| 2004-07-10 |
jason | allow alignment to be specified in run()
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commit | commitdiff | tree |
| 2004-07-09 |
jason | support more models
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commit | commitdiff | tree |
| 2004-06-30 |
jason | bug #1646; This should go with msf if gcg format is...
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commit | commitdiff | tree |
| 2004-06-30 |
jason | allow alignment methods (A=[01234]) to be specified...
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commit | commitdiff | tree |
| 2004-06-24 |
jason | let alpha be more free - don't try and restrict it
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commit | commitdiff | tree |
| 2004-06-24 |
jason | tests more resistant to rounding differences
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commit | commitdiff | tree |
| 2004-06-24 |
jason | This still needs an overhaul but fix minor doc bugs...
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commit | commitdiff | tree |
| 2004-06-24 |
jason | attempted cleanup of code for bug #1657
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commit | commitdiff | tree |
| 2004-06-02 |
jason | get rid of deprecation warning
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commit | commitdiff | tree |
| 2004-05-14 |
jason | small docu fixes
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commit | commitdiff | tree |
| 2004-05-14 |
jason | more, better tests for the new implementation for tree...
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commit | commitdiff | tree |
| 2004-02-20 |
jason | allow 0 value attributes per Susan Miller's bug report
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commit | commitdiff | tree |
| 2004-02-05 |
jason | adding Daniel's LVB wrapper
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commit | commitdiff | tree |
| 2004-01-02 |
jason | docfix, an array of genes can be returned
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commit | commitdiff | tree |
| 2003-12-30 |
jason | docu fix
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commit | commitdiff | tree |
| 2003-12-17 |
jason | stupid jason - it saves a syscall
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commit | commitdiff | tree |
| 2003-12-17 |
jason | what is that underscore in there for?
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commit | commitdiff | tree |
| 2003-12-17 |
jason | catfile not catdir
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commit | commitdiff | tree |
| 2003-11-19 |
jason | George Hartzell fixes
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commit | commitdiff | tree |
| 2003-09-30 |
jason | use save_tempfiles, use PROGRAMNAME as a variable,...
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commit | commitdiff | tree |
| 2003-09-30 |
jason | typo
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commit | commitdiff | tree |
| 2003-09-08 |
jason | default should be an arrayref
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commit | commitdiff | tree |
| 2003-09-03 |
jason | wait -this isn't necessary , we already pad the PROGRAMNAME...
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commit | commitdiff | tree |
| 2003-09-03 |
jason | bug #1507 add MSwin .exe extension where appropriate
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commit | commitdiff | tree |
| 2003-09-03 |
jason | bug #1507, SYNOPSIS is runnable now with API changes
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commit | commitdiff | tree |
| 2003-08-14 |
jason | can't declare are expect a variable at the same time
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commit | commitdiff | tree |
| 2003-08-14 |
jason | no need for this debugging
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commit | commitdiff | tree |
| 2003-08-14 |
jason | fix stupidity with tempfilehandle and outfh not being...
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commit | commitdiff | tree |
| 2003-07-11 |
jason | align the code
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commit | commitdiff | tree |
| 2003-07-11 |
jason | properly get the hash value
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commit | commitdiff | tree |
| 2003-06-28 |
jason | Mark Wagner's enhancements bug #1399
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commit | commitdiff | tree |
| 2003-05-30 |
jason | POD fixes
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commit | commitdiff | tree |
| 2003-05-21 |
jason | some code cleanup to avoid warnings and insure filehandles...
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commit | commitdiff | tree |
| 2003-05-21 |
jason | more modern use of hit/query instead of feature1/feature2...
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commit | commitdiff | tree |
| 2003-03-29 |
jason | begin documenting the necessary env variables
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commit | commitdiff | tree |
| 2003-03-29 |
jason | remove debugging code
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commit | commitdiff | tree |
| 2003-03-29 |
jason | update error message
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commit | commitdiff | tree |
| 2003-03-28 |
jason | rework tempfile handling to explicitly close a filehanle...
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commit | commitdiff | tree |
| 2003-03-28 |
jason | Handle interleaved output from phylip 3.6, handle 3...
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commit | commitdiff | tree |
| 2003-03-28 |
jason | test quiet
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commit | commitdiff | tree |
| 2003-03-24 |
jason | some scripts for running protdist and neighbor, for...
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commit | commitdiff | tree |
| 2003-03-23 |
jason | require jumble parameter to be odd or we get ina bad...
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commit | commitdiff | tree |
| 2003-03-17 |
jason | bug which was not caught before
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commit | commitdiff | tree |
| 2003-03-14 |
jason | test needs to be in same CVS module as the perl module
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commit | commitdiff | tree |
| 2003-02-25 |
jason | support -S and a place to put the 'output' data - although...
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commit | commitdiff | tree |
| 2003-02-24 |
jason | hmm, we should figure out how to support either fasta34...
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commit | commitdiff | tree |
| 2003-02-24 |
jason | need to override executable to store multiple program...
