Core 1.0.0 1.0.1 delta

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These are detailed notes on changes made between bioperl-release-1-0-0 and bioperl-release-1-0-1.

Bio::Align::AlignI
Merge doc changes to branch
Bio::Align::DNAStatistics
Objects for calculated DNA and pairwise statistics for AlignI objects
Bio::Align::PairwiseStatistics
Objects for calculated DNA and pairwise statistics for AlignI objects
Bio::Align::StatisticsI
Very initial interface definition for doing distance calculations
Objects for calculated DNA and pairwise statistics for AlignI objects
Bio::AlignIO
Update doc for link to simplealign
Update doc for link to simplealign
Bio::AlignIO::bl2seq
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::AlignIO::clustalw
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::AlignIO::emboss
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::AlignIO::fasta
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::AlignIO::mase
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::AlignIO::mega
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::AlignIO::msf
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::AlignIO::nexus
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::AlignIO::pfam
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::AlignIO::phylip
Added sub idlength to enable using phylip which accepts id names that are greater in length than the default 10
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::AlignIO::prodom
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::AlignIO::psi
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::AlignIO::selex
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::AlignIO::stockholm
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::Annotation::Collection
Documentation update including a synopsis
Added a synopsis
Bio::AnnotationCollectionI
Added more documentation
Bio::Biblio
Merged changes from trunk to branch
Bio::Biblio::BiblioBase
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::Cluster::UniGene
Initial commit of UniGene modules
Inherit from Bio::Factory::SequenceStreamI interface and utilize sequence_factory method for creating sequence objects (may be overkill)
Changed module to parse multiple chromosome lines after NCBI UniGene format was altered.
Multiple defined chromosome function removed
Bio::Cluster::UniGeneI
Initial commit of UniGene modules
Changed module to parse multiple chromosome lines after NCBI UniGene format was altered.
Bio::Cluster::dbSNP
Not finished - classes for dbSNP parsing
Bio::ClusterIO
Created ClusterIO.pm from UniGene.pm, moved it to top level directory and made code changes as appropriate
Change to runtime load
Improve dynamic module loading procedure
Bio::ClusterIO::UniGeneIO
Initial commit of UniGene modules
Removed UniGeneIO.pm having converted it to ClusterIO.pm
Bio::ClusterIO::dbsnp
Not finished - classes for dbSNP parsing
Bio::ClusterIO::unigene
Moved unigene.pm up a level into the ClusterIO dir
Changed next_unigene to next_cluster to override ClusterIO.pm
Quote to keep my emacs happy
Changed module to parse multiple chromosome lines after NCBI UniGene format was altered.
Bio::DB::Biblio::soap
Notion of the HTTP proxy added
HTTP proxy code migrated from HEAD
Bio::DB::BiblioI
Remove old reference to abstract_Death
Bio::DB::Fasta
Fixed RootI warnings in Bio::DB::Fasta
Fixed RootI inclusion errors when calling get_Seq_by_id(). added new regression tests
Bio::DB::Flat::OBDAIndex
Get_Seq_by_secondary returns array of Bio::Seq
Bio::DB::GFF
Multiple small fixes to graphics module; allow wildcard ID searches in Bio::DB::GFF module
Replaced a croak with a throw
Bio::DB::GFF::Feature now implements location() interface; replaced a croak() with a throw in Bio::DB::GFF
- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)
Added experimental support for a Genbank/EMBL proxy. If a landmark isn't in the local Bio::DB::GFF database, it will treat the landmark as an accession number, use biofetch to fetch the accession entry from EMBL, parse it, and place it in the local Bio::DB::GFF database. There is currently support for the feature table, the DNA, secondary accession numbers and the description line. Other fields are tossed 'cause I don't care.
Made aggregation type matching case insensitive
Bio::DB::GFF::Adaptor::biofetch
Added experimental support for a Genbank/EMBL proxy. If a landmark isn't in the local Bio::DB::GFF database, it will treat the landmark as an accession number, use biofetch to fetch the accession entry from EMBL, parse it, and place it in the local Bio::DB::GFF database. There is currently support for the feature table, the DNA, secondary accession numbers and the description line. Other fields are tossed 'cause I don't care.
