2008-12-24 19:01 cjfields
* [r15261] Changes, README: Updates for RC1
2008-12-24 06:53 cjfields
* [r15260] Build.PL: remove Microarray deps
2008-12-24 06:04 cjfields
* [r15258] t/RemoteDB/HIV/HIVQuery.t: Small fix for tests JIC there
is a network error
2008-12-24 05:27 cjfields
* [r15257] Bio/Biblio/IO.pm, Bio/DB/HIV.pm,
Bio/DB/HIV/HIVQueryHelper.pm, Bio/DB/Query/HIVQuery.pm,
Bio/DB/SeqFeature/Store/DBI/mysql.pm,
Bio/DB/SeqFeature/Store/FeatureFileLoader.pm, Bio/FeatureIO.pm,
Bio/Index/Abstract.pm, Bio/LiveSeq/IO/Loader.pm,
Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm,
Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm, Bio/Root/IO.pm,
Bio/SearchIO.pm, Bio/SeqFeature/SiRNA/Oligo.pm,
Bio/SeqFeature/SiRNA/Pair.pm, Bio/SeqIO.pm, Bio/SeqIO/agave.pm,
Bio/SeqIO/phd.pm, Bio/SeqIO/qual.pm, Bio/SeqIO/scf.pm,
Bio/Structure/IO.pm, Bio/Tools/Lucy.pm, Bio/Tools/SiRNA.pm,
Bio/Tools/SiRNA/Ruleset/saigo.pm,
Bio/Tools/SiRNA/Ruleset/tuschl.pm, DEPENDENCIES, INSTALL,
maintenance/dependencies.pl, maintenance/deprecated.pl,
t/RemoteDB/HIV/HIV.t, t/RemoteDB/HIV/HIVQuery.t,
t/Tools/rnamotif.t: Sync branch with trunk
2008-12-24 05:26 cjfields
* [r15256] Bio/Microarray/Tools/MitoChipV2Parser.pm,
Bio/Microarray/Tools/ReseqChip.pm,
t/Microarray/Tools/ReseqChip.t: Remove Bio::Microarray from
branch (still in development on trunk). May return later if API
stabilizes
2008-12-24 05:21 cjfields
* [r15255] Bio/Graph: Remove (merge didn't remove this for some
reason)
2008-12-24 05:20 cjfields
* [r15254] Bio/Tools/BPlite/HSP.pm, Bio/Tools/BPlite/Iteration.pm,
Bio/Tools/BPlite/Sbjct.pm: Remove (merge didn't remove this for
some reason)
2008-12-22 21:51 cjfields
* [r15231] Bio/DB/NCBIHelper.pm, Bio/DB/Qual.pm,
Bio/DB/SeqFeature/Store/FeatureFileLoader.pm,
Bio/Factory/SeqAnalysisParserFactory.pm, Bio/Root/Build.pm,
Bio/Root/Version.pm, Bio/Search/Iteration/GenericIteration.pm,
Bio/Search/Result/BlastResult.pm,
Bio/Search/Result/CrossMatchResult.pm,
Bio/SeqFeature/Annotated.pm, Bio/Tools/ERPIN.pm,
Bio/Tools/Infernal.pm, Bio/Tools/Phylo/PAML.pm,
Bio/Tools/RNAMotif.pm, Bio/Tools/Run/RemoteBlast.pm,
Bio/Tools/Run/StandAloneBlast.pm,
Bio/Tools/Run/StandAloneNCBIBlast.pm,
Bio/Tools/Run/StandAloneWUBlast.pm, Build.PL, DEPRECATED,
examples/tk/hitdisplay.pl, maintenance/deprecated.pl,
t/Tools/Run/StandAloneBlast.t: sync trunk with branch
2008-12-20 05:44 cjfields
* [r15214] .: Created branch branch-1-6.
2008-12-20 05:07 cjfields
* [r15213] 5.6.1 is min perl version required for all core modules
now
2008-12-19 05:47 cjfields
* [r15212] update NAMES
2008-12-19 03:41 cjfields
* [r15211] small typo
2008-12-18 09:26 heikki
* [r15208] skip right number of tests needing the network
2008-12-18 05:42 cjfields
* [r15207] typo
2008-12-18 05:33 cjfields
* [r15206] [bug 2714]
* patches to update Bio::DB::HIV and related (Mark Jensen)
2008-12-17 03:05 cjfields
* [r15195] fix test number
2008-12-17 03:03 cjfields
* [r15194] update Test::Warn (fixes Qual.t test problems with
warnings_like)
2008-12-17 00:07 sendu
* [r15193] no longer assumes added order of ids in tests
2008-12-17 00:06 sendu
* [r15192] passing $1 is bad in perl 5.10? - fixed
2008-12-16 20:26 cjfields
* [r15191] missed one
2008-12-16 20:18 cjfields
* [r15190] EUtilities remote tests back online (simple tests only)
2008-12-16 20:17 cjfields
* [r15189] EUtilities remote tests back online (simple tests only)
2008-12-16 17:42 sendu
* [r15180] added POD docs
2008-12-16 16:55 sendu
* [r15179] new transfac pro database parser
2008-12-16 12:48 sendu
* [r15178] new test method test_output_dir(), a wrapper around
Temp::File::tempdir
2008-12-16 07:49 jason
* [r15177] skip test count updated for instances when SVG::Graph is
not installed
2008-12-16 05:51 jason
* [r15176] parse DBlinks now supported
2008-12-16 05:11 cjfields
* [r15175] You must actually test data if you want this module to
be included in the release (this now fails two tests)
2008-12-16 05:10 cjfields
* [r15174] Don't use print! Changing to $self->debug or commenting
out
2008-12-16 04:58 jason
* [r15173] indentation and formatting only
2008-12-16 04:50 cjfields
* [r15172] Bio::Graph deprecated in 1.6
2008-12-16 03:28 cjfields
* [r15171] stifle warnings when passing string instead of integer
2008-12-16 03:25 cjfields
* [r15170] hash ref, not array ref
2008-12-16 03:24 cjfields
* [r15169] [bug 2637]
* Bio::DB::HIV and related need schema file installed along with
the modules
2008-12-16 03:19 cjfields
* [r15168] [bug 2637]
* tests (HIVQuery may be problematic so will need to keep an eye
on it)
2008-12-16 03:17 cjfields
* [r15167] [bug 2637]
* forgot one module!
* some fixes for tests: little known fact, warnings are good!
2008-12-16 03:17 cjfields
* [r15166] [bug 2637]
* forgot one module!
* some fixes for tests: little known fact, warnings are good!
2008-12-15 20:42 cjfields
* [r15165] [bug 2637]
* New modules for accessing HIV Sequence Database
* Thanks to Mark Jensen for the code!
* Tests to be committed soon
2008-12-15 19:30 cjfields
* [r15164] [bug 2712]
* allow unread lines (passes tests)
2008-12-15 18:39 cjfields
* [r15163] scores
2008-12-15 18:13 cjfields
* [r15162] remaining tests for Bio::Tool::EUtilities
2008-12-15 18:10 cjfields
* [r15161] more test data
2008-12-15 18:09 cjfields
* [r15160] Updates:
* simplify data dumping/printing (everything implements
to_string, calls as needed)
* round out the print_* methods (DocSums, LinkSets, LinkInfo,
FieldInfo, GlobalQuery, all)
2008-12-15 17:49 sendu
* [r15159] Bio::Map extended to model transcription factors and
their binding sites
2008-12-15 11:08 sendu
* [r15158] minor comment correntions
2008-12-14 17:55 jason
* [r15157] another example BLAST
2008-12-13 06:14 cjfields
* [r15156] initial batch of EUtilParameters tests
2008-12-13 01:14 cjfields
* [r15155] einfo tests
2008-12-12 21:33 cjfields
* [r15154] some EUtilities tests (parsing from files)
2008-12-12 21:32 cjfields
* [r15153] some test data for Bio::Tools::EUtilities
2008-12-12 21:29 cjfields
* [r15152] updates to EUtilities (getting ready for docs, tests,
etc)
2008-12-12 21:28 cjfields
* [r15151] Move EUtilParameters to Tools (seems more appropriate)
2008-12-12 13:47 sendu
* [r15150] new parser for the Match program from transfac
2008-12-12 10:52 heikki
* [r15149] Do not use "return undef" unless you really know that it
is necessary. Use plain "return". If you know what you are doing
and use "return undef", mark it: "# intended return undef"
2008-12-11 22:05 scain
* [r15148] Adding the postgres adaptor for SeqFeature::Store;
doesn't pass tests yet!
2008-12-11 21:49 cjfields
* [r15147] fix for bug when getting cached response with filename
or callback (prevents resubing the request)
2008-12-11 19:17 cjfields
* [r15146] small pointer to wiki page (will update along with wiki
closer to release)
2008-12-11 19:16 cjfields
* [r15145] small update
2008-12-11 19:16 cjfields
* [r15144] updates
2008-12-11 19:15 cjfields
* [r15143] return, not 'return undef'
2008-12-11 18:58 cjfields
* [r15142] return, not 'return undef'
2008-12-11 05:34 cjfields
* [r15141] [bug 2699]
* skip off by two
2008-12-11 05:30 cjfields
* [r15140] [bug 2699]
* addressing Heikki's comments
2008-12-11 05:02 cjfields
* [r15139] [bug 2707]
* temporarily quotemeta file names for BLAST output files
2008-12-10 18:27 lstein
* [r15138] added simple feature deletion script, take 2
2008-12-10 18:26 lstein
* [r15137] added simple feature deletion script
2008-12-10 16:52 cjfields
* [r15136] Removing from HEAD (deprecated for 1.6)
2008-12-10 16:46 cjfields
* [r15135] mini pod fix
2008-12-10 14:10 thm09830
* [r15134] use superclasses initialization and argument
processing/attribute setting as suggested in styleguide
2008-12-10 12:51 thm09830
* [r15133] Test/Example Data for ReseqChip
2008-12-10 12:49 thm09830
* [r15132] Providing Testscript for ReseqChip
2008-12-10 12:46 thm09830
* [r15131] Bug Fixes, New Feature: different Fasta Files (e.g.
comprising Basecalls with different Quality Thresholds) for
analyzing Insertion and Substitutions
2008-12-10 05:51 cjfields
* [r15130] update deprecation list
2008-12-10 05:48 cjfields
* [r15129] remove Bio::Graphics (separate package now)
2008-12-10 05:47 cjfields
* [r15128] [bug 2637]
* Add in Mark Jensen (working on adding Mark's Bio::DB::HIV
modules, which come with tests)
2008-12-10 01:27 cjfields
* [r15127] Remove dependencies for Bio::Graphics and deprecated
modules
2008-12-09 23:04 lstein
* [r15126] fixed issue of score and phase fields disappearing from
the first part of a multi-child feature
2008-12-09 21:46 lstein
* [r15125] removed Bio::Graphics itself
2008-12-09 06:03 cjfields
* [r15124] Squash warning
2008-12-09 06:02 cjfields
* [r15123] diag() only on verbose
2008-12-09 03:32 cjfields
* [r15122] Fix last loop tests, move some to can_ok
2008-12-09 03:19 cjfields
* [r15121] Modify to test new temp classes and ensure that added
methods do not pollute original namespace
2008-12-09 03:11 cjfields
* [r15120] update Mauricio's email
2008-12-09 02:08 lstein
* [r15119] Bio::Graphics has become its own module; latest version
is uploaded to CPAN
2008-12-08 21:55 scain
* [r15118] added my info
2008-12-08 21:35 dave_messina
* [r15117] adding myself to author list
2008-12-08 20:12 bosborne
* [r15116] I'm a core dev
2008-12-08 20:00 cjfields
* [r15115] Update Roy's email
2008-12-08 19:54 cjfields
* [r15114] Roy's email (and bioperl.org not bioperl.edu)
2008-12-08 19:51 cjfields
* [r15113] Updated emails
2008-12-08 18:12 sendu
* [r15112] BioperlTest -> Bio::Root::Test
2008-12-08 17:45 sendu
* [r15111] gain-of-function changes for mysql implementation only:
features are searchable by source, and you can avoid freezing
objects to the db for size and speed benefits; was unable to get
any feedback from the maintainer about this change - maintainer
may revert if this is undesireable
2008-12-08 17:31 sendu
* [r15110] new ability to define what is consered an overlap
2008-12-08 17:25 sendu
* [r15109] ModuleBuildBioperl -> Bio::Root::Build
2008-12-08 13:41 sendu
* [r15104] evalue now parsed and set as score
2008-12-07 15:36 cjfields
* [r15103] [bug 2699]
* Fix paths for Bio::DB::SeqFeature tests
* Restore BDB tests
2008-12-06 18:33 jason
* [r15097] demonstrate with a valid 'site_model' as 'codons' rather
than unimplemented 'syn'
2008-12-06 11:49 dave_messina
* [r15096] forgot a linebreak. Oh the irony...
2008-12-06 11:01 dave_messina
* [r15095] improved message for genemap read error to suggest
possible solution; also added test for catching this error.
2008-12-05 04:40 cjfields
* [r15094] Need to retrieve the tree for output
2008-12-05 02:46 cjfields
* [r15093] [bug 2450]
* aln-specific annotation in SimpleAlign->annotation
* seq-specific annotation in SimpleAlign's FeatureHolderI (and
tied to related sequence)
* Bio::Annotation::Target (which was DBLink-y) now inherits
DBLink (so we now have a DBLink that's RangeI)
* tests for above
2008-12-04 19:02 cjfields
* [r15092] Make Target a true DBLink
2008-12-04 12:00 heikki
* [r15091] interpro XML parser tries to assign "NA" into a numeric
"score" field. There does not seem to be an easy way to fix this
in there, so exluding all letters_only values to score()
2008-12-04 10:52 heikki
* [r15090] remove t/sequencetrace.t and add missing method tests
into t/SeqIO/scf (could be split into IO and storage class
spesific tests)
2008-12-04 04:35 cjfields
* [r15089] Directory is no longer needed (Heikki split this up into
LocalDB and RemoteDB)
2008-12-04 02:49 bosborne
* [r15088] svn propset Id
2008-12-04 02:48 bosborne
* [r15087] Add script that demonstrates reverse_tranlate_best()
2008-12-04 02:32 lstein
* [r15086] fixed default of ##index-subfeatures to true so that it
behaves the way that it is documented to work
2008-12-03 22:34 cjfields
* [r15085] add force_nse tests
2008-12-03 22:31 cjfields
* [r15084] leave ID undefined if it isn't present, but allow the
NSE to be created if forced (this may need revisiting in the
future)
2008-12-03 21:31 heikki
* [r15083] reorganising tests by group (5: rest)
2008-12-03 14:14 bosborne
* [r15082] Clarify what frame is used by count_codons
2008-12-03 13:34 cjfields
* [r15081] Remove files accidently added from last commit
2008-12-03 06:37 cjfields
* [r15080] Reorganize Tools tests (needs some more splitting)
2008-12-03 06:26 cjfields
* [r15079] Remove (tests are redundant, in Consed.t)
2008-12-03 06:17 cjfields
* [r15078] Merge tests and remove redundant file
2008-12-03 06:15 cjfields
* [r15077] Update test count
2008-12-03 06:13 cjfields
* [r15076] Merge tests
2008-12-03 05:56 cjfields
* [r15075] Remove redundant file
2008-12-03 04:57 bosborne
* [r15074] Add method that finds the most common codons for the
aa's, uses those to reverse-translate a nucleotide sequence
2008-12-03 03:40 cjfields
* [r15073] Remove old files
2008-12-03 03:34 cjfields
* [r15072] Start Tools move
2008-12-03 03:21 cjfields
* [r15071] small updates:
* fix svn tags
* add eval test to svggraph (failing for some reason)
* bsml test count was wrong
2008-12-03 03:05 cjfields
* [r15070] forgot to increment test count
2008-12-03 02:49 cjfields
* [r15069] Add a couple of tests for seq_id (small but significant
inconsistency btwn blast and blast_pull). Should rectify this
prior to 1.6.
2008-12-02 22:09 cjfields
* [r15068] [bug 2450]
* add -source
* more tests
2008-12-02 21:46 cjfields
* [r15067] [bug 2450]
* completely refactor stockholm to use a generic alignment
Handler object (worked better than I thought, should be
applicable to other formats)
* now captures sequence-based annotation
* now working on refactoring write_aln to get correct output
2008-12-02 21:44 cjfields
* [r15066] [bug 2450]
* more parameters for the constructor
* if using NSE for a lookup, one should use the NSE for storing
the name
2008-12-02 21:41 cjfields
* [r15065] [bug 2450]
* add parameter for passing in named meta tags as hash ref to the
constructor
2008-12-02 21:40 cjfields
* [r15064] some pod updates
2008-12-02 21:38 cjfields
* [r15063] [bug 2450]
* include version in NSE (Rfam/Pfam now does this)
2008-12-02 20:58 cjfields
* [r15062] fix erroneously renamed stockholm tests
2008-12-02 15:24 bosborne
* [r15061] Correct typos, runnable Synopsis
2008-12-02 13:40 cjfields
* [r15060] small pod fix
2008-12-02 08:24 heikki
* [r15059] reorganising tests by group (4: Map)
2008-12-02 08:24 heikki
* [r15058] reorganising tests by group (4: Map)
2008-12-02 08:20 heikki
* [r15057] reorganising tests by group (3: Root)
2008-12-02 08:02 heikki
* [r15056] reorganising tests by group (2: TreeIO plugins)
2008-12-02 07:37 heikki
* [r15055] reorganising tests by group (2: Tree)
2008-12-02 06:46 jason
* [r15054] XML::DOM dependancy
2008-12-02 04:32 heikki
* [r15053] reorganising tests by group (1)
2008-12-01 08:47 heikki
* [r15052] make SYNOPSIS code to compile
2008-11-30 22:19 cjfields
* [r15051] silence GuessSeqFormat.t warnings (not sure if old
version was even legal Stockholm format)
2008-11-30 21:04 bosborne
* [r15050] Bug 2336, test length of each sequence in tmp.fst
2008-11-29 19:45 dave_messina
* [r15049] adding more diagnostic messages to t/SeqIO/intepro.t
2008-11-28 13:24 dave_messina
* [r15048] verbose mistakenly left on in PrimarySeq->new, which was
causing RootIO to be verbose about its tempfile handling after. I
noticed this from running SeqIO/largefasta.t. Reverting r15026,
wherein Heikki went after the same problem in
Bio::Seq::LargeLocatableSeq. Also minor cleanup in
t/SeqIO/largefasta.t and t/EUtilities.t
2008-11-28 10:00 dave_messina
* [r15047] switching EUtilities.t over to BioperlTest style test
initialization. Was using DEBUG flag to choose whether to run
network tests.
