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

Bio::Das mumble mumble documentation mumble mumble, grrr.

Fixed "Useless use of a variable in void context" error in Slice

both the graphic and textual displays.  Mapping of the result
ranges into the query coordinates doesn't happen just yet.

performs a query for a disjoint segment if neccesary (a
continous segment on the query sequence that is mapped onto two
separate segements on the target).

Yay!

Doesn't yet map the result though.

them.

I also need to replace all "target" ID strings in the DAS server
replies with the "query" ID string that the user actually asked
for... or come up with another solution which doesn't break
links provided by the DAS server, or confuses the user too much
in other ways.

overridden by command line options or configuration file) and
environment variables removed (since the old valus are now the default
values of exonerate anyway).

Informs user of failed query.

myself (prefer seat-of-the-pants SQL), but someone might find a use
for it.

Bio::EnsEMBL::Mapper objects from cigar lines, but does not use
them yet (ranges are not supported and the reply will be in the
"other" coordinate system).  Relies on the availablility of a
<tab>-delimited file where each line has the following format:

QueryID TargetID QueryAlignBegin TargetAlignBegin CigarLine

The cigar line should be on the non-exonerate format
("218MI728M" rather than "M 218 I 1 728 M").  The *Begin values
are in "between"-type coodinates (like what exonerate uses).

It's messy, but it's not done yet...