Streamline XPRESS isotopic labeling support. XPRESS will now automatically determine if peptide is C13 or N15 light/heavy labeled based on modification state of peptide.
Per bug report by Oded Kleifeld in spctools-discuss, terminal mods were not handled correctly. Turns out issue was a string comparison for 'n' and 'c' terminal specification being compared against 'N' and 'C' terminus attribute in the terminal_modification element. Correcting this case comparison issue seems to solve the reported problem.
revert return value to true at end of PermuteMods, otherwise modification permutations don't continue
Add long overdue support for isotope peaks to XPRESS cgi. When C13 isotope peaks are used in the quantitation, the cgi XPressPeptideUpdateParser.cgi is now aware of them and will display the same ratio,taking into account the data in the C13 isotope peaks.
PEFF: add option to search just variants or modifications separately
add check to make sure variant position is within sequence length