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());
}