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AnnotationDbi
adding to the TODO list

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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
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
end of testing.
testing

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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 adds support for worm, pig and chicken.
Adds code for planned support (October release) of these additional
organisms. These organisms are not supported at this moment.

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AnnotationDbi
Adds convenience function for listing .db0 packages.

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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
Just the documentation.
This check in adds some more documentation to the man pages to better
describe some of the new helper functions used in AnnotationDbi.

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

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

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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
This update adds new methods for filtering Bimap objects.
These new methods allow users more flexible ways of toggling the
filters for Bimaps that contain probes which may map to multiple
targets. Also more permissive filtering is now possible for
inparanoid based bimaps.

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AnnotationDbi
Major overhaul of PFAM.db
These changes reflect a major overhaul of the new PFAM.db package to
squash bugs in there so that they won't burn users and also to provide
proper documentation.

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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
Fixes a bad bug in SQLForge introduced by Refseq vers. #s
This adds some debug code, and also fixes a bad bug introduced when I
added code that attempts to automatically scrub version numbers from

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AnnotationDbi
Changes and bug fixes for making chip based pkgs.
These changes and bug fixes allow things to work properly for making
chip based databases and bundling these into packages. There is still
a minor issue with arabidopsis to fix. And then the intermediate
databases need to be bundled into packages for easy distribution and
the default paths set for these helper functions.
Wrapper functions for chip packages
This update adds wrapper functions for chip packages along with man
pages. This code still needs to be much more thoroughly tested and
there are still problems here with support for Yeast and Arabidopsis
which both still need to have the portion of their code that maps data
set up for the mapping of non-affy packages. But at least now it
should be possible to call a function, and have it make a database,
and then wrap that up into a chip based package. Organism based
packages are more monolithic and so are not really expected to need a
wrapper package. Although the code to make the sqlite files and the
packages for these is already here.

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AnnotationDbi
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
Fixed mget(c("GO:0018075","GO:0018075"),GOTERM) bug (the problem was in the .toListOfLists() function which was affecting the "as.list" method for GOTermsAnnDbBimap objects). Version bump.

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AnnotationDbi
Fixes bug in inparanoid mappings.
This was a bad bug that prevented these mappings from filtering out all
the non-seed regions properly.

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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
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
Fixed bug where wrong type of ID causes ins. of spaces
This fixed a bug where R was automatically casting numeric IDs to be
numbers which would cause spaces to be inserted downstream when these
data would be stuck into the database.

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

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AnnotationDbi
Minor bug fixes for release of candidate 1.1.8
These include some small typo fixes to the .Rd files, corrections to
the author lists on some new packages and the usual required update to
the version numbers across the board.

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AnnotationDbi
Added Marc to the Author field. Updated dependencies. Version bump.
Clean up of the code in showQCdata()
Bug fix for shoqQCdata()
This time the bug fixes are actually in.
Fixed bugs in showQCdata()
This change just fixes the showQCdata function so that the counts are
displayed correctly.
Fixes a bug in the new shoqQCData function.
This function needs further work to get the mapped keys to be counted
correctly.
Cosmetic change only.
This adds a news section to the AnnotationDbi
This adds a news section to AnnotationDbi which will be used to
announce MAJOR "bullet point" changes that have been made to the
package since the last revision.
Modifications to schemas.
These are changes to the schema documentation so that they more
precisely align with what was in the sqlite files that are feeding
into AnnotationDbi. Also, code was added to
AnnotationDbi-internals.Rd so that it will not complain about the man
pages being in a sub-template within AnnotationDbi for the new
packages.
Applied Marc's big patch: switch to version 1.0 of the schemas + support for the Inparanoid packages + support for new PFAM.db + pkgname() function for displaying QC information. No version bump for now. inst/NEWS file is in preparation and will be added later.

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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
Fixed slowdown bugs
These bugs only impacts the speed at which SQLForge does it's job.
The results will be the same. But if you are building ~ 700 packages,
you might appreciate this change.
Bug fix for increased AnnBuilder file format compatibility
This fix makes things more compatible for people who are using classic
AnnBuilder style files.

