Examples of eu.isas.peptideshaker.filtering.PeptideFilter

eu.isas.peptideshaker.filtering.PeptideFilter
Peptide Filter. @author Marc Vaudel @author Harald Barsnes

     */
    private void editStarredPeptidesActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_editStarredPeptidesActionPerformed
        int row = starredPeptidesTable.getSelectedRow();
        if (row >= 0) {
            String selectedFilterName = (String) starredPeptidesTable.getValueAt(row, 2);
            PeptideFilter peptideFilter = peptideStarFilters.get(selectedFilterName);
            new FindDialog(peptideShakerGUI, this, null, peptideFilter, null, FilterType.STAR);
        }
    }//GEN-LAST:event_editStarredPeptidesActionPerformed

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     */
    private void editHiddenPeptidesActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_editHiddenPeptidesActionPerformed
        int row = hiddenPeptidesTable.getSelectedRow();
        if (row >= 0) {
            String selectedFilterName = (String) hiddenPeptidesTable.getValueAt(row, 2);
            PeptideFilter peptideFilter = peptideHideFilters.get(selectedFilterName);
            new FindDialog(peptideShakerGUI, this, null, peptideFilter, null, FilterType.HIDE);
        }
    }//GEN-LAST:event_editHiddenPeptidesActionPerformed

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                    validated = true;
                }
            }


            if (!validated) {
                PeptideFilter peptideFilter;
                if (!filterPreferences.getPeptideStarFilters().containsKey(MatchFilter.MANUAL_SELECTION)) {
                    peptideFilter = new PeptideFilter(MatchFilter.MANUAL_SELECTION);
                    peptideFilter.setDescription("Manual selection via the graphical interface");
                    filterPreferences.getPeptideStarFilters().put(peptideFilter.getName(), peptideFilter);
                } else {
                    peptideFilter = filterPreferences.getPeptideStarFilters().get(MatchFilter.MANUAL_SELECTION);
                }
                peptideFilter.addManualValidation(match);
            }


            psParameter.setStarred(true);
            identification.updatePeptideMatchParameter(match, psParameter);
            peptideShakerGUI.setDataSaved(false);

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                    validated = true;
                }
            }


            if (!validated) {
                PeptideFilter peptideFilter;
                if (!filterPreferences.getPeptideHideFilters().containsKey(MatchFilter.MANUAL_SELECTION)) {
                    peptideFilter = new PeptideFilter(MatchFilter.MANUAL_SELECTION);
                    peptideFilter.setDescription("Manual selection via the graphical interface");
                    filterPreferences.getPeptideHideFilters().put(peptideFilter.getName(), peptideFilter);
                } else {
                    peptideFilter = filterPreferences.getPeptideHideFilters().get(MatchFilter.MANUAL_SELECTION);
                }
                peptideFilter.addManualValidation(match);
            }


            psParameter.setHidden(true);
            identification.updatePeptideMatchParameter(match, psParameter);
            peptideShakerGUI.setDataSaved(false);

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     * Creates a peptide filter based on the users input.
     */
    public void createPeptideFilter() {
        if (validateInput()) {
            if (peptideFilter == null) {
                peptideFilter = new PeptideFilter("find peptide filter");
            } 
            ArrayList<String> modifications = new ArrayList<String>();
            for (int row = 0; row < modificationTable.getRowCount(); row++) {
                if ((Boolean) modificationTable.getValueAt(row, 0)) {
                    modifications.add((String) modificationTable.getValueAt(row, 2));

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        if (proteinFilter != null || peptideFilter != null || psmFilter != null) {
            exitButtonActionPerformed(null);
        }


        ProteinFilter newProteinFilter = null;
        PeptideFilter newPeptideFilter = null;
        PsmFilter newPsmFilter = null;


        if (proteinFilter == null && filterTypeJTabbedPane.getSelectedIndex() == 0) {
            if (!proteinInput()) {
                JOptionPane.showMessageDialog(this, "There seems to be no filters added.", "Empty Filter?", JOptionPane.INFORMATION_MESSAGE);

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     * @return the default filters for setting a match as doubtful
     */
    public static ArrayList<PeptideFilter> getDefaultPeptideFilters() {
        ArrayList<PeptideFilter> filters = new ArrayList<PeptideFilter>();


        PeptideFilter peptideFilter = new PeptideFilter("One confident PSM");
        peptideFilter.setDescription("No confident PSM");
        peptideFilter.setNConfidentSpectra(0); // @TODO: make the thresholds editable by the user!
        peptideFilter.setnConfidentSpectraComparison(RowFilter.ComparisonType.AFTER);
        filters.add(peptideFilter);


        return filters;
    }

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Related Classes of eu.isas.peptideshaker.filtering.PeptideFilter

com.compomics.util.experiment.identification.matches.PeptideMatch

com.compomics.util.experiment.identification.SequenceFactory

eu.isas.peptideshaker.gui.FiltersDialog

eu.isas.peptideshaker.gui.FindDialog

eu.isas.peptideshaker.myparameters.PSParameter

eu.isas.peptideshaker.scoring.PeptideSpecificMap

eu.isas.peptideshaker.utils.StarHider

java.util.regex.Pattern

java.util.regex.Matcher

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