}

        }

        // set the filtering import settings

        idFilter.setMinPepLength(cliInputBean.getMinPepLength());

        idFilter.setMaxPepLength(cliInputBean.getMaxPepLength());

        idFilter.setMaxMzDeviation(cliInputBean.getMaxMzDeviation());

        idFilter.setIsPpm(cliInputBean.isMaxMassDeviationPpm());

        idFilter.setRemoveUnknownPTMs(cliInputBean.excludeUnknownPTMs());

     * @param evt

     */

    private void importFilterMenuActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_importFilterMenuActionPerformed

        ImportSettingsDialog importSettingsDialog = new ImportSettingsDialog(this, getIdFilter(), true);

        if (newFilter != null) {

            setIdFilter(newFilter);

        }

    }//GEN-LAST:event_importFilterMenuActionPerformed

     * @param evt

     */

    private void editImportFilterButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_editImportFilterButtonActionPerformed

        ImportSettingsDialog importSettingsDialog = new ImportSettingsDialog(this, peptideShakerGUI.getIdFilter(), true);

        if (newFilter != null) {

            importFilterTxt.setText("User Defined");

            idFilter = newFilter;

        }

    }//GEN-LAST:event_editImportFilterButtonActionPerformed

            experimentSettings = new PeptideShakerSettings(tempSettings.getSearchParameters(), tempSettings.getAnnotationPreferences(),

                    tempSettings.getSpectrumCountingPreferences(), tempSettings.getProjectDetails(), tempSettings.getFilterPreferences(),

                    tempSettings.getDisplayPreferences(),

                    tempSettings.getMetrics(), tempProcessingPreferences, tempSettings.getIdentificationFeaturesCache(),

        } else {

            experimentSettings = (PeptideShakerSettings) experiment.getUrParam(experimentSettings);

        }

        searchParameters = new SearchParameters();

        processingPreferences = new ProcessingPreferences();

        genePreferences = new GenePreferences();

        sequenceMatchingPreferences = null;

    }

        processingPreferences = new ProcessingPreferences();

        ptmScoringPreferences = new PTMScoringPreferences();

        genePreferences = new GenePreferences();

        sequenceMatchingPreferences = SequenceMatchingPreferences.getDefaultSequenceMatching(searchParameters);

    }

     * deserializing a match

     */

    public void scoreProteinPtms(Identification identification, Metrics metrics, WaitingHandler waitingHandler, SearchParameters searchParameters,

            AnnotationPreferences annotationPreferences, PTMScoringPreferences ptmScoringPreferences, SequenceMatchingPreferences sequenceMatchingPreferences) throws Exception {

    }