2008-11-28 06:00 cjfields
* [r15046] rearrange to avoid unnecessary warnings
2008-11-28 05:58 cjfields
* [r15045] Add warning for missing data (real bug)
2008-11-28 05:47 cjfields
* [r15044] hash ref, not a hash
2008-11-28 05:42 cjfields
* [r15043] test file name and test # correction
2008-11-28 05:40 cjfields
* [r15042] correct test file name
2008-11-28 05:38 cjfields
* [r15041] '::', not ':'
2008-11-28 05:33 cjfields
* [r15040] rename (recursive tests think this is a test file)
2008-11-28 05:23 cjfields
* [r15039] recurse into test subdirectories (means any non-test
filed in t/ must not end in *.t!)
2008-11-28 04:51 cjfields
* [r15038] remove redundant copy
2008-11-28 04:50 cjfields
* [r15037] move into directory structure
2008-11-28 04:38 cjfields
* [r15036] move into directory structure (DaveM++)
2008-11-27 16:48 dave_messina
* [r15035] Big reorganization of SeqIO tests. Now each flavor of
SeqIO has its own test file (if it didn't already). Where
possible, test data files were renamed test.<module> e.g.
test.fasta so that it's easy to locate them and future code
refactoring is simplified.
2008-11-26 21:15 lstein
* [r15034] squashed occasional unit variable warning
2008-11-26 21:03 cjfields
* [r15033] [bug 2567]
* store sequence by placement in block (not by name)
* this will not fix locatableseqs with same id/start-end (which
are replaced in a SimpleAlign with a warning)
2008-11-26 18:19 cjfields
* [r15032] Redundant; file was renamed SearchIO_blast_pull.t.
2008-11-26 18:09 cjfields
* [r15031] [bug 2686]
* preliminary support for xmlcompact preprocessing (use
-xmlcompact => 1 to preprocess these files)
2008-11-26 08:27 heikki
* [r15029] POD fix
2008-11-26 08:12 heikki
* [r15028] get rid off "my" variable redeclaration warning
2008-11-26 07:41 heikki
* [r15027] fix POD syntax
2008-11-26 07:36 heikki
* [r15026] silence the warnings about removing the temporary files.
Tests in t/AlignIO_largemultifasta.t are now cleaner
2008-11-26 00:03 cjfields
* [r15025] fix subversion tags
2008-11-25 23:59 cjfields
* [r15024] po, not poa
2008-11-25 23:52 cjfields
* [r15023] fix undefined value warnings
2008-11-25 23:11 cjfields
* [r15022] [bug 2686]
* fix to support -m7 output from WU-BLAST (patch courtesy of
Jason Wood)
2008-11-25 23:09 cjfields
* [r15021] [bug 2641, 2642]
* patches for bioperl.lisp, courtesy of Mark Jensen
2008-11-25 22:03 cjfields
* [r15020] split up AlignIO tests
2008-11-25 20:48 fangly
* [r15019] Updated Bio::Assembly tests
2008-11-25 17:16 cjfields
* [r15018] [bug 2682]
* patch substr() to accept named arguments, optionally strip gaps
* patch courtesy of Mark Jensen
2008-11-25 15:40 cjfields
* [r15017] [bug 2630]
* more LocatableSeq tweaks.
* no_gaps() reverted (was not counting gaps accurately)
* notes (and TODO tests) about issues with using globals
variables and LocatableSeq; will fix in 1.7
2008-11-24 05:46 cjfields
* [r15016] [bug 2633]
* frac_* method values slightly changed (rounding instead of
floor'ing with int)
* total gap values were wrong (now corrected in parser)
2008-11-24 05:05 cjfields
* [r15015] [bug 2663]
* BLAST data checked for correct seq_inds() positions; gap
positions for translated sequences indicate the position just
before the gap
* the third codon position (not the first) to be precise
2008-11-24 05:02 cjfields
* [r15014] [bug 2663]
* overhaul seq_inds to handle frameshifts, true gap positions
(the position just prior to the gap)
* relevant data passed onto LocatableSeqs when needed
* added 'frameshift' as an option to seq_inds to grab the
positions a frameshift likely occurs in (for TFASTX/Y)
2008-11-24 04:52 cjfields
* [r15013] [bug 2630]
* small Simplealign fix to deal with symbols
2008-11-24 04:50 cjfields
* [r15012] [bug 2262]
* Warn about blessing into Bio::Seq, indicate Bio::LocatableSeq
needs some revision.
2008-11-24 02:33 cjfields
* [r15011] [bug 2630]
* add frameshift support
* add tests
* end() now takes frameshifts into account
2008-11-23 20:16 bosborne
* [r15010] Add test for bug 2339, and fix
2008-11-23 19:42 bosborne
* [r15009] Add for bug 2339
2008-11-21 21:33 scain
* [r15008] Fixes for the change to Bio::Annotation::Comment that
removed double quote overloading
2008-11-21 16:36 lstein
* [r15007] "blunting" of the generic glyph when the glyph goes off
the edge of the panel is now consistent between directional
(fillled arrow) and non-directional (simple box) renderings
2008-11-19 21:55 lstein
* [r15006] moved more glyphs from gbrowse into bioperl
2008-11-19 20:32 dave_messina
* [r15005] more sensitive fix for bug 2632, courtesy of Francisco
J. Ossandon
2008-11-18 03:46 cjfields
* [r15004] * Double-checked data, tested results were wrong
2008-11-18 02:58 cjfields
* [r15003] * seq_inds is not defined for Model-based HSPs
* remove redundant tests
2008-11-18 02:43 cjfields
* [r15002] * fix POD
* make verbose to trip evals
2008-11-17 22:59 cjfields
* [r15001] * 'highly' (and I get r15000!)
2008-11-17 22:57 cjfields
* [r15000] Remove redundant test files
2008-11-17 22:57 cjfields
* [r14999] [tests]
* split up SearchIO into more manageable bits
* relevant Bio::Tools parsers get their own Tools_* test files
where needed
2008-11-17 22:54 cjfields
* [r14998] move results2hash test utility sub to SearchUtils
2008-11-17 16:20 sendu
* [r14997] resolve long-standing issue with auto-install of
circular dependency: no more! Now you must choose to install
circular deps in interactive mode; they do not get installed when
installing "all" modules
2008-11-17 15:34 sendu
* [r14996] fixed bug 2667: no more complaints about code refs
2008-11-16 06:20 cjfields
* [r14995] [bug 2663]
* some fixes for seq_ind().
* 7 other SearchIO.t tests failing (all FASTA related), will look
into
2008-11-16 06:18 cjfields
* [r14994] perltidy
2008-11-16 06:14 cjfields
* [r14993] [bug 2635]
* new method cat()
* needs further evaluation using meta data, but code is iin place
which should take care of it.
* patch courtesy of Roy Chaudhuri
2008-11-14 03:29 cjfields
* [r14991] [bug 2656]
* fix mispelled module name - patch courtesy of Fernan Aguero
2008-11-11 19:55 cjfields
* [r14990] remove debugging lines
2008-11-11 19:52 cjfields
* [r14989] remove fixed verbose flag
2008-11-11 19:45 sendu
* [r14988] corrected test to test the hmmer parser, not the
hmmer_pull parser; test passes but generates big warning
2008-11-11 19:44 cjfields
* [r14987] [bug 2650]
* implement result_count for blastxml
2008-11-11 19:29 cjfields
* [r14986] Clarify result_count (discussions on mail list per Dan
Bolser and Sendu).
2008-11-11 19:21 cjfields
* [r14985] [bug 2632]
* added tests for plain ol' hmmer parsing
2008-11-11 18:39 sendu
* [r14984] fixed significant alignment parsing bug affecting hsps,
and also got rid of warnings when length not known
2008-11-11 18:37 sendu
* [r14983] test data for bug 2632
2008-11-11 16:03 lstein
* [r14982] migrated glyphs from gbrowse distribution into bioperl
main
2008-11-10 13:21 cjfields
* [r14981] [bug 2645]
* return assembly only when assembly contains contigs
* noticing that singlet.t tests are failing
2008-11-04 19:10 cjfields
* [r14980] wrap text
2008-11-04 19:08 cjfields
* [r14979] * parse 'Features in this part of subject sequence:' and
pass on data to GenericHSP
2008-11-04 19:07 cjfields
* [r14978] * parse 'Features in this part of subject sequence' data
from some NCBI output (string can be retrieved using new
GenericHSP::hit_features method)
* add test
2008-11-01 18:46 lstein
* [r14977] restored the ability of add_feature() to set the
feature's type. Unfortunately side-effect: feature is actually
altered during this operation
2008-11-01 18:28 lstein
* [r14976] fixed parsing of # characters so that HTML fragments are
not stripped out
2008-10-30 21:28 cjfields
* [r14975] [bug 2632]
* bypass CS lines (fix courtesy of Francisco Ossandon)
2008-10-29 18:17 cjfields
* [r14974] fix seq_inds(); wasn't calling identical residues for
FASTA parsing
2008-10-29 04:03 cjfields
* [r14973] [bug 2633]
* fasta.pm: switch out POSIX::ceil)( for sprintf() rounding
(off-by-one error)
* GenericHSP: switch out int() for sprintf() rounding. No
apparent effect, but int() is effectively a POSIX::floor() in
this case (no rounding)
* downside: 8 tests are failing. Need to evaluate further to
ensure whether the expected test results are erroneous, or
whether some changes need to be rolled back.
2008-10-28 17:26 jason
* [r14972] jasonfail. add missing test data file for FASTA v35.04
2008-10-28 16:08 cjfields
* [r14971] [bug 2630]
* initial Bio::LocatableSeq::mapping implementation (two element
array, maps # symbols to # positions)
* fixes GenericHSP warnings, but FastaHSP-generated LocatableSeqs
are still problematic
* removed redundant code from LargeLocatableSeq and fix some
inheritance tree problems
2008-10-26 15:47 dave_messina
* [r14968] clarifying example code. Credit to Nic Blouin.
2008-10-26 05:29 cjfields
* [r14967] Fix unlink() warning
2008-10-26 05:27 cjfields
* [r14966] end = start if only start is passed
2008-10-26 05:10 cjfields
* [r14965] use valid_Location to check Location state
2008-10-26 05:03 cjfields
* [r14964] add docs for LocationI method valid_Location
2008-10-26 04:54 cjfields
* [r14963] [bug 2621]
* add valid_Location method to LocationI and
Bio::Location::Atomic ( if ($location->valid_Location) {...} )
* checks state of Bio::LocationI (i.e. at check point, indicates
whether it represents a valid Bio::LocationI, which may be
implementation-specific)
* use in Bio::SF::Generic for checking for feature expansion
2008-10-26 04:02 cjfields
* [r14962] [bug 2621]
* ##sequence region directive should be:
##sequence-region seqid start end
2008-10-26 03:40 cjfields
* [r14960] [bug 2624]
* store score() as a tag (don't treat as a 'first-class'
attribute, but an optional value)
2008-10-26 03:25 cjfields
* [r14959] [bug 2621]
* end = start if not defined
* Throw warnings if the above condition occurs (likely a silent
bug as this is Bio::Location::Simple) or if start and end are not
defined
2008-10-25 23:37 cjfields
* [r14958] bullet-proof prototype test
2008-10-24 19:50 bosborne
* [r14957] Add tests for Index::Blast and RPSBLAST
2008-10-24 18:42 bosborne
* [r14956] Fix for RPS-BLAST
2008-10-24 07:02 heikki
* [r14955] typo in docs
2008-10-23 20:36 bosborne
* [r14954] Correct the example
2008-10-23 19:18 jason
* [r14953] support new method in API get_seq_by_id
2008-10-23 19:13 jason
* [r14952] FASTA - 35.04 Parameters section parsing for Matrix
2008-10-23 19:13 jason
* [r14951] FASTA - 35.04 Parameters section parsing for Matrix
2008-10-22 23:24 jason
* [r14950] Allow multi-ID indexing per sequence. This can be rolled
back later if it isn't appropriate
2008-10-22 06:42 sendu
* [r14949] Don't include potentially undefined variables in warning
message
2008-10-22 01:04 jason
* [r14948] more specific warning
2008-10-22 01:03 jason
* [r14947] fix email address
2008-10-22 00:52 cjfields
* [r14946] fix file properties
2008-10-22 00:49 cjfields
* [r14945] new module for parsing vecscreen -f 3 output, courtesy
of Robert Buels
2008-10-22 00:45 jason
* [r14944] fix email address
2008-10-21 18:22 fangly
* [r14943] Removed superfluous statement in Bio::Assembly::IO::ace
2008-10-21 04:01 fangly
* [r14942] [Bug 2455] Bio::Assembly::IO::ace singlet support
* the driver doesn't look for additional files to find the
singlets in
* in the ACE file, any contig of one sequence is loaded as a
Bio::Assembly::Singlet
2008-10-21 01:44 fangly
* [r14941] Fixed missing -end for the contig and singlet features
in Bio::Assembly::IO::tigr
2008-10-21 00:23 fangly
* [r14940] [Bug 2519] and [Bug 2459]
Changed the Bio::Assembly::IO::ace driver to parse more generic
contig IDs
2008-10-20 23:06 fangly
* [r14939] Additional checks in the singlet code
2008-10-20 03:56 fangly
* [r14938] Cleanup of the Bio::Assembly::Singlet module
2008-10-19 21:50 fangly
* [r14937] [bug 2441] Singlets as Bio::Assembly::Singlet objects
* documentation update of Bio::Assembly::ScaffoldI and
Bio::Assembly::Scaffold
* verification of input object type in Bio::Assembly::Scaffold
* Bio::Assembly::IO::phrap modification to generate
Bio::Assembly::Singlet objects
2008-10-18 06:23 heikki
* [r14936] revcom on a Bio::LocatableSeq does not change the
outcome of column_from_residue_number() no matter how
counterintutive it is. The main reason is that revcom on sequence
that is part of the alignment is a non-biological process.
2008-10-17 05:45 heikki
* [r14935] Write out tags color and label as a comment understood
by the FigTree program
2008-10-15 18:57 cjfields
* [r14934] add -source for ARP
2008-10-15 18:53 cjfields
* [r14933] [bug 2563]
* add TagTree convenience method 'pairs' (get a hash of key/val
for simple TagTree data)
* refactored ARP parsing - add annotation data, new tests
2008-10-15 04:11 hartzell
* [r14932] * commit a TODO test that catches a problem with getting
a column
from a locatable seq when the column is before the first residue
in the sequence and the sequences start != 1.
2008-10-15 03:47 hartzell
* [r14931] * touch up the documentation for
column_from_residue_number and
location_from_column.
There's still a problem with location_from_column, the docs say
it will return undef for the first column (given the example) but
the reality is that it returns an IN-BETWEEN. This is consistent
with how it behaves for column 11 (given the example).
I'll ask around about who might be depending on the current
behaviour.
2008-10-14 10:48 heikki
* [r14930] fix parsimony score of ps() to work with polytomies
2008-10-10 19:19 cjfields
* [r14929] typo
2008-10-10 19:18 cjfields
* [r14928] [bug 2519]
* forgot ace!
2008-10-10 19:17 cjfields
* [r14927] [bug 2519]
* fix bug introduced by previous patch (new patch courtesy of
Michael Kiwala)
2008-10-09 09:48 lstein
* [r14926] fixed broken primary_id generation in memory adaptor
2008-10-09 08:20 heikki
* [r14925] fixed ps() output; spotted by Mira Han
2008-10-08 22:11 lstein
* [r14924] removed stupid debugging statement
2008-10-08 22:10 lstein
* [r14923] added a workaround that prevents panel from crashing
when trying to draw an image with no tracks in it
2008-10-08 17:07 lstein
* [r14922] try to distinguish between #aabbcc colors and right-hand
comments
2008-10-07 22:06 cjfields
* [r14920] add svn tag
2008-10-07 22:06 cjfields
* [r14919] TODO's work
2008-10-07 18:38 cjfields
* [r14918] [bug 2612]
* undef the name, don't carry it over
2008-10-07 17:52 cjfields
* [r14917] [bug 2612]
Allow all-gap sequences; if start == 0, assume sequence is blank
and end no longer needs adjustment
2008-10-03 17:13 lstein
* [r14915] apply HTML escaping to imagemap title attributes rather
than URL escaping
2008-10-02 21:04 cjfields
* [r14914] clean up XMFA parsing, allow spaces in parsing (ende++,
from IRC)
2008-09-27 05:12 cjfields
* [r14913] [BUG] bug 2598
* added more for 'J'
* added pyrrolysine (O) data
* removed duplicated hash
2008-09-26 20:50 cjfields
* [r14912] [BUG] bugfix for # 2598 (add 'J')
2008-09-26 18:42 miraceti
* [r14911] add default first line to phyloXML output
2008-09-26 18:15 cjfields
* [r14910] [BUG] bug 2593
* works with Storable now and passes tests
2008-09-26 17:38 cjfields
* [r14909] [BUG] fix bug 2595
* fix comp. stats to check for 0/1 instead of yes/no
* check other yes/no for similar issues? or punt until someone
takes this over?
2008-09-26 13:39 sendu
* [r14908] keep memory leak fix from previous commit and solve the
Speciest.t test failures introduced. But there may be issues with
this kludge. See bug 2594.
2008-09-24 21:01 miraceti
* [r14907] add_phyloXML_annotation
2008-09-24 17:05 lstein
* [r14906] added documentation for bicolor options
2008-09-23 21:50 sendu
* [r14905] increased the version number to be higher than the
current release version
2008-09-19 16:17 heikki
* [r14904] method to add trait values in into leaf nodes
(add_trait), indicator values for trait distribution (ps, ai, mc)
and tree shape (cherries)
2008-09-18 19:45 lstein
* [r14903] killed a few uninit variable warnings
2008-09-18 19:04 lstein
* [r14902] added missing aggregator needed by default gbrowse
installation
2008-09-18 18:22 lstein
* [r14901] removed another text::shellwords dependency
2008-09-18 16:02 cjfields
* [r14900] Use 'warning_like' for instances where a regex match is
needed
2008-09-18 10:07 heikki
* [r14899] Tests for is_binary().Added set_tag_value(). Tests for
tags separately in trees and nodes. Ideally there should be a
separate class that is a superclass for both. After sequence
features moved to Bio::AnnotationI, I am not sure if it is worth
creating (TaggableI?)
2008-09-18 10:03 heikki
* [r14898] added is_binary()
2008-09-17 13:50 cjfields
* [r14897] * No longer a stub
* Appears to work fine with BioSQL, as evidenced by swissprot
tests, but needs additional bioperl-db tests to check for deeply
nested data
2008-09-17 04:14 cjfields
* [r14896] 1965 + 6 -1 = 1970, not 1999
2008-09-17 04:13 cjfields
* [r14895] passing TODO's (?!?)
2008-09-17 04:06 cjfields
* [r14894] update tests (seq length change in record verified)
2008-09-17 04:05 cjfields
* [r14893] set -end to coorespond to sequence end
2008-09-16 20:27 cjfields
* [r14892] test result changed (start always < end)
2008-09-16 20:22 cjfields
* [r14891] Fix nexus issues with seq. ambiguity symbol '.'
