added TYPE parameter to DBAdaptor constructor

entries.  Makes it easier to customize, and to remember.

sort on the first part of the "description" field.

bugfixes for ExternalFeatureAdaptor,support for assembly version/name in meta table, support for Glovar and removed some mysql-only DB dependencies

the client in the future.

client.

from other sources than the first one listed.

Fixed bug which restricted the client to exactly one type of
mapping (simple xor align).

Thinking of breaking the program apart into modules.

Updated requirements.
Other fixes.

mapped back to the query coordinate system.  The parts of these
features that maps into a "gap" are labelled as gaps.

Added alignment_length method again for use in homologous gene pairing pipeline, to regenerate the original perc_id and perc_pos that blast gives. The blast Runnable returns the perc_id based on the query length without indels

Added identical_matches and positive_matches methods mainly for use in homologous gene pairing pipeline, but may be useful for others

systems are tagged as "fragmented" and does not have their
coordinates mapped.

Features that are mapped into a region outside the query
coordinate system are tagged as "unmappable" and does not have
their coordinates mapped.

Features that are mapped into a region inside the query
coordinate system, without getting split, are tagged as "mapped"
and have their coordinates mapped.

Currently leaves any features that, when mapped back into the
query coordinate system, contains gaps or are split.  These will
still be shown in the target coordinate system but are tagged
"[unmappable]".

now works for RGDs format, rather than modified RGD format, also imports RatMap synonyms from RGD file