Bio::DB::GFF::Adaptor::dbi
Multiple small fixes to graphics module; allow wildcard ID searches in Bio::DB::GFF module
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required)
Bio::DB::GFF::Adaptor::dbi::caching_handle
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required)
Bio::DB::GFF::Adaptor::dbi::mysql
Multiple small fixes to graphics module; allow wildcard ID searches in Bio::DB::GFF module
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general
Allow get_feature_by_name() to accept wildcards
Allow get_feature_by_name() to accept wildcards
Bio::DB::GFF::Adaptor::memory
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required)
- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)
Bio::DB::GFF::Adaptor::memory_iterator
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required)
- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)
Bio::DB::GFF::Aggregator
Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway.
Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.
Bio::DB::GFF::Aggregator::alignment
Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway.
Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.
Bio::DB::GFF::Aggregator::wormbase_gene
Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs.
Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs. Fixed the SearchIO.t regression test to report the correct number of tests being performed. Under 5.6.1 it misreported the number of tests, causing spurious failed tests.
Bio::DB::GFF::Feature
Bio::DB::GFF::Feature now implements location() interface
Bio::DB::GFF::Feature now implements location() interface; replaced a croak() with a throw in Bio::DB::GFF
- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects.
- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)
Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway.
Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.
Removed a duplicated score() definition.
Removed a duplicated score() definition.
Added heterogeneous_segments glyph and removed wormbase_transcript glyph
Bio::DB::GFF::RelSegment
As it happens, the RangeI methods weren't really working for relative segments. This is now fixed.
Fixed overlaps() to work correctly with reverse-strand features when using relative addressing
Bio::DB::GFF::Segment
Added seq_id() method to Bio::DB::GFF::Segment and Bio::Graphics::Feature
Added seq_id() method to Bio::DB::GFF::Segment and Bio::Graphics::Feature
Now inherits from SeqI and can be directly written out with Bio::SeqIO
Bio::DB::WebDBSeqI
Verbosity is pushed into instantiated classes
Pass verbose state to instantiated classes
Bio::Das::FeatureTypeI
Added Bio::Das::FeatureTypeI
Bio::Das::SegmentI
Finished the Bio::DasI and Bio::Das::SegmentI interface definitions.
Added Bio::Das::FeatureTypeI
Bio::DasI
Was inheriting from Bio::Root (doesn't exist). now inherits from Bio::Root::Root. Should be Bio::Root::RootI? Well, it seems to be working.
Should inherit from Bio::Root::RootI, does not need Carp
Should inherit from Bio::Root::RootI, does not need Carp
Finished the Bio::DasI and Bio::Das::SegmentI interface definitions.
Added Bio::Das::FeatureTypeI
Bio::DasSegmentI
Finished the Bio::DasI and Bio::Das::SegmentI interface definitions.
Bio::Factory::MapFactoryI
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::Factory::Pise
Source code for Pise Factory and Application classes. Bio/Factory/Pise.pm: factory Bio/Tools/Run/PiseApplication.pm: base class for all programs Bio/Tools/Run/PiseJob.pm: class for a launched job Bio/Tools/Run/PiseJobParser.pm: XML parser for a job result page
Bio::Factory::SeqAnalysisParserFactory
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::Factory::SeqAnalysisParserFactoryI
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::Factory::SequenceBuilderI
New interface to handle generic sequence building
Modules renamed to be more GoF happy
Bio::Factory::SequenceFactoryI
Modules renamed to be more GoF happy
Update doc and method name from new_sequence to create_sequence to comply with design pattern standard
Bio::Factory::SequenceStreamI
Added new interface describin what SeqIO is
Bio::Factory::TreeFactoryI
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::Graphics
Multiple small fixes to graphics module; allow wildcard ID searches in Bio::DB::GFF module
Bumped up version number for Bio::Graphics to 1.03.
Bumped up version number for Bio::Graphics to 1.03.
Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway.
Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.
Bumped up version number of Graphics.pm to 1.05
Bio::Graphics::Feature
Simplified Bio::Graphics internals for stability and generality
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general
Added seq_id() method to Bio::DB::GFF::Segment and Bio::Graphics::Feature
Added seq_id() method to Bio::DB::GFF::Segment and Bio::Graphics::Feature
- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects.
- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)
Changed the tick mark code in arrow.pm to handle minus strand features differently. This might fix a bug -- or might introduce one.
Work around uninitialized variable warnings
Minor fixes to Bio::Graphics. Silenced various uninitialized variable warnings, and fixed the arrow glyph so that the reversal of coordinate labels only occurs when relative coordinate addressing is requested.
Audit of the glyphs. Fixed some minor bugs.
Bio::Graphics::FeatureFile
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required)
Moved changes from bioperl-live into release
Bio::DB::GFF::Feature now implements location() interface
Bio::DB::GFF::Feature now implements location() interface; replaced a croak() with a throw in Bio::DB::GFF
- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)
Modification to filehandle close() handling to accomodate perl 5.00503 backward compatibility
Aesthetic improvements to split-location features
Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs. Fixed the SearchIO.t regression test to report the correct number of tests being performed. Under 5.6.1 it misreported the number of tests, causing spurious failed tests.
Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.
Moved "use Bio::Location::Simple" from Glyph::transcript to Glyph::segments. transcript now inherits from segments.
Changed the tick mark code in arrow.pm to handle minus strand features differently. This might fix a bug -- or might introduce one.
Work around uninitialized variable warnings
Minor fixes to Bio::Graphics. Silenced various uninitialized variable warnings, and fixed the arrow glyph so that the reversal of coordinate labels only occurs when relative coordinate addressing is requested.
Bio::Graphics::Glyph
Multiple small fixes to graphics module; allow wildcard ID searches in Bio::DB::GFF module
Simplified Bio::Graphics internals for stability and generality
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general
Added an extra argument to the callback so that the callback can get at the glyph; restored dashed line for groups even when the right side of first feature is greater than the left side of second feature
Moved changes from bioperl-live into release
Fixed Glyph and Glyph::transcript2 so that the components always are drawn after the connectors. This cleans up some of the alignment glyphs in which the components overlap each other
Aesthetic improvements to split-location features
Fixed a bug that nuked connectors when both flanking parts are off screen.
Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs.
Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs. Fixed the SearchIO.t regression test to report the correct number of tests being performed. Under 5.6.1 it misreported the number of tests, causing spurious failed tests.
Changed the tick mark code in arrow.pm to handle minus strand features differently. This might fix a bug -- or might introduce one.
Minor fixes to Bio::Graphics. Silenced various uninitialized variable warnings, and fixed the arrow glyph so that the reversal of coordinate labels only occurs when relative coordinate addressing is requested.
Bio::Graphics::Glyph::Factory
Simplified Bio::Graphics internals for stability and generality
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general
Added an extra argument to the callback so that the callback can get at the glyph; restored dashed line for groups even when the right side of first feature is greater than the left side of second feature
Moved changes from bioperl-live into release
When I refactored the transcript and segments glyphs, I forgot to move the Bio::Location::Simple requiremejnt to where it belonged
Moved "use Bio::Location::Simple" from Glyph::transcript to Glyph::segments. transcript now inherits from segments.
Bio::Graphics::Glyph::anchored_arrow
Fixed anchored arrow off-by-one error
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general
Bio::Graphics::Glyph::arrow
Changed the tick mark code in arrow.pm to handle minus strand features differently. This might fix a bug -- or might introduce one.
Fixed tick mark code in arrow.pm so that ticks dont disappear when looking at reversed feature in absolute coordinate system
Reordered test of relative coordinate testing for efficiency.
Minor fixes to Bio::Graphics. Silenced various uninitialized variable warnings, and fixed the arrow glyph so that the reversal of coordinate labels only occurs when relative coordinate addressing is requested.
Fixed a new bug in the relative tickmarks in arrow.pm introduced when I fixed the old bug
Bio::Graphics::Glyph::crossbox
Audit of the glyphs. Fixed some minor bugs.
Bio::Graphics::Glyph::diamond
- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects.
- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)
Bio::Graphics::Glyph::ex
Audit of the glyphs. Fixed some minor bugs.
Bio::Graphics::Glyph::generic
Audit of the glyphs. Fixed some minor bugs.
