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2002-09-18	jason	default should be F3X4	commit \| commitdiff \| tree
2002-09-18	jason	Matthew's Changes committed: Add support to save_output...	commit \| commitdiff \| tree
2002-09-18	jason	handle exe apps	commit \| commitdiff \| tree
2002-09-05	jason	SAX/Sax -> PerlSAX	commit \| commitdiff \| tree
2002-08-14	jason	for building manifest	commit \| commitdiff \| tree
2002-08-14	jason	cosmetic code fix	commit \| commitdiff \| tree
2002-08-14	jason	describe the current state of affair	commit \| commitdiff \| tree
2002-07-30	jason	skip tests	commit \| commitdiff \| tree
2002-07-29	jason	test file for TCoffee	commit \| commitdiff \| tree
2002-07-29	jason	whoops,one more time, cleanup tempfiles and dirs	commit \| commitdiff \| tree
2002-07-29	jason	cleanup of tempfiles works	commit \| commitdiff \| tree
2002-07-29	jason	handle bad result err by skipping tests	commit \| commitdiff \| tree
2002-07-29	jason	tests updated to handle missing exe better	commit \| commitdiff \| tree
2002-07-29	jason	inherit from WrapperBase	commit \| commitdiff \| tree
2002-07-29	jason	code formatting	commit \| commitdiff \| tree
2002-07-29	jason	API changed a little bit with new parser	commit \| commitdiff \| tree
2002-07-29	jason	handle windows exes	commit \| commitdiff \| tree
2002-07-29	jason	fix test count	commit \| commitdiff \| tree
2002-07-29	jason	use new PAML parser API	commit \| commitdiff \| tree
2002-07-27	jason	codeml->protml doc fixes	commit \| commitdiff \| tree
2002-07-27	jason	added additions of .exe for on windows, allow alignment...	commit \| commitdiff \| tree
2002-07-27	jason	brought in line with WrapperBase	commit \| commitdiff \| tree
2002-07-27	jason	brought module in-line with new WrapperBase	commit \| commitdiff \| tree
2002-07-27	jason	bump test count	commit \| commitdiff \| tree
2002-07-27	jason	copy+paste error	commit \| commitdiff \| tree
2002-07-27	jason	fix internal parameter name	commit \| commitdiff \| tree
2002-07-27	jason	added ProtML wrapper - part of Molphy packager for...	commit \| commitdiff \| tree
2002-07-27	jason	test for protml running	commit \| commitdiff \| tree
2002-07-25	jason	migrate from PAMLBase to WrapperBase	commit \| commitdiff \| tree
2002-07-16	jason	print data to file right away rather than holding array...	commit \| commitdiff \| tree
2002-07-16	jason	don't redirect to /dev/null - make sure quiet really...	commit \| commitdiff \| tree
2002-07-16	jason	more robust program finding	commit \| commitdiff \| tree
2002-07-09	jason	changed to use PAML template for find executable insated...	commit \| commitdiff \| tree
2002-07-06	jason	explicitly closing some filehandles appears to do a...	commit \| commitdiff \| tree
2002-07-05	jason	tests find the mat and data file now, and will skip...	commit \| commitdiff \| tree
2002-07-05	jason	need to test when people run Makefile.PL, otherwise...	commit \| commitdiff \| tree
2002-07-05	jason	prompt user when Makefile.PL is run	commit \| commitdiff \| tree
2002-07-05	jason	update test count	commit \| commitdiff \| tree
2002-07-03	jason	makefile	commit \| commitdiff \| tree
2002-07-02	jason	added codeml data	commit \| commitdiff \| tree
2002-07-02	jason	removed run wrappers tests from core - they have been...	commit \| commitdiff \| tree
2002-06-26	jason	readme for run wrappers	commit \| commitdiff \| tree
2002-06-21	jason	testfile renamed	commit \| commitdiff \| tree
2002-06-21	jason	remove debug copyfile	commit \| commitdiff \| tree
2002-06-21	jason	shorten filename to avoid possible windows long filenames...	commit \| commitdiff \| tree
2002-06-19	jason	doc fix	commit \| commitdiff \| tree
2002-06-18	jason	use the determined path to RP when attempting to find...	commit \| commitdiff \| tree
2002-06-17	jason	return the values as hash of hashes as they are all...	commit \| commitdiff \| tree
2002-06-17	jason	small doc tweaks and added runnable synopsis	commit \| commitdiff \| tree
2002-06-17	jason	yn00 wrapper for PAML	commit \| commitdiff \| tree
2002-06-15	jason	quieter tests unless BIOPERLDEBUG env variable is set	commit \| commitdiff \| tree
2002-06-14	jason	set verbose to -1	commit \| commitdiff \| tree
