[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.
Last week I tested some data from Freiburg containing multiple runs. Because the PepXMLFile.store() supports multiple Identification runs now, we merged all the ID runs and then converted into only one pepXML file as the input. For now I am not sure if  it's necessary to support when we implement all the pipeline in TOPPAS.