Bio::Graphics::Glyph::graded_segments
Added heterogeneous_segments glyph and removed wormbase_transcript glyph
Bio::Graphics::Glyph::group
Simplified Bio::Graphics internals for stability and generality
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general
Bio::Graphics::Glyph::heterogeneous_segments
Added heterogeneous_segments glyph and removed wormbase_transcript glyph
Bio::Graphics::Glyph::primers
Audit of the glyphs. Fixed some minor bugs.
Bio::Graphics::Glyph::ruler_arrow
Audit of the glyphs. Fixed some minor bugs.
Bio::Graphics::Glyph::segmented_keyglyph
Moved changes from bioperl-live into release
- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)
Aesthetic improvements to split-location features
Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs. Fixed the SearchIO.t regression test to report the correct number of tests being performed. Under 5.6.1 it misreported the number of tests, causing spurious failed tests.
Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.
Moved "use Bio::Location::Simple" from Glyph::transcript to Glyph::segments. transcript now inherits from segments.
Minor fixes to Bio::Graphics. Silenced various uninitialized variable warnings, and fixed the arrow glyph so that the reversal of coordinate labels only occurs when relative coordinate addressing is requested.
Bio::Graphics::Glyph::segments
Simplified Bio::Graphics internals for stability and generality
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general
Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway.
Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.
When I refactored the transcript and segments glyphs, I forgot to move the Bio::Location::Simple requiremejnt to where it belonged
Moved "use Bio::Location::Simple" from Glyph::transcript to Glyph::segments. transcript now inherits from segments.
Changed the tick mark code in arrow.pm to handle minus strand features differently. This might fix a bug -- or might introduce one.
Minor fixes to Bio::Graphics. Silenced various uninitialized variable warnings, and fixed the arrow glyph so that the reversal of coordinate labels only occurs when relative coordinate addressing is requested.
Bio::Graphics::Glyph::track
Simplified Bio::Graphics internals for stability and generality
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general
Bio::Graphics::Glyph::transcript
Simplified Bio::Graphics internals for stability and generality
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general
Moved changes from bioperl-live into release
- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)
Aesthetic improvements to split-location features
Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs.
Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs. Fixed the SearchIO.t regression test to report the correct number of tests being performed. Under 5.6.1 it misreported the number of tests, causing spurious failed tests.
Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway.
Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.
When I refactored the transcript and segments glyphs, I forgot to move the Bio::Location::Simple requiremejnt to where it belonged
Moved "use Bio::Location::Simple" from Glyph::transcript to Glyph::segments. transcript now inherits from segments.
Minor fixes to Bio::Graphics. Silenced various uninitialized variable warnings, and fixed the arrow glyph so that the reversal of coordinate labels only occurs when relative coordinate addressing is requested.
Bio::Graphics::Glyph::transcript2
Simplified Bio::Graphics internals for stability and generality
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required)
Moved changes from bioperl-live into release
- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)
Fixed Glyph and Glyph::transcript2 so that the components always are drawn after the connectors. This cleans up some of the alignment glyphs in which the components overlap each other
Fixed irregularity involving features with no internal structure
Aesthetic improvements to split-location features
Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs.
Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs. Fixed the SearchIO.t regression test to report the correct number of tests being performed. Under 5.6.1 it misreported the number of tests, causing spurious failed tests.
Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.
Moved "use Bio::Location::Simple" from Glyph::transcript to Glyph::segments. transcript now inherits from segments.
Minor fixes to Bio::Graphics. Silenced various uninitialized variable warnings, and fixed the arrow glyph so that the reversal of coordinate labels only occurs when relative coordinate addressing is requested.
Bio::Graphics::Glyph::wormbase_transcript
Added heterogeneous_segments glyph and removed wormbase_transcript glyph
Bio::Graphics::Panel
Multiple small fixes to graphics module; allow wildcard ID searches in Bio::DB::GFF module
Simplified Bio::Graphics internals for stability and generality
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general
Added an extra argument to the callback so that the callback can get at the glyph; restored dashed line for groups even when the right side of first feature is greater than the left side of second feature
Moved changes from bioperl-live into release
Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway.
Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.
