Examples with ProteinMatch com.compomics.util.experiment.identification.matches.ProteinMatch used on opensource projects

Example 1 with ProteinMatch

use of com.compomics.util.experiment.identification.matches.ProteinMatch in project peptide-shaker by compomics.

the class ProteinStructurePanel method pdbMatchesJTableMouseReleased.

// GEN-LAST:event_peptideTableMouseReleased
/**
 * Update the PDB structure shown in the Jmol panel.
 *
 * @param evt
 */
private void pdbMatchesJTableMouseReleased(java.awt.event.MouseEvent evt) {
    // GEN-FIRST:event_pdbMatchesJTableMouseReleased
    setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
    boolean loadStructure = true;
    if (pdbMatchesJTable.getSelectedRow() != -1 && currentlyDisplayedPdbFile != null) {
        String tempPdbFile = (String) pdbMatchesJTable.getValueAt(pdbMatchesJTable.getSelectedRow(), pdbMatchesJTable.getColumn("PDB").getModelIndex());
        if (currentlyDisplayedPdbFile.equalsIgnoreCase(tempPdbFile)) {
            loadStructure = false;
        }
    }
    if (loadStructure) {
        // just a trick to make sure that the users cannot select
        // another row until the selection has been updated
        this.setEnabled(false);
        DefaultTableModel dm = (DefaultTableModel) pdbChainsJTable.getModel();
        dm.getDataVector().removeAllElements();
        dm.fireTableDataChanged();
        // clear the peptide to pdb mappings in the peptide table
        for (int i = 0; i < peptideTable.getRowCount(); i++) {
            peptideTable.setValueAt(false, i, peptideTable.getColumn("PDB").getModelIndex());
        }
        // select the peptide in the table again
        int peptideRow = 0;
        long peptideKey = peptideShakerGUI.getSelectedPeptideKey();
        if (peptideKey != NO_KEY) {
            peptideRow = getPeptideRow(peptideKey);
        }
        if (peptideTable.getRowCount() > 0) {
            peptideTable.setRowSelectionInterval(peptideRow, peptideRow);
            peptideTable.scrollRectToVisible(peptideTable.getCellRect(peptideRow, peptideRow, false));
        }
        // empty the jmol panel
        if (jmolStructureShown) {
            jmolPanel = new JmolPanel();
            pdbPanel.removeAll();
            pdbPanel.add(jmolPanel);
            pdbPanel.revalidate();
            pdbPanel.repaint();
            jmolStructureShown = false;
            currentlyDisplayedPdbFile = null;
            ((TitledBorder) pdbOuterPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "PDB Structure" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
            pdbOuterPanel.repaint();
        }
        if (pdbMatchesJTable.getSelectedRow() != -1) {
            currentlyDisplayedPdbFile = (String) pdbMatchesJTable.getValueAt(pdbMatchesJTable.getSelectedRow(), pdbMatchesJTable.getColumn("PDB").getModelIndex());
            // open protein link in web browser
            if (pdbMatchesJTable.getSelectedColumn() == pdbMatchesJTable.getColumn("PDB").getModelIndex() && evt.getButton() == MouseEvent.BUTTON1 && ((String) pdbMatchesJTable.getValueAt(pdbMatchesJTable.getSelectedRow(), pdbMatchesJTable.getSelectedColumn())).lastIndexOf("<a href=\"") != -1) {
                String temp = currentlyDisplayedPdbFile.substring(currentlyDisplayedPdbFile.indexOf("\"") + 1);
                currentlyDisplayedPdbFile = temp.substring(0, temp.indexOf("\""));
                this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
                BareBonesBrowserLaunch.openURL(currentlyDisplayedPdbFile);
