Revision history for Perl module Bio::DB::Das::Chado 0.2 Wed Apr 22 14:47:52 2009 - Stand alone module moved out of the GBrowse package 0.21 Thu May 7 20:17:33 EDT 2009 - Fixed Segment features method to support API needed for GBrowse2 - Fixed a bug that caused CDS inferrence to fail for single exon genes that have either a 5' or 3' UTR (but not both) to fail 0.22 Thu May 28 15:53:03 EDT 2009 - Added a rel2abs method to the Segment feature so that uploaded annotations will work correctly. 0.23 Thu Jun 4 11:55:24 EDT 2009 - Fixes to accomidate changes to the Chado GFF3 loader; there is still an outstanding bug associated with searching when the same ID is used in different GFF3 files. While this will be solved soon, a release is needed for a demo. 0.24 Wed Jun 17 03:29:06 EDT 2009 - made the srcfeature method always return something; it no longer depends on the call to the constructor to set it. - Made using organism information more robust; now checks abbreviation and "genus species", and if it fails at everything, throws an error. - Added an option to the Chado constructor called -reference_class that allows the user to specify what feature type_id to use as the srcfeature. For example, if you have motifs mapped to a polypeptide and that polypeptide mapped to a region, you can speicify either "region" or "polypeptide" for the reference_class. Note that this does not automatically turn on recursive mapping, so by default, the motifs wouldn't be visible on the region. I honestly don't know for sure if recursive mapping still works--I haven't tested it in a long time. - Fixed a bug that sometimes prevented GBrowse from finding the subfeatures of features (like mRNAs of genes couldn't be found). 0.25 Thu Apr 29 22:10:43 EDT 2010 - Bumping version number to make CPAN happy. 0.26 Fri May 14 11:37:37 EDT 2010 - Making the dbh method in Chado.pm create a db handle if one doesn't already exist (it is not clear to me how this happens, since the constructor for Chado.pm is supposed to create it, but whatever). - Silenced uninit squawks when gbrowse_details page is rendered 0.3 Fri Jun 25 09:32:01 EDT 2010 - Added documentation for the Chado constructor - Changed the class method so that it always returns 'Sequence', which is really the right thing for it to do: class only makes sense in the context of Bio::DB::GFF. - Added a -fulltext option for using full text searching in postgres 8.4 or better. See perldoc Bio::DB::Das::Chado and gmod_chado_fts_prep.pl for more info, as well as the web page on the GMOD wiki: http://gmod.org/wiki/Chado_Full_Text_Search - Added feature_summary and coverage_array methods to Chado.pm to support the feature summary functionality of GBrowse2; see the GMOD wiki page describing this feature: http://gmod.org/wiki/Chado_gbrowse_summary_view 0.31 Tue Apr 5 12:32:31 EDT 2011 - Added gmod_chado_fts_prep.pl and gmod_create_summary_statistics.pl to the MANIFEST. - Improved how the interval stats table data get generated. - Added support for the primary_seq method to the Segment object. - Added support for using srcfeatureslice in command line instances. - Improved GFF and other dump formats from GBrowse (though they are still probably less than perfect). 0.32 Thu Jun 23 16:08:33 EDT 2011 - Fixed a bug that caused the density plot to fail when in the summary view when the source of the feature isn't provided in the track def. 0.33 Thu Oct 20 10:52:55 EDT 2011 - Added rudimentary support for non-public schemas (mostly for Tripal). - Fixed a bug that caused all features to show up when only features for one seq_id was requested and srcfeatureslice isn't set. - Added a build time "recommends" for Bio::GMOD::DB::Config 1.22 so that the support for schemas will work. 0.34 Thu Sep 27 15:09:34 EDT 2012 - Made -srcfeatureslice on by default - Added a -tripal option to fix the adaptor's tendancy to find multiple features where there is only one when a foreign key links from analysisfeature to features to which those analyses don't belong (that is, Tripal links a BLAST result to the mRNA that was searched with, rather than the standard behavior of linking it with a match feature that has two srcfeatures in featureloc). 0.35 Thu Oct 25 15:53:05 EDT 2012 - Added "as_string" as an alias to asString (ugh--Javaish) in Segment.pm - Added ability to Segment's srcfeature_id method to introspect to find it. - Removed instances of "defined(@_)" because it's stupid and not allowed in perl 5.21.