Compliance with Bioc submission
changed database to db and modifications to mods to avoid mzID clash. Added all constructors
Added NEWS, tests and vignette
Updated documentation
Added small fasta example
Delete MS-GF+ executable from package
Update version and name
T => TRUE and function to fetch MS-GF+ remotely
database => db, modifications => mods + documentation
Documentation, validation logic, T => TRUE, setReplaceMethod('name') => setMethod('name<-'), Type checking in runMSGF
Remove printMSGFLicense as no longer included, T => TRUE