| 2003-03-10 |
lapp | Sync'ed RichSeqI with the implementation. RichSeq provides...
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commit | commitdiff | tree |
| 2003-03-07 |
lapp | Removed the backslashes and corrected the output stream...
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commit | commitdiff | tree |
| 2003-03-06 |
lapp | Few fixes to remove assumptions on precise format of...
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commit | commitdiff | tree |
| 2003-03-06 |
lapp | Added the additional formats that are supported.
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commit | commitdiff | tree |
| 2003-03-06 |
lapp | Final steps towards stabilizing and cleaning the ontology...
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commit | commitdiff | tree |
| 2003-03-06 |
lapp | Made the species map current with NCBI's repository...
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commit | commitdiff | tree |
| 2003-03-06 |
lapp | Removed left-over print statement.
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commit | commitdiff | tree |
| 2003-03-06 |
lapp | Added macro for array get/add/remove.
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commit | commitdiff | tree |
| 2003-03-04 |
lapp | Next round if Ontology and OntologyIO changes and fixes...
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commit | commitdiff | tree |
| 2003-02-28 |
lapp | Reworked the ontology to add ontology objects and interfaces...
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commit | commitdiff | tree |
| 2003-02-28 |
lapp | Like it or not, but the SeqIO swissprot format has...
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commit | commitdiff | tree |
| 2003-02-28 |
lapp | Added documentation.
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commit | commitdiff | tree |
| 2003-02-20 |
lapp | Fixed instantiation to recognize array ref for -keywords.
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commit | commitdiff | tree |
| 2003-02-18 |
lapp | Fixed the locuslink parser. Refactored RichSeq to delegate...
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commit | commitdiff | tree |
| 2003-02-12 |
lapp | Fixed a bug in the LL parser.
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commit | commitdiff | tree |
| 2003-02-11 |
lapp | Added forgotten file. Strange - has noone seen this...
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commit | commitdiff | tree |
| 2003-02-11 |
lapp | Fixed syntax error. Do people actually run the tests...
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commit | commitdiff | tree |
| 2003-02-06 |
lapp | Initial revision of SimpleOntologyEngine implementation...
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commit | commitdiff | tree |
| 2003-02-03 |
lapp | Added and updated a good deal of documentation. Fixed...
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commit | commitdiff | tree |
| 2003-02-03 |
lapp | Replaced the second 'require' by 'use' (had been changed...
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commit | commitdiff | tree |
| 2003-02-02 |
lapp | Applied Peter Chines' patch to genbank.pm to handle...
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commit | commitdiff | tree |
| 2002-12-29 |
lapp | Fixed bug #1321 (intron start/ends screwed up on negative...
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commit | commitdiff | tree |
| 2002-12-29 |
lapp | Fixed bug #1338 (write_line_GenBank_regex lost information...
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commit | commitdiff | tree |
| 2002-12-28 |
lapp | Fixed a number of bugs: LocusLink parser (#1353), SplitLocat...
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commit | commitdiff | tree |
| 2002-11-23 |
lapp | Allowed description to be set to undef.
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commit | commitdiff | tree |
| 2002-11-19 |
lapp | Small doc fix.
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commit | commitdiff | tree |
| 2002-11-18 |
lapp | Added FeatureHolderI. Migrated SeqI, Seq, SeqFeatureI...
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commit | commitdiff | tree |
| 2002-11-16 |
lapp | Added Graph::Directed as dependency.
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commit | commitdiff | tree |
| 2002-11-16 |
lapp | Applied proper case to names. Moved the parser to the...
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commit | commitdiff | tree |
| 2002-11-16 |
lapp | Fixed a bug report about Root::new() complaining about...
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commit | commitdiff | tree |
| 2002-11-11 |
lapp | Forgot to cvs add AnnotatableI. Also sorry about the...
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commit | commitdiff | tree |
| 2002-11-11 |
lapp | Added Bio::AnnotationI and have it implemented by Bio...
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commit | commitdiff | tree |
| 2002-11-09 |
lapp | Fixed version parsing in genbank and in embl. Believe...
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commit | commitdiff | tree |
| 2002-11-07 |
lapp | Fixed the bug Mat Wiepert reported: fasta seqs lost...