2008-09-16 20:18 cjfields
* [r14890] MEGA now resets $GAP_SYMBOLS and $OTHER_SYMBOLS to get
around sequence ambiguity issues
2008-09-16 20:09 cjfields
* [r14889] Test data matches new XMFA example
2008-09-16 20:07 cjfields
* [r14888] * XMFA alignment doesn't correspond to XMFA spec
(http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/mauve-output-file-formats.html);
changed to correct start/end coordinates (code checks this)
* fixed small warning, now passes AlignIO.t
2008-09-16 19:26 cjfields
* [r14887] fix xmfa.pm parsing oops
2008-09-16 19:20 cjfields
* [r14886] make LocatableSeq::end() consistent
2008-09-16 19:10 cjfields
* [r14885] * fix start/end/strand
* add alphabet() (and guess if not set)
2008-09-16 19:09 cjfields
* [r14884] typo
2008-09-16 18:27 jason
* [r14883] match '*' and '?' as well
2008-09-16 04:13 miraceti
* [r14882] Relation/AnnotatableNode correct pod
2008-09-16 03:59 miraceti
* [r14881] phyloxml correct pod format
2008-09-16 03:23 miraceti
* [r14880] phyloxml more documentation
2008-09-16 02:22 bosborne
* [r14879] Add Jason's script
2008-09-15 20:30 bosborne
* [r14878] Minor edits
2008-09-15 16:32 cjfields
* [r14877] remove debugging statement
2008-09-15 16:28 cjfields
* [r14876] partial fix for arp (-end now works and counts ? as
ambigious sequence instead of gap)
2008-09-15 16:27 cjfields
* [r14875] -end parameter does not take gaps into account
2008-09-15 16:26 cjfields
* [r14874] * always warn about passing wrong end() coordinate
* distinguish $GAP_SYMBOLS from sequence data for using in
_ungapped_length (more consistent)
* this unveils errors in end coordinate calculation in several
parsers (breaks some AlignIO tests)
2008-09-15 14:25 lstein
* [r14873] removed spurious dependency on Text::Shellwords
2008-09-14 20:41 cjfields
* [r14872] Create Data::Stag node lazily; always use node() to grab
node instance
2008-09-14 19:23 cjfields
* [r14871] add a few new (untested) URLAPI parameters
2008-09-14 19:23 cjfields
* [r14870] use direct object syntax
2008-09-13 19:10 heikki
* [r14869] Start counting internal IDs from 1. 0 as an index was
creating too much trouble.
Should not make any difference at code usage.
2008-09-10 22:30 lstein
* [r14864] fixed primary_id method to return a more rational result
2008-09-09 16:23 cjfields
* [r14863] bug 2579
* spliced_seq() shouldn't automatically sort circular sequences.
My question: should it be sorting a 'join' at all?
2008-09-09 15:51 cjfields
* [r14862] bug 2580
* add GO ID parsing (patch courtesy of John Osborne)
2008-09-08 17:36 fangly
* [r14861] Bug correction regarding read location in a contig
2008-09-08 17:34 fangly
* [r14860] Update number of sequences and their order when removing
a sequence from a contig
2008-09-08 17:32 fangly
* [r14859] Documentation improvement
2008-09-07 05:32 heikki
* [r14858] Document that get_tag_values() return variable is
context sensitive (array of scalar)
2008-09-04 22:21 lstein
* [r14857] fixed bugs that interfered with the display of stranded
features defined using the FeatureFile format
2008-09-04 19:18 lstein
* [r14856] essential ideogram glyph base class missing
2008-09-04 06:13 heikki
* [r14855] remove a spurious line creating an unneeded object
2008-09-03 23:02 hartzell
* [r14854] small documentation typo fix
2008-09-03 23:01 hartzell
* [r14853] small documentation typo and grammar fix
2008-09-03 23:00 hartzell
* [r14852] small documentation typo fix
2008-09-03 22:57 hartzell
* [r14851] small documentation typo fix
2008-09-03 22:54 hartzell
* [r14850] small documentation fix
2008-09-02 22:37 miraceti
* [r14849] testing translation between nhx and phyloxml
2008-08-29 16:45 cjfields
* [r14840] Allow other Bio::SeqFeature::CollectionI
2008-08-29 14:58 fangly
* [r14839] Fixed bug: not using gapped length to calculate
LocatableSeq->end in _overlap_alignment. Letting the default
behavior use ungapped length instead
2008-08-29 14:49 fangly
* [r14838] Fixed bug: all LocatableSeq->end specified based on
gapped length (instead of ungapped) now not specified
2008-08-29 14:36 fangly
* [r14837] Fixed bug for add_seq: $seq->end now based on ungapped
length
2008-08-29 14:17 fangly
* [r14836] Fixed bug for set_consensus_sequence->end: end needs to
take into account sequence gaps
2008-08-28 14:59 cjfields
* [r14835] [bug 2576]
* explicitly leave hit table block if a blank line is encountered
after the hit table (passes all SearchIO.t tests)
2008-08-27 20:44 hartzell
* [r14834] Fix a typo in pod doc
2008-08-27 16:37 cjfields
* [r14833] grep not needed (check for ontology is in
Ontology::get_predicate_terms)
2008-08-27 16:33 cjfields
* [r14832] [bug 2573]
* only work with Bio::Ontology::Relationship instances with a set
Bio::Ontology::Ontology
2008-08-27 15:00 cjfields
* [r14831] Update documentation
2008-08-27 14:59 cjfields
* [r14830] complete sentence
2008-08-27 06:19 heikki
* [r14829] _build_nt_matrix() now uses $self->warn rather than
straight print to report on ambiguous residues (suggested by
Dominic Rose on the bioperl mailing list)
2008-08-26 18:39 lstein
* [r14828] quashed an uninit variable warning
2008-08-25 23:35 lstein
* [r14827] set the mysql autoreconnect flag
2008-08-25 17:42 cjfields
* [r14826] Add some print_* methods for einfo, esummary, etc.
2008-08-25 15:40 lstein
* [r14825] added an option to bp_seqfeature_load to ignore
##sequence-region directives in the gff3 file
2008-08-22 14:57 lstein
* [r14823] added a background color fallback option
2008-08-22 14:35 sendu
* [r14821] don't complain if there's no scripts directory
2008-08-22 13:31 lstein
* [r14820] added get_feature_by_primary_id() method
2008-08-21 20:51 lstein
* [r14817] added a get_feature_by_id() method to
Bio::DB::SeqFeature::Store as an alias for the non-intuitive
fetch() method that does the same thing
2008-08-21 16:00 cjfields
* [r14816] * write PROJECT support
* test case
* round-trip tests
* WGS, similar should conform with other annotation tag names
(all lc)
* bring handler-based parser up-to-date
2008-08-21 13:37 cjfields
* [r14815] add PROJECT support (bug 2569)
2008-08-20 23:02 lstein
* [r14814] fixed rotation of imagemaps, which was not correct
2008-08-20 21:24 lstein
* [r14813] added regression tests for the safe() flag
2008-08-19 21:06 lstein
* [r14812] fixed bugs in the ideogram glyphs that caused them to
draw the label and description incorrectly
2008-08-19 21:06 lstein
* [r14811] fixed bugs in the ideogram glyphs that caused them to
draw the label and description incorrectly
2008-08-18 06:45 miraceti
* [r14810] phyloxml documentation
2008-08-18 05:25 miraceti
* [r14809] phyloxml use filehandle instead of file name
2008-08-17 07:00 heikki
* [r14808] deprecate findnode_by_id
2008-08-17 03:32 jason
* [r14807] fully implement Bio::LocationI
2008-08-16 08:02 miraceti
* [r14806] phyloxml more tests
2008-08-16 02:35 miraceti
* [r14805] phyloxml: bug fixes and tests
2008-08-15 21:57 miraceti
* [r14804] added nowarnonempty arg to Bio::PrimarySeq
2008-08-15 19:39 scain
* [r14803] fix for windows: glob() isn't working for paths with
spaces in them
2008-08-15 06:01 miraceti
* [r14802] get_nested_Annotations
2008-08-14 15:23 lstein
* [r14801] made -gff an alias for -dsn in
Bio::DB::Seqfeature::Store::memory adaptor new() call, since
people are having trouble adapting to shift between Bio::DB::GFF
and Bio::Db::SeqFeature::Store
2008-08-14 08:14 heikki
* [r14800] the new method
Bio::Tree::Tree::subtree_length($internal_node) is identical to
total_branch_length when no Bio::Tree::NodeI object is given as
an argument
2008-08-14 02:21 scain
* [r14799] Getting ready for a GBrowse release
2008-08-11 15:55 lstein
* [r14798] for some reason the failure to open a Bio::DB::Fasta
file was not generating an error message; this is now fixed
2008-08-11 15:22 miraceti
* [r14797] phyloxml: add clade_relation to node instead of tree,
write clade_relation
2008-08-10 23:34 lstein
* [r14795] improved the way that several glyphs are grouped when
exporting panels as SVG
2008-08-10 22:16 lstein
* [r14794] added feature grouping to SVG output from Bio::Graphics
2008-08-09 23:34 hartzell
* [r14793] Use weaken to avoid a circular reference in the tree
that's
allocated, thus avoiding a memory leak.
2008-08-09 17:16 bosborne
* [r14792] POD was a bit misleading, remove_SeqFeatures just
removes features, sub- or not
2008-08-07 15:28 avilella
* [r14791] adding parsing support for the Standard Errors (SE line)
-- this goes into tags doing the clever mapping as in the branch
mode -- only tested with Baseml executions
2008-08-06 20:25 lstein
* [r14790] fixed a display bug that appeared when feature
start=stop=0
2008-08-06 15:56 miraceti
* [r14789] phyloxml: new module for clade_relation seq_relation
2008-08-05 22:48 fangly
* [r14788] Used weak references (Scalar::Util::weaken) in a
circular reference to fix memory leak
2008-08-05 22:07 cjfields
* [r14787] For new NCBI blasttable format
2008-08-05 22:00 cjfields
* [r14786] Previous changes killed RemoteBlast again; make a little
more bulletproof
2008-08-04 20:57 cjfields
* [r14784] Add a few new GET/PUT parameters.
2008-08-04 17:10 cjfields
* [r14783] Sequences weren't being parsed correctly; unfortunately
this breaks multiple alignments in one ARP file, so using
todo_skip() to pass over tests until bug fix is in place.
2008-08-02 16:20 lstein
* [r14782] fixes to "safe callbacks" feature
2008-08-02 03:56 ymc
* [r14780] edited comments related to DNA IUPAC code
2008-08-01 21:34 lstein
* [r14777] did work necessary to process option callbacks in a
Safe::World context
2008-07-31 14:44 lstein
* [r14775] fixed zero-width rectangles which were breaking GD::SVG
representations of xyplot data
2008-07-30 21:33 cjfields
* [r14774] tests should use is/isnt when possible, not ok()
2008-07-30 19:01 cjfields
* [r14772] revert Roy's patch (my bad)
2008-07-30 14:14 cjfields
* [r14771] bug 2556:
* patch courtesy of Roy Chaudhuri
2008-07-30 14:09 cjfields
* [r14770] Bug 2546
* cleanup RemoteBlast a bit
* blasttable now works with BLAST 2.2.18+ (extra column in new
version broke parser)
* added some tests
2008-07-29 05:12 miraceti
* [r14769] phyloxml seq_relation clade_relation
2008-07-29 03:48 cjfields
* [r14768] bug 2555
2008-07-29 03:36 cjfields
* [r14767] bug 2549; fixed small bug in Bio::Taxon which doesn't
catch -common_name
2008-07-29 00:30 lstein
* [r14766] modified fix so that it doesn't break compatibility with
those who use '+' to describe the strand of the target
2008-07-29 00:26 lstein
* [r14765] pretty formatting of gff3 attributes
2008-07-29 00:19 lstein
* [r14764] fixed error in which spaces are not properly escaped in
GFF3 files
2008-07-28 17:30 cjfields
* [r14763] add multiple record support (courtesy of Jorge Duarte,
per mail list)
2008-07-24 00:36 lstein
* [r14762] glyphs will now display the first alias as the label if
the display_name() is not defined
2008-07-21 05:55 miraceti
* [r14761] phyloxml: create Bio::Seq for <sequence>
2008-07-18 23:09 lstein
* [r14760] fixed bug in the memory adapter which prevented features
with a primary ID of "0" from being loaded
2008-07-18 20:05 cjfields
* [r14759] bulletproof test; remote tabular BLAST is failing for
some reason...
2008-07-17 02:18 lstein
* [r14758] workaround a bug that emerges when the memory adapter
automatically assigns a primary id of 0
2008-07-13 04:56 miraceti
* [r14757] phyloxml: taxonomy, distribution, annotation, events,
date, etc
2008-07-09 16:05 cjfields
* [r14756] bug 2534
2008-07-08 16:54 lstein
* [r14755] accept $seq_id or $seqid in link substitution rules
2008-07-08 04:05 cjfields
* [r14754] Can't inherit from oneself
2008-07-08 03:39 cjfields
* [r14753] bug 2539
2008-07-04 20:07 bosborne
* [r14752] Minor edits
2008-07-04 19:45 miraceti
* [r14751] phyloxml write_tree
2008-07-02 21:05 miraceti
* [r14750] element_default instead of element_name _branch
_confidence
2008-07-02 06:06 miraceti
* [r14749] nested annotation collection instead of structuredValue
2008-07-01 22:12 miraceti
* [r14748] phyloxml to_string <name>,<branch_length>
2008-06-30 23:02 miraceti
* [r14747] _to_string callback for AnnotatableNode and phyloxml
2008-06-21 05:06 miraceti
* [r14746] <property> using id_source and id_ref
2008-06-20 03:16 miraceti
* [r14745] <property> using id_source and id_ref
2008-06-19 23:17 jason
* [r14744] AAML parsing was failing on runmode=0 data (usertree)
2008-06-18 19:44 miraceti
* [r14741] <property> via Bio::Annotation
2008-06-18 00:29 jason
* [r14739] avoid undefined warnings when start/end are empty.
Causing weird slowdowns in Gbrowse
2008-06-17 23:19 cjfields
* [r14738] bug 2423
2008-06-17 23:11 cjfields
* [r14737] bug 2423
2008-06-16 18:29 miraceti
* [r14736] changed NodePhyloXML to AnnotatableNode
2008-06-16 18:08 miraceti
* [r14735] changed NodePhyloXML to AnnotatableNode
2008-06-14 22:16 lstein
* [r14734] Bio::Graphics::Glyph::minmax is the base class that
defines midpoint(); fixed bug that mistakenly called
SUPER::minmax()
2008-06-14 19:52 jason
* [r14733] set the ID, typo
2008-06-14 19:48 jason
* [r14732] More GFF3 like output
2008-06-14 19:48 jason
* [r14731] simplify list of special ID tags and their preferred
order, still needs some more work; Indentation standardization
from emacs
2008-06-14 17:14 lstein
* [r14730] added a bicolor_pivot option to the xyplot glyph to
allow the color switch to occur at non-zero values
2008-06-14 04:52 cjfields
* [r14729] bug 2512 (Gene Ontology changes)
2008-06-14 04:29 cjfields
* [r14728] bug 2519
2008-06-14 04:20 cjfields
* [r14727] bug 2518
2008-06-14 02:04 cjfields
* [r14726] bug 2517
2008-06-13 18:58 jason
* [r14725] doc expansion
2008-06-12 17:11 jason
* [r14724] some whitespace cleanup
2008-06-12 17:10 jason
* [r14723] inherit from Bio::Root::RootI instead of NodeI
2008-06-12 02:54 miraceti
* [r14722] Removed TreePhyloXML.pm
2008-06-12 02:51 miraceti
* [r14721] Removed TreePhyloXML.pm
2008-06-11 19:42 miraceti
* [r14720] test new module TreePhyloXML
2008-06-11 19:37 miraceti
* [r14719] phyloxml: name, confidence
2008-06-11 19:35 miraceti
* [r14718] New module TreePhyloXML.pm for phyloxml specific
variables.
2008-06-11 06:48 heikki
* [r14716] Why is Bio::SeqFeature::Annotated object creation
downloading so.obo from sourceforge? This is an emergency fix
disabling these tests if no network is available. Better solution
needed ASAP.
2008-06-10 05:04 miraceti
* [r14712] use function hash instead of if-else
2008-06-10 00:42 heikki
* [r14710] POD fixes
2008-06-10 00:08 heikki
* [r14708] fixing POD whitespaceissues
2008-06-09 18:02 miraceti
* [r14707] requires_modules XML::LibXML
2008-06-09 17:58 miraceti
* [r14706] requires_modules XML::LibXML
2008-06-09 04:09 miraceti
* [r14705] phyloxml: next_tree and basic parsing of <clade>
2008-06-09 04:09 miraceti
* [r14704] phyloxml: next_tree and basic parsing of <clade>
2008-06-06 22:10 miraceti
* [r14703] Change phyloxml to using libxml instead of SAX
2008-06-06 22:06 miraceti
* [r14702] Change phyloxml to using libxml instead of SAX
2008-06-06 22:02 miraceti
* [r14701] Change phyloxml to using libxml instead of SAX
2008-06-06 22:00 miraceti
* [r14700] Change phyloxml to using libxml instead of SAX
2008-06-06 15:37 lstein
* [r14699] fixed the positioning of the '0' coordinate on the scale
so that it doesn't clash with the midpoint coordinate
2008-06-05 16:42 lstein
* [r14698] fixed scale on xyplot so that scale values < 0 are
rendered correctly
2008-06-04 14:22 heikki
* [r14697] fix POD errors
2008-06-04 14:21 heikki
* [r14696] point searches to bioperl-run assuming that it is at the
same directory as bioperl-live
2008-06-03 19:59 heikki
* [r14695] use uniform notice string when skipping network tests
2008-06-03 14:45 heikki
* [r14694] skip tests that need networking using the same logic
that all other modules use.
fix number of enzyme prototypes returned
2008-06-03 14:22 heikki
* [r14693] skip tests when XML::Writer is not installed
2008-06-03 13:54 heikki
* [r14692] correct number of tests
2008-06-03 13:39 heikki
* [r14691] fix number of tests
2008-06-03 13:38 heikki
* [r14690] fixed POD errors
2008-06-02 20:06 miraceti
* [r14689] start_element/end_element clade
2008-06-02 20:05 miraceti
* [r14688] start_element/end_element clade
2008-05-29 14:17 lstein
* [r14687] added some more special cases to the gene glyph so that
it "behaves right" with unusual data
2008-05-29 09:55 heikki
* [r14685] Added support for long IDs (give -longid => 1 to
constuctor). They can be optionally surrounded by single quotes.
A warning is printed out if the length of an ID is over 50
characters long. Updated docs to show that both interleaved and
sequential formats can be read and written.
2008-05-28 19:47 miraceti
* [r14684] test scripts for phyloxml modules
2008-05-28 19:42 miraceti
* [r14683] New module to handle phyloxml
2008-05-27 17:52 cjfields
* [r14682] RT#12802 (via CPAN RT)
2008-05-23 14:35 faga
* [r14679] Now, the loader passes unrecognized meta tags to the
store object (if it can). Also, it handles the ### pragma.
