Changes from the lost phospho branch
Merge branch 'devel' into ptm
annotateSpectraPhosphoRS fixes
Merge branch 'devel' into ptm
Updated DESCRIPTION also to 1.1.3 for ptm
Merge branch 'devel' into ptm
resolved merge
Merge branch 'devel' into git-svn

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/isobar@64890 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'devel' into git-svn

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/isobar@64890 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'devel' into ptm

Conflicts:
	R/IBSpectra-class.R
	R/ProteinGroup-class.R
	R/report-utils.R
added phospho.sites and fixed typo
Merge branch 'devel' into ptm

Conflicts:
	R/IBSpectra-class.R
	R/report-utils.R
Merge branch 'devel' into ptm

Conflicts:
	R/IBSpectra-class.R
Merge branch 'devel' into ptm

Conflicts:
	R/IBSpectra-class.R
Merge branch 'devel' into git-svn

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/isobar@65209 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'devel' into git-svn

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/isobar@65209 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'devel' into ptm
allow 'data' being a file for annotateSpectraPhosphoRS
Merge branch 'devel' into ptm
Merge branch 'devel' into ptm