OpenMS/OpenMS — pull request #814 by grosenberger (2014-05-09 11:27:57+00:00)
Title: [FEATURE] ConvertTSVToTraML: Support for SpectraST MRM Transition Lists

This pull request enable SpectraST MRM transition list support in ConvertTSVToTraML.

The functionality is implemented as following:

1) A SpectraST MRM file is identified as .mrm. No other tests are conducted since the .mrm files don't contain any headers.

2) TransitionTSVReader assigns the columns to header names compatible with the TSV/CSV implementation.

3) SpectraST MRM specific parsers extract and generate information like transition_group_id or transition_name or RT / iRT.

4) The likeliest fragment ion annotation is parsed if possible and translated to the correct CV term. SpectraST also reports many other ions (immonium, precursors, non-unique annotations, etc.) which annotations are not parsed.

Please find below more comments in the code.