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commit | commitdiff | tree |
| 2002-11-07 |
lapp | Committed locuslink parser, sample, and test.
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commit | commitdiff | tree |
| 2002-11-05 |
lapp | Fixed setting seq_id to top location.
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commit | commitdiff | tree |
| 2002-11-04 |
lapp | Doc fix in Location::Split. Fixed FTHelper to set location...
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commit | commitdiff | tree |
| 2002-11-02 |
lapp | Added recognition of all IdentifiableI parameters to...
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commit | commitdiff | tree |
| 2002-10-31 |
lapp | Added a couple of object factories. Fixed Ontology...
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commit | commitdiff | tree |
| 2002-10-25 |
lapp | Added species() to Cluster::UniGene and interface....
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commit | commitdiff | tree |
| 2002-10-25 |
lapp | Fully moved most of the extended UniGene properties...
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commit | commitdiff | tree |
| 2002-10-25 |
lapp | First step towards migrating most properties into the...
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commit | commitdiff | tree |
| 2002-10-25 |
lapp | Tidied up Cluster interfaces. Changed Cluster::UniGene...
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commit | commitdiff | tree |
| 2002-10-24 |
lapp | Interface and base implementation, first revision....
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commit | commitdiff | tree |
| 2002-10-23 |
lapp | Fixed namespace_string() in IdentifiableI. Added recognition...
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commit | commitdiff | tree |
| 2002-10-22 |
lapp | Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl...
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commit | commitdiff | tree |
| 2002-10-22 |
lapp | Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl...
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commit | commitdiff | tree |
| 2002-10-19 |
lapp | Made -seqname for SeqFeature::Generic deprecated.
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commit | commitdiff | tree |
| 2002-10-19 |
lapp | Added check to PrimarySeq::length that throws an exception...
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commit | commitdiff | tree |
| 2002-10-12 |
lapp | Fixed write_seq() to terminate species with a dot....
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commit | commitdiff | tree |
| 2002-10-11 |
lapp | Added documentation to SeqBuilder. Unified and fixed...
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commit | commitdiff | tree |
| 2002-10-10 |
lapp | Made genbank and embl to force the species classification...
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commit | commitdiff | tree |
| 2002-10-10 |
lapp | Implemented SeqBuilder. Adopted in the genbank parser...
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commit | commitdiff | tree |
| 2002-10-09 |
lapp | Intermediate commit of ObjectBuilderI and its implementation...
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commit | commitdiff | tree |
| 2002-10-08 |
lapp | Renamed seqname() to seq_id() and display_id() to display_na...
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commit | commitdiff | tree |
| 2002-10-07 |
lapp | Based on the fall-out from swissprot->biosql, some...
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commit | commitdiff | tree |
| 2002-10-07 |
lapp | Added second form of calling to Species::classification...
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commit | commitdiff | tree |
| 2002-10-04 |
lapp | Moved debug() from RootI to Root and allowed an array...
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commit | commitdiff | tree |
| 2002-10-03 |
lapp | Cosmetic and doc fixes. Changed the new get/set method...
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commit | commitdiff | tree |
| 2002-10-02 |
lapp | Small fixes. Added -namespace as parameter to Bio:...
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commit | commitdiff | tree |
| 2002-10-02 |
lapp | Fixed bugs introduced into Bio::Seq (does it really...
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commit | commitdiff | tree |
| 2002-10-01 |
lapp | Added tagvalue_object_factory().
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commit | commitdiff | tree |
| 2002-09-29 |
lapp | Added Bio::SeqFeature::AnnotationAdaptor and its test...
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commit | commitdiff | tree |
| 2002-09-27 |
lapp | Added documentation to SeqFeatureI::attach_seq. Also...
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commit | commitdiff | tree |
| 2002-09-26 |
lapp | Promoted seq(), entire_seq(), seqname(), and attach_seq...
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commit | commitdiff | tree |
| 2002-09-26 |
lapp | Fixed setters such that setting to an empty string...
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commit | commitdiff | tree |
| 2002-09-25 |
lapp | Fixed order of inheritance.
