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2002-12-17	jason	catfile inputfilename was not being called correctly	commit \| commitdiff \| tree
2002-12-16	jason	made docs slightly more clear (still long ways to go...	commit \| commitdiff \| tree
2002-12-16	jason	proper use of the Root::IO->catfile and slightly simplified...	commit \| commitdiff \| tree
2002-12-16	jason	let's create one less temporary file -- also - let...	commit \| commitdiff \| tree
2002-12-13	jason	this is really what I meant by splitting up these conditiona...	commit \| commitdiff \| tree
2002-12-13	jason	oops - meant to set the HMMER param in the right place...	commit \| commitdiff \| tree
2002-12-13	jason	support HMMER filetype parameter	commit \| commitdiff \| tree
2002-12-04	jason	oops - use class state not class variable for the tempdir...	commit \| commitdiff \| tree
2002-12-03	jason	clean up to make -w clean	commit \| commitdiff \| tree
2002-12-03	jason	test the distance value	commit \| commitdiff \| tree
2002-12-03	jason	use tempdir to run things	commit \| commitdiff \| tree
2002-12-01	jason	refer to the correct base class	commit \| commitdiff \| tree
2002-11-30	jason	doc + code formatting cleanup	commit \| commitdiff \| tree
2002-11-30	jason	use the new Phylip base wrapper	commit \| commitdiff \| tree
2002-11-30	jason	tree drawing modules	commit \| commitdiff \| tree
2002-11-30	jason	tests and data files for drawing trees and phylo/phenograms	commit \| commitdiff \| tree
2002-11-29	jason	should read correct filename for output, and allows...	commit \| commitdiff \| tree
2002-11-29	jason	small formatting changes	commit \| commitdiff \| tree
2002-11-29	jason	handle different expected results for different versions...	commit \| commitdiff \| tree
2002-11-29	jason	more robust parameter handling, matrix is not a required...	commit \| commitdiff \| tree
2002-11-29	jason	new generic 'run' method	commit \| commitdiff \| tree
2002-11-13	jason	support -u and -v settings, support passing in file...	commit \| commitdiff \| tree
2002-11-13	jason	fail gracefully - remove Fugu group Ensembl cruft here	commit \| commitdiff \| tree
2002-11-13	jason	more graceful exiting	commit \| commitdiff \| tree
2002-11-13	jason	add an Id header	commit \| commitdiff \| tree
2002-11-13	jason	can run tests if we let executeable find the exe	commit \| commitdiff \| tree
2002-11-13	jason	ah hah, test will run without fugu specific stuff	commit \| commitdiff \| tree
2002-11-13	jason	Name of program is pfscan	commit \| commitdiff \| tree
2002-11-13	jason	fail gracefully -- and secret message for Fugu guys...	commit \| commitdiff \| tree
2002-11-13	jason	free resources	commit \| commitdiff \| tree
2002-11-13	jason	use new API	commit \| commitdiff \| tree
2002-11-13	jason	make sure resources are freed	commit \| commitdiff \| tree
2002-11-13	jason	codeml --> tcoffee copy+paste silliness	commit \| commitdiff \| tree
2002-11-13	jason	Convert StandAloneBlast to WrapperBase (finallyperl...	commit \| commitdiff \| tree
2002-11-13	jason	use proper Tools::WrapperBase now	commit \| commitdiff \| tree
2002-11-13	jason	missing input files for StandAloneBlast	commit \| commitdiff \| tree
2002-11-13	jason	insure filehandles are closed	commit \| commitdiff \| tree
2002-11-13	jason	17 tests now?	commit \| commitdiff \| tree
2002-11-13	jason	Brought up to spec with the new Objects and seqname...	commit \| commitdiff \| tree
2002-11-13	jason	remove Fugu system stuff and insure that File tmp handles...	commit \| commitdiff \| tree
2002-11-10	jason	fixed to work with new base object and use bioperl...	commit \| commitdiff \| tree
2002-11-10	jason	skip if ret val is 0	commit \| commitdiff \| tree
2002-11-10	jason	consistency	commit \| commitdiff \| tree
2002-11-10	jason	code beautification	commit \| commitdiff \| tree
2002-11-10	jason	platform independent filename	commit \| commitdiff \| tree
2002-11-09	jason	respect the original cwd	commit \| commitdiff \| tree
2002-09-18	jason	synopsis doc	commit \| commitdiff \| tree
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
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