| 2002-07-30 |
jason | skip tests
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commit | commitdiff | tree |
| 2002-07-29 |
jason | test file for TCoffee
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commit | commitdiff | tree |
| 2002-07-29 |
jason | whoops,one more time, cleanup tempfiles and dirs
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commit | commitdiff | tree |
| 2002-07-29 |
jason | cleanup of tempfiles works
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commit | commitdiff | tree |
| 2002-07-29 |
jason | handle bad result err by skipping tests
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commit | commitdiff | tree |
| 2002-07-29 |
jason | tests updated to handle missing exe better
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commit | commitdiff | tree |
| 2002-07-29 |
jason | inherit from WrapperBase
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commit | commitdiff | tree |
| 2002-07-29 |
jason | code formatting
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commit | commitdiff | tree |
| 2002-07-29 |
jason | API changed a little bit with new parser
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commit | commitdiff | tree |
| 2002-07-29 |
jason | handle windows exes
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commit | commitdiff | tree |
| 2002-07-29 |
jason | fix test count
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commit | commitdiff | tree |
| 2002-07-29 |
jason | use new PAML parser API
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commit | commitdiff | tree |
| 2002-07-27 |
jason | codeml->protml doc fixes
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commit | commitdiff | tree |
| 2002-07-27 |
jason | added additions of .exe for on windows, allow alignment...
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commit | commitdiff | tree |
| 2002-07-27 |
jason | brought in line with WrapperBase
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commit | commitdiff | tree |
| 2002-07-27 |
jason | brought module in-line with new WrapperBase
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commit | commitdiff | tree |
| 2002-07-27 |
jason | bump test count
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commit | commitdiff | tree |
| 2002-07-27 |
jason | copy+paste error
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commit | commitdiff | tree |
| 2002-07-27 |
jason | fix internal parameter name
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commit | commitdiff | tree |
| 2002-07-27 |
jason | added ProtML wrapper - part of Molphy packager for...
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commit | commitdiff | tree |
| 2002-07-27 |
jason | test for protml running
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commit | commitdiff | tree |
| 2002-07-25 |
jason | migrate from PAMLBase to WrapperBase
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commit | commitdiff | tree |
| 2002-07-16 |
jason | print data to file right away rather than holding array...
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commit | commitdiff | tree |
| 2002-07-16 |
jason | don't redirect to /dev/null - make sure quiet really...
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commit | commitdiff | tree |
| 2002-07-16 |
jason | more robust program finding
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commit | commitdiff | tree |
| 2002-07-09 |
jason | changed to use PAML template for find executable insated...
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commit | commitdiff | tree |
| 2002-07-06 |
jason | explicitly closing some filehandles appears to do a...
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commit | commitdiff | tree |
| 2002-07-05 |
jason | tests find the mat and data file now, and will skip...
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commit | commitdiff | tree |
| 2002-07-05 |
jason | need to test when people run Makefile.PL, otherwise...
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commit | commitdiff | tree |
| 2002-07-05 |
jason | prompt user when Makefile.PL is run
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commit | commitdiff | tree |
| 2002-07-05 |
jason | update test count
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commit | commitdiff | tree |
| 2002-07-03 |
jason | makefile
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commit | commitdiff | tree |
| 2002-07-02 |
jason | added codeml data
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commit | commitdiff | tree |
| 2002-07-02 |
jason | removed run wrappers tests from core - they have been...
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commit | commitdiff | tree |
| 2002-06-26 |
jason | readme for run wrappers
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commit | commitdiff | tree |
| 2002-06-21 |
jason | testfile renamed
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commit | commitdiff | tree |
| 2002-06-21 |
jason | remove debug copyfile
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commit | commitdiff | tree |
| 2002-06-21 |
jason | shorten filename to avoid possible windows long filenames...
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commit | commitdiff | tree |
| 2002-06-19 |
jason | doc fix
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commit | commitdiff | tree |
| 2002-06-18 |
jason | use the determined path to RP when attempting to find...
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commit | commitdiff | tree |
| 2002-06-17 |
jason | return the values as hash of hashes as they are all...
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commit | commitdiff | tree |
| 2002-06-17 |
jason | small doc tweaks and added runnable synopsis
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commit | commitdiff | tree |
| 2002-06-17 |
jason | yn00 wrapper for PAML
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commit | commitdiff | tree |
| 2002-06-15 |
jason | quieter tests unless BIOPERLDEBUG env variable is set
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commit | commitdiff | tree |
| 2002-06-14 |
jason | set verbose to -1
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commit | commitdiff | tree |
| 2002-06-14 |
jason | PAML package -- codeml wrapper and test committed
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commit | commitdiff | tree |
| 2002-05-31 |
jason | doc fix
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commit | commitdiff | tree |
| 2002-05-31 |
jason | handle case when PHYLIP is installed but not clustalw
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commit | commitdiff | tree |
| 2002-05-30 |
jason | handle some weird boundary cases
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commit | commitdiff | tree |
| 2002-05-21 |
jason | update some of the docs
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commit | commitdiff | tree |
| 2002-05-21 |
jason | test value for protdist
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commit | commitdiff | tree |
| 2002-04-22 |
jason | fixes to remove warnings
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commit | commitdiff | tree |
| 2002-04-22 |
jason | fix warnings
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commit | commitdiff | tree |
| 2002-04-18 |
jason | POD fix
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commit | commitdiff | tree |
| 2002-03-22 |
jason | updated tests for v 1.22 problems on main trunk
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commit | commitdiff | tree |
| 2002-03-21 |
jason | simple align has overall percent id method
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commit | commitdiff | tree |
| 2002-03-19 |
jason | cleanup before each run of an application
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commit | commitdiff | tree |
| 2002-03-15 |
jason | merge from branch
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commit | commitdiff | tree |
| 2002-03-15 |
jason | merge changes from branch
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commit | commitdiff | tree |
| 2002-03-15 |
jason | updated to handle tests with SearchIO object returned...