                this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
            }
            // get the pdb file
            int selectedPdbTableIndex = (Integer) pdbMatchesJTable.getValueAt(pdbMatchesJTable.getSelectedRow(), 0);
            PdbParameter lParam = uniProtPdb.getPdbs().get(selectedPdbTableIndex - 1);
            chains = lParam.getBlocks();
            // get the protein sequence
            SelfUpdatingTableModel proteinTableModel = (SelfUpdatingTableModel) proteinTable.getModel();
            int proteinIndex = proteinTableModel.getViewIndex(proteinTable.getSelectedRow());
            long proteinKey = proteinKeys[proteinIndex];
            ProteinMatch proteinMatch = peptideShakerGUI.getIdentification().getProteinMatch(proteinKey);
            String proteinSequence = peptideShakerGUI.getSequenceProvider().getSequence(proteinMatch.getLeadingAccession());
            // add the chain information to the table
            for (int j = 0; j < chains.length; j++) {
                XYDataPoint temp = new XYDataPoint(chains[j].getStartProtein(), chains[j].getEndProtein());
                if (chains[j].getStartProtein() != chains[j].getEndProtein()) {
                    ((DefaultTableModel) pdbChainsJTable.getModel()).addRow(new Object[] { (j + 1), chains[j].getBlock(), temp, (((double) chains[j].getEndProtein() - chains[j].getStartProtein()) / proteinSequence.length()) * 100 });
                }
            }
            ((JSparklinesIntervalChartTableCellRenderer) pdbChainsJTable.getColumn("PDB-Protein").getCellRenderer()).setMaxValue(proteinSequence.length());
            if (pdbChainsJTable.getRowCount() > 0) {
                ((TitledBorder) pdbChainsPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "PDB Chains (" + pdbChainsJTable.getRowCount() + ")" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
            } else {
                ((TitledBorder) pdbChainsPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "PDB Chains" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
            }
            pdbChainsPanel.repaint();
            if (pdbChainsJTable.getRowCount() > 0) {
                pdbChainsJTable.setRowSelectionInterval(0, 0);
                pdbChainsJTable.scrollRectToVisible(pdbChainsJTable.getCellRect(0, 0, false));
                pdbChainsJTableMouseReleased(null);
            }
        } else {
            ((TitledBorder) pdbChainsPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "PDB Chains" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
            pdbChainsPanel.repaint();
        }
        // give the power back to the user ;)
        this.setEnabled(true);
    } else {
        // open protein link in web browser
        if (pdbMatchesJTable.getSelectedColumn() == pdbMatchesJTable.getColumn("PDB").getModelIndex() && evt.getButton() == MouseEvent.BUTTON1 && ((String) pdbMatchesJTable.getValueAt(pdbMatchesJTable.getSelectedRow(), pdbMatchesJTable.getSelectedColumn())).lastIndexOf("<a href=\"") != -1) {
            String temp = currentlyDisplayedPdbFile.substring(currentlyDisplayedPdbFile.indexOf("\"") + 1);
            currentlyDisplayedPdbFile = temp.substring(0, temp.indexOf("\""));
            this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
            BareBonesBrowserLaunch.openURL(currentlyDisplayedPdbFile);
            this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
        }
    }
    setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}