2002-06-14	jason	PAML package -- codeml wrapper and test committed	commit \| commitdiff \| tree
2002-05-31	jason	doc fix	commit \| commitdiff \| tree
2002-05-31	jason	handle case when PHYLIP is installed but not clustalw	commit \| commitdiff \| tree
2002-05-30	jason	handle some weird boundary cases	commit \| commitdiff \| tree
2002-05-21	jason	update some of the docs	commit \| commitdiff \| tree
2002-05-21	jason	test value for protdist	commit \| commitdiff \| tree
2002-04-22	jason	fixes to remove warnings	commit \| commitdiff \| tree
2002-04-22	jason	fix warnings	commit \| commitdiff \| tree
2002-04-18	jason	POD fix	commit \| commitdiff \| tree
2002-03-22	jason	updated tests for v 1.22 problems on main trunk	commit \| commitdiff \| tree
2002-03-21	jason	simple align has overall percent id method	commit \| commitdiff \| tree
2002-03-19	jason	cleanup before each run of an application	commit \| commitdiff \| tree
2002-03-15	jason	merge from branch	commit \| commitdiff \| tree
2002-03-15	jason	merge changes from branch	commit \| commitdiff \| tree
2002-03-15	jason	updated to handle tests with SearchIO object returned...	commit \| commitdiff \| tree
2002-03-15	jason	better synopsis and doc update	commit \| commitdiff \| tree
2002-03-14	jason	io cleanup called at outset of an analyses -- from...	commit \| commitdiff \| tree
2002-03-14	jason	merged exe checking from branch	commit \| commitdiff \| tree
2002-03-14	jason	skip nicely, handle case where server is down	commit \| commitdiff \| tree
2002-03-11	jason	use SearchIO not Tools::Blast	commit \| commitdiff \| tree
2002-03-09	jason	turn of clustalw debugging	commit \| commitdiff \| tree
2002-03-05	jason	unlink test file output	commit \| commitdiff \| tree
2002-03-04	jason	added ability to dump alignments as well as sequences...	commit \| commitdiff \| tree
2002-02-18	jason	added example documentation to the POD	commit \| commitdiff \| tree
2002-02-18	jason	test for cmd line argument where value is a Bio::PrimarySeqI...	commit \| commitdiff \| tree
2002-02-18	jason	handle cmd line arguments pointing to a Bio::PrimarySeqI...	commit \| commitdiff \| tree
2002-02-06	jason	params should be appended not overwriting	commit \| commitdiff \| tree
2002-01-30	jason	verbosity=-1 is same as quiet()	commit \| commitdiff \| tree
2002-01-11	jason	debug message now uses the debug method	commit \| commitdiff \| tree
2002-01-09	jason	warn about not using old clustalw	commit \| commitdiff \| tree
2002-01-09	jason	use the updated PROGRAM exe location information to...	commit \| commitdiff \| tree
2002-01-09	jason	check to insure defined object before calling ISA	commit \| commitdiff \| tree
2001-12-14	jason	skip msg updated due to clustal 1.81 bug	commit \| commitdiff \| tree
2001-12-14	jason	nice message printing when blast is not runnable	commit \| commitdiff \| tree
2001-12-14	jason	more quiet warning so tests are less chatty	commit \| commitdiff \| tree
2001-12-14	jason	issue nice message when skipping EMBOSS tests	commit \| commitdiff \| tree
2001-12-14	jason	skip can print a nice message about why it skipped	commit \| commitdiff \| tree
2001-12-14	jason	emboss factory behaves more quietly when EMBOSS is...	commit \| commitdiff \| tree
2001-11-19	jason	EMBOSS more runnable and w/ tests	commit \| commitdiff \| tree
2001-08-10	jason	don't have clustalw tests fail for 0.9 release	commit \| commitdiff \| tree
2001-08-07	jason	documentation for retrieve_blast method	commit \| commitdiff \| tree
2001-06-15	jason	minium identity score required instead of hard value...	commit \| commitdiff \| tree
2001-06-14	jason	status set to invalid on a failed retrieval	commit \| commitdiff \| tree
2001-06-12	jason	using private state outside of class, must change the...	commit \| commitdiff \| tree
2001-04-30	jason	migrated test data files to dir t/data	commit \| commitdiff \| tree
2001-04-16	jason	Tests pass even when IO::String is not installed	commit \| commitdiff \| tree
2001-04-09	jason	updated to use ncbi Blast.cgi script rather than blast.cgi	commit \| commitdiff \| tree
2001-04-07	jason	updated num of tests	commit \| commitdiff \| tree
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