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2009-09-02	Christopher Lee	split up bullet points to integrate into the code example	commit \| commitdiff \| tree
2009-09-02	Christopher Lee	revised sequence tutorial intro (first part)	commit \| commitdiff \| tree
2009-09-02	Christopher Lee	Merge commit 'remotes/ctb/xmlrpc_tutorial' into tutorial	commit \| commitdiff \| tree
2009-09-02	Christopher Lee	Merge commit 'remotes/ctb/doc_alignment' into tutorial	commit \| commitdiff \| tree
2009-09-02	Christopher Lee	revised gff3 code	commit \| commitdiff \| tree
2009-09-02	Christopher Lee	added GFF3 example of gene building	commit \| commitdiff \| tree
2009-09-01	Christopher Lee	Merge commit 'remotes/mkszuba/xmlrpc_tutorial' into...	commit \| commitdiff \| tree
2009-09-01	Christopher Lee	Merge commit 'remotes/ctb/doc_annotations' into tutorial	commit \| commitdiff \| tree
2009-09-01	Christopher Lee	extracted material for separate database tutorial	commit \| commitdiff \| tree
2009-08-29	Christopher Lee	removed unnecessary stat and shutil import from setup.py	commit \| commitdiff \| tree
2009-08-14	Christopher Lee	fixed easy_install bug by protecting coordinator.ResourceFil...	commit \| commitdiff \| tree
2009-08-04	Christopher Lee	fixed blast_test: renamed test_seq_without_db() to...	commit \| commitdiff \| tree
2009-08-04	Christopher Lee	Merge commit 'remotes/ctb/minor_fixes' into minor_fixes	commit \| commitdiff \| tree
2009-08-04	Christopher Lee	fix port passing in testutil.TestXMLRPCServer	commit \| commitdiff \| tree
2009-08-04	Christopher Lee	use pair_identity_tuple() for blast_test formatting...	commit \| commitdiff \| tree
2009-08-04	Christopher Lee	added BlastBase.tearDown() to close seqdbs as they...	commit \| commitdiff \| tree
2009-08-04	Christopher Lee	Merge commit 'remotes/mkszuba/doc_make'	commit \| commitdiff \| tree
2009-08-04	Christopher Lee	Merge commit 'remotes/mkszuba/rpm'	commit \| commitdiff \| tree
2009-07-29	Christopher Lee	got rid of BlastMapping.warn_about_self_matches()	commit \| commitdiff \| tree
2009-07-29	Christopher Lee	changed NLMSA pairwiseMode to allow reporting of self...	commit \| commitdiff \| tree
2009-07-29	Christopher Lee	Merge commit 'remotes/mkszuba/debian'	commit \| commitdiff \| tree
2009-07-29	Christopher Lee	retry reading port_file in TestXMLRPCServer several...	commit \| commitdiff \| tree
2009-07-29	Christopher Lee	added comments to process_blast()	commit \| commitdiff \| tree
2009-07-29	Christopher Lee	fix problem introduced in process_blast() by commit...	commit \| commitdiff \| tree
2009-07-28	Christopher Lee	handle missing WINDIR case on Windows	commit \| commitdiff \| tree
2009-07-28	Christopher Lee	added SeqTranslator.__repr__()	commit \| commitdiff \| tree
2009-07-28	Christopher Lee	Merge commit 'remotes/ctb/simpleframe_formatdb_cleanup...	commit \| commitdiff \| tree
2009-07-28	Christopher Lee	Merge branch 'master' into simpleframe	commit \| commitdiff \| tree
2009-07-28	Christopher Lee	added SeqTranslator.iter_frames() method, used in BlastxMapp...	commit \| commitdiff \| tree
2009-07-28	Christopher Lee	Merge commit 'remotes/ctb/simpleframe_doc_align' into...	commit \| commitdiff \| tree
2009-07-27	Christopher Lee	protect 2 more tests using blast_enabled() check	commit \| commitdiff \| tree
2009-07-27	Christopher Lee	fixed syntax error	commit \| commitdiff \| tree
2009-07-27	Christopher Lee	added python 2.3 code for FilePopen to detect bad exit...	commit \| commitdiff \| tree
