| 2011-04-12 |
Chris Fields | squash local warnings
|
commit | commitdiff | tree |
| 2011-04-12 |
Chris Fields | default to memory if the adaptor is SQLite
|
commit | commitdiff | tree |
| 2011-04-07 |
Chris Fields | enable fast loading with namespaces; empty tables were...
|
commit | commitdiff | tree |
| 2011-04-07 |
Chris Fields | make sure short params don't conflict, make them explicit
|
commit | commitdiff | tree |
| 2011-04-07 |
Chris Fields | comment out overzealous error checking, which caused...
|
commit | commitdiff | tree |
| 2011-04-07 |
Chris Fields | fix test fail from bad file name
|
commit | commitdiff | tree |
| 2011-04-06 |
Chris Fields | Allow falling back to any strigified Bio::AnnotationI...
|
commit | commitdiff | tree |
| 2011-04-06 |
Chris Fields | * add tests that check trucated sequence length matches...
|
commit | commitdiff | tree |
| 2011-04-06 |
Chris Fields | * 'use vars' -> our
|
commit | commitdiff | tree |
| 2011-04-05 |
Chris Fields | moved functions to Bio::SearchIO so they can be used...
|
commit | commitdiff | tree |
| 2011-04-04 |
Chris Fields | sizes() now allows for a Bio::Restriction::EnzymeI...
|
commit | commitdiff | tree |
| 2011-04-04 |
Chris Fields | rework to optimize a bit, again for bug #3172
|
commit | commitdiff | tree |
| 2011-04-04 |
Chris Fields | potential fix for bug #3172, but needs to be checked...
|
commit | commitdiff | tree |
| 2011-04-04 |
Chris Fields | Revert "test hook again (anyone getting annoyed by...
|
commit | commitdiff | tree |
| 2011-04-04 |
Chris Fields | test hook again (anyone getting annoyed by this yet?)
|
commit | commitdiff | tree |
| 2011-04-04 |
Chris Fields | use residue count for calcs instead of length, fixes...
|
commit | commitdiff | tree |
| 2011-04-04 |
Chris Fields | test hook
|
commit | commitdiff | tree |
| 2011-04-04 |
Chris Fields | test hook
|
commit | commitdiff | tree |
| 2011-04-04 |
Chris Fields | test hook, fingers crossed
|
commit | commitdiff | tree |
| 2011-04-04 |
Chris Fields | add patch that fixes #3190, courtesy Ali Walsh
|
commit | commitdiff | tree |
| 2011-03-31 |
Chris Fields | test hook again
|
commit | commitdiff | tree |
| 2011-03-31 |
Chris Fields | test hook again
|
commit | commitdiff | tree |
| 2011-03-31 |
Chris Fields | test post-receive again
|
commit | commitdiff | tree |
| 2011-03-29 |
Chris Fields | retest hook to make sure it works, refs #3189
|
commit | commitdiff | tree |
| 2011-03-29 |
Chris Fields | test post-receive hook, post-SSL
|
commit | commitdiff | tree |
| 2011-03-29 |
Chris Fields | retest using https post-rec hook: refs #3181, @2.5
|
commit | commitdiff | tree |
| 2011-03-29 |
Chris Fields | remove comment: refs #3181, @2.5
|
commit | commitdiff | tree |
| 2011-03-29 |
Chris Fields | add tests: refs #3181
|
commit | commitdiff | tree |
| 2011-03-29 |
Chris Fields | add tests for bug 3181
|
commit | commitdiff | tree |
| 2011-03-29 |
Chris Fields | revert some changes from the global redmine conversion
|
commit | commitdiff | tree |
| 2011-03-17 |
Chris Fields | Revert "volatile data broke test". Remote database...
|
commit | commitdiff | tree |
| 2011-03-17 |
Chris Fields | update manifest
|
commit | commitdiff | tree |
| 2011-03-13 |
Chris Fields | within_element works better
|
commit | commitdiff | tree |
| 2011-03-13 |
Chris Fields | reduce warning message, was overly verbose and gave...
