initial checkin, only one function works (get.genes.by.pathway())

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72144 bc3139a8-67e5-0310-9ffc-ced21a209358
rename file

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72145 bc3139a8-67e5-0310-9ffc-ced21a209358
more accurate description

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72146 bc3139a8-67e5-0310-9ffc-ced21a209358
tweaks.....

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72147 bc3139a8-67e5-0310-9ffc-ced21a209358
implemented some more APIs

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72149 bc3139a8-67e5-0310-9ffc-ced21a209358
implement a couple more APIs

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72150 bc3139a8-67e5-0310-9ffc-ced21a209358
some ideas about how to implement mark.pathway.by.objects/color.pathway.by.objects

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72151 bc3139a8-67e5-0310-9ffc-ced21a209358
implemented mark.pathway.by.objects()/color.pathway.by.objects(), general cleanup

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72155 bc3139a8-67e5-0310-9ffc-ced21a209358
cleanup, add questions for KEGG

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72159 bc3139a8-67e5-0310-9ffc-ced21a209358
implemented bconv()

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72161 bc3139a8-67e5-0310-9ffc-ced21a209358
passes check

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72162 bc3139a8-67e5-0310-9ffc-ced21a209358
add questions about some SOAP APIs called by gene2pathway

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72163 bc3139a8-67e5-0310-9ffc-ced21a209358
implement suggestions from Martin

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72174 bc3139a8-67e5-0310-9ffc-ced21a209358
more tidying

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72175 bc3139a8-67e5-0310-9ffc-ced21a209358
cleanup....

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72194 bc3139a8-67e5-0310-9ffc-ced21a209358
Extensive rewrite, deciding to expose all functionality in KEGG REST
API, rather than trying to create a drop-in replacement for KEGGSOAP
which is not widely used (and much of its functionality did not
make the transition to REST). 
Passes check with --no-tests, because tests have not been rewritten
yet. Also still need to add a vignette.



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72211 bc3139a8-67e5-0310-9ffc-ced21a209358
keggGet with aaseq or ntseq option now returns an AAStringSet object

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72220 bc3139a8-67e5-0310-9ffc-ced21a209358
add vignette stub, start on flat-file parsing code

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72223 bc3139a8-67e5-0310-9ffc-ced21a209358
added valid unit tests, small tweaks

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72250 bc3139a8-67e5-0310-9ffc-ced21a209358
progress on vignette

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGREST@72345 bc3139a8-67e5-0310-9ffc-ced21a209358