Changed proposed by Bo Wen and Attila Kertesz-Farkas
Changes proposed by Bo Wen and Attila Kertesz-Farkas
Merge branch 'PTMTreeSearch' of ssh://gh/Frederic-bioinfo/rTANDEM into PTMTreeSearch
Merge branch 'PTMTreeSearch' of ssh://gh/Frederic-bioinfo/rTANDEM into PTMTreeSearch
Merge branch 'PTMTreeSearch' of ssh://gh/Frederic-bioinfo/rTANDEM into PTMTreeSearch
Corrected linking problem between PTMTreeSearchScore and mscore.

The mconvert function from mscore was redeclared in PTMTreeSearchScore.
Renamed the stack header with correct extension and changed the 'include' statements.
Redirected output to R console (cout becomes Rprintf).
Reverted some variable renaming proposed by Bo, but not justified by PTMTreeSearch.
PTMTS parameters added. New function to set PTMTS params to default values.
Modified documentation to present the scoring functions k, hrk, PTMTS.
Small corrections to the Rprintf calls.
Setting a 7th round to mrefine is now done only when PTMTS is selected.
Adding 'virtual' to seq_mh declaration makes PTMTS finally work in rTANDEM.
Commented-out parts of PTMTreeSearch that must not run on rTANDEM.
Added data file (PTM lists) for PTMTS in inst/extdata.
Corrected PTMTS parameters and the setParamPTMTS to match source code
Added references to the vignette
Version change to 1.3.6