2008-05-21 21:04 dave_messina
* [r14678] Added support for WU-BLAST tabular output. Tests added
to SearchIO.t and all tests pass.
2008-05-11 07:21 jason
* [r14677] first crack at a sort_hsps option in a Hit object,
impemented in GenericHit object
2008-05-11 06:41 jason
* [r14676] code simplification
2008-05-11 06:40 jason
* [r14675] bug #2492, credit to K.Thornton's implementation
2008-05-11 06:36 jason
* [r14674] bug 2492
2008-04-25 19:51 dave_messina
* [r14673] uneven tr///, thanks to Lskatz for the report.
2008-04-22 21:42 cjfields
* [r14672] bug 2485 and related fixes
2008-04-22 21:26 cjfields
* [r14671] correct # of skipped tests
2008-04-22 21:23 cjfields
* [r14670] bug 2490 (small test)
2008-04-22 21:03 cjfields
* [r14669] bug 2490
2008-04-22 18:44 cjfields
* [r14668] new NCBI BLAST URL (works with RemoteBlast.t)
2008-04-22 16:34 jason
* [r14667] bug #2491
2008-04-22 00:20 cjfields
* [r14666] bug 2490
2008-04-21 15:43 cjfields
* [r14665] Fix failing tests
2008-04-21 15:28 cjfields
* [r14664] update test (seq in remote db has changed)
2008-04-21 15:25 cjfields
* [r14663] bullet-proof; this needs more stringent tests
2008-04-17 21:13 lstein
* [r14662] added ability to get at the parent feature in callbacks
2008-04-15 00:03 thm09830
* [r14660] Function for counting number of alternative probes added
2008-04-14 23:42 thm09830
* [r14659] Minor changes in the main processing function
calc_sequence(), Logmessages are buffered, hence only one file
open/write/close operation is needed per processed chip, udpated
version of testscript is provided via Bug #2332 in Bioperl
bugzilla, Documentation updated
2008-04-14 21:06 jason
* [r14658] typo
2008-04-14 17:56 cjfields
* [r14657] bug 2484
2008-04-14 15:05 lstein
* [r14656] added a clone() method to support the (uncommon) case of
passing database adaptors across a fork()
2008-04-11 23:19 lapp
* [r14655] Applied SYNOPSIS patch by Adam Sjogre (asjo at koldfront
dot dk).
2008-04-10 21:10 lstein
* [r14654] corrected case in which seq_id of Bio::Location::Split
could unintentionally be set to undef
2008-04-08 16:05 cjfields
* [r14653] bug 2479
2008-04-08 15:58 cjfields
* [r14652] bug 2478
2008-04-07 18:24 cjfields
* [r14651] updates; may switch some data objects over to
(lightweight) Data::Stag implementation at some point
2008-04-03 13:58 lstein
* [r14650] added an API to prevent FeatureFile->render() from
rendering indiscriminately without paying attention to the seq_id
of the underlying reference sequence
2008-04-03 13:24 lstein
* [r14649] restored the ability to have a "tag=value #comment"
style comment
2008-04-02 21:36 fangly
* [r14648] Misc cleaning, and bug fixing
Bio::Assembly::Contig
Fixed bug: replaced an occurence of 'elem' by '_elem'
Bio::Assembly::Scaffold
Fixed bug: scaffold source is implemented, stored in the scaffold
at scaffold creation
Fixed bug: contig or singlet addition to a scaffold now really
creates a reference to that scaffold as a contig or singlet
attribute
Improvement: a list of singlets can be given at scaffold creation
(just like a list of contigs can be specified)
Improvement: adding a non singlet object using the add_singlet
method is now a fatal error (like all other such errors)
Improvement: adding singlet to scaffold now generates a singlet
name if singlet is unnamed
Improvement: method update_seq_list now also updates singlets
Improvement: adding a singlet to a scaffold now puts the singlet
sequence in the list of sequences belonging to the scaffold (just
like for contigs)
Improvement: implemented 'remove_features_collection' method
Bio::Assembly::IO::Ace
Fixed bug: under certain conditions, the list of scaffold
sequences ('_seqs') was not populated
2008-04-02 16:28 cjfields
* [r14647] Add some tests to catch tag naming
2008-04-02 16:24 cjfields
* [r14646] Fix bad silent bug which doesn't set exon tags correctly
(showed up when using -W flag with tests)
2008-04-02 15:52 cjfields
* [r14645] merge back previous commits from Sendu and I
2008-04-02 04:23 cjfields
* [r14643] get rid of variable redefined warnings
2008-04-02 04:22 cjfields
* [r14642] test not matching error message (oops!)
2008-04-02 04:14 cjfields
* [r14641] RefSeq redirection now requires explicit setting (note
that sequence length returned by Bio::DB::RefSeq is off by one,
needs investigating).
2008-04-02 03:57 cjfields
* [r14640] Squash uninit. value warnings
2008-04-01 16:39 cjfields
* [r14639] Remove extraneous code; update docs
2008-04-01 16:31 cjfields
* [r14638] bug 2466 :
* change default behavior of Bio::DB::GenBank to always retrieve
from NCBI
* deprecate 'no_redirect' in favor of 'redirect_refseq', which
must be set for RefSeq redirection (see note above)
* make explicit getter/setters out of redirect_refseq,
no_redirect, seq_start, seq_end, strand, complexity along with
docs
2008-04-01 00:02 cjfields
* [r14637] Make regex matches safer
2008-03-31 14:51 sendu
* [r14635] added POD warning about coordinate issue
2008-03-28 18:22 cjfields
* [r14633] add some seq_inds() tests (appears fine)
2008-03-28 17:14 cjfields
* [r14632] * revert symbol passing (forgot query and hit have
different gap symbols)
* add in Marc's fix for converting model gaps to '-', changed
tests to reflect different output
2008-03-28 15:58 cjfields
* [r14630] * Allow gap symbol to be set
* Add symbol passing to hmmer parsing
* Needs additional tests
2008-03-27 16:13 cjfields
* [r14629] remove extraneous comment
2008-03-27 16:12 cjfields
* [r14628] using seq_inds() with 'gaps' now repeats sequence
indices based on the number of inserted gaps; repeated indices
now collapsed into one
2008-03-27 16:07 cjfields
* [r14627] Collapse repeated sequence indices into one position
2008-03-27 15:37 cjfields
* [r14626] Marc's bug from mail list; repeat the seq position for
gaps > 1.
2008-03-25 01:12 cjfields
* [r14625] bug 2473 (with tests)
2008-03-19 16:07 sendu
* [r14623] final (?!) changes now that B::SF::Annotated behaves
more like Generic
2008-03-19 15:59 sendu
* [r14622] futher changes now that B::SF::Annotated to behave more
like Generic
2008-03-19 13:27 sendu
* [r14621] added -i option to choose format; improved docs; now
clusters modules in the same subdir; now colours edges according
to inheritance or usage
2008-03-19 04:03 jason
* [r14620] tag/value pairing associating with Trees
2008-03-19 04:02 jason
* [r14619] quiet some warnings on initialization
2008-03-18 14:21 sendu
* [r14618] new script to look at BioPerl module usage
2008-03-18 09:37 heikki
* [r14617] use base, not ISA
2008-03-18 09:35 heikki
* [r14616] No need to use Bio::AnnotationI
2008-03-17 21:28 lstein
* [r14615] under some circumstances, the link_pattern() routine
might think the reference sequence for a feature is empty and
fail to replace $ref correctly
2008-03-17 12:39 sendu
* [r14614] use base, not ISA
2008-03-17 12:32 sendu
* [r14613] use base, not ISA
2008-03-17 12:30 sendu
* [r14612] use base, not ISA
2008-03-17 11:16 sendu
* [r14611] slightly improved docs
2008-03-12 18:51 jason
* [r14610] split sequence database into individual sequence files
2008-03-12 11:28 thm09830
* [r14609] Updated Documentation
2008-03-11 12:22 thm09830
* [r14608] Removed obsolete Function _get_refseq_max_ins_offset()
2008-03-10 22:08 lstein
* [r14607] killed horrible bug that was preventing segmented
features from loading correctly
2008-03-10 21:41 lstein
* [r14606] bitten by "!=" ne "ne"
2008-03-10 17:15 thm09830
* [r14605] Minor Changes
2008-03-07 22:19 scain
* [r14604] adding an option for `perl Build.PL` to accept the
default of asked questions.
To use, do `perl Build.PL --accept 1`
2008-03-06 15:38 lstein
* [r14603] fixed loading problem that arose when a feature had two
parents but feature repeated twice on different lines
2008-03-05 16:48 bosborne
* [r14600] Add example
2008-03-05 05:42 lstein
* [r14598] fixed an issue that prevented DAS features from
rendering correctly on Bio::Graphics::Panels (label missing)
2008-03-05 01:26 lstein
* [r14597] quenched many warnings and small bugs that crop up when
processing slightly invalid config files
2008-03-04 22:22 lstein
* [r14596] config file parser should be more stable in the face of
odd blank lines, funny comments, etc
2008-03-04 19:44 lstein
* [r14595] fix problems parsing configuration files containing
embedded "[" characters inside option values
2008-03-04 17:41 lstein
* [r14594] fixes out-of-memory problems during gff3 file loading
(at the cost of reduced performance), and should fix the problem
of bio::graphics dying when a feature does not have the
source_tag method
2008-03-04 05:21 cjfields
* [r14592] bug 1707
2008-03-03 21:05 cjfields
* [r14591] bug 2465
2008-03-03 20:16 cjfields
* [r14590] bug 2449
2008-03-03 19:37 cjfields
* [r14589] some more for bug 2349
2008-03-03 17:19 lstein
* [r14588] added missing Loader.pm file
2008-03-03 17:14 lstein
* [r14587] removed dangling debug statement
2008-03-03 04:15 cjfields
* [r14586] partial fix for bug 2439
2008-03-03 00:20 lstein
* [r14585] added a version method to featurefile so that GBrowse
can warn when the module is not up to date
2008-03-03 00:05 lstein
* [r14584] revamped featurefile significantly in order for syntax
to be compatible with GBrowse, and to support loading of
featurefiles into GFF3 databases
2008-03-02 23:28 cjfields
* [r14583] Bug 2378
2008-03-01 17:28 cjfields
* [r14582] fix undef. variable issue when no ancestor indicated (no
root and not passed in).
2008-03-01 17:15 cjfields
* [r14581] add some flexibility for name length, defaulting to 10
2008-03-01 17:01 cjfields
* [r14580] bug 2356 (check for correct number with multiple trees)
2008-03-01 16:58 cjfields
* [r14579] bug 2356
2008-03-01 14:26 cjfields
* [r14578] add driver/handler support (will clean these up more for
1.7)
2008-03-01 04:51 cjfields
* [r14577] add some docs
2008-03-01 04:15 cjfields
* [r14576] added prototype-checking method (bug 2179)
2008-03-01 02:32 cjfields
* [r14575] clean up inheritance tree; add remote database test
2008-02-29 23:03 cjfields
* [r14574] Add in support for grabbing most current data via ftp;
add prototype/neoschizomer support
2008-02-29 23:02 cjfields
* [r14573] parser for neo/prototype format from REBASE
2008-02-29 05:52 cjfields
* [r14572] bug 2179
2008-02-29 01:31 cjfields
* [r14571] bug 2128
2008-02-29 01:04 cjfields
* [r14570] Note about XML format (related to bug 2018)
2008-02-28 18:16 sendu
* [r14569] tests for bug6421
2008-02-28 18:16 sendu
* [r14568] fixed bug6421: reimplemented main code to cope with
non-unique names in a lineage. Also fixed child-related bug.
2008-02-28 16:41 cjfields
* [r14567] fix Handler tests
2008-02-28 16:28 cjfields
* [r14566] * Implement StructureValue-like get_all_values()
(flattened value array)
* remove TODOs (all pass now)
2008-02-28 14:53 cjfields
* [r14565] add Data::Stag to require (may change to recommend based
on other core dev input)
2008-02-28 14:34 cjfields
* [r14564] minor word wrapping for error message
2008-02-28 14:30 cjfields
* [r14563] bug 1825
2008-02-28 14:30 cjfields
* [r14562] bug 1825: updating swiss.pm/tests to try out TagTree
(passes all tests). Need to update Handler.t and related modules
still...
2008-02-28 12:03 heikki
* [r14561] removed unused dependency to Dumpvalue module
2008-02-28 03:54 cjfields
* [r14560] check tagtree in collection
2008-02-28 02:13 cjfields
* [r14559] More tests
2008-02-27 21:21 cjfields
* [r14558] bug 2462
2008-02-27 20:29 lstein
* [r14557] worked around different behavior in
Text::ParseWords::shellwords under perl 5.8 and 5.10 -- should be
relatively stable over various versions
2008-02-27 20:20 cjfields
* [r14556] Change name to TagTree
2008-02-27 20:19 cjfields
* [r14555] changes and additions (can't fairly implement
StructureValue's methods, so we'll go another route)...
2008-02-27 17:30 cjfields
* [r14554] Add some tests, more to follow upon implementation...
2008-02-27 16:43 cjfields
* [r14553] Remove Data::Stag cruft (use a reimplementation instead)
2008-02-27 16:41 cjfields
* [r14552] StructuredTag - AnnotationI which uses Data::Stag for
structured tag representation. Just the basic implementation;
needs get/set tag value methods implemented.
2008-02-27 16:38 cjfields
* [r14551] add error message for callbacks if no code reference
2008-02-26 17:18 sendu
* [r14549] No longer makes db test if user chose not to run them
2008-02-26 17:17 sendu
* [r14548] No longers stores code refs via Data::Dumper, avoiding
possible warnings
2008-02-26 04:13 cjfields
* [r14547] bug 2458
2008-02-26 01:02 cjfields
* [r14546] Russell's fixes
2008-02-25 09:46 heikki
* [r14544] RC (reference comment) line was printed in wrong place.
It belongs right after RN line.
2008-02-25 08:22 heikki
* [r14543] better roundtip when preventing line wrapping between
author surname and initials
2008-02-25 06:19 heikki
* [r14542] minor edits to docs
2008-02-25 06:10 heikki
* [r14541] documentation for the GN line parsing and management
2008-02-24 02:47 cjfields
* [r14540] GN changes
2008-02-23 15:10 heikki
* [r14539] AC (accession) line now wraps if there are too many
accession to fit one line
2008-02-23 14:48 heikki
* [r14538] GN (Gene Name) line parsing rewrite. Breaks backward
compatibility. Can now deal with >1 gene per entry and four
categories of names per gene. Parses old style syntax (...OR ...
OR ... ) into one gene name and synonyms for each gene. Docs to
follow.
2008-02-22 17:18 cjfields
* [r14537] revert last commit (good catch Sendu)
2008-02-22 16:10 lstein
* [r14536] these loaders allow gff2 and featurefile-format data to
be stored into gff3 databases
2008-02-22 16:09 lstein
* [r14535] improved behavior of xy and density plots when spanning
regions that contained undefined scores; now just skips over
these regions
2008-02-22 08:09 heikki
* [r14534] Do not print out empty KW (keyword) lines.
2008-02-21 22:09 cjfields
* [r14533] run tests directly in Build.PL (don't pass code refs on
to Module::Build)
2008-02-21 20:21 cjfields
* [r14532] TODO now works
2008-02-21 20:18 cjfields
* [r14531] fall back to empty set
2008-02-21 20:17 cjfields
* [r14530] now deprecated
2008-02-21 19:48 cjfields
* [r14529] Sequence gained a nucleotide
2008-02-21 19:48 cjfields
* [r14528] bug 2438. 'X' can't be completely disambiguated from a
protein sequence anymore
2008-02-21 19:32 cjfields
* [r14527] add file test, unlink if already present
2008-02-21 19:20 cjfields
* [r14526] add Graph::Directed to requirements for tests
2008-02-21 18:45 cjfields
* [r14525] fix CUTG tests
2008-02-21 17:30 cjfields
* [r14524] Now passes tests; added warnings for no returned exons
when called
2008-02-20 22:38 cjfields
* [r14523] tests for bug 2453
2008-02-20 21:51 cjfields
* [r14522] Bug 2453; needs tests
2008-02-20 21:30 cjfields
* [r14521] Oops! Bug 2453 again.
2008-02-20 21:13 cjfields
* [r14520] small fix for bug 2453, but see bugzilla for reasons on
not closing this out
2008-02-20 17:03 cjfields
* [r14519] bug 2452
2008-02-20 01:15 fangly
* [r14517] New module Bio::Assembly::Tools::ContigSpectrum for
dealing with contig spectra obtained from metagenome assembly
2008-02-19 08:51 heikki
* [r14516] FTId is no longer treated a part of the description of
an FT key but similarly to EMBL FT qualifiers. This allows for
100% roundtrip of the Feature Table.
2008-02-19 08:17 heikki
* [r14515] Reindenting the code. Too many lines were slightly off
making reading difficult. No code changes.
2008-02-19 06:57 heikki
* [r14514] Reindenting the code. Too many lines were slightly off
making reading difficult. No code changes.
2008-02-19 02:31 cjfields
* [r14513] TODO now works
2008-02-17 11:36 heikki
* [r14512] DOI can include
2008-02-17 11:29 heikki
* [r14511] prevent line wrapping within author name (RA lines) and
withing key frase (KW lines), but allow wrapping at hyphen in a
title (RT lines)
2008-02-17 10:00 heikki
* [r14510] GN line output now follows the new format. BioPerl would
need new objects to store all infomation so for now only the
official name (Name=) and synonym categories are kept. ORFNames
and OrderedLocusNames are treated as synonyms.
2008-02-17 09:48 heikki
* [r14509] removed extra space chars and a full stop at the end of
the FT HELIX and STRAND lines. No more extra spaces at the end of
the line. The line length in this format is 76, not 80. Changeing
that solved a lot of line differences
2008-02-13 20:38 cjfields
* [r14508] update interface documentation
2008-02-13 20:31 cjfields
* [r14507] not 1.5.3 (modules don't work anymore)
2008-02-13 08:08 heikki
* [r14506] Rewrote RX line parsing and writing to allow DOI values
seen and printed out
2008-02-13 06:51 heikki
* [r14505] PE (evidence) line was printed out between CC and DR
lines when it needs to be between DR and KW lines
2008-02-13 06:39 heikki
* [r14504] Changed the swissprot parser to work regardless of the
end full stop character in DT lines. This solved an old problem
with a workaround in the swiss.t: "grabbing seq_update with old
SwissProt seqs fails roundtrip tests" Now make sure to print it
out for each DT line.
2008-02-13 05:54 heikki
* [r14503] removed BASE COUNT line printing code. Genbank does not
use it any more. This should be safe, because GenPept has never
had it and all (most?) genbank format parsers can deal with both
formats
2008-02-13 05:36 heikki
* [r14502] do not write a full stop at the end of the SOURCE line
2008-02-12 05:11 cjfields
* [r14501] missing getter/setter added
2008-02-12 04:09 cjfields
* [r14500] bug 2440
2008-02-11 01:55 cjfields
* [r14499] remove comment (make sure tempfile/tempdirs stored in
WrapperBase are removed).