Example 2 with ProteinMatch

use of com.compomics.util.experiment.identification.matches.ProteinMatch in project peptide-shaker by compomics.

the class ProteinStructurePanel method updatePdbTable.

/**
 * Update the PDB table according to the selected protein in the protein
 * table.
 *
 * @param proteinKey the current protein key
 */
private void updatePdbTable(long aProteinKey) {
    final long proteinKey = aProteinKey;
    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.setPrimaryProgressCounterIndeterminate(true);
    new Thread(new Runnable() {

        public void run() {
            progressDialog.setTitle("Getting PDB Data. Please Wait...");
            try {
                progressDialog.setVisible(true);
            } catch (IndexOutOfBoundsException e) {
            // ignore
            }
        }
    }, "ProgressDialog").start();
    new Thread("ExtractThread") {

        @Override
        public void run() {
            try {
                // get the accession number of the main match
                ProteinMatch proteinMatch = peptideShakerGUI.getIdentification().getProteinMatch(proteinKey);
                String tempAccession = proteinMatch.getLeadingAccession();
                // find the pdb matches
                // @TODO: make it possible to cancel this process...
                uniProtPdb = new FindPdbForUniprotAccessions(tempAccession, progressDialog);
                // delete the previous matches
                DefaultTableModel dm = (DefaultTableModel) pdbMatchesJTable.getModel();
                dm.getDataVector().removeAllElements();
                dm.fireTableDataChanged();
                dm = (DefaultTableModel) pdbChainsJTable.getModel();
                dm.getDataVector().removeAllElements();
                dm.fireTableDataChanged();
                // clear the peptide to pdb mappings in the peptide table
                for (int i = 0; i < peptideTable.getRowCount() && !progressDialog.isRunCanceled(); i++) {
                    peptideTable.setValueAt(false, i, peptideTable.getColumn("PDB").getModelIndex());
                }
                int maxNumberOfChains = 1;
                // add the new matches to the pdb table
                for (int i = 0; i < uniProtPdb.getPdbs().size() && !progressDialog.isRunCanceled(); i++) {
                    PdbParameter lParam = uniProtPdb.getPdbs().get(i);
                    ((DefaultTableModel) pdbMatchesJTable.getModel()).addRow(new Object[] { i + 1, addPdbDatabaseLink(lParam.getPdbaccession()), lParam.getTitle(), lParam.getExperiment_type(), lParam.getBlocks().length });
                    if (lParam.getBlocks().length > maxNumberOfChains) {
                        maxNumberOfChains = lParam.getBlocks().length;
                    }
                }
                if (!progressDialog.isRunCanceled()) {
                    ((JSparklinesBarChartTableCellRenderer) pdbMatchesJTable.getColumn("Chains").getCellRenderer()).setMaxValue(maxNumberOfChains);
                    if (!uniProtPdb.urlWasRead()) {
                        ((TitledBorder) pdbMatchesPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "PDB Matches - Not Available Without Internet Connection!" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
                    } else {
                        ((TitledBorder) pdbMatchesPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "PDB Matches (" + pdbMatchesJTable.getRowCount() + ")" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
                    }
                    pdbMatchesPanel.repaint();
                    ((TitledBorder) pdbChainsPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "PDB Chains" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
                    pdbChainsPanel.repaint();
                }
                progressDialog.setRunFinished();
            } catch (Exception e) {
                progressDialog.setRunFinished();
                peptideShakerGUI.catchException(e);
            }
        }
    }.start();
}

Example 3 with ProteinMatch

use of com.compomics.util.experiment.identification.matches.ProteinMatch in project peptide-shaker by compomics.

the class ProteinStructurePanel method updateSelection.