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commit | commitdiff | tree |
| 2003-02-21 |
jason | added BLAST and FASTA
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commit | commitdiff | tree |
| 2003-02-04 |
jason | JIT should be JTT
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commit | commitdiff | tree |
| 2003-02-04 |
jason | formatting
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commit | commitdiff | tree |
| 2003-01-18 |
jason | added Bala's email
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commit | commitdiff | tree |
| 2003-01-18 |
jason | an authors file
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commit | commitdiff | tree |
| 2003-01-18 |
jason | use Root::IO
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commit | commitdiff | tree |
| 2003-01-18 |
jason | remove Kiran's hardcoded path to exe
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commit | commitdiff | tree |
| 2003-01-18 |
jason | support the 'Boolean Yes/No' as well as 'Yes/No' that...
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commit | commitdiff | tree |
| 2003-01-10 |
jason | add some debugging support
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commit | commitdiff | tree |
| 2003-01-10 |
jason | test Yn00
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commit | commitdiff | tree |
| 2003-01-04 |
jason | some changes to deal with dec_osf bug
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commit | commitdiff | tree |
| 2002-12-23 |
jason | use debug to print out the dumper info
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commit | commitdiff | tree |
| 2002-12-23 |
jason | deal with changes needed as seen by Bug #1359, mostly...
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commit | commitdiff | tree |
| 2002-12-18 |
jason | quiet properly
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commit | commitdiff | tree |
| 2002-12-17 |
jason | make sure we've closed temporary file handles
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commit | commitdiff | tree |
| 2002-12-17 |
jason | make sure we cleanup tempfiles before each run
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commit | commitdiff | tree |
| 2002-12-17 |
jason | catfile inputfilename was not being called correctly
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commit | commitdiff | tree |
| 2002-12-16 |
jason | made docs slightly more clear (still long ways to go...
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commit | commitdiff | tree |
| 2002-12-16 |
jason | proper use of the Root::IO->catfile and slightly simplified...
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commit | commitdiff | tree |
| 2002-12-16 |
jason | let's create one less temporary file -- also - let...
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commit | commitdiff | tree |
| 2002-12-13 |
jason | this is really what I meant by splitting up these conditiona...
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commit | commitdiff | tree |
| 2002-12-13 |
jason | oops - meant to set the HMMER param in the right place...
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commit | commitdiff | tree |
| 2002-12-13 |
jason | support HMMER filetype parameter
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commit | commitdiff | tree |
| 2002-12-04 |
jason | oops - use class state not class variable for the tempdir...
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commit | commitdiff | tree |
| 2002-12-03 |
jason | clean up to make -w clean
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commit | commitdiff | tree |
| 2002-12-03 |
jason | test the distance value
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commit | commitdiff | tree |
| 2002-12-03 |
jason | use tempdir to run things
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commit | commitdiff | tree |
| 2002-12-01 |
jason | refer to the correct base class
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commit | commitdiff | tree |
| 2002-11-30 |
jason | doc + code formatting cleanup
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commit | commitdiff | tree |
| 2002-11-30 |
jason | use the new Phylip base wrapper
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commit | commitdiff | tree |
| 2002-11-30 |
jason | tree drawing modules
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commit | commitdiff | tree |
| 2002-11-30 |
jason | tests and data files for drawing trees and phylo/phenograms
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commit | commitdiff | tree |
| 2002-11-29 |
jason | should read correct filename for output, and allows...
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commit | commitdiff | tree |
| 2002-11-29 |
jason | small formatting changes
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commit | commitdiff | tree |
| 2002-11-29 |
jason | handle different expected results for different versions...
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commit | commitdiff | tree |
| 2002-11-29 |
jason | more robust parameter handling, matrix is not a required...
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commit | commitdiff | tree |
| 2002-11-29 |
jason | new generic 'run' method
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commit | commitdiff | tree |
| 2002-11-13 |
jason | support -u and -v settings, support passing in file...
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commit | commitdiff | tree |
| 2002-11-13 |
jason | fail gracefully - remove Fugu group Ensembl cruft here
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commit | commitdiff | tree |
| 2002-11-13 |
jason | more graceful exiting
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commit | commitdiff | tree |
| 2002-11-13 |
jason | add an Id header
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commit | commitdiff | tree |
| 2002-11-13 |
jason | can run tests if we let executeable find the exe
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commit | commitdiff | tree |
| 2002-11-13 |
jason | ah hah, test will run without fugu specific stuff
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commit | commitdiff | tree |
| 2002-11-13 |
jason | Name of program is pfscan
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commit | commitdiff | tree |
| 2002-11-13 |
jason | fail gracefully -- and secret message for Fugu guys...
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commit | commitdiff | tree |
| 2002-11-13 |
jason | free resources
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commit | commitdiff | tree |
| 2002-11-13 |
jason | use new API
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commit | commitdiff | tree |
| 2002-11-13 |
jason | make sure resources are freed
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commit | commitdiff | tree |
| 2002-11-13 |
jason | codeml --> tcoffee copy+paste silliness
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commit | commitdiff | tree |
| 2002-11-13 |
jason | Convert StandAloneBlast to WrapperBase (finallyperl...
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commit | commitdiff | tree |
| 2002-11-13 |
jason | use proper Tools::WrapperBase now
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commit | commitdiff | tree |
| 2002-11-13 |
jason | missing input files for StandAloneBlast
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commit | commitdiff | tree |
| 2002-11-13 |
jason | insure filehandles are closed
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commit | commitdiff | tree |