2008-02-11 01:41 cjfields
* [r14498] Fix for bug 2413. Shouldn't we delegate all IO-related
functions to the internal IO object?
2008-02-10 04:37 cjfields
* [r14497] test commit msgs from /usr/local/bin
2008-02-10 04:29 cjfields
* [r14496] checking svn post commits to list
2008-02-07 19:26 cjfields
* [r14495] bug 2445: clean up hit table regex to skip N (Bernd's
suggestion); passes tests but needs more testing
2008-02-07 18:29 bosborne
* [r14494] Remove dead links, don't know what should replace them,
unfortunately
2008-02-07 14:33 lstein
* [r14493] Added missing documentation for memory and berkeleydb
adaptors.
2008-02-05 21:39 cjfields
* [r14491] changed URL
2008-02-05 20:39 cjfields
* [r14490] handles Bio::Taxon as well as Bio::Species now (might be
worth propogating to other SeqIO modules?)
2008-02-05 20:35 cjfields
* [r14489] * small rnamotif fix
* significance conforms to spec (evalue, then pvalue)
* update tests
2008-02-05 20:04 cjfields
* [r14488] bug 2444 (HSP::significance returning wrong value)
2008-02-05 16:35 lstein
* [r14485] fixed bug in featurefile processing that inappropriately
grouped features with no name
2008-02-05 03:46 lstein
* [r14484] fixed a logic error which caused undefined end
coordinates when creating a feature with abs=>1, a start and an
undefined end
2008-02-05 03:11 cjfields
* [r14483] bug 2438; 'X' no longer completely ambiguous
2008-02-05 02:37 cjfields
* [r14482] bug 2415
2008-02-05 02:16 cjfields
* [r14481] bug 2442
2008-02-04 23:41 cjfields
* [r14480] Fixed bits/raw_score issue related to GenericHit changes
to raw_score/bits
2008-01-31 23:02 cjfields
* [r14460] bug 2436; add option for 'mismatch' (no match w/o gaps)
2008-01-30 19:54 cjfields
* [r14459] Add simple method to retrieve parameter settings
2008-01-25 22:00 cjfields
* [r14458] Returned value from EntrezGene is different
2008-01-24 13:51 cjfields
* [r14457] Stefan's fix for entrezgene which includes a fix for
pseudohash warnings; works now using perl 5.10.
2008-01-22 20:49 lstein
* [r14456] new feature of -strand_arrow option allows you to
specify arrowheads only on first and last segment
2008-01-22 20:48 lstein
* [r14455] fixed up the gene glyph so that it works properly with
CDS-only genes
2008-01-22 00:16 cjfields
* [r14454] revert last commit; problem more serious than initially
appears (will require more debugging)
2008-01-21 23:57 cjfields
* [r14453] get rid of annoying 'pseudohashes' error; tests now pass
on perl 5.8.8, perl 5.10
2008-01-21 22:41 cjfields
* [r14452] Use db settings for both BioDBGFF and
BioDBSeqFeature_mysql (needs bypass testing for Pg and other
drivers)
2008-01-17 19:26 cjfields
* [r14451] remove format option for EMBL just in case...
2008-01-17 18:58 cjfields
* [r14450] bug 2433
2008-01-17 18:11 cjfields
* [r14449] Starter cross_match tests and sample data. Needs much
more testing (see notes in test file)
2008-01-17 17:35 cjfields
* [r14448] Tentative fix for bug 2427
2008-01-17 11:15 sendu
* [r14447] more fixes for synopsis code, added warning to
description
2008-01-17 11:08 sendu
* [r14446] fixed synopsis code to work
2008-01-17 06:09 cjfields
* [r14445] bug 2423
2008-01-17 02:57 cjfields
* [r14444] bug 2431
2008-01-16 10:54 sendu
* [r14443] improved handling of different kinds of feature object
2008-01-16 10:51 sendu
* [r14442] first version of Gerp parser, usable
2008-01-16 02:46 scain
* [r14440] fixing the missing space between the feature type name
and the location when the type name is longer than 15 char.
2008-01-15 21:56 cjfields
* [r14439] Bug 2426
2008-01-14 05:31 cjfields
* [r14437] test post-commit after fsfs transfer (2nd try)
2008-01-14 05:19 cjfields
* [r14436] test commits after fsfs transfer
2008-01-07 23:37 hartzell
* [r14435] * a simple test commit, added a blank line to the
bottom of the README file. I'll remove it in a moment.
README (modified)
2008-01-07 21:58 cjfields
* [r14429] Test
2007-12-15 19:32 jason
* [r11793] Short circuit if the a1 is 0 to avoid divide by zero
2007-12-15 19:30 jason
* [r11792] some formatting -- committing before SVN merge
2007-12-06 17:58 cjfields
* [r11791] small fix for VERSIONing issue, POD fixes
2007-12-05 20:31 skirov
* [r11790] Fixes sequence parsing for gapless alignments from
codeml (Bug 2416)
2007-12-04 04:13 scain
* [r11789] oops--missed a failed test because of a missing prereq.
2007-12-03 23:37 jason
* [r11788] actually parse percent similar numbers out properly, add
some tests to this effect, percent_conserved for nucleotide
alignments now represents ungapped numbers from FASTA/SSEARCH
2007-12-03 19:55 scain
* [r11787] the check for '>' was actually swallowing the first line
of a fasta file (where the fasta file was masquerading as a GFF3
file without any features). Now that works.
2007-12-03 08:29 heikki
* [r11786] correct syntax in the example; doc formatting
2007-11-29 22:54 cjfields
* [r11785] bug 2333; first pass at PSIBLAST XML parsing
2007-11-29 06:10 cjfields
* [r11784] Match HSP, not hit table
2007-11-29 06:09 cjfields
* [r11783] more memory-friendly
2007-11-28 21:21 cjfields
* [r11782] WUBLAST signif gets pvalue, NCBI BLAST signif gets
evalue
2007-11-28 06:29 cjfields
* [r11781] Several fixes
* bug 2409
* code to pull out the GI if present
* resolve most of the NCBI/WUBLAST bits/raw_score confusion,
changed tests to reflect (needs warnings, more docs)
* several tests added
* one test still failing for WU-BLAST reports and significance
parsing, so beware!
2007-11-27 23:14 jason
* [r11780] dependancies enumearated for Bio::PhyloNetwork
2007-11-27 23:13 jason
* [r11779] Initial commit of Phylogenetic Network code from Gabriel
Valiente and Gabriel Cardona
2007-11-27 23:07 jason
* [r11778] I'm pretty sure this returning correct values and tests
don't need to be TODOed
2007-11-25 18:50 cjfields
* [r11777] bug 2329
* code added to Bio::SeqIO::abi to optionally grab trace data
* tests added to abi.t, requires newest staden::read (1.52).
2007-11-25 17:06 cjfields
* [r11776] bug 2329, example script to generate a SVG chromatogram
2007-11-25 16:50 cjfields
* [r11775] bug 2329
2007-11-25 16:37 cjfields
* [r11774] get rid of 'Use of uninitialized value in concatenation'
warnings
2007-11-25 15:37 cjfields
* [r11773] Related to Albert's fix
2007-11-25 11:49 avilella
* [r11772] speed boost by not calculating _symbols -- because this
will be calculated anyway when calling symbol_chars, we dont need
to calculate it here for all alns
2007-11-23 09:27 heikki
* [r11771] no more hardcoded line length, default changed to 25
values, value for
width() can be given to the constructor. Uniform indentation of
code
to avoid excessively long lines.
2007-11-23 09:01 heikki
* [r11770] write_seq() now writes out desc string
2007-11-21 17:49 cjfields
* [r11769] bug 2399
2007-11-21 17:26 cjfields
* [r11768] a bit more for bug 2391
2007-11-21 17:15 cjfields
* [r11767] bug 2391
2007-11-21 16:48 cjfields
* [r11766] bug 2406
2007-11-21 15:56 smckay
* [r11765] Changes to allow non-coding RNA genes and pseudogenes.
2007-11-19 18:37 cjfields
* [r11764] bug 2392
2007-11-19 18:31 cjfields
* [r11763] bug 2399
2007-11-18 01:30 jason
* [r11762] add trailing newline
2007-11-16 19:37 cjfields
* [r11761] fix fuzzy location bug
2007-11-16 02:35 bosborne
* [r11760] Jeffrey's patch, tests pass
2007-11-13 18:28 cjfields
* [r11759] Now catches primary GI
2007-11-10 04:47 cjfields
* [r11758] Fix for mysql adaptor to recursively remove child
features only if when all parents are removed
2007-11-08 05:36 cjfields
* [r11757] fix arg list not being passed along if GFF3 is intended
2007-11-08 02:20 cjfields
* [r11756] Allow phase to be set
2007-11-08 02:19 cjfields
* [r11755] * alias delete_features (for GBrowse plugins)
* allow IO::String (for GBrowse plugins)
2007-11-06 19:47 jason
* [r11745] allow . in the names
2007-11-06 19:43 jason
* [r11744] Don't we need to include Bio::Tools::GFF
2007-11-05 15:27 scain
* [r11741] adding name to sort order options
2007-11-04 00:11 dave_messina
* [r11740] Bug 2388 fix - added support for WU-BLAST -echofilter
option. added test to SearchIO.t.
All SearchIO tests pass.
2007-11-02 16:29 sendu
* [r11739] fixed error when source() sets its own default value
2007-11-01 14:52 jason
* [r11738] Parsing PAML4 and PAML3.15 should work now. Dealing with
variable order for the sequences and summary results in the top
of the MLC files
2007-11-01 14:51 jason
* [r11737] add Codeml pairwise result for PAML4
2007-10-31 09:45 avilella
* [r11736] using Bio::Tools::GuessSeqFormat
2007-10-30 16:33 jason
* [r11735] Fixes from Claude Rispe and Fabrice Legeai for RST
parsing.
2007-10-26 18:39 avilella
* [r11734] render a svg of a multiple sequence alignment -- green
boxes for matches/mismatches vs lines for gapped regions
2007-10-26 18:22 jason
* [r11733] fix Genewise data moving and tests
2007-10-26 16:47 sendu
* [r11732] Changed B::SF::Annotated to behave more like Generic
(seq_id, score, phase, frame all return strings) and be more
internally consistent: source() and type() only accepts and
returns objects, source_tag() and primary_tag() accept and return
strings. Other modules and test scripts updated as appropriate
2007-10-23 19:31 cjfields
* [r11731] error in test script
2007-10-23 16:50 cjfields
* [r11730] bug 2385
2007-10-23 16:18 cjfields
* [r11729] bug 2368
2007-10-23 16:11 cjfields
* [r11728] bug 2367
2007-10-18 03:34 cjfields
* [r11727] some tweaks
2007-10-17 01:31 lstein
* [r11726] accepted Danny Rice's proposed patch for improving
performance and accuracy of %GC glyph
2007-10-17 01:22 lstein
* [r11725] squelched warning about empty sequence in
Bio::DB::GFF::Feature->seq() call when no DNA has been attached
2007-10-16 19:28 lstein
* [r11724] all GFF and GFF3 stores now return the type of the
feature in the information returned by search_notes()
2007-10-16 14:19 bosborne
* [r11723] Check frame of 2, just for the sake of completeness
2007-10-15 15:39 cjfields
* [r11722] bug 2332
2007-10-09 04:19 cjfields
* [r11721] start must always be < end; strand determines
directionality
2007-10-08 21:34 cjfields
* [r11720] capture display_name, score data for Glimmer3 predict
file
2007-10-05 16:36 cjfields
* [r11719] typo
2007-10-05 00:27 cjfields
* [r11718] * bug fix from Jeffrey Barrick for cases where empty
midline data occurs
* add simple synopsis, update POD
2007-10-04 19:03 jason
* [r11717] force MYISAM for FULLTEXT indexed tables
2007-10-04 15:13 cjfields
* [r11716] always use table type to MyISAM for FULLTEXT indexing
2007-10-01 15:18 scain
* [r11715] Fix for the case when the Parent tag isn't present; also
improving regex in GFF tool
2007-09-28 18:00 jason
* [r11714] allow -ID to be set on init
2007-09-28 15:37 cjfields
* [r11713] don't use Carp, use $self->warn()
2007-09-28 03:17 cjfields
* [r11712] fix bug with multiple ID, DE, AC lines
2007-09-27 22:10 cjfields
* [r11711] * add line_length parameter for stockholm to print
blocks; default is all on one line (Pfam-like)
* hacked in meta support for SimpleAlign::slice()
2007-09-27 19:45 cjfields
* [r11710] Add meta data to alignments if present
2007-09-27 19:43 cjfields
* [r11709] remove nonexistent exported sub
2007-09-27 15:47 cjfields
* [r11708] minor change to prevent scripts from dying
2007-09-27 15:40 cjfields
* [r11707] Add obo to registry
2007-09-27 15:40 cjfields
* [r11706] Switch to using SO and OBO
2007-09-26 14:06 jason
* [r11705] POD copy+paste fix
2007-09-25 22:08 cjfields
* [r11704] Rollback last commit, don't want to change lca node data
directly
2007-09-25 21:50 cjfields
* [r11703] bug 2219
2007-09-24 13:27 sendu
* [r11702] removed repeated print of version line
2007-09-24 13:13 cjfields
* [r11701] POD fix
2007-09-21 10:00 sendu
* [r11700] compatability changes with recent feature annotation
rollback
2007-09-21 08:46 sendu
* [r11699] safer open, corrected throw message in sort_by_list
2007-09-20 16:23 lstein
* [r11698] was incorrectly adding vertical spacing to the
description's vertical offset twice
2007-09-20 15:51 sendu
* [r11697] in GTF mode, allow the setting of transcript id and gene
id independently, allow no score, allow frame to be supplied with
frame()
2007-09-20 15:21 sendu
* [r11696] major bugfix: this module now actually does something!
2007-09-20 15:07 lstein
* [r11695] removed a spurious lock() call which caused
Bio::Graphics::Panel to fail under some versions of perl
2007-09-19 19:17 lstein
* [r11694] documented -fallback_to_rectangle option
2007-09-17 20:54 cjfields
* [r11693] remove overloading exceptions (more trouble than they're
worth)
2007-09-17 06:47 jason
* [r11692] lowercase typo
2007-09-14 16:37 cjfields
* [r11691] mail list patch from Jay Hannah
2007-09-14 11:53 cjfields
* [r11690] bug 2352
2007-09-13 14:29 skirov
* [r11689] copy/paste error fixed: module name in Synopsis
2007-09-13 14:19 skirov
* [r11688] ->new repeated
2007-09-11 00:58 cjfields
* [r11687] bug 2358
2007-09-10 17:34 cjfields
* [r11686] bug 2350
2007-09-10 17:04 cjfields
* [r11685] bug 2354
2007-09-10 16:42 cjfields
* [r11684] bug 2358, added some more tests for Assembly objects
2007-09-08 03:14 cjfields
* [r11683] bug 2358
2007-09-06 06:57 lstein
* [r11682] minor change to featurebase to allow gbrowse das
entry_points request to work properly
2007-09-05 22:16 cjfields
* [r11681] Shouldn't use Carp, use throw/warn instead
2007-09-05 20:29 cjfields
* [r11680] 2357
2007-09-05 14:36 cjfields
* [r11679] add in hack for alignment viewer
2007-09-05 12:14 sendu
* [r11678] added GPL License
2007-09-05 11:00 sendu
* [r11677] changed license to "perl", ie. artistic or GPL
2007-09-05 03:59 cjfields
* [r11676] change sub redefining to to simple handler dispatch
2007-09-05 02:57 cjfields
* [r11675] parses 0.81 output (still throwing a warning...)
2007-09-03 01:45 cjfields
* [r11674] doc fixes
2007-08-31 03:03 cjfields
* [r11673] doc fixes
2007-08-31 00:22 cjfields
* [r11672] bug 2203
2007-08-30 18:46 cjfields
* [r11671] * Annotation : explain display_text() more explicitly;
remove commented out overloads
* Ontology fixes: dagflat/obo parsers now make DBLinks, use
add_dbxref
* tests : added note on changes; DBLinks call display_text for
simple sort or comparison
2007-08-29 22:07 cjfields
* [r11670] get rid of extra 'my' declarations
2007-08-29 21:39 cjfields
* [r11669] Feature-Annotation rollback (merged over from branch)
2007-08-29 18:07 cjfields
* [r11668] add note about graphics tests; we'll need to allow
regenerating the test files at some point
2007-08-29 15:45 cjfields
* [r11667] remote data from server has changed
2007-08-29 15:13 cjfields
* [r11666] committed file with DOS line endings which caused
warnings, change data file to UNIX
2007-08-29 15:01 cjfields
* [r11665] fix redefined sub warning
2007-08-27 16:31 jason
* [r11654] return undef when demon is 0 for now in Tajima's D
2007-08-27 15:55 lstein
* [r11653] killed redundant my declaration in order to get rid of
-w warning
2007-08-27 15:47 lstein
* [r11652] line glyph was not respecting the linewidth option!
2007-08-26 23:33 jason
* [r11650] for now let's report the offending codon in the message
2007-08-26 22:29 jason
* [r11649] some small code compaction in attempt to optimize, not
sure it actually helped
2007-08-26 22:29 jason
* [r11648] Fix some POD that was wrong. Test for completely missing
outgroup and throw on error.McDonald-Kreitman returns a 5th
value, hashref of warning messages about codons states (gapped,
too many alleles, etc).
2007-08-26 22:27 jason
* [r11647] Code optimization. Can skip ISA checking when building
Population. Streamline code for building populations from
alignments. Seems to have small perf improvement based on
profiling
2007-08-26 22:27 jason
* [r11646] Code optimization. Can force a skip ISA checking for
small speed boost
2007-08-26 20:13 jason
* [r11645] skip when we encounter gaps -- to better parameterize
this in the future
2007-08-24 21:15 lstein
* [r11629] linewidth setting was being ignored when drawing filled
arrows
2007-08-23 04:02 cjfields
* [r11625] fix POD syntax
2007-08-21 21:55 cjfields
* [r11624] initial commit; simple index class for Rfam/Pfam
alignments
2007-08-21 16:14 cjfields
* [r11623] catch ERROR flag
2007-08-20 21:08 jason
* [r11622] get the count right every time
2007-08-20 11:21 cjfields
* [r11621] speed up indexing, add id_parser() method
2007-08-20 01:01 cjfields
* [r11620] add convenience method to munge IDs from file if asked
(still working on)
2007-08-20 01:00 cjfields
* [r11619] add docsum printing convenience method.
2007-08-20 00:58 cjfields
* [r11618] Catch algorithm and version if -m 9
2007-08-20 00:57 cjfields
* [r11617] Initial commit; index class for -m 9 BLAST output
2007-08-15 15:24 sendu
* [r11616] removed debugging throw from last commit
2007-08-15 15:11 sendu
* [r11615] added tests for bug 2344
2007-08-15 15:10 sendu
* [r11614] bug 2344 fixed
2007-08-15 15:06 sendu
* [r11613] end() now allows getting and setting of 0, allowing the
representation of gaps-only in a sequence alignment
2007-08-15 08:55 heikki
* [r11612] hack to get LiveSeq working with newer EMBL seqs with
more verbose
molecule type strings. (Method is still misleadingly called
alphabet.)
