[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.
@hroest So before PepXMLFile().store() successfully supports other search engine results, I will put a error message here. #933 is tracking this.