|
commit | commitdiff | tree |
| 2011-03-13 |
Chris Fields | fix CUTG skipped test count
|
commit | commitdiff | tree |
| 2011-03-13 |
Chris Fields | volatile data broke test
|
commit | commitdiff | tree |
| 2011-03-13 |
Chris Fields | make exception messages match whether one has Error...
|
commit | commitdiff | tree |
| 2011-03-13 |
Chris Fields | a bit more perl 5.12 warning squashing
|
commit | commitdiff | tree |
| 2011-03-13 |
Chris Fields | use Test::Exception methods exported from Bio::Root...
|
commit | commitdiff | tree |
| 2011-03-13 |
Chris Fields | squash XML::Writer issue, still get a warning though
|
commit | commitdiff | tree |
| 2011-03-13 |
Chris Fields | use 'ace' as the default source, make sure that undef...
|
commit | commitdiff | tree |
| 2011-03-13 |
Chris Fields | commented out accidentally uncommented code
|
commit | commitdiff | tree |
| 2011-03-13 |
Chris Fields | squash warning
|
commit | commitdiff | tree |
| 2011-03-12 |
Chris Fields | only add tags if the value is defined
|
commit | commitdiff | tree |
| 2011-03-12 |
Chris Fields | please use a source tag
|
commit | commitdiff | tree |
| 2011-03-11 |
Chris Fields | test redmine post-receive hook
|
commit | commitdiff | tree |
| 2011-03-11 |
Chris Fields | test redmine
|
commit | commitdiff | tree |
| 2011-03-11 |
Chris Fields | not using subversion
|
commit | commitdiff | tree |
| 2011-03-04 |
Chris Fields | add tests and a few other fixes to account for cut...
|
commit | commitdiff | tree |
| 2011-03-04 |
Chris Fields | fix for bad condition check, via Elia Stupka
|
commit | commitdiff | tree |
| 2011-02-27 |
Chris Fields | -tag and -attribute are synonyms with SeqFeatureI
|
commit | commitdiff | tree |
| 2011-02-23 |
Chris Fields | actually have an error message
|
commit | commitdiff | tree |
| 2011-02-14 |
Chris Fields | Merge branch 'master' of github.com:bioperl/bioperl...
|
commit | commitdiff | tree |
| 2011-02-14 |
Chris Fields | checked each line for definedness, not falseness
|
commit | commitdiff | tree |
| 2011-01-31 |
Chris Fields | translate() changes
|
commit | commitdiff | tree |
| 2011-01-31 |
Chris Fields | consolidate tests, fix exception string
|
commit | commitdiff | tree |
| 2011-01-31 |
Chris Fields | correct test count
|
commit | commitdiff | tree |
| 2011-01-31 |
Chris Fields | can have a -string option as well
|
commit | commitdiff | tree |
| 2011-01-31 |
Chris Fields | future-proof test
|
commit | commitdiff | tree |
| 2011-01-31 |
Chris Fields | [bug 3165] quick fix for fastq indexing, this parser...
|
commit | commitdiff | tree |
| 2011-01-31 |
Chris Fields | squash minor warning
|
commit | commitdiff | tree |
| 2011-01-31 |
Chris Fields | [bug RT#58492] small synopsis fix, update->store
|
commit | commitdiff | tree |
| 2011-01-31 |
Chris Fields | [bug RT#54590] add some docs on the -blasttype parameter
|
commit | commitdiff | tree |
| 2011-01-31 |
Chris Fields | RT#47704: recursively remove code refs for any SeqFeatureI
|
commit | commitdiff | tree |
| 2011-01-18 |
Chris Fields | rectify a conflict in behavior between PrimarySeq:...
|
commit | commitdiff | tree |
| 2011-01-11 |
Chris Fields | Merge branch 'master', remote branch 'origin'
|
commit | commitdiff | tree |
| 2011-01-03 |
Chris Fields | tweak SeqIO to catch odd file types, add generic SeqIO...
|
commit | commitdiff | tree |
| 2010-12-23 |
Chris Fields | deal with OX lines and TaxIDs (patch courtesy Jacob...
