Added the mgsa package to the repository.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@52070 bc3139a8-67e5-0310-9ffc-ced21a209358
Added the m4 files required for building the configure script.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@52082 bc3139a8-67e5-0310-9ffc-ced21a209358
Fixed contents of \VignetteIndexEntry

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@53025 bc3139a8-67e5-0310-9ffc-ced21a209358
Added biocViews field as recommended by Dan Tenenbaum

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@54488 bc3139a8-67e5-0310-9ffc-ced21a209358
Bumped version numbers for BioC 2.8 release.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@54800 bc3139a8-67e5-0310-9ffc-ced21a209358
Bumped version numbers again for new BioC 2.9 devel cycle.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@54802 bc3139a8-67e5-0310-9ffc-ced21a209358
Added missing close.screen() call.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@54907 bc3139a8-67e5-0310-9ffc-ced21a209358
vignette update for term definition and setsResults() example
there is a CHANGES file

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@55116 bc3139a8-67e5-0310-9ffc-ced21a209358
Fixed some typos.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@55122 bc3139a8-67e5-0310-9ffc-ced21a209358
createMGsaGoSets is now exported. This function is useful for people working with IDs that are different from those in the GAF file (example Ensembl transcript ID vs Uniprot ID in human)

Append set annotations to set results when mgsa() is called on an MgsaSets. This gives more verbose output than before.
To do this the following changes have been made:
mgsa-methods: append set annotations when called wit an MgsaSets
MgsaResults: dotted table for the results
dottedTable: only add dots on factor and characters so that numbers are still completely displayed

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@57273 bc3139a8-67e5-0310-9ffc-ced21a209358
adding drop=FALSE to keep column names in returned setsResults when setAnnotations have a single column

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@57639 bc3139a8-67e5-0310-9ffc-ced21a209358
Added docs for data set.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@57730 bc3139a8-67e5-0310-9ffc-ced21a209358
Regenerated using buildman.sh

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@57731 bc3139a8-67e5-0310-9ffc-ced21a209358
Manual fixes to the doc.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@57732 bc3139a8-67e5-0310-9ffc-ced21a209358
Added mgsa.pdf to keep R CMD check happy.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@57733 bc3139a8-67e5-0310-9ffc-ced21a209358
Removed as this is not really needed. Suggested by Martin Morgan.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@57743 bc3139a8-67e5-0310-9ffc-ced21a209358
bumped package version numbers prior to creating 2.9 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@59920 bc3139a8-67e5-0310-9ffc-ced21a209358
version bump for start of 2.10 development cycle

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@59924 bc3139a8-67e5-0310-9ffc-ced21a209358
first version bump prior to creating 2.10 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@64678 bc3139a8-67e5-0310-9ffc-ced21a209358
bumped version numbers after creating 2.10 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa@64680 bc3139a8-67e5-0310-9ffc-ced21a209358