Core 1.2.0 1.2.1 delta

These are detailed notes on changes made between bioperl-release-1-2-0 and bioperl-release-1-2-1.

Bio::AlignIO::bl2seq

Pass in report_type to bl2seq -- for now, until we get patches to auto-detect

Bio::AlignIO::clustalw

Pass the verbosity down

Bio::AlignIO::phylip

Sunday morning Issue #1373

Merge changes for Issue #1373 onto branch

Parse interleaved files where id and first sequence bit run into one another

Bio::AlignIO::psi

Update documentation

Bio::AlignIO::stockholm

Fix to allow AlignIO to read multiple stockholm format entries from a file. Contributed by Andreas Kahari

Fix to allow AlignIO to read multiple stockholm format entries from a file. Contributed by Andreas Kahari

Bio::AlternativeLocationHolderI

Added speculative code for multiple alternative feature locations

Bio::AnalysisI

Added interfaces AnalysisI and Factory::AnalysisI; the rest goes to Bio::Tools::Run in bioperl-run

Bio::Annotation::DBLink

Now a GloballyIdentifiableI (was an IdentifiableI)

Bio::Annotation::OntologyTerm

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Bio::Annotation::SimpleValue

Sync'ed RichSeqI with the implementation. RichSeq provides backward compatibility to the old API. Fixed doc bug in SimpleValue.

Migrated 1.9->1.10 (doc bug fix).

Bio::Cluster::ClusterFactory

Added factories for relationships and terms (the latter aren't used at this time because none of the engine implementations create term objects).

Bio::Cluster::UniGene

Made the species map current with NCBI's repository of UniGene sequences.

Migrated fix to UniGene to make species list current.

Documentation change only; reflects being a GloballyIdentifiableI versus an IdentifiableI

Bio::ClusterIO

Fixed Issue #1369

Fixed Issue #1369 on branch.

Bio::ClusterIO::unigene

(on branch) fix Issue #1370, parse Celegans cluster IDs which have 3 letters instead of 2

Fix Issue #1370, parse Celegans cluster IDs which have 3 letters instead of 2

Bio::Coordinate::Collection

Upgrade to handle split locations. They are needed for example to map features from cds to genomic level with all details. Next todo: documentation!

Deep cloning of mapper elements to make them independet of each other, merge split sub locations when they are adjacent to each other.

Cleaning, adding documentation

Moving fully functional coordinate code from head

Make error message informative

Make sure err msg is informative

Bio::Coordinate::ExtrapolatingPair

Fix chr<->gene coordinates when gene is on reverse strand

Upgrade to handle split locations. They are needed for example to map features from cds to genomic level with all details. Next todo: documentation!

Deep cloning of mapper elements to make them independet of each other, merge split sub locations when they are adjacent to each other.

Cleaning, adding documentation

Moving fully functional coordinate code from head

Bio::Coordinate::GeneMapper

Upgrade to handle split locations. They are needed for example to map features from cds to genomic level with all details. Next todo: documentation!

Deep cloning of mapper elements to make them independet of each other, merge split sub locations when they are adjacent to each other.

Cleaning, adding documentation

Cleaning code and documentation

Moving fully functional coordinate code from head

three fixes: 1. Constructor was reading the parameters in wrong order 2. exons() defaulted strand in one mapper to 1 3. map() returned split locations with only only one sublocation and a feature enhancement: 4. if you did not define cds() you got the split locations in reverse strand back in reverse order. Now exons() calls cds() automatically and sets it to span all the exons.

Fixes from HEAD

Doc fix, mispelling

Bio::Coordinate::Graph

Cleaning, adding documentation

Moving fully functional coordinate code from head

Bio::Coordinate::Pair

Upgrade to handle split locations. They are needed for example to map features from cds to genomic level with all details. Next todo: documentation!

Cleaning, adding documentation

Moving fully functional coordinate code from head

Bio::Coordinate::Result

Deep cloning of mapper elements to make them independet of each other, merge split sub locations when they are adjacent to each other.

