[PARAM,INTERNAL] use parameter lists instead of strings in 'QProcess::execute'; shortened Java parameter names
[FEATURE,TEST] added utility function to get index of element in vector ('ListUtils::getIndex')
[PARAM,DOC] replaced magic numbers in parameters by descriptive names; other parameter (handling and documentation) improvements
[INTERNAL] improved parameter handling
[INTERNAL] coding style: append '_' to names of protected methods
[FIX] don't forget to clean up temporary files
[INTERNAL] code simplification and formatting
[TEST] renamed mzML and FASTA file used in search engine tests to signify general usage
[FIX] fixed conversion of numbers to QStrings
[TEST] added test for MSGFPlusAdapter