2009-07-27	Christopher Lee	Merge branch 'no_edge_db'	commit \| commitdiff \| tree
2009-07-27	Christopher Lee	Merge branch 'silencio'	commit \| commitdiff \| tree
2009-07-27	Christopher Lee	added showFormatdbMessages option to BlastMapping	commit \| commitdiff \| tree
2009-07-25	Christopher Lee	added support for no-edgeDB case in mapping.Graph:...	commit \| commitdiff \| tree
2009-07-23	Christopher Lee	added option for latex output of the reference manual	commit \| commitdiff \| tree
2009-07-16	Christopher Lee	Merge commit 'remotes/ctb/blast_test_rc' into simpleframe	commit \| commitdiff \| tree
2009-07-16	Christopher Lee	added more docstrings for blast.py	commit \| commitdiff \| tree
2009-07-16	Christopher Lee	removed old BlastxMapping code	commit \| commitdiff \| tree
2009-07-16	Christopher Lee	new, greatly simplified BlastxMapping	commit \| commitdiff \| tree
2009-07-16	Christopher Lee	switched test_blastx_server to use new TranslationDB...	commit \| commitdiff \| tree
2009-07-16	Christopher Lee	added read_blast_alignment() translateDest option	commit \| commitdiff \| tree
2009-07-16	Christopher Lee	added NLMSA.edges() method	commit \| commitdiff \| tree
2009-07-16	Christopher Lee	switched test_tblastn_parser to use new TranslationDB...	commit \| commitdiff \| tree
2009-07-16	Christopher Lee	switch tblastn to use new TranslationDB approach	commit \| commitdiff \| tree
2009-07-15	Christopher Lee	added translationDB.py	commit \| commitdiff \| tree
2009-07-15	Christopher Lee	moved dbname default into get_bound_subclass()	commit \| commitdiff \| tree
2009-07-15	Christopher Lee	make CoordsToIntervals / get_interval() use seq.absolute_sli...	commit \| commitdiff \| tree
2009-07-15	Christopher Lee	cleaned up SeqPath.classySlice()	commit \| commitdiff \| tree
2009-07-15	Christopher Lee	Merge commit 'remotes/mkszuba/nlmsa_no_verbose' into...	commit \| commitdiff \| tree
2009-07-15	Christopher Lee	Merge commit 'remotes/mkszuba/cnestedlist_notice' into...	commit \| commitdiff \| tree
2009-07-15	Christopher Lee	incomplete new code for TranslationDB	commit \| commitdiff \| tree
2009-07-15	Christopher Lee	cleaned up reversePath construction	commit \| commitdiff \| tree
2009-07-15	Christopher Lee	add absolute_slice() method to SeqPath	commit \| commitdiff \| tree
2009-07-14	Christopher Lee	Merge commit 'remotes/mkszuba/cnestedlist_logger' into...	commit \| commitdiff \| tree
2009-07-14	Marek Szuba	Given existing isolation problems between tests run...	commit \| commitdiff \| tree
2009-07-14	Christopher Lee	Merge branch 'master' into megatests	commit \| commitdiff \| tree
2009-07-03	Christopher Lee	Merge branch 'formatdb_fail'	commit \| commitdiff \| tree
2009-07-03	Christopher Lee	improved whitespace path warning	commit \| commitdiff \| tree
2009-07-03	Christopher Lee	added warning for whitespace in path	commit \| commitdiff \| tree
2009-07-01	Christopher Lee	Merge commit 'remotes/mkszuba/megatests'	commit \| commitdiff \| tree
2009-07-01	Christopher Lee	use glob.glob() instead of os.listdir(); cleaned up...	commit \| commitdiff \| tree
2009-07-01	Christopher Lee	Merge commit 'remotes/mkszuba/mimetext'	commit \| commitdiff \| tree
2009-07-01	Christopher Lee	Merge commit 'remotes/mkszuba/docfixes'	commit \| commitdiff \| tree
2009-07-01	Christopher Lee	Merge commit 'remotes/mkszuba/hashlib'	commit \| commitdiff \| tree
