Package eu.isas.peptideshaker.filtering

Examples of eu.isas.peptideshaker.filtering.ProteinFilter

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            // has to be done like this on order to avoid a ConcurrentModificationException
            final Collection<ProteinFilter> values = proteinStarFilters.values();
            Iterator<ProteinFilter> iterator = values.iterator();

            while (iterator.hasNext()) {
                ProteinFilter proteinFilter = iterator.next();

                if (!others.contains(proteinFilter.getName())) {
                    String oldName = proteinFilter.getName();
                    proteinFilter.setName(newName);
                    proteinStarFilters.remove(oldName);
                    proteinStarFilters.put(newName, proteinFilter);
                }
            }
        }
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     */
    private void editStarredProteinActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_editStarredProteinActionPerformed
        int row = starredProteinsTable.getSelectedRow();
        if (row >= 0) {
            String selectedFilterName = (String) starredProteinsTable.getValueAt(row, 2);
            ProteinFilter proteinFilter = proteinStarFilters.get(selectedFilterName);
            new FindDialog(peptideShakerGUI, this, proteinFilter, null, null, FilterType.STAR);
        }
    }//GEN-LAST:event_editStarredProteinActionPerformed
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     */
    private void editHiddenProteinActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_editHiddenProteinActionPerformed
        int row = hiddenProteinsTable.getSelectedRow();
        if (row >= 0) {
            String selectedFilterName = (String) hiddenProteinsTable.getValueAt(row, 2);
            ProteinFilter proteinFilter = proteinHideFilters.get(selectedFilterName);
            new FindDialog(peptideShakerGUI, this, proteinFilter, null, null, FilterType.HIDE);
        }
    }//GEN-LAST:event_editHiddenProteinActionPerformed
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    public static ArrayList<ProteinFilter> getDefaultProteinFilters() {
        ArrayList<ProteinFilter> filters = new ArrayList<ProteinFilter>();

        // @TODO: make the thresholds editable by the user!
       
        ProteinFilter proteinFilter = new ProteinFilter(">=2 confident peptides"); // the name is used to show what we expect
        proteinFilter.setDescription("<2 confident peptides"); // the description is displayed as failure explanation
        proteinFilter.setnConfidentPeptides(1);
        proteinFilter.setnConfidentPeptidesComparison(RowFilter.ComparisonType.AFTER);
        filters.add(proteinFilter);

        proteinFilter = new ProteinFilter(">=2 confident spectra");
        proteinFilter.setDescription("<2 confident spectra");
        proteinFilter.setProteinNConfidentSpectra(1);
        proteinFilter.setnConfidentSpectraComparison(RowFilter.ComparisonType.AFTER);
        filters.add(proteinFilter);

        return filters;
    }
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    /**
     * Set up the initial filters.
     */
    public void setUpInitialFilters() {
        Enzyme enzyme = getSearchParameters().getEnzyme();
        ProteinFilter proteinFilter = new ProteinFilter(enzyme.getName());
        proteinFilter.setIdentifierRegex(enzyme.getName());
        proteinFilter.setDescription("Hides " + enzyme.getName() + " related proteins.");
        proteinFilter.setActive(false);
        getFilterPreferences().addHidingFilter(proteinFilter);
        proteinFilter = new ProteinFilter("Keratin");
        proteinFilter.setIdentifierRegex("keratin");
        proteinFilter.setDescription("Hides keratin.");
        proteinFilter.setActive(false);
        getFilterPreferences().addHidingFilter(proteinFilter);
    }
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                    validated = true;
                }
            }

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

            psParameter.setStarred(true);
            identification.updateProteinMatchParameter(match, psParameter);
            peptideShakerGUI.setDataSaved(false);
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                    validated = true;
                }
            }

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

            psParameter.setHidden(true);
            identification.updateProteinMatchParameter(match, psParameter);
            peptideShakerGUI.setDataSaved(false);
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            Integer pi = null;
            if (proteinPICmb.getSelectedIndex() != 0) {
                pi = proteinPICmb.getSelectedIndex() - 1;
            }
            if (proteinFilter == null) {
                proteinFilter = new ProteinFilter("find protein filter");
            }
            if (!proteinAccessionTxt.getText().trim().equals("")) {
                proteinFilter.setIdentifierRegex(proteinAccessionTxt.getText().trim());
            }
            if (pi != null) {
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        // if filters have been updated, close dialog
        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()) {
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Related Classes of eu.isas.peptideshaker.filtering.ProteinFilter

  • com.compomics.util.experiment.identification.matches.ProteinMatch
  • com.compomics.util.experiment.identification.SequenceFactory
  • eu.isas.peptideshaker.gui.FiltersDialog
  • eu.isas.peptideshaker.gui.FindDialog
  • eu.isas.peptideshaker.gui.PeptideShakerGUI
  • eu.isas.peptideshaker.myparameters.PSParameter
  • eu.isas.peptideshaker.scoring.ProteinMap
  • eu.isas.peptideshaker.utils.StarHider
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