter : newParameters.getPsmFilters()) {
                PsmFilter psmFilter = (PsmFilter) filter;
                AssumptionFilter assumptionFilter = psmFilter.getAssumptionFilter();
                assumptionFilter.clear();
                for (String itemName : psmFilter.getItemsNames()) {
                    assumptionFilter.setFilterItem(itemName, psmFilter.getComparatorForItem(itemName), psmFilter.getValue(itemName));
                }
            }
            progressDialog = new ProgressDialogX(PeptideShakerGUI.this, Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")), Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker-orange.gif")), true);
            progressDialog.setTitle("Validating. Please Wait...");
            progressDialog.setPrimaryProgressCounterIndeterminate(false);
            new Thread(new Runnable() {

                public void run() {
                    try {
                        progressDialog.setVisible(true);
                    } catch (IndexOutOfBoundsException e) {
                    // ignore
                    }
                }
            }, "ProgressDialog").start();
            new Thread("RecalculateThread") {

                @Override
                public void run() {
                    PeptideShakerGUI peptideShakerGUI = PeptideShakerGUI.this;
                    try {
                        PSMaps pSMaps = new PSMaps();
                        pSMaps = (PSMaps) peptideShakerGUI.getIdentification().getUrParam(pSMaps);
                        MatchesValidator matchesValidator = new MatchesValidator(pSMaps.getPsmMap(), pSMaps.getPeptideMap(), pSMaps.getProteinMap());
                        matchesValidator.validateIdentifications(peptideShakerGUI.getIdentification(), peptideShakerGUI.getMetrics(), pSMaps.getInputMap(), progressDialog, exceptionHandler, peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getSequenceProvider(), peptideShakerGUI.getProteinDetailsProvider(), peptideShakerGUI.getSpectrumProvider(), peptideShakerGUI.getGeneMaps(), peptideShakerGUI.getIdentificationParameters(), peptideShakerGUI.getProjectType(), peptideShakerGUI.getProcessingParameters());
                        progressDialog.setPrimaryProgressCounterIndeterminate(true);
                        ProteinProcessor proteinProcessor = new ProteinProcessor(peptideShakerGUI.getIdentification(), peptideShakerGUI.getIdentificationParameters(), peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getSequenceProvider());
                        proteinProcessor.processProteins(new ModificationLocalizationScorer(), peptideShakerGUI.getMetrics(), modificationFactory, progressDialog, peptideShakerGUI.getExceptionHandler(), peptideShakerGUI.getProcessingParameters());
                        if (!progressDialog.isRunCanceled()) {
                            // update the other tabs
                            peptideShakerGUI.getMetrics().setnValidatedProteins(-1);
                            peptideShakerGUI.getMetrics().setnConfidentProteins(-1);
                            peptideShakerGUI.setUpdated(PeptideShakerGUI.OVER_VIEW_TAB_INDEX, false);
                            peptideShakerGUI.setUpdated(PeptideShakerGUI.PROTEIN_FRACTIONS_TAB_INDEX, false);
                            peptideShakerGUI.setUpdated(PeptideShakerGUI.STRUCTURES_TAB_INDEX, false);
                            peptideShakerGUI.setUpdated(PeptideShakerGUI.MODIFICATIONS_TAB_INDEX, false);
                            peptideShakerGUI.setUpdated(PeptideShakerGUI.QC_PLOTS_TAB_INDEX, false);
                            peptideShakerGUI.setUpdated(PeptideShakerGUI.SPECTRUM_ID_TAB_INDEX, false);
                            peptideShakerGUI.setDataSaved(false);
                        } else {
                            idValidationParameters.setValidationQCParameters(validationQCParameters);
                        }
                    } catch (Exception e) {
                        peptideShakerGUI.catchException(e);
                    }
                    progressDialog.setRunFinished();
                    PeptideShakerGUI.this.repaintPanels();
                }
            }.start();
        }
    }
}

Example 5 with ModificationLocalizationScorer

use of eu.isas.peptideshaker.ptm.ModificationLocalizationScorer in project peptide-shaker by compomics.

the class ValidationPanel method validateButtonActionPerformed.

