7 Commits (420725441afd116aa181a18e2e21307aa79f27f1)

Author	SHA1	Message	Date
hanna	a78bc60c0f	Minor tweak to improve ease-of-use of iterator system. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2104 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-20 18:24:19 +00:00
hanna	4fbb6d05d0	Refactoring. Push the revisions to the common aligner interface down into ... the aligner base classes. Hack the managed implementation to support the new interface. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2103 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-20 17:08:09 +00:00
hanna	38a030f2ba	Finishing off data transfer conduits for single alignment generator. ... Misc bug fixes elsewhere. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2101 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-20 15:21:59 +00:00
hanna	a95302fe98	Single alignment generator, another checkpoint. Does generate single alignments, but some of the data still ... needs to plumbed through and it may leak memory. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2095 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-19 21:20:03 +00:00
hanna	a972b2769f	Checkpoint. Add first phase of single alignment interface. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2094 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-19 19:03:43 +00:00
hanna	ce5034dc5d	Finally reinstate the iterator-style interface. Get rid of some scaffolding code. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2052 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-16 02:34:19 +00:00
hanna	15c14add4d	Repackage the aligner for better partitioning. The C aligner, for example, is now ... partitioned from the Java aligner, and both are partitioned from the more general- purpose BWT reader. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2045 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-13 22:55:27 +00:00