Bio::Index::GenBank
Doc fix -- seq->layout no longer exists
Doc fix -- seq->layout no longer exists
Bio::LiveSeq::SeqI
Explicitly include Bio::PrimarySeqI interface
Bio::Location::Simple
Warning should not print if we've already specified minus strand
Bio::LocationI
Documentation fix
Add docs - convert to throw_not_implemented not _abstractDeath
Bio::Map::MapI
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::Map::PositionI
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::Map::SimpleMap
Issue #1154 fixed
Issue #1154 fixed
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::MapIO
Documentation fix
Merged changes from trunk to branch
Bio::MapIO::mapmaker
Remove abstract reference
Remove abstractDeath --branch
Bio::PrimarySeq
Protect against calling length on empty string
Update doc to describe circular feature
Optimize PrimarySeq _guess_alphabet to be more efficient using tr// to count rather than editing the sequence string
Bio::Root::Exception
Fixes bg #1146 as suggested by Martin. Steve, there are not tests for Bio::Root::Exception!
Fixes bg #1146 as suggested by Martin. Steve, there are not tests for Bio::Root::Exception!
Modified _reformat_stacktrace() to get the top-most file:linenum data (name of the script)
Migrating fixe 1.13 to branch-1-0-0
Bio::Root::RootI
Remove abstractDeath
Remove abstractDeath from branch
Moved code from HEAD: replaced _abstractDeath() by throw_not_implemented() fixes Issue #1155
Only print warnings when BIOPERLDEBUG env variable is set
No warnings for RootI on _cleanup_object either unless ->verbose or BIOPERLDEBUG defined
Bio::Search::HSP::BlastHSP
Some changes to have Blast* and Generic* play nicer
Bio::Search::HSP::GenericHSP
Update docs to clearly state that frame is GFF not BLAST
Added caveat in docs about how frame works and removed warning when HSP gaps param is unspecified
Doc fix
Bio::Search::HSP::HSPI
Fix doc to say pvalue not p
Use pvalue instead of p in docs -- merge from trunk
Bio::Search::Hit::BlastHit
Implementing accession() as required by HitI. Addresses Issue #1139
Migrating fix 1.10 to branch-1-0-0.
Bio::Search::Hit::GenericHit
Migrated some of SteveC's psiblast specific methods into the interfaces
Some changes to have Blast* and Generic* play nicer
Allow a Hit to have a bit score which is typically the best bit score of the contained HSPs
Bio::Search::Hit::HitI
Migrated some of SteveC's psiblast specific methods into the interfaces
Doc fixes
Allow a Hit to have a bit score which is typically the best bit score of the contained HSPs
Bio::Search::Processor
Processor module is not part of branch
Bio::Search::Result::BlastResult
Some changes to have Blast* and Generic* play nicer
Bio::Search::Result::GenericResult
Migrated some of SteveC's psiblast specific methods into the interfaces
Some changes to have Blast* and Generic* play nicer
Doc fixes
Bio::Search::Result::ResultI
Migrated some of SteveC's psiblast specific methods into the interfaces
Some changes to have Blast* and Generic* play nicer
Doc fixes
Bio::SearchIO::Writer::HSPTableWriter
Fixed method name (psiblast_round -> iteration). Fixes the 'all zeros' bug with default table.
Migrating fix 1.6.2.1 to the trunk.
Enable some debugging when -verbose => 1 and tracked down problems with different API from Interface
Bio::SearchIO::Writer::HTMLResultWriter
Added BLAST/FASTA reference generator and more detailed statistics/parameter value, also allow linkout to be set to empty to omit linking out
Handle cases when parser didn't pull in values (BlastHSP)
Bio::SearchIO::Writer::HitTableWriter
Fixed method name (psiblast_round -> iteration). Fixes the 'all zeros' bug with default table.
Migrating fix 1.6.2.1 to the trunk.
Enable some debugging when -verbose => 1 and tracked down problems with different API from Interface
Bio::SearchIO::Writer::ResultTableWriter
More debugging in ResultTableWriter
Enable some debugging when -verbose => 1 and tracked down problems with different API from Interface
Bio::SearchIO::blast
Fixed bug reported by Bill Morgart with wublast output - missing 'Sum P(D)' handler
Branch fix of bug reported by Bill Morgart with wublast output - missing 'Sum P(D)' handler
Handle wu-blast P values and desc-lines that have line wrappings
Handle parsing wu-blast reports where frame is listed on same line as the score
Merge blast parsing fixes for wu-blast from trunk to branch
Handle NOTE or WARNING lines in WU-BLAST reports, what a just, excellent, report format....
