private Semaphore proteinsMutex;
private ArrayList<ModificationMatch> modifications = null;
private ArrayList<VariantMatch> variants = null;
private HashMap<String, HashMap<Integer, ArrayList<Variant>>> variantsMap = null;
public final static String MODIFICATION_LOCALIZATION_SEPARATOR = "-ATAA-";
<BUG>public final static String MODIFICATION_SEPARATOR = "_";
public Peptide() {</BUG>
}
public Peptide(String aSequence, ArrayList<ModificationMatch> modifications, boolean sanityCheck) {
this.sequence = aSequence;

private Semaphore proteinsMutex;
private ArrayList<ModificationMatch> modifications = null;
private ArrayList<VariantMatch> variants = null;
private HashMap<String, HashMap<Integer, ArrayList<Variant>>> variantsMap = null;
public final static String MODIFICATION_LOCALIZATION_SEPARATOR = "-ATAA-";
public final static String MODIFICATION_SEPARATOR = "_";
public final static char MODIFICATION_SEPARATOR_CHAR = '_';
public Peptide() {
}
public Peptide(String aSequence, ArrayList<ModificationMatch> modifications, boolean sanityCheck) {
this.sequence = aSequence;