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commit | commitdiff | tree |
| 2002-09-25 |
lapp | Added tagname() to Bio::AnnotationI and adapted the...
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commit | commitdiff | tree |
| 2002-09-24 |
lapp | Added Bio::Annotation::OntologyTerm. The rest is insignifica...
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commit | commitdiff | tree |
| 2002-09-22 |
lapp | Retired Bio/Annotation.pm. Everything else is minor...
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commit | commitdiff | tree |
| 2002-09-16 |
lapp | SequenceFactoryI wasn't inheriting from ObjectFactoryI...
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commit | commitdiff | tree |
| 2002-09-10 |
lapp | Added capability to deal with locations enclosed in...
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commit | commitdiff | tree |
| 2002-09-10 |
lapp | Almost revoked the changes to FTLocationFactory, tests...
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commit | commitdiff | tree |
| 2002-09-10 |
lapp | Renamed SeqAnal.t to IUPAC.t as advised by SteveC.
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commit | commitdiff | tree |
| 2002-09-10 |
lapp | Fixed messed up decision whether or not to guess the...
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commit | commitdiff | tree |
| 2002-09-10 |
lapp | Added alias accession for accession_number, with deprecation...
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commit | commitdiff | tree |
| 2002-09-06 |
lapp | Separated IdentifiableI and DescribableI from PrimarySeqI...
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commit | commitdiff | tree |
| 2002-09-04 |
lapp | Simplified and cleaned up subseq().
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commit | commitdiff | tree |
| 2002-09-02 |
lapp | You should not try to check $start and $end here for...
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commit | commitdiff | tree |
| 2002-08-30 |
lapp | Fixed broken validation of names and species.
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commit | commitdiff | tree |
| 2002-08-30 |
lapp | Replaced with new version (the old one had a superfluous...
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commit | commitdiff | tree |
| 2002-08-30 |
lapp | Fixes small bug (missing 'use' statement).
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commit | commitdiff | tree |
| 2002-08-29 |
lapp | Fixed a missing double quote in the POD section. Fixed...
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commit | commitdiff | tree |
| 2002-08-22 |
lapp | Fixed a couple of small omissions.
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commit | commitdiff | tree |
| 2002-08-12 |
lapp | Need to check is_remote() before propagating strand...
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commit | commitdiff | tree |
| 2002-08-12 |
lapp | Adapted FTHelper and the parsers for genbank, embl...
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commit | commitdiff | tree |
| 2002-08-12 |
lapp | Added Bio::Factory::LocationFactoryI with one method...
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commit | commitdiff | tree |
| 2002-08-07 |
lapp | fixed to output correct number of tests/oks w/ and...
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commit | commitdiff | tree |
| 2002-08-07 |
lapp | Adapted to use _load_module() in Root.pm.
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commit | commitdiff | tree |
| 2002-08-07 |
lapp | Propagated Lincoln's untainting fix to SeqIO module...
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commit | commitdiff | tree |
| 2002-08-07 |
lapp | Added _load_module().
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commit | commitdiff | tree |
| 2002-07-23 |
lapp | Small mostly cosmetic changes (like, added $ID$ line...
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commit | commitdiff | tree |
| 2002-07-12 |
lapp | Added each_Location() to Location/Atomic.pm and removed...
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commit | commitdiff | tree |
| 2002-06-14 |
lapp | Removed upper-casing of sequence.
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commit | commitdiff | tree |
| 2001-11-30 |
lapp | Fixed bug reported by Brian Osborne (module dies if...
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commit | commitdiff | tree |
| 2001-11-26 |
lapp | Removed overloaded double-quotes examples from the...
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commit | commitdiff | tree |
| 2001-11-21 |
lapp | Applied Malcolm Cook's fix to read/write secondary...
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commit | commitdiff | tree |
| 2001-11-18 |
lapp | Fixed bug #1019 by the fix suggested by carl virtanen
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commit | commitdiff | tree |
| 2001-08-25 |
lapp | Small fix to shut up File::Spec.
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commit | commitdiff | tree |
| 2001-08-25 |
lapp | Added report_type(). Rearranged report type interpretation...
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commit | commitdiff | tree |
