OpenMS/OpenMS — pull request #927 by hendrikweisser (2014-08-07 10:14:10+00:00)
Title: PeptideIndexer: support for treating isoleucine/leucine as equivalent (resolves #872)

Added the option "IL_equivalent" to PeptideIndexer, that enables treating isoleucine/leucine as indistinguishable.

I had wanted to explicitly replace "I" and "L" with "J" also in the output, but it's not straightforward to make these changes in the AASequence instances (how to deal with modifications?). So now the replacement only happens for the search; the peptide hits appear unchanged in the output (apart from the protein associations, of course).