added first version of MSGFplusAdapter
Merge branch 'fix-pepxml-load' into FFId
Merge branch 'FFId' of https://github.com/hendrikweisser/OpenMS into FFId
[BUG-FIX #753] MyrimatchAdapter

process.start doesn't call the myrimatch. Replaced process.start with process.execute to fix the problem. Myrimatch also needs the parameter -workdir to set the directory for writing the output.pepXML

modified:   ../src/topp/MyriMatchAdapter.cpp
Merge branch 'fix-myrimatchadapter' into develop
Merge branch 'MSGF+-Adapter' of https://github.com/mwalzer/OpenMS into test-msgfadapter
Renamed the Adaper to MSGFPlusAdapter
Extended the parameter definition
Added the adapter to de make files

modified:   ../doc/doxygen/public/TOPP.doxygen
modified:   ../src/openms/source/APPLICATIONS/ToolHandler.cpp
modified:   ../src/openms/source/CHEMISTRY/AASequence.cpp
new file:   ../src/topp/MSGFPlusAdapter.cpp
modified:   ../src/topp/executables.cmake
Merge branch 'feature/AASequence_refactoring' of https://github.com/timosachsenberg/OpenMS into test-msgfadapter
[PARAM] added flag 'all_features' to FeatureFinderIdentification (return all features found by OpenSWATH per peptide ID, instead of best one only)
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into FFId
[MSGFPlusAdapter extension]

- added input parameters for the search
- replaced the static parameter values with the input parameter values
- write the idXML based on the tsv file
  - added search parameters
  - add protein_identifications
  - parse the input mzML File to get the RT information in the idXML file
- extended IDPosteriorErrorProbability with MSGF+ search engine

modified:   ../src/topp/IDPosteriorErrorProbability.cpp
modified:   ../src/topp/MSGFPlusAdapter.cpp
deleted:    ../src/topp/MSGFplusAdapter.C
Merge branch 'fix-msgfplusadapter' of https://github.com/PetraGutenbrunner/OpenMS into fix-msgfplusadapter
Undo changes for MyriMatchAdapter in branch fix-msgfplusadapter

modified:   ../src/topp/MyriMatchAdapter.cpp
[FEATURE,PARAM] reworked parameter handling, added internal feature detection (not yet finished)
Merge branch 'develop' into fix-msgfplusadapter
[FEATURE] more work on feature detection (adding meta data to features: m/z, charge, peptide IDs)
[MSGFPlus Adapter Coding Conventions]

2 spaces instead of tab

modified:   ../src/openms/source/APPLICATIONS/ToolHandler.cpp
[FIX] various fixes to get feature (elution peak) detection working
[FIX] write original intensities instead of scaled ones
[FIX] Get m/z from input file, because after converting to tsv the value is rounded.
The searchengine throws an error if you create an outputnode for the .mzid file, because the file doesn't ends with .mzid. To solve this problem add .mzid to the filename and rename the file at the end to the original filename.

modified:   ../src/topp/MSGFPlusAdapter.cpp