DBNAME is no longer a required attribute as we now allow for direct DB connections. SQLHelper is now an attribute of a DBConnection. Methods added to avoid unintentional DB disconnections, working with the DBH safely and quote DB identifiers if required (useful to avoid SQL injection attacks with auto-generated code). Equals method also improved. Associated test cases written.

Added RefSeq_mRNA, RefSeq_mRNA_predicted, RefSeq_ncRNA and RefSeq_ncRNA_predicted external db names to the nucleotide sql.

Removing URIParser sub-package. It was nice in theory but I'd rather support different schemes using extensions to the URI package

Minor POD corrections

Changes to get_official_domain_name, if we can't eliminate multiple HGNCs based on priority, and most common name not found via vega, eliminate HGNCs with worse % identity.

Removing URIParser sub-package. It was nice in theory but I'd rather support different schemes using extensions to the URI package

Remove getting species_id from filename if they are not set. As these have to be set or it dies before that bit is reached.

Remove getting source_id or species_id from filename if they are not set. As these have to be set or it dies before that bit is reached.

Removed the database connection, database creation and process control from the module as this is different to the actual parsing of the data files. See Database.pm and ProcessData.pm  So now module should only deal with the parsing of data and release files

Controls the overall process of the parsing. Makes calls for the creation of the database and then subsequent calls to fetch and parse the data files.

Rolling back the code to 1.20 because of issues with re-binning the human Y chromsome density values resulting in a -ve value.

Commit moved to HEAD from branch-64. Moved the slice fetch into the knowngenedensity/genedensity loop so we can continue to use shift to iterate through them

According to test cases adaptor() should be nullable by passing an undef through to the mutator. Detection of a purposful undef is by checking the length of @_

db_name in external_db. Clean up a few bugs while I'm at it.

Bugs corrected:

  A list (rather than a list reference) was returned if the
  external_db_id for the given db_name could not be found.

  The list returned from list_gene_ids_by_external_db_id() (in
  DBEntryAdaptor) was used as a hash.

Storing 'intersection_of' lines for terms, storing relationships between terms not defined in the current ontology.