added first version of MSGFplusAdapter
[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
[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
Merge branch 'develop' into fix-msgfplusadapter
[MSGFPlus Adapter Coding Conventions]

2 spaces instead of tab

modified:   ../src/openms/source/APPLICATIONS/ToolHandler.cpp
[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
[FIX #803] Add decoy hits to output

Set show_decoy = 1 to keep the decoy hits

modified:   ../src/topp/MSGFPlusAdapter.cpp
Merge branch 'develop' into fix-msgfplusadapter
[#803] Extensions

- added min/max values for options
- changeComma -> fixDecimalSeparator
- reformated brackets
- added max java heap size as parameter
- changes error message from MzIDToTSVConverter
- renamed parameter precursor_mass_tolerance_unit to precursor_error_units
- removed unused variable precursor_mz

modified:   ../src/topp/MSGFPlusAdapter.cpp
[FIX-#803] amino acid specific n-term modifications

If amino acid specific n-term modifications occur in the tsv output, the amino acid must be before the mass, otherwise a parsing error will be thrown.

modified:   ../src/topp/MSGFPlusAdapter.cpp
[FEATURE #803] add parameter setting thread to execute statement of the search engine
[FEATURE #802] Add parameter to define the java param XX:MaxPermSize, needed for conversion to tsv

modified:   ../src/topp/MSGFPlusAdapter.cpp
tested under Windows (success); added some TODO's (e.g. current calling method not robust against spaces in path)
[FIX,PARAM] use Java memory setting (parameter 'java_memory_size') also for MzIDToTsv tool