Cleaning, adding documentation

Moving fully functional coordinate code from head

Bio::Coordinate::Result::Gap

Cleaning, adding documentation

Moving fully functional coordinate code from head

Bio::Coordinate::Result::Match

Cleaning, adding documentation

Moving fully functional coordinate code from head

Bio::Coordinate::ResultI

Initial commit

Moved from head

Bio::Coordinate::Utils

Cleaning, adding documentation

Moving fully functional coordinate code from head

Bio::DB::Ace

Old school - changed from -type to -alphabet

Bio::DB::AggregatingFeatureProviderI

A Bio::DB::FeatureProviderI with additional methods to support the use of Bio::SeqFeature::AggregatorI objects for creating meta-features.

Bio::DB::BioFetch

Renamed OBDAIndex.pm => BinarySearch.pm and got Bio::DB::Flat to work uniformly with both

Changed config biodbname -> dbname according to new OBDA specs

Added some OBDA documentation plus flat file index load script

Added new heading to biodatabase access doc for Heikki to fill in

Added the dbfetch script

Added a forward-compatibility type() method to Segment

Bio::DB::Failover

Use accession when fetching by accession

Bio::DB::Fasta

Begin addressing concern raised in Issue #1363

Bio::DB::FeatureProviderI

New interfaces; initial docs are in the cvs add.

Minor bugfix

Minor updates

Bio::DB::FileCache

Fix Issue #1376; Make sure we use Bio::Species

Make sure we use Bio::Species

Linewraps

Bio::DB::Flat

Renamed OBDAIndex.pm => BinarySearch.pm and got Bio::DB::Flat to work uniformly with both

Fixed multiple feature inconsistencies between the bdb and binary search versions of the flat databases

ODBA flat file indexers support swiss,fasta,genbank and embl formats

Added some OBDA documentation plus flat file index load script

Make creating directory information quieter

Bio::DB::Flat::BDB

Renamed OBDAIndex.pm => BinarySearch.pm and got Bio::DB::Flat to work uniformly with both

Fixed multiple feature inconsistencies between the bdb and binary search versions of the flat databases

Added some OBDA documentation plus flat file index load script

Respect wantarray

Merge improvements from main trunk

Bio::DB::Flat::BDB::embl

Renamed OBDAIndex.pm => BinarySearch.pm and got Bio::DB::Flat to work uniformly with both

Fixed multiple feature inconsistencies between the bdb and binary search versions of the flat databases

Added some OBDA documentation plus flat file index load script

Bio::DB::Flat::BDB::fasta

Added some OBDA documentation plus flat file index load script

Bio::DB::Flat::BDB::genbank

ODBA flat file indexers support swiss,fasta,genbank and embl formats

Added some OBDA documentation plus flat file index load script

Bio::DB::Flat::BDB::swiss

Check in reasonable howtos for database access and flat databases

Bio::DB::Flat::BDB::swissprot

Added some OBDA documentation plus flat file index load script

Bio::DB::Flat::Binary

Renamed OBDAIndex.pm => BinarySearch.pm and got Bio::DB::Flat to work uniformly with both

Added some more verbiage to OBDA HOWTO

Bio::DB::Flat::BinarySearch

Renamed OBDAIndex.pm => BinarySearch.pm and got Bio::DB::Flat to work uniformly with both

Fixed multiple feature inconsistencies between the bdb and binary search versions of the flat databases

Tighten up code, allow cross-platform ability w/ Bio::Root::IO->catfile

ODBA flat file indexers support swiss,fasta,genbank and embl formats

Added some OBDA documentation plus flat file index load script

Code cleanup, documentation added to many more APIs and tests should now pass

Bio::DB::Flat::OBDAIndex

Renamed OBDAIndex.pm => BinarySearch.pm and got Bio::DB::Flat to work uniformly with both

Bio::DB::GFF

Added some more explanation about how group fields work in GFF2.