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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 sqlForge involving primarily fly and arabidopsis.
These bug fixes only affect the sqlForge portion of the codebase and
primarily are concerned with getting the output perfect for the sqlite
files generarted for flies and arabidposis.
Updating the license reference to reflect R standards.

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AnnotationDbi
Addition of code to package up intermediate DBs.
This checkin adds the code that will be used to make biannual updates
of the intermediate databases. These databases will be shipped out to
developers as very large R packages, and will allow us to ensure that
everyone has the correct intermediate database installed in the
correct place. One package is planned per supported organism. The
sqlForge code has been modified to find these databases as a default
parameter so that everyone should be able to just use biocLite to get
the latest intermediate DBs (if they want to make annotation packages)
and then to just use the wrapper functions to crank out .db packages
for supported organisms.

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AnnotationDbi
Modified schema definitions to match 1.0
These schema definitions should now match what is planned for 1.0
including my new tables for ensembl and flybase_cg.
This adds files that were previously missing from the 1.0 schemas.
These still need more changes to be full 1.0 compliant. But at least
now they are here.
Update the schemas for human and rodents for new tables.
Added ensembl tables to these schemas so I have to also add this into
the schema definition.
Added maps for Flybase CG IDs and ensembl.
These changes add maps and fine tune the man pages for the ensemble
and the flybase CG IDs. Now users should be able to easily get the
IDs used by ensembl for mammals and fly packages.
Adds the man pages for the ensembl maps.
This just adds man pages for the planned ensembl maps with changes and
concessions as appropriate to context of whether its a chip package or
an organism based one.
Adds man pages for the new FLYBASE CG maps.
This adds a man page to the FLYCHIP.DB and the FLY.DB packages with
appropriate concessions.

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AnnotationDbi
Minor bug fixes for cross platform compatibility of sqlForge
These minor fixes should ensure that sqlForge will work better across
OS platforms when looking for the standard DB packages.
Fixed mget(c("969","969"),org.Hs.egGO) bug (was in "as.list" method for GoAnnDbBimap objects). Version bump.

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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
Fixes minor bug with the package checking code.
This bug would have prevented some packages which legitimately might
have had some empty fields for GO terms (this came up with the Sakai
strain of E coli), from passing check.

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AnnotationDbi
Major overhaul of PFAM.db
These changes reflect a major overhaul of the new PFAM.db package to
squash bugs in there so that they won't burn users and also to provide
proper documentation.

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AnnotationDbi
Fixes a bug in the display of chrlengths vectors
There was a bug in the creation of the chrlengths vectors that was
introduced with the 1.0 schema changes. Bug only affected the display
of the data and not the underlying data, so only AnnotationDbi needs
to be updated to clear this up.

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AnnotationDbi
Bug fix for missing keys.
This fixes a problem introduced when the maps were enabled for
supporting probes that map to multiple targets. It basically fixes
Lkeys() and Llength() so that they return the correct (complete) key
sets on maps regardless of which mappings are "exposed" or "masked"
depending on their status as being probes that match multiple targets
or not. The Lkeys() and Llength() methods should always give the FULL
set of probes even when some of the values for those probes have been
masked by a filter.
This update adds new methods for filtering Bimap objects.
These new methods allow users more flexible ways of toggling the
filters for Bimaps that contain probes which may map to multiple
targets. Also more permissive filtering is now possible for
inparanoid based bimaps.

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AnnotationDbi
Further changes to clean up the role of probeMappings.
ProbeXXX mappings are used by all the probe package schemas, and these
changes just clean that relationship up so that methods like
toggleKeys will be used only when appropriate. This change just makes
things safer for the end users.
Bug fix for missing keys.
This fixes a problem introduced when the maps were enabled for
supporting probes that map to multiple targets. It basically fixes
Lkeys() and Llength() so that they return the correct (complete) key
sets on maps regardless of which mappings are "exposed" or "masked"
depending on their status as being probes that match multiple targets
or not. The Lkeys() and Llength() methods should always give the FULL
set of probes even when some of the values for those probes have been
masked by a filter.

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