/**
 * Update the selected protein and peptide.
 *
 * @param scrollToVisible if true the table also scrolls to make the
 * selected row visible
 */
public void updateSelection(boolean scrollToVisible) {
    int proteinRow = 0;
    long proteinKey = peptideShakerGUI.getSelectedProteinKey();
    long peptideKey = peptideShakerGUI.getSelectedPeptideKey();
    String spectrumFile = peptideShakerGUI.getSelectedSpectrumFile();
    String spectrumTitle = peptideShakerGUI.getSelectedSpectrumTitle();
    Identification identification = peptideShakerGUI.getIdentification();
    if (proteinKey == NO_KEY && peptideKey == NO_KEY && spectrumFile != null && spectrumTitle != null) {
        long psmKey = SpectrumMatch.getKey(spectrumFile, spectrumTitle);
        SpectrumMatch spectrumMatch = identification.getSpectrumMatch(psmKey);
        if (spectrumMatch != null && spectrumMatch.getBestPeptideAssumption() != null) {
            Peptide peptide = spectrumMatch.getBestPeptideAssumption().getPeptide();
            peptideKey = peptide.getMatchingKey(peptideShakerGUI.getIdentificationParameters().getSequenceMatchingParameters());
        }
    }
    if (proteinKey == NO_KEY && peptideKey != NO_KEY) {
        final long peptideKeyFinal = peptideKey;
        ProteinMatch tempProteinMatch = identification.getProteinIdentification().parallelStream().map(key -> identification.getProteinMatch(key)).filter(proteinMatch -> Arrays.stream(proteinMatch.getPeptideMatchesKeys()).anyMatch(key -> key == peptideKeyFinal)).findAny().orElse(null);
        if (tempProteinMatch != null) {
            proteinKey = tempProteinMatch.getKey();
            peptideShakerGUI.setSelectedItems(proteinKey, peptideKey, spectrumFile, spectrumTitle);
        }
        if (proteinKey != NO_KEY) {
            proteinRow = getProteinRow(proteinKey);
        }
        if (proteinKeys.length == 0) {
            clearData();
            return;
        }
        if (proteinRow == -1) {
            peptideShakerGUI.resetSelectedItems();
            proteinTableMouseReleased(null);
        } else if (proteinTable.getSelectedRow() != proteinRow) {
            proteinTable.setRowSelectionInterval(proteinRow, proteinRow);
            if (scrollToVisible) {
                proteinTable.scrollRectToVisible(proteinTable.getCellRect(proteinRow, 0, false));
            }
            proteinTableMouseReleased(null);
        }
        int peptideRow = 0;
        if (peptideKey != NO_KEY) {
            peptideRow = getPeptideRow(peptideKey);
        }
        if (peptideTable.getSelectedRow() != peptideRow && peptideRow != -1) {
            peptideTable.setRowSelectionInterval(peptideRow, peptideRow);
            if (scrollToVisible) {
                peptideTable.scrollRectToVisible(peptideTable.getCellRect(peptideRow, 0, false));
            }
            peptideTableMouseReleased(null);
        }
        if (spectrumFile != null && spectrumTitle != null) {
            peptideShakerGUI.setSelectedItems(peptideShakerGUI.getSelectedProteinKey(), peptideShakerGUI.getSelectedPeptideKey(), spectrumFile, spectrumTitle);
        }
    }
}

Example 4 with ProteinMatch

use of com.compomics.util.experiment.identification.matches.ProteinMatch in project peptide-shaker by compomics.

the class ModificationLocalizationScorer method scorePTMs.

