2007-05-12 |
jason | TreeIO magic to now automatically move bootstrap values...
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commit | commitdiff | tree |
2007-05-12 |
jason | test for method to move bootstrap values from id values...
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commit | commitdiff | tree |
2007-05-12 |
jason | method to move bootstrap values from id values for...
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commit | commitdiff | tree |
2007-04-26 |
jason | whoops, I made a bug, test if we are in Result before...
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commit | commitdiff | tree |
2007-04-22 |
jason | Handle reports with no ending stanza
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commit | commitdiff | tree |
2007-04-22 |
jason | move some cached-handler code over from blast to help...
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commit | commitdiff | tree |
2007-04-17 |
jason | special MrBayes macro case, cleanup err msg a little...
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commit | commitdiff | tree |
2007-04-13 |
jason | some error checking
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commit | commitdiff | tree |
2007-04-13 |
jason | do not need to include Root.pm
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commit | commitdiff | tree |
2007-03-19 |
jason | correct package name in POD, use the seqname parsed...
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commit | commitdiff | tree |
2007-03-01 |
jason | bug #2220
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commit | commitdiff | tree |
2007-02-06 |
jason | remove errant reference to ENV variable in POD - this...
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commit | commitdiff | tree |
2007-02-02 |
jason | bug #2201
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commit | commitdiff | tree |
2007-01-31 |
jason | Need to split the range up into start/end if you want...
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commit | commitdiff | tree |
2007-01-29 |
jason | POD typo
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commit | commitdiff | tree |
2007-01-26 |
jason | insure that length is positive and location object...
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commit | commitdiff | tree |
2006-12-31 |
jason | indenting fix
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commit | commitdiff | tree |
2006-12-19 |
jason | email address obscuring
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commit | commitdiff | tree |
2006-12-19 |
jason | indented code simplification
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commit | commitdiff | tree |
2006-12-19 |
jason | indentification...
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commit | commitdiff | tree |
2006-12-19 |
jason | specify validate_seq specific to LocatableSeq objects...
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commit | commitdiff | tree |
2006-12-19 |
jason | better detection of error if arrayref is passed in
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commit | commitdiff | tree |
2006-12-12 |
jason | migrate to Test::More; this needs to be tested on system...
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commit | commitdiff | tree |
2006-12-12 |
jason | add features to alignments to allow for better NEXUS...
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commit | commitdiff | tree |
2006-12-12 |
jason | even if this is not quite correct english make spelling...
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commit | commitdiff | tree |
2006-11-25 |
jason | indentation I think, this was old chgs not checked in
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commit | commitdiff | tree |
2006-11-25 |
jason | get rid of cleanup methods for serialize success
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commit | commitdiff | tree |
2006-11-25 |
jason | comment fix
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commit | commitdiff | tree |
2006-11-25 |
jason | doc fix
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commit | commitdiff | tree |
2006-11-25 |
jason | use Comment object
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commit | commitdiff | tree |
2006-11-25 |
jason | weaken refs to avoid circular references
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commit | commitdiff | tree |
2006-11-09 |
jason | remove unecessary use lib
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commit | commitdiff | tree |
2006-11-07 |
jason | insure that STH is finish-ed before returing from these...
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commit | commitdiff | tree |
2006-11-07 |
jason | More API doc in the SYNOPSIS
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commit | commitdiff | tree |
2006-11-03 |
jason | test model num as well in this example
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commit | commitdiff | tree |
2006-11-03 |
jason | test for trees in the model result object for an M0...
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commit | commitdiff | tree |
2006-10-19 |
jason | indentation madness
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commit | commitdiff | tree |
2006-10-19 |
jason | small POD fixes
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commit | commitdiff | tree |
2006-10-19 |
jason | dblink fix to keep version and accession separate
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commit | commitdiff | tree |
2006-10-19 |
jason | tests for dblink fixes
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commit | commitdiff | tree |
2006-10-19 |
jason | simplified dblink parsing and setting, code indenting
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commit | commitdiff | tree |
2006-10-19 |
jason | indenting code and init DBlink all at once
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commit | commitdiff | tree |
2006-10-19 |
jason | more tests for dblinks
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commit | commitdiff | tree |
2006-10-19 |
jason | typo in new function initing wrong field, copy+paste...
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commit | commitdiff | tree |
2006-10-10 |
jason | POD fix
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commit | commitdiff | tree |
2006-10-10 |
jason | POD fix: format is GFF version is 3
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commit | commitdiff | tree |
2006-10-01 |
jason | the API has changed... binomial_name --> binomial
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commit | commitdiff | tree |
2006-09-29 |
jason | deal with WU-BLAST weird case
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commit | commitdiff | tree |
2006-09-28 |
jason | API changed and this is no longer a Taxonomy::Node...
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commit | commitdiff | tree |
2006-09-03 |
jason | hackily parse score and associate it with a tree
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commit | commitdiff | tree |
2006-08-30 |
jason | be explicit
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commit | commitdiff | tree |
2006-08-16 |
jason | move debug init into BEGIN otherwise it isn't initialized...