2007-08-14 08:13 nathan
* [r11611] Changed variable name so that multiple "my" statements
don't mask others in the same scope
2007-08-08 20:38 cjfields
* [r11610] add use statement if only wanting to index; fix
debugging
2007-08-02 20:47 cjfields
* [r11609] infernal 0.81 parsing not implemented yet
2007-08-02 17:48 cjfields
* [r11608] bug fix and cleanup; genemap not loaded in some cases,
so let Bio::Root::IO do the error throwing.
2007-08-02 09:42 sendu
* [r11607] test for 0 valued positions
2007-08-02 09:15 sendu
* [r11606] fixed bug in setting position value of 0
2007-08-02 03:35 scain
* [r11605] removing a deadly debugging statement
2007-08-02 03:29 scain
* [r11604] fixing empty fasta database (the adaptor was partially
changed to use locally scoped filehandles)
2007-07-31 15:32 sendu
* [r11603] no longer prints a space at the end of the sequence name
in write_aln()
2007-07-30 15:46 cjfields
* [r11602] bug 2335
2007-07-28 06:41 jason
* [r11601] don't force blankallele matching to be case insensitive.
Update pattern to take this into account
2007-07-24 20:22 cjfields
* [r11600] forogt to commit docs
2007-07-24 20:22 cjfields
* [r11599] take out history setting from LinkSet for now until I
can work out the kinks
2007-07-24 19:03 cjfields
* [r11598] small fix for entrez links
2007-07-24 18:08 cjfields
* [r11597] Simplify; remove history queue and make epost part of
Query; parser now has-a HistoryI (not is-a HistoryI)
2007-07-24 16:46 lstein
* [r11596] forgot to flip the GC content glyph when panel is
flipped
2007-07-23 14:42 cjfields
* [r11595] Catch failing tie'd DB_File handle
2007-07-19 01:10 cjfields
* [r11594] bug 2334
2007-07-18 17:37 cjfields
* [r11593] Bug 2212
2007-07-18 04:56 cjfields
* [r11592] bug 2286
2007-07-17 21:00 cjfields
* [r11591] add XML::DOM::XPath
2007-07-17 18:40 cjfields
* [r11590] Stop complaints with '.' (attributeless features);
should we change to a warning?
2007-07-17 18:37 cjfields
* [r11589] Bug 2302
2007-07-17 17:21 cjfields
* [r11588] bug 2178
2007-07-17 16:07 cjfields
* [r11587] doc fixes for ace parsing, clarify warning more
2007-07-17 16:03 cjfields
* [r11586] fix use base()
2007-07-17 16:02 cjfields
* [r11585] add unimplemented method write_assembly; removed SeqIO
carryover
2007-07-17 15:58 cjfields
* [r11584] bug 2320
2007-07-16 19:11 jason
* [r11583] move transcript score to transcript, set gene score as
overall score FWIW
2007-07-16 14:04 cjfields
* [r11582] is, not ok
2007-07-16 04:14 cjfields
* [r11581] bug 2282
2007-07-16 03:53 cjfields
* [r11580] use CORE::close() to close file
2007-07-16 03:41 cjfields
* [r11579] test out getting rid of some of the multiple regex
matches (to simplify things...)
2007-07-16 02:53 cjfields
* [r11578] bug 1986 and GCG BLAST fixes (got the TODO working)
2007-07-16 01:12 cjfields
* [r11577] bug 1986 (part deux)
2007-07-15 21:40 cjfields
* [r11576] bug 1986 (second bit)
2007-07-15 19:55 cjfields
* [r11575] bug 1986 tests
2007-07-15 19:46 cjfields
* [r11574] BPLite (and ilk) deprecated
2007-07-15 19:45 cjfields
* [r11573] unnecessary use Carp
2007-07-15 19:43 cjfields
* [r11572] small fix to deal with attribute-less GFF files (prob.
should be a warn() here...)
2007-07-15 19:41 cjfields
* [r11571] partial fix for bug 1986
2007-07-13 20:12 jason
* [r11570] unique_id not person_id
2007-07-13 20:12 jason
* [r11569] Add test for remove Individuals and allele freq
2007-07-13 16:00 sendu
* [r11568] only id, start, end are required: fixed to not require
optional fields
2007-07-12 10:42 sendu
* [r11567] cleaned up to avoid warnings
2007-07-09 08:54 sendu
* [r11566] removed pointless print of 0-length string
2007-07-09 01:35 cjfields
* [r11565] Use double quotes to interpolate
2007-07-09 01:34 cjfields
* [r11564] $value is undef in some cases (apparently from
GBrowseGFF SearchIO writer)
2007-07-09 01:33 cjfields
* [r11563] eutils fixes
2007-07-06 22:51 jason
* [r11562] remove debugging
2007-07-06 22:40 jason
* [r11561] more FASTA-35 fixes, support multi-report files, parse
Library section properly
2007-07-06 04:59 cjfields
* [r11560] Must allow other SearchIO readmethods (anything that
starts with 'blast')
2007-07-05 15:51 sendu
* [r11559] changed to use Test::Exception and Test::Warn syntax
2007-07-05 15:49 sendu
* [r11558] throw() fixed to print throw message starting with a
dash when Error.pm is not loaded; debug() reimplemented with
CORE::warn
2007-07-05 15:46 sendu
* [r11557] warn() reimplemented to use CORE::warn instead of print
STDERR, for Test::Warn compatability
2007-07-05 15:43 sendu
* [r11556] adjusted for new Bioperl warning output
2007-07-05 13:05 sendu
* [r11555] Added copy of Test::Warn, its dependencies and
Test::Warn::Bioperl subclass
2007-07-05 12:58 sendu
* [r11554] loads Test::Warn::Bioperl to allow the testing of
warnings
2007-07-05 09:34 sendu
* [r11553] added copy of Test::Exception and its dependencies
2007-07-05 09:33 sendu
* [r11552] now loads in Test::Exception
2007-07-05 09:31 sendu
* [r11551] improved syntax
2007-07-04 22:08 jason
* [r11550] minor reformatting
2007-07-04 22:08 jason
* [r11549] Changed API to used named parameters and only need
ingroup and outgroup not total population. Polarized now works
2007-07-03 21:32 jason
* [r11548] FASTA-35 parsing tweak
2007-07-03 14:07 cjfields
* [r11547] lightweight HistoryI holder (used in a queue in place of
parser)
2007-07-03 14:06 cjfields
* [r11546] introduce lightweight HistoryI (aka cookies) to decouple
data from parser
2007-07-03 12:14 sendu
* [r11545] added -mixed_dash option to _setparams()
2007-07-03 12:05 sendu
* [r11544] fixed compression test for cases that a temp file has to
be made
2007-07-03 07:59 sendu
* [r11543] fixed skips, typos
2007-07-02 16:55 cjfields
* [r11542] Changed class name to something more relevant
2007-07-02 16:53 cjfields
* [r11541] A few changes; changed poorly named GenericWebDBI to
GenericWebAgent, clean up some methods, etc.
2007-07-02 14:51 cjfields
* [r11540] bug 2321
2007-07-02 12:49 cjfields
* [r11539] bug 2325
2007-07-02 06:22 jason
* [r11538] McDonald-Kreitman implementation
2007-07-02 02:53 cjfields
* [r11537] bug 2262
2007-07-02 02:52 cjfields
* [r11536] bug 2262 (add caveat, TODO about Meta::Array interface
ambiguity)
2007-07-02 01:15 cjfields
* [r11535] bug 2305
2007-07-02 01:01 cjfields
* [r11534] bug 2288
2007-07-01 22:52 cjfields
* [r11533] bug 2317
2007-07-01 22:02 cjfields
* [r11532] bug 2299
2007-07-01 21:43 cjfields
* [r11531] bug 2295
2007-06-28 18:06 cjfields
* [r11530] Add optional history queueing, other things
2007-06-28 18:04 cjfields
* [r11529] added a few new methods
2007-06-27 15:14 sendu
* [r11528] fixed handling of compressing/uncompressing files not
owned by user
2007-06-27 10:58 sendu
* [r11527] corrected in/outfile problem
2007-06-27 10:27 sendu
* [r11526] corrected in/outfile problem
2007-06-27 10:16 sendu
* [r11525] reimplemented with BioperlTest
2007-06-27 10:15 sendu
* [r11524] Test.pm no longer used by any test script
2007-06-27 08:34 sendu
* [r11523] added missing use Bio::Range statement
2007-06-26 15:43 sendu
* [r11522] allowed specification of a minimum version of a required
module, improved missing module feedback
2007-06-26 14:41 cjfields
* [r11521] obsolete (functionality moved to Bio::Tools::EUtilities)
2007-06-26 14:38 cjfields
* [r11520] commits for overhaul (finally got POST working)
2007-06-26 13:50 sendu
* [r11519] allow the skipping of all tests due to deprecation
2007-06-26 12:49 sendu
* [r11518] removed empty lines at start to avoid meaningless diff
in new SeqIO test
2007-06-26 12:48 sendu
* [r11517] obsolete, tests moved to SeqIO.t
2007-06-26 09:37 sendu
* [r11516] flush after every write_result
2007-06-26 08:55 sendu
* [r11515] revcom no longer tries to multiply strand if it is not
set
2007-06-25 19:06 cjfields
* [r11514] Implement eutils callbacks, iterator generation, lazy
parsing. Need to make seekable iterators (for rewind()) and clean
up POD.
2007-06-25 14:25 sendu
* [r11513] bug fix: flush on write!
2007-06-25 14:00 sendu
* [r11512] be silent if verbose 0 or less
2007-06-25 12:06 sendu
* [r11511] solved uninitialized value in -x
2007-06-25 03:43 cjfields
* [r11510] Cleaning up API, need to clean up POD and make callbacks
more consistent
2007-06-23 04:43 cjfields
* [r11509] eutils parsers, part of EUtilities overhaul (still need
some work and tests)
2007-06-23 01:38 jason
* [r11508] use DEBUG instead of STDERR
2007-06-23 01:37 jason
* [r11507] refixed - now will get NHX bootstraps properly and parse
empty [&&NHX] fields
2007-06-23 01:19 jason
* [r11506] deal with empty NHX fields as seen in NJTREE
2007-06-22 16:07 rdobson
* [r11505] Initial submission
2007-06-22 15:55 sendu
* [r11504] more POD, catch more user errors
2007-06-22 10:52 sendu
* [r11503] added test_output_file() and test_input_file() methods
2007-06-22 09:42 sendu
* [r11502] added -requires_module option to compliment
-requires_modules
2007-06-21 15:55 sendu
* [r11501] print only when verbose
2007-06-21 14:51 sendu
* [r11500] converted to BioperlTest
2007-06-21 14:50 sendu
* [r11499] improved output, docs
2007-06-21 14:11 sendu
* [r11498] added protection again arg typos, new option excludes_os
2007-06-21 08:25 sendu
* [r11497] added more POD
2007-06-21 08:17 sendu
* [r11496] added test_skip() method
2007-06-20 15:15 sendu
* [r11495] reimplemented with BioperlTest
2007-06-20 15:14 sendu
* [r11494] new base module for Bioperl tests
2007-06-19 18:41 scain
* [r11493] fixing polypeptide features so that they use
'Derives_from' instead of 'Parent'
2007-06-19 16:38 scain
* [r11492] fixing a minor bug
2007-06-19 14:58 cjfields
* [r11491] taking tests offline for the time being until I finish
updates
2007-06-19 06:46 sendu
* [r11490] revert last change: its not supposed to access the db to
find descendents
2007-06-19 00:57 jason
* [r11489] this method needs to delegate to the db handle to get
the children
2007-06-18 17:44 jason
* [r11488] Converted to Test::More
2007-06-18 10:45 sendu
* [r11487] removed extraneous code
2007-06-18 09:46 sendu
* [r11486] implemented the --network option to request network
tests
2007-06-14 22:50 jason
* [r11485] add $
2007-06-14 22:49 jason
* [r11484] Added support for printing bootstrap values
2007-06-14 21:35 sac
* [r11483] Removed the obsolete Bio::Root::Global module and use of
the
verbosity() method (not essential for demo-ing this module).
2007-06-14 18:39 cjfields
* [r11482] Removed two tests; the warning that these tests caught
is no
longer there (the parser just bypasses blank lines, so no need).
2007-06-14 18:01 nathan
* [r11481] POD corrections
2007-06-14 14:16 sendu
* [r11480] removed bad "new Bio::Module" syntax, replaced with
"Bio::Module->new"
2007-06-14 14:00 sendu
* [r11479] removed bad "new Bio::Module" syntax, replaced with
"Bio::Module->new"
2007-06-14 13:38 sendu
* [r11478] moved to Test::More, 2 tests currently failing
2007-06-14 13:13 sendu
* [r11477] fixed skipping
2007-06-13 22:47 nathan
* [r11476] Test for checking POD syntax
2007-06-11 15:58 heikki
* [r11475] overall_percentage_identity() enhancements by Hongyu
Zhang. Bugzilla #2304
2007-06-11 15:55 heikki
* [r11474] I always forget to increase NUMTESTS!
2007-06-11 15:52 heikki
* [r11473] tests for overall_percentage_identity() enhancements by
Hongyu Zhang. Bugzilla #2304
2007-06-08 10:49 sendu
* [r11472] added a little extra advice on what to do when
encountering test failures
2007-06-07 17:49 cjfields
* [r11471] Some more fixes for bug 2305
2007-06-07 16:00 sendu
* [r11470] corrected skips
2007-06-07 15:48 sendu
* [r11469] corrected skip behaviour; still need a solution for when
server fails to return any data
2007-06-07 15:13 sendu
* [r11468] corrected number of tests
2007-06-05 23:46 cjfields
* [r11467] Partial fix for bug 2305
2007-06-05 15:07 cjfields
* [r11466] prettify verbose warnings a little more
2007-06-03 21:19 lstein
* [r11465] added optional debug statements to the xyplot glyph
2007-05-31 16:41 mcook
* [r11464] add newline at end of file
2007-05-31 16:29 mcook
* [r11463] improved diagnostic error message when reporting on
Incorrect parameters
2007-05-31 16:25 mcook
* [r11462] add 'Name' as column 9 attribute if feature implements
'name' such as might be for Bio::DB::SeqFeature
2007-05-31 16:08 dave_messina
* [r11461] Correcting docs per bug #2303. Thanks to Heikki
Lehvaslaiho for the report.
2007-05-31 15:57 dave_messina
* [r11460] Correcting docs per bug #2303. Thanks to Heikki
Lehvaslaiho for the report.
2007-05-29 04:51 jason
* [r11459] don't need to guess the alphabet if we already know it
2007-05-29 04:28 jason
* [r11458] revert ... my mistake
2007-05-29 04:27 jason
* [r11457] POD fix in SYNOPSIS
2007-05-25 10:11 sendu
* [r11456] tempered last commit to avoid warnings when there is no
significance
2007-05-25 10:10 sendu
* [r11455] _set_from_args fixed to return 0 from created methods if
set with 0
2007-05-23 22:42 lstein
* [r11454] fixed a problem which caused scale not to match upper
values correctly
2007-05-23 05:52 dave_messina
* [r11453] Fix for Bug 2300 -- thanks to Wayne Clarke for reporting
it and supplying the patch.
2007-05-21 20:41 cjfields
* [r11452] Remove incomplete module (OK'd per Allen Day)
2007-05-17 10:51 lstein
* [r11451] fixed documentation for map_pt()
2007-05-16 14:12 sendu
* [r11450] moved to Test::More, no longer tests the deprecated
BPLite _READMETHOD, tests the new blast_pull instead
2007-05-16 14:11 sendu
* [r11449] reimplemented to use _set_from_args and _setparams;
wublast params now properly case insensitive and do not get
infected by NCBI params; NCBI switches can be set with boolean;
param values with spaces now auto-quoted
2007-05-16 13:25 sendu
* [r11448] _setparams now quotes values that contain spaces
2007-05-16 09:29 sendu
* [r11447] bodge fix for commas leaking into evalues somewhere in
Bio::SearchIO::blast
2007-05-16 07:49 sendu
* [r11446] hit table can be empty?
2007-05-16 07:43 sendu
* [r11445] fixed hit table parsing error: scores can contain e
2007-05-15 10:20 sendu
* [r11444] fixed hit table parsing bug and hsp evalues: evalues can
start with an e (ie no number)
2007-05-14 15:48 sendu
* [r11443] bug2293
2007-05-14 15:39 sendu
* [r11442] fix for hits with no descriptions
2007-05-14 15:38 sendu
* [r11441] fix to use the correct new module
2007-05-14 14:17 sendu
* [r11440] roundinc accuracy increased, tests updated to match
2007-05-14 12:58 sendu
* [r11439] undo debugging step of last commit
2007-05-14 12:55 sendu
* [r11438] dependencies can be in parents
2007-05-14 12:53 sendu
* [r11437] reimplemented start() and end() for speed - tiling not
necessary
2007-05-14 12:49 sendu
* [r11436] initial commit of blast pull modules and tests
2007-05-14 12:46 sendu
* [r11435] bug fix: get chunk methods no longer travel outside
chunk bounds
2007-05-14 12:23 sendu
* [r11434] added -code and -case_sensitve options to
set_from_args()
2007-05-12 22:59 jason
* [r11433] TreeIO magic to now automatically move bootstrap values
over if the user requests this - made it a global Bio::TreeIO
flag but is really only used in Bio::TreeIO::newick and nexus
2007-05-12 22:58 jason
* [r11432] test for method to move bootstrap values from id values
for internal nodes automatically
2007-05-12 22:58 jason
* [r11431] method to move bootstrap values from id values for
internal nodes automatically
2007-05-12 12:04 cjfields
* [r11430] initial commit; part of EUtilities overhaul
2007-05-12 04:20 dave_messina
* [r11429] NEW: initial import of
Bio::Search::Result::CrossMatchResult and
Bio::SearchIO::cross_match. Many thanks to Shin Leong for these.
2007-05-08 23:01 cjfields
* [r11428] small comment for tracking bug 1986
2007-05-08 23:00 cjfields
* [r11427] New generic interface encapsulating parameters and
helper methods
2007-05-03 21:14 mcook
* [r11426] redefine gff3_string to:
# Return GFF3 format for the feature $self. Optionally
# $recurse to include GFF for any subfeatures of the feature. If
# recursing, provide special handling to "remove an extraneous
level
# of parentage" (unless $preserveHomegenousParent) for features
# which have at least one subfeature with the same type as the
# feature itself (thus redefining Lincoln's "homogenous
# parent/child" case, which previously required all children to
have
# the same type as parent). This usage is a convention for
# representing discontiguous features; they may be created by
using
# the -segment directive without specifying a distinct -subtype
to
# Bio::Graphics::FeatureBase->new (or to Bio::DB::SeqFeature,
# Bio::Graphics::Feature). Such homogenous subfeatures created in
# this fashion TYPICALLY do not have the parent (GFF column 9)
# attributes propogated to them; but, since they are all part of
the
# same parent, the ONLY difference relevant to GFF production
SHOULD
# be the $start and $end coordinates for their segment, and ALL
# THIER OTHER ATTRIBUTES should be taken from the parent
(including:
# score, Name, ID, Parent, etc), which happens UNLESS
# $dontPropogateParentAttrs is passed.
2007-05-03 20:04 mcook
* [r11425] fixing up the RCS ID line
2007-05-03 20:00 mcook
* [r11424] initial checkin
2007-05-01 17:45 cjfields
* [r11423] small bug fixes
2007-05-01 17:43 cjfields
* [r11422] Update on v.0.81 output; will try to add parsing support
soon.