/**
 * Scores PTMs in a protein match.
 *
 * @param identification The identification object containing the matches.
 * @param proteinMatch The protein match.
 * @param identificationParameters The identification parameters.
 * @param scorePeptides If true, peptides will be scored as well.
 * @param modificationProvider The modification provider to use.
 * @param waitingHandler The waiting handler to sue, ignored if null.
 */
public void scorePTMs(Identification identification, ProteinMatch proteinMatch, IdentificationParameters identificationParameters, boolean scorePeptides, ModificationProvider modificationProvider, WaitingHandler waitingHandler) {
    HashMap<Integer, ArrayList<String>> confidentSites = new HashMap<>();
    HashMap<Integer, HashMap<Integer, HashSet<String>>> ambiguousSites = new HashMap<>();
    for (long peptideKey : proteinMatch.getPeptideMatchesKeys()) {
        PeptideMatch peptideMatch = identification.getPeptideMatch(peptideKey);
        Peptide peptide = peptideMatch.getPeptide();
        PSParameter psParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
        if (psParameter.getMatchValidationLevel().isValidated() && peptide.getNVariableModifications() > 0) {
            PSModificationScores peptideScores = (PSModificationScores) peptideMatch.getUrParam(PSModificationScores.dummy);
            if (peptideScores == null || scorePeptides) {
                scorePTMs(identification, peptideMatch, identificationParameters, modificationProvider, waitingHandler);
                peptideScores = (PSModificationScores) peptideMatch.getUrParam(PSModificationScores.dummy);
            }
            if (peptideScores != null) {
                int[] peptideStart = peptide.getProteinMapping().get(proteinMatch.getLeadingAccession());
                for (int confidentSite : peptideScores.getConfidentSites()) {
                    for (int peptideTempStart : peptideStart) {
                        int siteOnProtein = peptideTempStart + confidentSite - 1;
                        ArrayList<String> modificationsAtSite = confidentSites.get(siteOnProtein);
                        if (modificationsAtSite == null) {
                            modificationsAtSite = new ArrayList<>();
                            confidentSites.put(siteOnProtein, modificationsAtSite);
                        }
                        for (String modName : peptideScores.getConfidentModificationsAt(confidentSite)) {
                            if (!modificationsAtSite.contains(modName)) {
                                modificationsAtSite.add(modName);
                            }
                        }
                    }
                }
                for (int representativeSite : peptideScores.getRepresentativeSites()) {
                    HashMap<Integer, HashSet<String>> peptideAmbiguousSites = peptideScores.getAmbiguousModificationsAtRepresentativeSite(representativeSite);
                    for (int peptideTempStart : peptideStart) {
                        int proteinRepresentativeSite = peptideTempStart + representativeSite - 1;
                        HashMap<Integer, HashSet<String>> proteinAmbiguousSites = ambiguousSites.get(proteinRepresentativeSite);
                        if (proteinAmbiguousSites == null) {
                            proteinAmbiguousSites = new HashMap<>(peptideAmbiguousSites.size());
                            ambiguousSites.put(proteinRepresentativeSite, proteinAmbiguousSites);
                        }
                        for (int peptideSite : peptideAmbiguousSites.keySet()) {
                            int siteOnProtein = peptideTempStart + peptideSite - 1;
                            proteinAmbiguousSites.put(siteOnProtein, peptideAmbiguousSites.get(peptideSite));
                        }
                    }
                }
            }
        }
    }
    // remove ambiguous sites where a confident was found and merge overlapping groups
    PSModificationScores proteinScores = new PSModificationScores();
    ArrayList<Integer> representativeSites = new ArrayList<>(ambiguousSites.keySet());
    Collections.sort(representativeSites);
    for (Integer representativeSite : representativeSites) {
        HashMap<Integer, HashSet<String>> secondarySitesMap = ambiguousSites.get(representativeSite);
        ArrayList<Integer> secondarySites = new ArrayList<>(secondarySitesMap.keySet());
        for (int secondarySite : secondarySites) {
            ArrayList<String> confidentModifications = confidentSites.get(secondarySite);
            if (confidentModifications != null) {
                boolean sameModification = confidentModifications.stream().map(modName -> modificationProvider.getModification(modName)).anyMatch(confidentModification -> secondarySitesMap.get(secondarySite).stream().map(modName -> modificationProvider.getModification(modName)).anyMatch(secondaryModification -> secondaryModification.getMass() == confidentModification.getMass()));
                if (sameModification) {
                    ambiguousSites.remove(representativeSite);
                    break;
                }
            }
            if (secondarySite != representativeSite) {
                ArrayList<Integer> tempRepresentativeSites = new ArrayList<>(ambiguousSites.keySet());
                Collections.sort(tempRepresentativeSites);
                for (Integer previousSite : tempRepresentativeSites) {
                    if (previousSite >= representativeSite) {
                        break;
                    }
                    if (previousSite == secondarySite) {
                        HashMap<Integer, HashSet<String>> previousSites = ambiguousSites.get(previousSite);
                        HashSet<String> previousModifications = previousSites.get(previousSite);
                        boolean sameModification = previousModifications.stream().map(modName -> modificationProvider.getModification(modName)).anyMatch(previousModification -> secondarySitesMap.get(secondarySite).stream().map(modName -> modificationProvider.getModification(modName)).anyMatch(secondaryModification -> secondaryModification.getMass() == previousModification.getMass()));
                        if (sameModification) {
                            for (int tempSecondarySite : secondarySitesMap.keySet()) {
                                if (!previousSites.containsKey(secondarySite)) {
                                    previousSites.put(tempSecondarySite, secondarySitesMap.get(tempSecondarySite));
                                }
                            }
                            ambiguousSites.remove(representativeSite);
                        }
                    }
                }
            }
        }
    }
    for (int confidentSite : confidentSites.keySet()) {
        for (String modName : confidentSites.get(confidentSite)) {
            proteinScores.addConfidentModificationSite(modName, confidentSite);
        }
    }
    for (int representativeSite : ambiguousSites.keySet()) {
        proteinScores.addAmbiguousModificationSites(representativeSite, ambiguousSites.get(representativeSite));
    }
    proteinMatch.addUrParam(proteinScores);
}