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commit | commitdiff | tree |
| 2002-03-15 |
jason | better synopsis and doc update
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commit | commitdiff | tree |
| 2002-03-14 |
jason | io cleanup called at outset of an analyses -- from...
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commit | commitdiff | tree |
| 2002-03-14 |
jason | merged exe checking from branch
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commit | commitdiff | tree |
| 2002-03-14 |
jason | skip nicely, handle case where server is down
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commit | commitdiff | tree |
| 2002-03-11 |
jason | use SearchIO not Tools::Blast
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commit | commitdiff | tree |
| 2002-03-09 |
jason | turn of clustalw debugging
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commit | commitdiff | tree |
| 2002-03-05 |
jason | unlink test file output
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commit | commitdiff | tree |
| 2002-03-04 |
jason | added ability to dump alignments as well as sequences...
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commit | commitdiff | tree |
| 2002-02-18 |
jason | added example documentation to the POD
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commit | commitdiff | tree |
| 2002-02-18 |
jason | test for cmd line argument where value is a Bio::PrimarySeqI...
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commit | commitdiff | tree |
| 2002-02-18 |
jason | handle cmd line arguments pointing to a Bio::PrimarySeqI...
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commit | commitdiff | tree |
| 2002-02-06 |
jason | params should be appended not overwriting
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commit | commitdiff | tree |
| 2002-01-30 |
jason | verbosity=-1 is same as quiet()
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commit | commitdiff | tree |
| 2002-01-11 |
jason | debug message now uses the debug method
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commit | commitdiff | tree |
| 2002-01-09 |
jason | warn about not using old clustalw
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commit | commitdiff | tree |
| 2002-01-09 |
jason | use the updated PROGRAM exe location information to...
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commit | commitdiff | tree |
| 2002-01-09 |
jason | check to insure defined object before calling ISA
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commit | commitdiff | tree |
| 2001-12-14 |
jason | skip msg updated due to clustal 1.81 bug
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commit | commitdiff | tree |
| 2001-12-14 |
jason | nice message printing when blast is not runnable
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commit | commitdiff | tree |
| 2001-12-14 |
jason | more quiet warning so tests are less chatty
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commit | commitdiff | tree |
| 2001-12-14 |
jason | issue nice message when skipping EMBOSS tests
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commit | commitdiff | tree |
| 2001-12-14 |
jason | skip can print a nice message about why it skipped
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commit | commitdiff | tree |
| 2001-12-14 |
jason | emboss factory behaves more quietly when EMBOSS is...
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commit | commitdiff | tree |
| 2001-11-19 |
jason | EMBOSS more runnable and w/ tests
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commit | commitdiff | tree |
| 2001-08-10 |
jason | don't have clustalw tests fail for 0.9 release
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commit | commitdiff | tree |
| 2001-08-07 |
jason | documentation for retrieve_blast method
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commit | commitdiff | tree |
| 2001-06-15 |
jason | minium identity score required instead of hard value...
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commit | commitdiff | tree |
| 2001-06-14 |
jason | status set to invalid on a failed retrieval
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commit | commitdiff | tree |
| 2001-06-12 |
jason | using private state outside of class, must change the...
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commit | commitdiff | tree |
| 2001-04-30 |
jason | migrated test data files to dir t/data
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commit | commitdiff | tree |
| 2001-04-16 |
jason | Tests pass even when IO::String is not installed
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commit | commitdiff | tree |
| 2001-04-09 |
jason | updated to use ncbi Blast.cgi script rather than blast.cgi
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commit | commitdiff | tree |
| 2001-04-07 |
jason | updated num of tests
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commit | commitdiff | tree |
| 2001-04-07 |
jason | quieter tests when verbose == 0, use tempfile for HTML...
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commit | commitdiff | tree |
| 2001-04-07 |
jason | Pure perl (via HTTP) Remote blast submission and retrieval...
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commit | commitdiff | tree |
| 2001-04-07 |
jason | io was not initialized, meaning tempfiles were not...
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commit | commitdiff | tree |
| 2001-04-07 |
jason | io was not initialized, meaning tempfiles were not...
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commit | commitdiff | tree |
| 2001-02-28 |
jason | properly removing tempfiles
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commit | commitdiff | tree |
| 2001-02-26 |
jason | fixed TCoffee changes to properly output seqs to temp...
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commit | commitdiff | tree |
| 2001-02-19 |
jason | BPlite changes to make BPlite a SeqAnalysisParserI...
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commit | commitdiff | tree |