2007-04-30 16:58 scain
* [r11421] added a GMOD-specific custom tag: CRUD (Create, Replace,
Update, or Delete)
2007-04-27 15:05 cjfields
* [r11420] possible fix for bug 2279
2007-04-26 23:11 jason
* [r11419] whoops, I made a bug, test if we are in Result before
deciding to close it.
2007-04-22 20:17 jason
* [r11418] Handle reports with no ending stanza
2007-04-22 19:55 jason
* [r11417] move some cached-handler code over from blast to help in
speedup.
2007-04-22 17:08 lstein
* [r11416] another fix for negative coordinates
2007-04-22 11:07 spiros
* [r11415] Test::More migration
2007-04-20 22:43 cjfields
* [r11414] revamping eutils tests; ramping up for refactoring
2007-04-20 19:47 bosborne
* [r11413] Don's patch to the patch
2007-04-20 19:17 lstein
* [r11412] whitespace fix as per AJM's letter of 20 April 2007
2007-04-20 18:34 dave_messina
* [r11411] FIX: fixing typo for cvs-less Aaron Mackey.
2007-04-20 16:13 lstein
* [r11410] applied patch from Aaron Mackey that escapes source and
method values from inappropriate regexp matching
2007-04-19 21:55 spiros
* [r11409] test::more migration
2007-04-19 21:32 spiros
* [r11408] small typo fix
2007-04-19 20:53 cjfields
* [r11407] Fix for recent DB.t woes
2007-04-19 19:24 spiros
* [r11406] test::more migration
2007-04-19 14:21 cjfields
* [r11405] separate ID string generation into a private method
2007-04-19 13:13 sendu
* [r11404] cleanup, corrected perl syntax
2007-04-19 13:12 sendu
* [r11403] no more printing of non-existant values
2007-04-19 13:11 sendu
* [r11402] cleanup and skip all if necessary
2007-04-19 10:04 sendu
* [r11401] fix for "bizarre copy of array" bug
2007-04-19 09:54 sendu
* [r11400] corrected number of tests
2007-04-18 19:30 lstein
* [r11399] fixed Bio::DB::GFF and Bio::DB::SeqFeature::Store to
handle negative coordinates
2007-04-18 16:23 sendu
* [r11398] corrected skip numbers, but are the "No seqs returned"
skips valid?
2007-04-18 15:21 mcook
* [r11397] throw DBI error on failed DBI-connection
2007-04-17 21:14 jason
* [r11396] special MrBayes macro case, cleanup err msg a little
more
2007-04-17 17:16 cjfields
* [r11395] change odd messages to diag(); use isa_ok(), not ok
$obj->isa()
2007-04-17 10:36 spiros
* [r11394] test::more migration
2007-04-16 21:03 mcook
* [r11393] build_object_tree_in_tables died when its globalID was
0. Changing to hash existence test avoids this bug.
2007-04-16 19:55 lstein
* [r11392] added load_gff_file() and load_fasta_file() to
Bio::DB::GFF to avoid problems with the load_gff() and
load_fasta() methods when run in FastCGI/mod_perl environments
2007-04-16 18:27 cjfields
* [r11391] cleanup and convert to Test::More
2007-04-15 15:38 bosborne
* [r11390] Minor edits
2007-04-15 10:48 spiros
* [r11389] test commit, a single whitespace
2007-04-13 21:23 cjfields
* [r11388] bug 2271
2007-04-13 20:40 cjfields
* [r11387] bug 2272
2007-04-13 20:04 cjfields
* [r11386] fix Location.t; MitoProt.t now runs under BIOPERLDEBUG=1
2007-04-13 19:33 cjfields
* [r11385] cleanup from Test::More conversion
2007-04-13 19:24 cjfields
* [r11384] cleanup from Test::More conversion
2007-04-13 19:04 cjfields
* [r11383] forgot to uncomment
2007-04-13 19:04 cjfields
* [r11382] cleanup from Test::More conversion
2007-04-13 18:53 cjfields
* [r11381] cleanup from Test::More conversion
2007-04-13 18:32 cjfields
* [r11380] cleanup from Test::More conversion
2007-04-13 18:13 cjfields
* [r11379] cleanup from Test::More conversion
2007-04-13 17:57 cjfields
* [r11378] cleanup from Test::More convesion
2007-04-13 17:45 cjfields
* [r11377] cleanup from Test::More conversion
2007-04-13 17:31 cjfields
* [r11376] Small DB.t fixes; GenBank query is failing but may be
network issue
2007-04-13 17:30 cjfields
* [r11375] convert to Test::More
2007-04-13 16:50 cjfields
* [r11374] convert to Test::More; IMAGE_TESTS seem to fail but are
not run by default, not sure why yet...
2007-04-13 16:48 cjfields
* [r11373] convert to Test::More
2007-04-13 16:35 cjfields
* [r11372] cleanup tests; set network tests so they won't run
unless BIOPERLDEBUG is set
2007-04-13 05:43 jason
* [r11371] some error checking
2007-04-13 05:41 jason
* [r11370] do not need to include Root.pm
2007-04-12 22:57 cjfields
* [r11369] Convert to Test::More
2007-04-12 22:56 cjfields
* [r11368] cleanup cruft
2007-04-12 04:36 cjfields
* [r11367] moved to Test::More
2007-04-12 04:15 cjfields
* [r11366] bug 2270
2007-04-12 04:07 cjfields
* [r11365] move to Test::More
2007-04-12 03:41 cjfields
* [r11364] Finish M-N (convert to Test::More)
2007-04-11 21:50 cjfields
* [r11363] Don't forget lucy!
2007-04-11 21:48 cjfields
* [r11362] Finished L's (move to Test::More)
2007-04-11 20:22 cjfields
* [r11361] convert to Test::More
2007-04-11 19:26 cjfields
* [r11360] convert to Test::More
2007-04-11 19:17 cjfields
* [r11359] convert to Test::More
2007-04-11 19:08 cjfields
* [r11358] Convert to Test::More
2007-04-11 18:54 cjfields
* [r11357] convert to Test::More
2007-04-11 17:37 cjfields
* [r11356] convert to Test::More
2007-04-11 14:01 sendu
* [r11355] removed extraneous line from select_noncont, check also
that input contains appropriate numbers before attmepting a
numerical sort
2007-04-11 13:04 cjfields
* [r11354] select_noncont() sorts numerically by default (fixed),
pass 'nosort' to prevent sorting
2007-04-11 01:22 cjfields
* [r11353] bug 2264, 2265
2007-04-10 13:55 bosborne
* [r11352] Don's patch
2007-04-06 19:42 mcook
* [r11351] pass the "safest" value, 3, for $if_active parameter to
DBD::prepare_cached, as we don't know how caller may be using the
SeqFeatureStore
2007-04-05 17:07 cjfields
* [r11350] bug 2263
2007-04-05 14:35 bosborne
* [r11349] Don's patch, this allows simple Target values and
supports existing Bioperl scripts
2007-04-02 15:55 scain
* [r11348] added support for a new directive: ##organism (should
use common name if available)
2007-04-02 14:41 cjfields
* [r11347] write_seq() is not implemented
2007-04-02 01:18 cjfields
* [r11346] bug 2246
2007-04-02 00:47 cjfields
* [r11345] bug 2237
2007-03-30 21:17 dave_messina
* [r11344] FIX: skip of 'Text BLAST' section caused subsequent
tests to fail when BIOPERLDEBUG=0. Fixed.
2007-03-30 14:05 cjfields
* [r11343] Small bug which botches some report parsing
2007-03-30 12:59 sendu
* [r11342] any version of Scalar::Util will do?
2007-03-30 11:43 heikki
* [r11341] initial commit
2007-03-30 07:51 heikki
* [r11340] doc typos
2007-03-29 15:50 sendu
* [r11339] fix for get_tree - load Bio::Tree::Tree
2007-03-29 15:33 cjfields
* [r11338] Fix '.' being appended to scientific_name
2007-03-29 14:27 sendu
* [r11337] remove trailing dot from bracketed scientific names
2007-03-29 13:38 sendu
* [r11336] bodge for OS lines with brackets that none-the-less are
a complete scientific species names
2007-03-29 13:36 sendu
* [r11335] no re-declaration of variables
2007-03-29 13:34 sendu
* [r11334] fix for angle-bracket queries
2007-03-28 22:39 bosborne
* [r11333] Don's fixes, related to new version of genbank2gff3.pl
2007-03-28 03:39 cjfields
* [r11332] is(), not ok()
2007-03-28 02:18 bosborne
* [r11331] Don's changes
2007-03-27 15:09 scain
* [r11330] allowing special handling of 'comment' tags since they
have a special meaning in Bio::Annotation::Collection
2007-03-27 15:08 scain
* [r11329] allowing 'value' as an alias for the 'text' method, to
make it more interoperable with the Bio::Annotation::SimpleValue
object
2007-03-27 13:19 bosborne
* [r11328] Command line options
2007-03-27 12:56 cjfields
* [r11327] reroute data flow through data_handler() for centralized
control
2007-03-27 12:43 heikki
* [r11326] 'use base'
2007-03-27 09:54 sendu
* [r11325] author is Chris Fields
2007-03-26 19:38 cjfields
* [r11324] pass data in chunks using element_hash()
2007-03-26 18:36 cjfields
* [r11323] tests changes and additions
2007-03-26 18:35 cjfields
* [r11322] add warnings for unsupported methods
2007-03-26 18:17 cjfields
* [r11321] rnamotif fixes
2007-03-26 17:58 cjfields
* [r11320] parsing fixes
2007-03-26 15:57 scain
* [r11319] allowing Bio::FeatureIO::gff to diverge (ever so
slightly) from the GFF3 spec, to allow dbxref tags to be treated
the same as Dbxref tags.
2007-03-22 19:14 cjfields
* [r11318] bug 2246 tentative fix
2007-03-22 18:30 cjfields
* [r11317] bug 2245 (enhancement to allow relative paths for index
files)
2007-03-22 04:00 cjfields
* [r11316] fix some tests
2007-03-22 03:51 cjfields
* [r11315] test data for BIC tests
2007-03-21 17:34 cjfields
* [r11314] Removing redundant module; passes flat.t
2007-03-21 16:22 cjfields
* [r11313] bug 2242
2007-03-21 04:14 cjfields
* [r11312] Now passes v3 tests (at least the v3 output we have...)
2007-03-21 04:11 cjfields
* [r11311] Neil & Co.'s modified Signalp parser (bug 2203) - passes
Signalp.t/Signalp2.t
2007-03-20 22:43 bosborne
* [r11310] More recent spec, version 3
2007-03-20 16:31 cjfields
* [r11309] Changed throw() due to verbose output from Infernal
programs choking the stockholm parser
2007-03-19 20:37 cjfields
* [r11308] TargetP parser, data, and tests
2007-03-19 20:23 cjfields
* [r11307] bug 2240
2007-03-19 18:53 jason
* [r11306] correct package name in POD, use the seqname parsed from
the first ID since that will be full length, rather than what is
presented in the NN output
2007-03-19 16:42 bosborne
* [r11305] Don's patch for GFF3
2007-03-19 15:41 lstein
* [r11304] Fixed bug in which all featurefiles returned an
extraneous undef feature in response to features() method
2007-03-17 02:53 bosborne
* [r11303] Daniel's patch
2007-03-16 21:21 lstein
* [r11302] fixed bug in FeatureFile caused by changed behavior of
Text::ParseWords
2007-03-16 20:41 cjfields
* [r11301] getter/setter for comment type (not implemented yet)
2007-03-16 20:40 cjfields
* [r11300] tests (write_seq() for drivers not implemented yet)
2007-03-16 20:39 cjfields
* [r11299] seq format drivers and single handler module for
GenBank/EMBL/Swiss
2007-03-16 20:38 cjfields
* [r11298] Handler-based parsing interface
2007-03-15 17:30 cjfields
* [r11297] Move to Test::More
2007-03-15 17:10 cjfields
* [r11296] moved to Test::More
2007-03-15 16:23 cjfields
* [r11295] move to Test::More
2007-03-15 14:22 cjfields
* [r11294] new signalp parser (need to merge code and tests for
both parsers ala glimmer)
2007-03-15 14:20 cjfields
* [r11293] signalp test data
2007-03-15 14:20 cjfields
* [r11292] new signalp tests; change to Test::More
2007-03-14 19:14 cjfields
* [r11291] Move to Test::More
2007-03-14 19:13 cjfields
* [r11290] Fix which checks for BLAST header for text/tabular
output; the QBlast status field has disappeared causing an
infinite loop
2007-03-13 22:20 cjfields
* [r11289] Bug 2221
2007-03-13 22:15 cjfields
* [r11288] TandemRepeatsFinder parser (bug 2233)
2007-03-11 19:06 bosborne
* [r11287] Bio::Graph is deprecated
2007-03-11 15:21 bosborne
* [r11286] Rename
2007-03-11 15:19 bosborne
* [r11285] Rename, no bp_
2007-03-11 15:13 bosborne
* [r11284] Correct POD
2007-03-08 18:40 cjfields
* [r11283] switch to XML::SAX (not heavily tested); this module
needs to be heavily refactored per bug 2018
2007-03-08 17:44 nathan
* [r11282] added POD for name() method, an alias for asString().
2007-03-08 17:40 nathan
* [r11281] added POD for deprecated moltype() method.
2007-03-08 17:38 cjfields
* [r11280] params use '-'
2007-03-08 17:38 cjfields
* [r11279] add simple bracket_string() tests
2007-03-08 17:34 nathan
* [r11278] added POD for deprecated members() method.
2007-03-08 17:16 nathan
* [r11277] added POD for trunc()
2007-03-08 17:02 nathan
* [r11276] added POD for cuts_after(), an alias for cut() method
2007-03-08 17:00 nathan
* [r11275] added POD for model method, an alias for descriptor()
method
2007-03-08 16:53 nathan
* [r11274] POD method name correction
2007-03-08 16:51 nathan
* [r11273] added POD for get_feature_by_name
2007-03-08 16:41 nathan
* [r11272] POD method name correction
2007-03-08 16:32 nathan
* [r11271] POD method name correction
2007-03-08 16:26 cjfields
* [r11270] D* tests to Test::More
2007-03-08 16:12 nathan
* [r11269] POD added for deprecated program_reference() method.
2007-03-08 16:02 nathan
* [r11268] POD method name correction
2007-03-08 15:56 cjfields
* [r11267] Finish converting C* tests to Test::More
2007-03-08 14:40 cjfields
* [r11266] removed tests from old bracket_string method (will add
to Simplealign tests)
2007-03-08 04:53 cjfields
* [r11265] change to Test::More
2007-03-08 03:54 cjfields
* [r11264] change to Test::More
2007-03-08 01:49 cjfields
* [r11263] convert to Test::More
2007-03-08 00:36 cjfields
* [r11262] move to Test::More
2007-03-07 16:00 sendu
* [r11261] bug 2133: code matches docs
2007-03-07 15:06 sendu
* [r11260] added Scalar::Util as a requirment
2007-03-07 14:53 cjfields
* [r11259] bug 2221; this should catch most translate data out
there; passes all tests
2007-03-07 14:51 cjfields
* [r11258] Added data to spaces.nex for NEXUS TreeIO tests, no
longer need this file
2007-03-07 14:49 cjfields
* [r11257] this should deal with all varieties of translate lines
(fingers crossed!)
2007-03-07 14:36 sendu
* [r11256] corrected previously commited test, added new test for
bug 2193
2007-03-07 14:35 sendu
* [r11255] test data for bug 2193
2007-03-07 14:34 sendu
* [r11254] bug 2193 should now be fixed
2007-03-07 14:15 sendu
* [r11253] frac_aligned_sbjct method alias now points to the
correct method
2007-03-07 13:55 cjfields
* [r11252] Bug 2221
2007-03-07 03:46 cjfields
* [r11251] bug 2205
2007-03-06 21:56 cjfields
* [r11250] perltidy and untabify (no bug fix for 2221 yet)
2007-03-06 21:46 cjfields
* [r11249] change to Test::More; added some tests for bug 2221, but
skip until patch is fixed
2007-03-02 16:15 sendu
* [r11248] test for frac_aligned_hit: used to be over 1 with this
data
2007-03-02 16:00 sendu
* [r11247] fix for incorrect frac_aligned_query() etc. caused by
bug in contig merging
2007-03-02 02:38 cjfields
* [r11246] additional spliced_seq tests (per Jay Hannah)
2007-03-01 20:28 jason
* [r11245] bug #2220
2007-03-01 16:36 scain
* [r11244] allowing featureloc entries for top level features when
an external srcfeature is specified
2007-03-01 07:49 heikki
* [r11243] typo in documentation
2007-03-01 04:57 scain
* [r11242] added GFF source handling; also added defaults for some
values that were ending up uninitialized
2007-02-27 18:37 cjfields
* [r11241] Add doi() get/setter
2007-02-27 13:40 cjfields
* [r11240] move to Test::More
2007-02-27 00:26 lstein
* [r11239] fixed various problems with gff3_string formatting of
Bio::Graphics::FeatureBase; (1) was dumping empty Alias
attributes and (2) was not dumping phase 0 CDS fields
2007-02-26 18:02 cjfields
* [r11238] Some POD fixes for bracket_string and sort_by_start
2007-02-26 17:47 cjfields
* [r11237] Made bracket_string a class method
2007-02-26 17:46 cjfields
* [r11236] remove bracket_strings (moving to SimpleAlign)
2007-02-26 17:26 scain
* [r11235] fixed GFF3 Dbxref handling
2007-02-26 15:47 scain
* [r11234] adding an override of write_seq to provide an explicit
close of the chado tag to mimic the original chadoxml.pm behavior
2007-02-25 11:06 sac
* [r11233] Added more tests for other methods.
Included some tests that depend on external binaries but left
them
commented out.
2007-02-25 11:03 sac
* [r11232] Major cleanup:
* Removed dependency on Bio::Root::Global and Object (now gone).
* Removed dependency on POSIX (now uses Bio::Root::IO for temp
filenames).
* Added find_exe() to avoid hard-coding paths to executables.
* Fixed bug in date_format().
* Updated pod.
