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AnnotationDbi
Overloads the Term and related methods for GOTERM
This update overloads the Term, Ontology etc. methods for GOTERM so
that they can take IDs or GOTermsAnnDbBimap.

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AnnotationDbi
Bug fixes for intraIDMapper
This just fixes some small bugs present in intraIDMapper. Mostly,
these have to do with the use of unlist() which is a dangerous
function to have to use.

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AnnotationDbi
Fixes a small bug in SQLForge and expands inpIDMapper.
This fixes a small bug where SQLForge fails when organsisms don't have
unigene IDs, and also expands the number of species that inpIDMapper
should work for.

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AnnotationDbi
This consolidates the INPARANOID_DB schemas into one.
By consolodating the INPARANOID schemas into one INPARANOID_DB schema,
I can now add more inparanoid packages without bloating up
AnnotationDbi any more than is strictly necessary...

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AnnotationDbi
Removed the some unnecessary comments from NAMESPACE.

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AnnotationDbi
Major overhaul for chip packages.
This checkin includes changes to allow chip packages to be lightweight
and instead depend on organism packages for their data. It also adds
organism support for rhesus monkeys, chimpanzees, Anopheles mosquito,
Arabidopsis and Xenopus laevis.

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AnnotationDbi
Major overhaul for chip packages.
This checkin includes changes to allow chip packages to be lightweight
and instead depend on organism packages for their data. It also adds
organism support for rhesus monkeys, chimpanzees, Anopheles mosquito,
Arabidopsis and Xenopus laevis.

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AnnotationDbi
This just adds the two new package listings to the internal file.
This ci is basically, bioconductor bookkeeping.

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AnnotationDbi
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.

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AnnotationDbi
Improved manual pages for makeXXXXXCHIP_DB() functions.

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AnnotationDbi
Adds ensembl for more species, fixes many man pages.
This update adds better support for ensembl IDs for many species, and
also updates several man pages to accurately reflect the more complex
origins of this data. In brief, when both NCBI and ensembl provide
data mapping entrez genes to ensembl gene IDs, we now will use data
from BOTH of these sources. However sometimes only one source is
available. In each case the manual pages have to be correct.

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AnnotationDbi
More updates to the manual pages.

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AnnotationDbi
This updates the manual pages for Annotation Packages.
The man pages for the Annotation packages had to be updated because of
improvements to R's check parser.

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AnnotationDbi
Exported the AnnObj class so people can extend the AnnDbBimap class in their own packages without getting a warning. Bumped version to 1.5.19

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AnnotationDbi
Patches bug in inpIDMapper and sqlForge_baseMapBuilder
This fixes a bug in inpIDMapper and lays groundwork for more functions
that act similarly. Also, this fixes a bug in baseMapBuilder to help
with getting the Affy annotations updated.

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AnnotationDbi
inpIDMapper() is now compatible with org.Sc.sgd.db
I thought that I had checked this in, but apparently I was mistaken.
This fixes the inpIDMapper function so that it depends on an available
(and upgraded) yeast package instead of on a package that we decided
against distributing.

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AnnotationDbi
Added 'drop.invalid.keys' arg to "subset" methods for Bimap and AnnDbBimap
objects (default is FALSE). Bumped version to 1.5.16

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AnnotationDbi
Moved the whole makeProbePackage() functionality (S3 methods + functions + pkg template + datasets + doc) from matchprobes to AnnotationDbi. Bumped versions: matchprobes -> 1.15.3 and AnnotationDbi -> 1.5.14

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AnnotationDbi
Improvements to the org.Sc.sgd.db package.
These changes add new mappings to the org.Sc.sgd.db package for Entrez
Gene IDs, Refseq accessions, SGD accessions, and Uniprot IDs.

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AnnotationDbi
preemptive bug fixes for inpIDMapper.
These are some code changes that will be needed once I have updated
the org.Sc.sgd.db package database to have a few new flavors of
mappings. This should allow this code to work with the new database
once I have it ready.

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AnnotationDbi
Fixes a bug in inpIDMapper when the src IDs are Entrez Gene IDs
This just skips an unecessary mapping step when the src IDs are
already Entrez Gene IDs.

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AnnotationDbi
Adds parameter for the inpIDMapper function.
This just adds another parameter so that you can choose to have the
final results limited to only one answer per initial ID even if you
map to something like a uniprot which may have many IDs for each
entrez gene ID. Default will still give you all of whatever you asked
for.
Added convenience function inpIDMapper
This function allows for easy mapping (using the appropriate
inparanoid packages) for IDs between species.

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AnnotationDbi
Adds support for a new org package for yeast.
The previous org package for yeast was org.Sc.sgd and was based on the
SGD, which is sensible because that is the standard for that
community. This package is based on NCBI data and is an org.Sc.eg
package, which should hopefully reduce some of the complaints I get
about there not being an eg based yeast package. Also, we needed a
package to map the standard yeast ORF IDs to both EG and uniprot IDs,
and neither of these is available at SGD.

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AnnotationDbi
Minor tweaks to enable chrlengths in Cross-db Bimaps.

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AnnotationDbi
removed quotes from do.call
Major change to SQL.R. Now Bimaps can join across DBs.
This updates AnnotationDbi so that Bimaps can be generated across
SQLite databases from multiple different installed packages.
Providing that the databases are indexed appropriately, there does not
seem to be a huge time penalty to such shenanigans, but there is still
some performance lost when doing this (on the order of a tenth of a
second for most maps tested). However this will hopefully be offset
by the fact that we will no longer have to have data in all of the
chip packages which is identical to the data in all our org
packages...

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AnnotationDbi
Bug fix for unigene/SQLForge
Fixes a bug that would cause problems for people using only unigene
IDs and SQLForge.

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AnnotationDbi
Adds missing documentation.

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AnnotationDbi
Adds convenience function for listing .db0 packages.

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AnnotationDbi
Adds convenience function for listing .db0 packages.

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AnnotationDbi
minor tweak to man page
trying to do a little more cross-linking of the man pages

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AnnotationDbi
Forgot to svn add the help file. How embarrasing...

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AnnotationDbi
Fix for arabidopsis custom packages.
This just fixes a bug that would prevent custom made Arabidopsis
packages from loading.

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AnnotationDbi
Added item to TODO which needs to be done in January.
Adds custom mappings capability to AnnotationDbi
This change adds a simple function for users who wish to customize
their standard annotation packages so that they can have new mappings
in addition to standard ones. Users can add extra data to their
databases, and then make mappings for this new data without modifying
AnnotationDbi.

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AnnotationDbi
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.

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AnnotationDbi
Minor adjustments.
This change just removes RSQLite and DBI from the search path.
DBI and RSQLite have both been imported here for some time, this just
gets them out of the DEPENDS field, and cleans up any in-package
consequences.

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AnnotationDbi
Updated to add CHRLENGTHS to arabidopsis packages.

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AnnotationDbi
added unlist2()

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AnnotationDbi
normalized the default License field for packages made with makeAnnDbPkg()

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AnnotationDbi
normalized the default License field for packages made with makeAnnDbPkg()

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AnnotationDbi
Final changes for Worm, Pig & Chicken, adds new info. to most pkgs.
This update adds support for Worms, pigs and chicken. It also adds
suport for uniprot IDs to most packages, ZFIN IDs to zebrafish
packages, and Wormbase IDs to worm packages. Finally, it also adds a
CHRLOCEND mapping to most packages which will allow the inclusion of
gene ending locations into most annotation packages in addition to the
usual CHRLOC mapping that already provides the start positions.

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