Save whole line as version not just first \S+
Support extracting more parameters and statistics from wu-blast reports
Merged changes from trunk to branch
Split out accession and description from query name
Split the query_name and description into 2 fields
Bio::SearchIO::fasta
Fixed bug that would have parser lose place when HSP is at the end of hit seq and the flanking region of the query is displayed on a line by itsself
Migrated bug fix to branch that deals with trailing query/hit seq when HSP is at the end of one seq
Added fix for fasta33 which doesn't produce percent gapped
Changes to parse fasta33 reports properly
Bio::Seq
Handle object init of features and annotation object - this allows for delayed object instantiation in Bio::SeqIO
Update version number for release
Some doc updates propigated in
Version number for release
Bio::Seq::PrimaryQual
Modules renamed to be more GoF happy
Some minor changes in primary qual and a change in the way that contig keys are treated in consed.
Prettier, less chatty code - better logic for setting qual() data
Remove debug stmt which will cause uninit val wrns when @args is empty
Drop alphabet(), it is not proper to be part of the API
Merged changes for Issue #1202 and cleanup of primaryseq/qual methods
Handle empty strs,undefs, and zeros identically
Handle empty strs,undefs, and zeros identically
Bio::Seq::SeqBuilder
Implement interface to handle generic sequence building
Modules renamed to be more GoF happy
Bio::Seq::SeqFactory
Modules renamed to be more GoF happy
Bio::Seq::SeqWithQuality
Modules renamed to be more GoF happy
Drop alphabet(), it is not proper to be part of the API
Merged changes for Issue #1202 and cleanup of primaryseq/qual methods
Bio::SeqAnalysisParserI
Remove abstractDeath for throw_not_implemented
Remove abstractDeath for throw_not_implemented
Bio::SeqFeature::Collection
New collection object to allow for efficient sub querying of features that fall within a range
Bio::SeqFeature::Computation
More tests for computation object for Issue #1165
Merged computation bugs from trunk to branch
Bio::SeqFeature::Gene::ExonI
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::SeqFeature::Gene::GeneStructureI
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::SeqFeature::Gene::NC_Feature
Renamed utr to UTR, fixed Issue #1181
Merged changes to branch wrt the renamed UTR class (wasn't completely done right before release, this is not an API chg) and fixed Issue #1181
Bio::SeqFeature::Gene::Promoter
Some more documentation
Bio::SeqFeature::Gene::Transcript
Renamed utr to UTR, fixed Issue #1181
Merged changes to branch wrt the renamed UTR class (wasn't completely done right before release, this is not an API chg) and fixed Issue #1181
Some more documentation
Bio::SeqFeature::Gene::TranscriptI
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::SeqFeature::Gene::UTR
Renamed utr to UTR, fixed Issue #1181
Merged changes to branch wrt the renamed UTR class (wasn't completely done right before release, this is not an API chg) and fixed Issue #1181
Enforce that primary tag with be uniform (this all may change soon anyways...)
Bio::SeqI
Don't need Carp anymore
Some doc updates propigated in
Bio::SeqIO
Migrate to using new Factory object for sequence building
Inherit from Bio::Factory::SequenceStreamI
Bio::SeqIO::FTHelper
Migrate to using new Factory object for sequence building
Bio::SeqIO::ace
Migrate to using new Factory object for sequence building
Bio::SeqIO::bsml
Noted that the XML::DOM::Parser object was becoming undef before DESTROY was called, so put a test in DESTROY to see if that object exists before trying to call dispose() on it.
