[FEATURE] ProteinProphetAdapter

TPP PeptideProphet and ProteinProphet adapter. This version is working for XTandemAdapter idXML results. TPP/xinteract program will do the PeptideProphet analysis on the peptideID results and TPP/ProteinProphet will do the protein inference. 
Tests are added into the SEARCHENGINES folder.
I am also unsure whether this is really a smart idea to treat all unknown enzymes as Trypsin. I would be much more in favor to not change the code and give out some error and make the caller code put trypsin as enzyme than to simply makes these assumptions