2007-02-23 21:53 mcook
* [r11231] handle Multiple attributes of the same type in GFF
output correctly
2007-02-23 19:17 scain
* [r11230] added Ontology_term handling
2007-02-23 18:05 lstein
* [r11229] fixed problems related to retrieving segments with
negative coordinates
2007-02-23 09:56 sendu
* [r11228] added new files and tests for mlagan matrix handling
2007-02-22 21:38 scain
* [r11227] adding Alias tag handling (requiring the addition of
synonym to chadoxml.pm)
I think flybase_chadoxml.pm might be broken, as it is using
'polypeptide' in
the resulting xml where it should be using 'protein'.
2007-02-22 00:17 cjfields
* [r11226] Bug 2215
2007-02-21 18:33 lapp
* [r11225] Fixed the bug reported by Samuel GRANJEAUD - adding an
empty list of members
was broken.
2007-02-20 17:26 lstein
* [r11224] made seq_id settable
2007-02-20 13:33 cjfields
* [r11223] Removed per Chris Mungall's request
2007-02-19 18:35 cjfields
* [r11222] Typo; add CVS tag
2007-02-19 18:15 sendu
* [r11221] first working version of parser for gumby .align output
2007-02-19 17:55 sendu
* [r11220] futher correction to Caroline's patch: be less annoying
2007-02-19 17:46 sendu
* [r11219] fix for tag-value pairs separated by tabs in GFF2
2007-02-17 05:20 cjfields
* [r11218] infernal parsing fixes
2007-02-16 13:56 sendu
* [r11217] now recommends Storable 2.05 which supports subroutine
refs
2007-02-16 05:21 sac
* [r11216] Adding the test script for the recently resurrected
Bio::Root::Utilities. Still needs fleshing out.
2007-02-16 01:47 cjfields
* [r11215] Remove XEMBL tests (no longer active)
2007-02-16 01:45 cjfields
* [r11214] Add deprecation warning
2007-02-16 01:21 cjfields
* [r11213] Removed extraneous line.
2007-02-15 23:33 dave_messina
* [r11212] left a testing print statement behind -- oops. Removed.
2007-02-15 23:29 dave_messina
* [r11211] Adding Stephen Montgomery's subtract method to RangeI
(Bug 2207)
2007-02-15 23:28 dave_messina
* [r11210] Added subtract unit tests (Bug 2207) and updated simple
method tests
2007-02-15 21:35 cjfields
* [r11209] Add back per sac's request...
2007-02-15 21:19 cjfields
* [r11208] XEMBL no longer is available
2007-02-15 20:14 cjfields
* [r11207] No longer needed; tests should use Glimmer*.out and
Glimmer3.detail
2007-02-15 19:36 cjfields
* [r11206] Bug 2206 - updates to allow all Glimmer formats to be
parsed
2007-02-15 14:29 cjfields
* [r11205] Fix for remote DB sort order change
2007-02-14 17:32 sendu
* [r11204] added get_tree method
2007-02-14 16:42 sendu
* [r11203] fixed typo bug in last commit
2007-02-14 14:21 sendu
* [r11202] Caroline Johnston's patch to executable() to warn about
using system path when program path was set but had no exe
2007-02-14 12:02 sendu
* [r11199] Bundle::BioPerl::XMLSimple now obsolete with XML::SAX
0.15
2007-02-12 10:21 sendu
* [r11197] added simplify_to_leaves_string()
2007-02-11 00:44 lstein
* [r11196] don't create a link unless there is an href
2007-02-10 03:42 cjfields
* [r11195] XML::SAX 0.15 is req'd; may not need Bundle for
XML::Simple now
2007-02-08 14:17 cjfields
* [r11194] fixed saxparser(), made tests stricter(!)
2007-02-08 13:36 cjfields
* [r11193] blastxml should now return all description data for
every (!?!) XML::SAX backend; no need for warnings
2007-02-07 15:40 lstein
* [r11192] fixed nonfunctional -temporary-directory option
2007-02-07 12:21 lstein
* [r11191] fixed map_pt to round correctly
2007-02-06 23:35 lstein
* [r11190] finished documentation for stackedplot glyph
2007-02-06 04:13 jason
* [r11189] remove errant reference to ENV variable in POD - this
only relates to the scripts bp_fetch and bp_index
2007-02-05 23:05 lstein
* [r11188] changes to glyph creation to more easily allow glyphs to
explicitly control types of their subglyphs
2007-02-04 06:21 cjfields
* [r11187] our->my; fix GI error
2007-02-04 05:55 cjfields
* [r11186] erpin, rnamotif SearchIO-based parsers with some tests
(need more work)
2007-02-04 05:14 cjfields
* [r11185] use quotemeta JIC for regexes
2007-02-04 05:13 cjfields
* [r11184] small changes
2007-02-04 05:11 cjfields
* [r11183] RNA-based SearchIO stuff (keep separate from SearchIO.t
for now)
2007-02-04 05:06 cjfields
* [r11182] cmsearch (Infernal) SearchIO-based parser; HSP model for
above; get/setter in GenericHit for storing NCBI GI
2007-02-04 02:41 cjfields
* [r11181] Add private sub for getting GI/accession/version if
present
2007-02-03 21:44 lstein
* [r11180] did a little work on the stackedplot glyph; bounding box
is still slightly off
2007-02-02 21:51 mcook
* [r11179] fixup whitespace in regexp which was causing any ID
attribute to get incorrectly lower-cased during GFF3 production
2007-02-02 21:46 mcook
* [r11178] - ensure that subfeatures get the `source` of their
parent
- comment on (bizarro?) treatment of -segment optio to ->new
2007-02-02 21:05 mcook
* [r11177] _create_subfeatures : subfeatures get the `source` of
their parent
2007-02-02 18:11 mcook
* [r11176] When score is defined and 0, print 0, not '.'. Only
print '.' if score is undefined.
2007-02-02 17:28 scain
* [r11175] breaking flybase specific stuff out into a subclass
(which should make
it easier for dialect-specific creation of chadoxml--which is not
really a good thing!! (even if it make design easier and
cleaner))
2007-02-02 16:25 cjfields
* [r11174] Move to Test::More
2007-02-02 00:19 jason
* [r11173] bug #2201
2007-02-01 21:15 scain
* [r11172] another flybase/standard difference: protein vs
polypeptide
2007-02-01 20:47 scain
* [r11171] fixing a typo
2007-02-01 20:27 scain
* [r11170] adding options to control printing of residues
2007-02-01 20:02 cjfields
* [r11169] bug 2189
2007-02-01 18:19 scain
* [r11168] adding is_circular to Graphics::FeatureBase because it
is required by Bio::PrimarySeqI; adding more flexible
functionality to SeqIO::chadoxml while introducing a
-flybase_compat arg to allow it to continue to work like they
expect
2007-01-31 18:07 jason
* [r11167] Need to split the range up into start/end if you want to
sort on that. Let's test before we commit.
2007-01-31 14:49 sendu
* [r11166] when Store::delete() is working on multiple features,
fix here allows all those features to be deleted
2007-01-30 23:01 mcook
* [r11165] provide fallback of operator overloading
2007-01-30 22:41 lstein
* [r11164] made Bio::Graphics::FeatureBase more consistent with
annotatableI interface
2007-01-30 22:21 lstein
* [r11163] fixed some of the Glyph documentation;
Bio::Graphics::FeatureBase->to_FTString() behaves a little more
rationally on minus strand features
2007-01-30 19:30 cjfields
* [r11162] XML::SAX::Expat (v. 0.38) works for XML parsing now;
catch fails in testing.
2007-01-30 18:24 cjfields
* [r11161] Added tests for sort_by_start
2007-01-30 18:12 scain
* [r11160] Now accepts a Bio::SeqFeature::Annotated (though it
still complains and doesn't create complete chadoxml--hey, one
step at a time :-)
2007-01-30 15:17 cjfields
* [r11159] Grr... remove Data::Dumper (from debugging)
2007-01-30 15:12 cjfields
* [r11158] tests for bug 2195
2007-01-30 15:04 cjfields
* [r11157] Bug 2195
2007-01-30 05:39 cjfields
* [r11156] Bugs 2197, 2092
2007-01-29 23:30 cjfields
* [r11155] Bug 2198
2007-01-29 21:50 jason
* [r11154] POD typo
2007-01-29 14:40 cjfields
* [r11153] Bug 2197
2007-01-29 11:46 sendu
* [r11152] bug 2194 fixed
2007-01-27 04:25 cjfields
* [r11151] small tweak to get rid of warning
2007-01-26 23:13 jason
* [r11150] insure that length is positive and location object has
segment's strandedness
2007-01-25 17:25 cjfields
* [r11149] Move to Test::More; clean up; make WGS tests more
explicit
2007-01-24 16:22 cjfields
* [r11148] Bulletproof some more...
2007-01-24 16:10 mcook
* [r11147] Improved error reporting on non-strider formatted file
2007-01-23 20:04 lstein
* [r11146] use Bio::DB::SeqFeatureI methods rather than generic
methods
2007-01-23 16:24 sendu
* [r11145] ignore header lines during input
2007-01-23 11:12 sendu
* [r11141] use a bundle to install XML::SAX::ExpatXS and
XML::Simple in the correct order
2007-01-22 17:17 sendu
* [r11140] removed code that kept pre-reqs ordered, improved
detection of running under CPAN
2007-01-22 15:28 weigang
* [r11139] add test files for Annotation.t
2007-01-19 23:34 mcook
* [r11138] tests for 1.3.7 fixes
2007-01-19 23:32 mcook
* [r11137] allow for setting score to 0 without auto-resetting it
to '.'
2007-01-19 22:04 cjfields
* [r11136] BIC format stuff
2007-01-19 19:47 cjfields
* [r11135] bracketed consensus (BIC?)
2007-01-19 16:24 sendu
* [r11134] File::Path::rmtree verbose when Bioperl is
2007-01-19 15:14 cjfields
* [r11133] change File::Path verbosity to only be TRUE when
debugging
2007-01-19 13:21 sendu
* [r11132] no setting own version
2007-01-18 19:44 cjfields
* [r11131] small change (bad example data)
2007-01-18 18:38 cjfields
* [r11130] for future SearchIO-based tests
2007-01-18 17:51 cjfields
* [r11129] remove comments; cleanup() should now work (fingers
crossed)
2007-01-18 17:47 cjfields
* [r11128] revert back to normal from debugging
2007-01-18 17:45 cjfields
* [r11127] Bug 2183
2007-01-18 06:00 cjfields
* [r11126] small POD change
2007-01-18 05:59 cjfields
* [r11125] POD changes
2007-01-18 05:58 cjfields
* [r11124] Added Bio::Tools::Infernal tests
2007-01-18 01:58 cjfields
* [r11123] Bug 2189; did some pre-spring cleaning
2007-01-17 20:50 cjfields
* [r11122] Small change
2007-01-17 20:42 bosborne
* [r11121] Better example
2007-01-17 14:11 sendu
* [r11120] fix to never confuse "Score E" line for an actual score,
evalue
2007-01-17 04:35 lstein
* [r11119] added a new base class for use with fixed-width glyphs
2007-01-17 03:54 lstein
* [r11118] fixed (and grossly simplified) behavior of
print_description()
2007-01-16 21:21 lstein
* [r11117] that wasn't the right fix; reverted
2007-01-16 21:14 lstein
* [r11116] description printing now takes overridden pad_bottom
into account correctly
2007-01-16 19:37 cjfields
* [r11115] fix filehandle issue for NEXUS parsing
2007-01-16 19:34 cjfields
* [r11114] file handle tests (NEXUS still doesn't work)
2007-01-16 19:31 cjfields
* [r11113] fix for filehandle IO
2007-01-16 18:08 cjfields
* [r11112] Bug 2185
2007-01-16 17:24 sendu
* [r11111] added rerooting option to contract_linear_paths
2007-01-16 12:42 lstein
* [r11110] fixed documentation bug
2007-01-14 22:00 bosborne
* [r11109] Complete list of glyphs
2007-01-12 11:54 sendu
* [r11108] new test script for Bio::Tools::Run::WrapperBase
2007-01-12 11:53 sendu
* [r11107] reimplemented save_tempfiles as a strict boolean
get/setter and clarified docs for it; added new method
_setparams()
2007-01-11 16:04 cjfields
* [r11106] Bug 2182
2007-01-11 16:02 cjfields
* [r11105] revert rnamotif.t changes (committed accidentally along
with DB.t)
2007-01-11 14:38 sendu
* [r11104] tests for _set_from_args() method, moved to Test::More
2007-01-11 14:37 sendu
* [r11103] added _set_from_args() method
2007-01-11 14:17 cjfields
* [r11102] removed extraneous (now wrong) comment
2007-01-11 14:15 cjfields
* [r11101] Bug 2182
2007-01-10 22:22 mcook
* [r11100] test implemention of offsetStranded:
2007-01-10 22:21 mcook
* [r11099] implement offsetStranded
2007-01-10 22:01 weigang
* [r11098] 6 tests added for Bio::Annotation::Tree
2007-01-10 21:55 weigang
* [r11097] New module (Bio::Annotation::Tree) to associate a tree
to an alignment
2007-01-10 11:58 sendu
* [r11096] added naive read capability
2007-01-10 11:52 sendu
* [r11095] get_taxonids can now search for synonym names with
user-input underscores intead of spaces, just like entrez
2007-01-09 23:12 mcook
* [r11094] added myself
2007-01-08 22:14 weigang
* [r11093] set_displayname_safe: now assigns id of user-defined
length
2007-01-08 16:17 cjfields
* [r11092] bug 2172
2007-01-07 22:36 cjfields
* [r11091] small changes
2007-01-07 22:33 cjfields
* [r11090] POD changes
2007-01-04 16:55 sendu
* [r11089] added quiet() method
2007-01-03 17:56 weigang
* [r11088] Add test for the method: sort_by_list
2007-01-03 17:54 weigang
* [r11087] Add new method: sort_by_list; also, bug fix in uniq_seq
2007-01-03 17:43 weigang
* [r11086] This is a test file for the SimpleAlign method
sort_by_list
2007-01-02 20:01 lstein
* [r11085] added better explanation of how to use dna glyph with a
generic seqfeature object
2006-12-31 19:35 cjfields
* [r11084] bug 2167
2006-12-31 03:05 jason
* [r11083] indenting fix
2006-12-30 22:12 cjfields
* [r11082] small change reg. HTML::Entities
2006-12-30 22:02 cjfields
* [r11081] small changes
2006-12-30 21:57 cjfields
* [r11080] Bug 2166
2006-12-30 20:52 cjfields
* [r11079] Removed debugging cruft
2006-12-30 20:36 cjfields
* [r11078] tentative fix for bug 2166
2006-12-28 22:34 cjfields
* [r11077] Moving BLAST XML SAX methods to separate class
2006-12-24 17:21 lstein
* [r11076] fixed division by zero error when sequence GC content ==
0
2006-12-22 15:27 lstein
* [r11075] stacked plot basically working --needs to have scale
reimplemented
2006-12-21 17:59 cjfields
* [r11074] XML::SAX::PurePerl works with older BLAST XML report
tests, must skip on newer ones.
2006-12-21 17:56 cjfields
* [r11073] add tests for 'unisave', move to Test::More, minor stuff
otherwise
2006-12-21 16:47 sendu
* [r11072] added force_binary() method
2006-12-21 14:29 cjfields
* [r11071] added 'unisave'
2006-12-20 23:35 lstein
* [r11070] featurefile no longer ignores #anchor notation in
configured urls; added a primitive stackplot glyph
2006-12-20 22:39 cjfields
* [r11069] Bug fix for env_proxy
2006-12-20 18:38 skirov
* [r11068] Added threshold to cigar_line, default is still 100
2006-12-19 22:02 lstein
* [r11067] fixed a bug that would crash the database (possibly
corrupting it) when adding a splice form to an existing gene or
any other three-part feature
2006-12-19 16:35 jason
* [r11066] email address obscuring
2006-12-19 16:34 jason
* [r11065] indented code simplification
2006-12-19 16:34 jason
* [r11064] indentification...
2006-12-19 16:33 jason
* [r11063] specify validate_seq specific to LocatableSeq objects so
that numeric values can be set - eventually make this regexp
get/settable. This is per hackathon use case requirement of
morphological and numeric coded data storage in Nexus data files.
2006-12-19 16:32 jason
* [r11062] better detection of error if arrayref is passed in
2006-12-18 19:13 sendu
* [r11061] speedup for merge_lineage()
2006-12-15 13:49 sendu
* [r11060] added Weigang Qiu's set_displayname_safe() and
restore_displayname() methods, for avoiding truncated alignment
names in eg. Phylip
2006-12-14 21:53 lstein
* [r11059] fixed egregious error in the plot which caused all
content to be display off to the right of the correct position
2006-12-14 14:08 sendu
* [r11058] clarified POD
2006-12-13 23:47 dave_messina
* [r11057] Fixing typo and updating return value info in
end_element's POD.
2006-12-13 22:40 cjfields
* [r11056] If parser overheats, turn off and back slowly away
(small edits)
2006-12-13 21:20 cjfields
* [r11055] Very experimental Infernal (cmsearch) parser.
Do not taunt parser.
If bitten by parser, go to nearest emergency room.
2006-12-13 17:17 scain
* [r11054] fixing a problem where the group would be missed due to
case sensitivity
2006-12-13 16:02 sendu
* [r11053] no longer creates features with no sequences
2006-12-12 22:37 cjfields
* [r11052] small change for phase test
2006-12-12 22:19 jason
* [r11051] migrate to Test::More; this needs to be tested on system
without some modules before I am sure it is totally done
2006-12-12 21:36 jason
* [r11050] add features to alignments to allow for better NEXUS
integration
2006-12-12 20:44 cjfields
* [r11049] Add convenience parameter '-phase' to spliced_seq()
2006-12-12 20:21 cjfields
* [r11048] spliced_seq() phase tests
2006-12-12 19:43 jason
* [r11047] even if this is not quite correct english make spelling
consistency: add_Descendant -> add_Descendent in the POD
2006-12-08 10:46 sendu
* [r11046] recommend PostScript::TextBlock for
Bio::Tree::Draw::Cladogram
2006-12-08 10:43 sendu
* [r11045] install order MUSTN'T matter; recommend XML::DOM::XPath
0.13 (no longer needs XML::XPath), note that we need to make a
bundle for XML::Simple
2006-12-07 19:31 bosborne
* [r11044] Dashed parameters
2006-12-06 18:18 sendu
* [r11041] update from wiki
2006-12-06 17:57 cjfields
* [r11040] Update from wiki
2006-12-06 17:42 cjfields
* [r11039] Update from wiki
2006-12-06 17:02 sendu
* [r11038] corrected Bio::Root::Version version number output in
ppds for non-core packages
2006-12-06 16:34 avilella
* [r11037] deals roughly with multiple blocks
2006-12-06 15:44 avilella
* [r11036] basic next_aln should work
2006-12-06 11:31 sendu
* [r11034] workaround for ppm bug: create fake bundle for pre-reqs
2006-12-05 22:31 cjfields
* [r11033] Grr...refix Bug 2159
2006-12-05 22:30 cjfields
* [r11032] bug 2159