Merged changes from trunk to branch
Migrate to using new Factory object for sequence building
Bio::SeqIO::embl
Migrate to using new Factory object for sequence building
Small correct to set desc
Don't assume that a SeqI object has a primary_seq object underneath
Bio::SeqIO::fasta
Migrate to using new Factory object for sequence building
Slight optimization with fasta reading
Use the object method not the hash key
Bio::SeqIO::fastq
Migrate to using new Factory object for sequence building
Bio::SeqIO::game
Migrate to using new Factory object for sequence building
Updated DTDs, added an empty field yto PREFIX_MAP to keep undef warnings out of XML::Writer call, and explicitly set strand in feature creation
Skip cases when score is undefined
Merge GAME parsing and writing changes to trunk
Explicitly use STDOUT if fh is not defined rather than sending in an undef - this should prevent problems with autoflush on STDOUT
Remove sequence_builder reference cause it just isn't going to work easily with game right now - and use STDOUT as fh explicitly when no fh set for the object to help with autoflushing problems seen when running in a CGI
Bio::SeqIO::game::featureHandler
Updated DTDs, added an empty field yto PREFIX_MAP to keep undef warnings out of XML::Writer call, and explicitly set strand in feature creation
Merge GAME parsing and writing changes to trunk
Bio::SeqIO::game::seqHandler
Migrate to using new Factory object for sequence building
Bio::SeqIO::gcg
Migrate to using new Factory object for sequence building
Bio::SeqIO::genbank
Migrate to using new Factory object for sequence building
Forgot leading slash in specified params PID and DATE
Issue #1062
Merge Issue #1062 from branch to trunk
Bio::SeqIO::largefasta
Migrate to using new Factory object for sequence building
Bio::SeqIO::phd
Migrate to using new Factory object for sequence building
Bio::SeqIO::pir
Migrate to using new Factory object for sequence building
Bio::SeqIO::qual
Migrate to using new Factory object for sequence building
Fixed Issue #1108 on branch - doc fix and return a 1 on successful writing
Fixed Issue #1108 on trunk - doc fix and return 1 on successful writing.
Fix for Issue #1202
Merged changes for Issue #1202 and cleanup of primaryseq/qual methods
Bio::SeqIO::raw
Migrate to using new Factory object for sequence building
Bio::SeqIO::scf
Migrate to using new Factory object for sequence building
Bio::SeqIO::swiss
Migrate to using new Factory object for sequence building
Bio::SimpleAlign
Simple align has overall percent id method
Doc fixes
Fixes Issue #1205
Fixes Issue #1205
Added contributor names
Bio::Structure::Entry
Make seqres() work when entry contains chains Bug reported by Yan-Yuan Tseng <ytseng3@uic.edu>
Make seqres() work when entry contains chains Bug reported by Yan-Yuan Tseng <ytseng3@uic.edu>
Make seqres() work on more then first chain
Make seqres() work with more then one chain
Make seqres work with default chain (bug reported by ytseng3@uic.edu)
Make seqres work with default chain (bug reported by ytseng3@uic.edu)
Bio::Structure::StructureI
Fixed package statement. Added 'use Bio::Root::RootI'.
Migrating fix 1.2 to the 1.0 branch.
Bio::Symbol::AlphabetI
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::Symbol::SymbolI
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::Tools::Alignment::Consed
Some minor changes in primary qual and a change in the way that contig keys are treated in consed.
Updated to use a pure-perl implementation and no grep
Merged consed no-use-grep changes to trunk
Bio::Tools::BPlite
Added eof bugfix
Protect the EOF call in the event we're talking to an IO::String which apparently doesn't implement all of IO::Handle...