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commit | commitdiff | tree |
2006-08-15 |
jason | fix return type - thanks to Ryan Morin @ BCGSC.ca
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commit | commitdiff | tree |
2006-06-20 |
jason | Ryan's fix to deal with inclusion of internal stops...
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commit | commitdiff | tree |
2006-06-14 |
jason | Ryan Golhar's fixes for 3.15 parsing
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commit | commitdiff | tree |
2006-06-08 |
jason | revert to non-forced haploid population call
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commit | commitdiff | tree |
2006-06-07 |
jason | I *HATE* overloaded ""- it is a pain when you expect...
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commit | commitdiff | tree |
2006-06-07 |
jason | ticky-tack changes
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commit | commitdiff | tree |
2006-06-07 |
jason | cleanup doc versus implementation consistency
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commit | commitdiff | tree |
2006-06-07 |
jason | silence failures, but really I don't think this module...
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commit | commitdiff | tree |
2006-06-07 |
jason | update test count and skip two tests that are not currently...
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commit | commitdiff | tree |
2006-06-07 |
jason | a graceful death
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commit | commitdiff | tree |
2006-06-07 |
jason | a better death
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commit | commitdiff | tree |
2006-06-07 |
jason | fix mistake in ID names being identical
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commit | commitdiff | tree |
2006-06-07 |
jason | Fix RepeatMasking - features were flipped 1/2
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commit | commitdiff | tree |
2006-06-07 |
jason | email obscuring
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commit | commitdiff | tree |
2006-06-07 |
jason | BFS and DFS searching properly
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commit | commitdiff | tree |
2006-06-07 |
jason | rejigger sort order so it doesn't require query to...
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commit | commitdiff | tree |
2006-06-06 |
jason | need to 'use' module for using module
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commit | commitdiff | tree |
2006-05-20 |
jason | drop debug and reformat indents
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commit | commitdiff | tree |
2006-05-17 |
jason | bug #1989 - don't reset the primary_id if it is a GI...
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commit | commitdiff | tree |
2006-05-17 |
jason | remove redundancy in collection accession numbers
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commit | commitdiff | tree |
2006-05-01 |
jason | obfuscation is fun
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commit | commitdiff | tree |
2006-04-27 |
jason | bug #1986 and allow SREB to be swapped back into IteratedREB
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commit | commitdiff | tree |
2006-04-21 |
jason | further removing myself from direct responsibility...
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commit | commitdiff | tree |
2006-04-21 |
jason | bug #1983, parse NEB and BEB sites from PAML 3.15 properly...
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commit | commitdiff | tree |
2006-04-03 |
jason | paml 3.15 test
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commit | commitdiff | tree |
2006-04-03 |
jason | PAML 3.15 parsing supported
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commit | commitdiff | tree |
2006-04-03 |
jason | PAML 3.15 tests
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commit | commitdiff | tree |
2006-04-03 |
jason | remove use lib stmt and comments
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commit | commitdiff | tree |
2006-04-03 |
jason | simplify covoluted logic
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commit | commitdiff | tree |
2006-03-06 |
jason | pod typos and sortby default
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commit | commitdiff | tree |
2006-02-15 |
jason | tabnabbit- be fixed
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commit | commitdiff | tree |
2006-02-15 |
jason | typo
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commit | commitdiff | tree |
2006-02-15 |
jason | synopsis snafu
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commit | commitdiff | tree |
2006-02-14 |
jason | make synopsis runnable, since this is needed on initial...
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commit | commitdiff | tree |
2006-02-11 |
jason | added F* which was present but not listed here
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commit | commitdiff | tree |
2006-02-11 |
jason | use internal warn instead of STDERR
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commit | commitdiff | tree |
2006-02-11 |
jason | ID and SCORE are settable at init time
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commit | commitdiff | tree |
2006-02-11 |
jason | allow shorthand u and p
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commit | commitdiff | tree |
2006-01-15 |
jason | missing :
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commit | commitdiff | tree |
2006-01-11 |
jason | set gff3_flag properly
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commit | commitdiff | tree |
2006-01-02 |
jason | when reporting the pattern mismatch, list it out with...
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commit | commitdiff | tree |
2005-12-30 |
jason | taxa->taxon
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commit | commitdiff | tree |
2005-12-20 |
jason | bug #1923
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commit | commitdiff | tree |
2005-11-30 |
jason | Jason gets bad marks in spelling. Jason gets bad marks in spelling.
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commit | commitdiff | tree |
2005-11-25 |
jason | POD fix?
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commit | commitdiff | tree |
2005-11-25 |
jason | create nodes of the same type as the existing nodes...
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commit | commitdiff | tree |
2005-11-25 |
jason | only write NHX block when there is something to write
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commit | commitdiff | tree |
2005-11-25 |
jason | allow newline separated clustalW dendogram style output
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commit | commitdiff | tree |