/**
* Get the non-terminal modifications as a string in the Tide format.
*
* @param modifications the modifications to check
* @param fixed if the modifications are to to be added as fixed or variable
* @return the non-terminal modifications as a string in the Tide forma
*/
private String getNonTerminalModifications(ArrayList<String> modifications, boolean fixed) {
// tide ptm pattern: [max_per_peptide]residues[+/-]mass_change
String nonTerminalModifications = "";
for (String ptmName : modifications) {
PTM ptm = ptmFactory.getPTM(ptmName);
if (!ptm.isNTerm() && !ptm.isCTerm()) {
if (!nonTerminalModifications.isEmpty()) {
nonTerminalModifications += ",";
}
// add the number of allowed ptms per peptide
if (!fixed) {
nonTerminalModifications +=
tideParameters
.getMaxVariablePtmsPerTypePerPeptide(); // @TODO: make this modification specific?
}
// add the residues affected
AminoAcidPattern ptmPattern = ptm.getPattern();
if (ptmPattern != null && ptmPattern.length() > 0) {
for (Character aminoAcid : ptmPattern.getAminoAcidsAtTarget()) {
nonTerminalModifications += aminoAcid;
}
}
// add the ptm mass
if (ptm.getRoundedMass() > 0) {
nonTerminalModifications += "+";
}
nonTerminalModifications += ptm.getRoundedMass();
}
}
return nonTerminalModifications;
}
