Core 1.5.2 1.6.0 delta

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NOTE : This is just the raw svn2cl changelog dump and will be reformatted for the final release!

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

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