|
commit | commitdiff | tree |
| 2010-11-20 |
Chris Fields | add length so this matches to_string documentation...
|
commit | commitdiff | tree |
| 2010-11-11 |
Chris Fields | add Error as a recommends, but indicate it as very...
|
commit | commitdiff | tree |
| 2010-11-11 |
Chris Fields | fix test that relied on the highly optional Error.pm
|
commit | commitdiff | tree |
| 2010-11-10 |
Chris Fields | use throw() as a class method, since next_token() is...
|
commit | commitdiff | tree |
| 2010-11-09 |
Chris Fields | rm $Id
|
commit | commitdiff | tree |
| 2010-11-09 |
Chris Fields | fixes to deal with changes in sort order of nodes due...
|
commit | commitdiff | tree |
| 2010-11-09 |
Chris Fields | Revert "Merge branch 'topic/tree_dbsqlite_memoryfix...
|
commit | commitdiff | tree |
| 2010-11-09 |
Chris Fields | Merge branch 'topic/gjuggler_tree_fixes'
|
commit | commitdiff | tree |
| 2010-11-09 |
Chris Fields | add simple test for number of nodes returned
|
commit | commitdiff | tree |
| 2010-11-08 |
Chris Fields | remove given/when :(
|
commit | commitdiff | tree |
| 2010-11-08 |
Chris Fields | kill our reliance on Switch, but add a temp reliance...
|
commit | commitdiff | tree |
| 2010-11-08 |
Chris Fields | Merge branch 'master' of https://github.com/gjuggler...
|
commit | commitdiff | tree |
| 2010-11-05 |
Chris Fields | check for definedness prior to calling methods
|
commit | commitdiff | tree |
| 2010-11-03 |
Chris Fields | display_name should be settable, like name()
|
commit | commitdiff | tree |
| 2010-10-27 |
Chris Fields | even more DBFetch changes, yay!
|
commit | commitdiff | tree |
| 2010-10-27 |
Chris Fields | more DBFetch URL changes (might be nice to centralize...
|
commit | commitdiff | tree |
| 2010-10-27 |
Chris Fields | future-proof a test
|
commit | commitdiff | tree |
| 2010-10-27 |
Chris Fields | URL changed for DBFetch
|
commit | commitdiff | tree |
| 2010-10-27 |
Chris Fields | [bug 3148] URL change at DBFetch was the culprit; default...
|
commit | commitdiff | tree |
| 2010-10-24 |
Chris Fields | [bug 3148] switch default to "expasy" until we can...
|
commit | commitdiff | tree |
| 2010-10-15 |
Chris Fields | fix get_count so it returns the actual number of IDs...
|
commit | commitdiff | tree |
| 2010-10-13 |
Chris Fields | catch using simple string instead of array ref for...
|
commit | commitdiff | tree |
| 2010-10-11 |
Chris Fields | [bug 3133] add some ducmentation on the quality_header...
|
commit | commitdiff | tree |
| 2010-10-11 |
Chris Fields | [bug 3145] fix courtesy Aaron Goodman. AXT parsing...
|
commit | commitdiff | tree |
| 2010-09-22 |
Chris Fields | update MANIFEST.SKIP
|
commit | commitdiff | tree |
| 2010-09-22 |
Chris Fields | update manifest
|
commit | commitdiff | tree |
| 2010-09-06 |
Chris Fields | remove IO::String dependency
|
commit | commitdiff | tree |
| 2010-09-02 |
Chris Fields | add check for undef in array of IDs
|
commit | commitdiff | tree |
| 2010-08-25 |
Chris Fields | add primary_id as a constructor parameter
|
commit | commitdiff | tree |
| 2010-08-23 |
Chris Fields | remove Id tags (strangely not removed from the last...
|
commit | commitdiff | tree |
| 2010-08-23 |
Chris Fields | more docs, for esummary
|
commit | commitdiff | tree |
| 2010-08-23 |
Chris Fields | more docs
|
commit | commitdiff | tree |
