Added a specific option in the mapping_conf file for NCBI prediction. Flaged the different entries retrieved in get_Xmapping.pl; KNOWN for SPTR and curated Refseq, XREF for all of the entries retrieved from the KNOWN matches and then PRED for all of the sequences predicted by other teams (in that case NCBI for human but can be anything).

Feature are not storable.

added test_db. Will return a DBAdaptor. On first call uploads test-db subdir into named database. Then only connects to that db. Is not auto removed, so doesnt cost much time on multiple test runs.

in test-db subdirectory in t. Database handle for this db is static in EnsTestDB so
not regenerated for each subtest.

some tables missing, not yet best area of genome.

them into Fpc tables. Missing: Accessions for the clones.

Added a method fetch_Protein_ligth, method used by the protein pipeline to be able to get protein objects without the presence of stable IDs in the database.

Renamed _contig_from_arrayref into _fill_contig_from_arrayref

hopefully useful for comeing schema conversions.

documentation and fetch_by_dbID for CloneAdaptor; RawContig still cycling badly with recursive fetch calls...

and if query length/3 != hit length for DnaPep

Added exceptions and pod.

added exon test - failing because CloneAdaptor is not to spec! Start of the testing and bug hunting ...

serious clean out commit - moved table.clean to table.sql; removed all tests and dumps --- a new, all useful testing system

moved sub's to bottom to make it readable