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
[FEATURE,PARAM,TEST,DOC] Added option to annotate protein hits with target/decoy tags in PeptideIndexer.

Also made cosmetic changes in PeptideIndexer documentation/log output and added a test for the protein annotation.
[FEATURE] Added new TOPP tool FidoAdapter (runs the protein inference engine Fido).

Work in progress.
Merge branch 'fix-idpep-mascot' of https://github.com/hendrikweisser/OpenMS into FidoAdapter

Need the fix of the "prob_correct" option in IDPosteriorErrorProbability.
[FIX] fixed clang compiler warnings
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into FidoAdapter
[FEATURE,DOC] completed implementation of Fido adapter, added documentation
[DOC] added FidoAdapter to TOPP docu page (and removed broken links to SILACAnalyzer/FeatureFinderRaw)
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