// GEN-LAST:event_formComponentResized
/**
 * Validate the data using the current settings.
 *
 * @param evt
 */
private void validateButtonActionPerformed(java.awt.event.ActionEvent evt) {
    // GEN-FIRST:event_validateButtonActionPerformed
    double lastThreshold = Double.valueOf(thresholdInput.getText());
    thresholdInputActionPerformed(null);
    if (lastThreshold < 0 || lastThreshold > 100) {
        JOptionPane.showMessageDialog(this, "Please verify the given threshold. Interval: [0, 100].", "Threshold Error", JOptionPane.WARNING_MESSAGE);
    } else {
        progressDialog = new ProgressDialogX(peptideShakerGUI, Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")), Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker-orange.gif")), true);
        progressDialog.setTitle("Recalculating. Please Wait...");
        progressDialog.setPrimaryProgressCounterIndeterminate(false);
        new Thread(new Runnable() {

            public void run() {
                try {
                    progressDialog.setVisible(true);
                } catch (IndexOutOfBoundsException e) {
                // ignore
                }
            }
        }, "ProgressDialog").start();
        new Thread("RecalculateThread") {

            @Override
            public void run() {
                try {
                    PSMaps pSMaps = new PSMaps();
                    pSMaps = (PSMaps) peptideShakerGUI.getIdentification().getUrParam(pSMaps);
                    MatchesValidator matchesValidator = new MatchesValidator(pSMaps.getPsmMap(), pSMaps.getPeptideMap(), pSMaps.getProteinMap());
                    matchesValidator.validateIdentifications(peptideShakerGUI.getIdentification(), peptideShakerGUI.getMetrics(), pSMaps.getInputMap(), progressDialog, peptideShakerGUI.getExceptionHandler(), peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getSequenceProvider(), peptideShakerGUI.getProteinDetailsProvider(), peptideShakerGUI.getSpectrumProvider(), peptideShakerGUI.getGeneMaps(), peptideShakerGUI.getIdentificationParameters(), peptideShakerGUI.getProjectType(), peptideShakerGUI.getProcessingParameters());
                    progressDialog.setPrimaryProgressCounterIndeterminate(true);
                    if (peptideShakerGUI.getProjectType() == ProjectType.protein) {
                        ProteinProcessor proteinProcessor = new ProteinProcessor(peptideShakerGUI.getIdentification(), peptideShakerGUI.getIdentificationParameters(), peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getSequenceProvider());
                        proteinProcessor.processProteins(new ModificationLocalizationScorer(), peptideShakerGUI.getMetrics(), modificationFactory, progressDialog, peptideShakerGUI.getExceptionHandler(), peptideShakerGUI.getProcessingParameters());
                    }
                    if (!progressDialog.isRunCanceled()) {
                        // update the other tabs
                        peptideShakerGUI.getMetrics().setnValidatedProteins(-1);
                        peptideShakerGUI.getMetrics().setnConfidentProteins(-1);
                        peptideShakerGUI.setUpdated(PeptideShakerGUI.OVER_VIEW_TAB_INDEX, false);
                        peptideShakerGUI.setUpdated(PeptideShakerGUI.PROTEIN_FRACTIONS_TAB_INDEX, false);
                        peptideShakerGUI.setUpdated(PeptideShakerGUI.STRUCTURES_TAB_INDEX, false);
                        peptideShakerGUI.setUpdated(PeptideShakerGUI.MODIFICATIONS_TAB_INDEX, false);
                        peptideShakerGUI.setUpdated(PeptideShakerGUI.QC_PLOTS_TAB_INDEX, false);
                        peptideShakerGUI.setUpdated(PeptideShakerGUI.SPECTRUM_ID_TAB_INDEX, false);
                        dataValidated = true;
                        validateButton.setEnabled(false);
                        double input = Double.valueOf(thresholdInput.getText());
                        int inputType = thresholdTypeCmb.getSelectedIndex();
                        TargetDecoyResults currentResults = currentTargetDecoyMap.getTargetDecoyResults();
                        currentResults.setUserInput(input);
                        currentResults.setInputType(inputType);
                        String selectedGroup = (String) groupSelectionTable.getValueAt(groupSelectionTable.getSelectedRow(), 1);
                        originalThresholds.put(selectedGroup, input);
                        originalThresholdTypes.put(selectedGroup, inputType);
                        peptideShakerGUI.setDataSaved(false);
                    } else {
                    // @TODO: ideally the validation settings ought to be reset as well..?
                    }
                } catch (Exception e) {
                    peptideShakerGUI.catchException(e);
                }
                progressDialog.setRunFinished();
            }
        }.start();
    }
}