Example 5 with ProteinMatch

use of com.compomics.util.experiment.identification.matches.ProteinMatch in project peptide-shaker by compomics.

the class QCPanel method getProteinDataset.

/**
 * Returns the dataset to use for the protein QC plot.
 */
private void getProteinDataset() {
    progressDialog.setPrimaryProgressCounterIndeterminate(false);
    progressDialog.setMaxPrimaryProgressCounter(peptideShakerGUI.getIdentification().getProteinIdentification().size());
    progressDialog.setValue(0);
    IdentificationFeaturesGenerator identificationFeaturesGenerator = peptideShakerGUI.getIdentificationFeaturesGenerator();
    maxValue = Double.MIN_VALUE;
    validatedValues = new ArrayList<>();
    validatedDoubtfulValues = new ArrayList<>();
    nonValidatedValues = new ArrayList<>();
    validatedDecoyValues = new ArrayList<>();
    nonValidatedDecoyValues = new ArrayList<>();
    ProteinMatchesIterator proteinMatchesIterator = peptideShakerGUI.getIdentification().getProteinMatchesIterator(progressDialog);
    ProteinMatch proteinMatch;
    while ((proteinMatch = proteinMatchesIterator.next()) != null) {
        long proteinKey = proteinMatch.getKey();
        if (progressDialog.isRunCanceled()) {
            break;
        }
        double value = 0;
        if (proteinNumberValidatedPeptidesJRadioButton.isSelected()) {
            value = identificationFeaturesGenerator.getNValidatedPeptides(proteinKey);
        } else if (proteinSpectrumCountingScoreJRadioButton.isSelected()) {
            value = identificationFeaturesGenerator.getSpectrumCounting(proteinKey);
        } else if (proteinSequenceCoverageJRadioButton.isSelected()) {
            HashMap<Integer, Double> sequenceCoverage = peptideShakerGUI.getIdentificationFeaturesGenerator().getSequenceCoverage(proteinKey);
            Double sequenceCoverageConfident = 100 * sequenceCoverage.get(MatchValidationLevel.confident.getIndex());
            Double sequenceCoverageDoubtful = 100 * sequenceCoverage.get(MatchValidationLevel.doubtful.getIndex());
            value = sequenceCoverageConfident + sequenceCoverageDoubtful;
        } else if (proteinSequenceLengthJRadioButton.isSelected()) {
            String proteinSequence = peptideShakerGUI.getSequenceProvider().getSequence(proteinMatch.getLeadingAccession());
            value = proteinSequence.length();
        }
        PSParameter proteinParameter = (PSParameter) proteinMatch.getUrParam(PSParameter.dummy);
        if (!proteinParameter.getHidden()) {
            if (value > maxValue) {
                maxValue = value;
            }
            if (!proteinMatch.isDecoy()) {
                if (proteinParameter.getMatchValidationLevel().isValidated()) {
                    if (proteinParameter.getMatchValidationLevel() == MatchValidationLevel.confident) {
                        validatedValues.add(value);
                    } else {
                        validatedDoubtfulValues.add(value);
                    }
                } else {
                    nonValidatedValues.add(value);
                }
            }
        }
        progressDialog.increasePrimaryProgressCounter();
    }
}