060e75a7a19e01075314d68576134d3b53aff09a,src/main/java/eu/isas/peptideshaker/gui/protein_inference/ProteinInferencePeptideLevelDialog.java,ProteinInferencePeptideLevelDialog,addPeptide,#String#HashMap#ArrayList#HashMap#ArrayList#HashMap#HashMap#,243

Before Change



                    Protein protein = sequenceFactory.getProtein(tempProteinAccession);
                    Boolean enzymatic = protein.isEnzymaticPeptide(peptideMatch.getTheoreticPeptide().getSequence(),
                            peptideShakerGUI.getIdentificationParameters().getSearchParameters().getEnzyme(),
                            peptideShakerGUI.getIdentificationParameters().getSequenceMatchingPreferences());

                    edgeProperties.put(peptideNodeName + "|" + proteinNodeKey, enzymatic.toString());

After Change



                    Protein protein = sequenceFactory.getProtein(tempProteinAccession);
                    Boolean enzymatic = false;
                    DigestionPreferences digestionPreferences = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getDigestionPreferences();
                    if (digestionPreferences.getCleavagePreference() == DigestionPreferences.CleavagePreference.enzyme) {
                        enzymatic = protein.isEnzymaticPeptide(peptideMatch.getTheoreticPeptide().getSequence(),
                                digestionPreferences.getEnzymes(),
                                peptideShakerGUI.getIdentificationParameters().getSequenceMatchingPreferences());
                    }