Bio::Tools::GFF
Simplify parsing loop for extra textfields
Bio::Tools::Gel
Protect against log of 0 callsmore flexible cmd line arguments parsed in
Merged changes from trunk to branch
Bio::Tools::HMMER::Results
Fixed Issue #1172
Fixed Issue #1172 (main trunk)
Fixed Issue #1178 to use the Root::IO destructor
Fixed Issue #1178 to use the Root::IO destructor
Bio::Tools::RestrictionEnzyme
Added debuggin capability and better seq object validataion
Merged changes from trunk to branch
Bio::Tools::Run::EMBOSSApplication
Cleanup before each run of an application
Merged changes from trunk to branch
Handle some weird boundary cases
Bio::Tools::Run::PiseApplication
Source code for Pise Factory and Application classes. Bio/Factory/Pise.pm: factory Bio/Tools/Run/PiseApplication.pm: base class for all programs Bio/Tools/Run/PiseJob.pm: class for a launched job Bio/Tools/Run/PiseJobParser.pm: XML parser for a job result page
Bio::Tools::Run::PiseJob
Source code for Pise Factory and Application classes. Bio/Factory/Pise.pm: factory Bio/Tools/Run/PiseApplication.pm: base class for all programs Bio/Tools/Run/PiseJob.pm: class for a launched job Bio/Tools/Run/PiseJobParser.pm: XML parser for a job result page
Bio::Tools::Run::PiseJobParser
Source code for Pise Factory and Application classes. Bio/Factory/Pise.pm: factory Bio/Tools/Run/PiseApplication.pm: base class for all programs Bio/Tools/Run/PiseJob.pm: class for a launched job Bio/Tools/Run/PiseJobParser.pm: XML parser for a job result page
Bio::Tools::Run::RemoteBlast
SYNOPSIS needed -readmethod argument
Bio::Tools::Run::RepeatMasker
Alpha Wrapper for RepeatMasker
Bio::Tools::SeqWords
Fixed bugs in synopsis reported by Will Hsiao
Fixed bugs in synopsis reported by Will Hsiao
Bio::Tree::NodeI
Handle empty branch lengths (a common occurance) by not whining so much
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::Tree::TreeI
Remove abstract death in favor of throw_not_implemented()
Remove abstract death in favor of throw_not_implemented() - on branch
Bio::TreeIO::newick
Added test for non-branch length tree files
Merged changes from trunk to branch
Bio::Variation::AAChange
Cleaning constructors
Cleaning constructors
Bio::Variation::AAReverseMutate
Cleaning constructors
Cleaning constructors
Bio::Variation::Allele
Cleaning constructors
Cleaning constructors
Added frequency() and count() methods to be used by Bio::Variation::SNP
Bio::Variation::DNAMutation
Cleaning constructors
Cleaning constructors
Bio::Variation::RNAChange
Cleaning constructors
Cleaning constructors
Bio::Variation::SNP
Not finished - classes for dbSNP parsing
Bio::Variation::SeqDiff
Cleaning constructors
Cleaning constructors
Added Eckhard Lehmann's code for calculating the mutated DNA sequence from the original using DNAMutations
FAQ
Minor updates
Merged changes from trunk to branch
Added some new contributor questions to the FAQ
Added mention of fuzzpro and fuzznuc
Added question/answer on BPLite's frame-change
Added answer to question about how to parse Sequence data from a $string.
Generated from doc/faq/faq.xml
Added mention of Pise
Prettier...
Merged changes from trunk to 1.0 release branch.
Makefile.PL
Missing extra slashes
Added missing section
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required)
Update version required for GD
Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs. Fixed the SearchIO.t regression test to report the correct number of tests being performed. Under 5.6.1 it misreported the number of tests, causing spurious failed tests.
Version number for release
biodesign.pod
Added mention of Bio::Root example scripts, some L<>s
Merged changes from trunk to branch
bioperl.pod
Added mention of flanks.pl revcom_dir.pl entropy.pl cat.pl ds.pl loocv_cat.pl info.pl loocv_ds.pl loocv_info.pl loocv_t.pl loocv_t_cc.pl loocv_u.pl loocv_u_rank.pl relation.pl relrand t_test.pl u_test.pl test-genscan.pl test1.pl test2.pl test3.pl test4.pl vector.pl destroy.pl error.pl filehandle.pl read.pl utilities.pl use_registry.pl scripts.
Merged changes from trunk to branch
Added mention of gb2features.pl, Damien's script
Added mention of the examples/pise scripts
bptutorial.pl
Changes for doc references
Soap -> SOAP
Changed Sigcleave section
Minor fixes to bptutorial code, need to do more...
Added more eval{ require } statements
Added mention of Parse-RecDescent, a dependency
Fixed run_remoteblast example, needed -readmethod argument
Removed list of recommended CPAN modules, maintaining these equivalent lists in bptutorial and in INSTALL is not wise
examples/biblio.pl
Notion of the HTTP proxy added
HTTP proxy code migrated from HEAD
models/bioperl.dia
Minor changes to the dia diagram -- I think
scripts/Bio-DB-GFF/bulk_load_gff.pl
Bulk_load_gff.pl will no longer become inoperative if interrupted during load
scripts/Bio-DB-GFF/load_gff.pl
FNOTE=>fnote table
scripts/render_sequence.pl
Teeny doc fix
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general
Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required)
scripts/seq_length.pl
Simple script for displaying length and # residues in a db file
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