2009-06-26	Christopher Lee	fixed caching bug introduced in commit 8d9966 in PrefixUnion...	commit \| commitdiff \| tree
2009-06-20	Christopher Lee	deprecated cursor argument to SQLTable	commit \| commitdiff \| tree
2009-06-20	Christopher Lee	fixed issue 99	commit \| commitdiff \| tree
2009-06-20	Christopher Lee	added test for issue 99	commit \| commitdiff \| tree
2009-06-20	Christopher Lee	cleaned up SQLiteServerInfo	commit \| commitdiff \| tree
2009-06-20	Christopher Lee	added DBServerInfo.new_cursor() method	commit \| commitdiff \| tree
2009-06-13	Christopher Lee	Merge commit 'remotes/mkszuba/issue97_test' into issue97_test	commit \| commitdiff \| tree
2009-06-13	Christopher Lee	removed redundant and buggy rstrip(".py") call from...	commit \| commitdiff \| tree
2009-06-12	Christopher Lee	fix pyrex cdef	commit \| commitdiff \| tree
2009-06-12	Christopher Lee	fix issue97	commit \| commitdiff \| tree
2009-06-12	Christopher Lee	raised minimum identity for relaxed blast tests to 60%	commit \| commitdiff \| tree
2009-06-09	Christopher Lee	replaced a few remaining refs in the docs to pygr.Data...	commit \| commitdiff \| tree
2009-06-09	Christopher Lee	Merge commit 'remotes/mkszuba/deb'	commit \| commitdiff \| tree
2009-06-09	Christopher Lee	Merge commit 'remotes/mkszuba/renames'	commit \| commitdiff \| tree
2009-06-09	Christopher Lee	Merge branch 'interval_filters' into blast_tests	commit \| commitdiff \| tree
2009-06-09	Christopher Lee	relaxed-tests had a bug that made them pass the comparison...	commit \| commitdiff \| tree
2009-06-04	Christopher Lee	must close FilePopen object before exiting BlastxMapping...	commit \| commitdiff \| tree
2009-06-04	Christopher Lee	merged in ctb/blastx_database	commit \| commitdiff \| tree
2009-06-04	Christopher Lee	Merge commit 'remotes/ctb/blastx_generator' into ctb_tmp	commit \| commitdiff \| tree
2009-06-04	Christopher Lee	PEP8 and whitespace fixes to nlmsa_utils.py; no functionalit...	commit \| commitdiff \| tree
2009-06-04	Christopher Lee	converted add_aligned_intervals functionality into...	commit \| commitdiff \| tree
2009-06-04	Christopher Lee	clean up AttributeInterface according to Titus suggestions	commit \| commitdiff \| tree
2009-06-04	Christopher Lee	Merge commit 'remotes/ctb/ctb_intervals' into interval_filters	commit \| commitdiff \| tree
2009-06-03	Christopher Lee	Merge commit 'remotes/ctb/ctb_blast2' into ctb_tmp	commit \| commitdiff \| tree
2009-06-03	Christopher Lee	Merge commit 'remotes/ctb/minor_doc_fixes' into ctb_tmp	commit \| commitdiff \| tree
2009-06-03	Christopher Lee	merged in ctb/annotation	commit \| commitdiff \| tree
2009-06-03	Christopher Lee	merged in ctb/blast_skip conflict with ctb/blast_cache	commit \| commitdiff \| tree
2009-06-03	Christopher Lee	Merge commit 'remotes/ctb/blast_cache' into ctb_tmp	commit \| commitdiff \| tree
2009-05-29	Christopher Lee	Merge commit 'remotes/ctb/nlmsa_iter_repr'	commit \| commitdiff \| tree
2009-05-29	Christopher Lee	removed unnecessary import	commit \| commitdiff \| tree
2009-05-29	Christopher Lee	converted test_multiblast_single() back to test against...	commit \| commitdiff \| tree
2009-05-29	Christopher Lee	rename to avoid false implication this test involves...	commit \| commitdiff \| tree
2009-05-28	Titus Brown	fixed typo in cnestedlist: MaskEnd => maskEnd	commit \| commitdiff \| tree
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Graph database interfaces in Python

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