Joyous (initial) integration with the collection consolodation

Fixed uc/lc bug in aggregator names; added ability to specify BioGraphics fonts as strings

Bio::DB::GFF::Adaptor::dbi::mysql

Removed binary from the declaration of gname, since most people do not expect object names to be case sensitive

Bio::DB::GFF::Aggregator

Now isa Bio::SeqFeature::AggregatorI

Fixed uc/lc bug in aggregator names; added ability to specify BioGraphics fonts as strings

Bio::DB::GFF::Aggregator::none

Overrides disaggregate_types instead of disaggregate

Bio::DB::GFF::Aggregator::ucsc_acembly

Refining source/method tags for faster querying w/ new gbrowse

Bio::DB::GFF::Aggregator::ucsc_ensgene

Refining source/method tags for faster querying w/ new gbrowse

Bio::DB::GFF::Aggregator::ucsc_genscan

Refining source/method tags for faster querying w/ new gbrowse

Bio::DB::GFF::Aggregator::ucsc_refgene

Refining source/method tags for faster querying w/ new gbrowse

Bio::DB::GFF::Aggregator::ucsc_sanger22

Refining source/method tags for faster querying w/ new gbrowse

Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo

Refining source/method tags for faster querying w/ new gbrowse

Bio::DB::GFF::Aggregator::ucsc_softberry

Refining source/method tags for faster querying w/ new gbrowse

Bio::DB::GFF::Aggregator::ucsc_twinscan

Refining source/method tags for faster querying w/ new gbrowse

Bio::DB::GFF::Aggregator::ucsc_unigene

Refining source/method tags for faster querying w/ new gbrowse

Bio::DB::GFF::Featname

Joyous (initial) integration with the collection consolodation

Bio::DB::GFF::Feature

Added attach_seq() dummy method

Initial attempt to merge this into the collection consolodation. Note that RelSegment is now obsolete.

Joyous (initial) integration with the collection consolodation

Bio::DB::GFF::Homol

Joyous (initial) integration with the collection consolodation

Bio::DB::GFF::RelSegment

Now obsolete. TO BE REMOVED.

Bio::DB::GFF::Segment

Added a forward-compatibility type() method to Segment

Initial attempt to merge this into the collection consolodation.

Joyous (initial) integration with the collection consolodation

Added primary_seq() method to Bio::DB::GFF::Segment

Bio::DB::GFF::Typename

Joyous (initial) integration with the collection consolodation

Bio::DB::GFFI

Interface for GFF.pm, was DasI.pm, now isa thin addition to Bio::DB::SegmentProviderI and Bio::DB::AggregatingFeatureProviderI

Bio::DB::NCBIHelper

Hedge bets and use full URL

Hedge bets and use full URL

Bio::DB::Query::GenBank

Get_Ids -> ids

Bio::DB::Registry

Renamed OBDAIndex.pm => BinarySearch.pm and got Bio::DB::Flat to work uniformly with both

* finds seqdatabase.ini from directory in env variable $BIOINFORMATICS * if ini file not found from local directories, copies the default one from net into users home directory

Added some more verbiage to OBDA HOWTO

ODBA flat file indexers support swiss,fasta,genbank and embl formats

Changes to conform to OBDA specs 1.00

Made registry keywords case insensitive by lowercasing them all

Added a forward-compatibility type() method to Segment

Bio::DB::SegmentProviderI

An interface for objects that are both Bio::DB::SequenceProviderIs and Bio::DB::FeatureProviderIs.

An interface for objects that are both Bio::DB::SequenceProviderIs and Bio::DB::FeatureProviderIs.

Minor updates

Bio::DB::SeqI

Minor bugfix: documentation only

Bio::DB::SequenceProviderI

A provider of Bio::PrimarySeqI objects.

Minor updates

Made get_PrimarySeq_stream an alias to whatever get_Seq_stream happens to be, as opposed to a glob ref alias, which isn't very OO-friendly

Bio::DB::SimpleFeatureProvider

A simple implementation of Bio::DB::FeatureProviderI with an in-memory backing store, for testing purposes.

Bio::DB::Taxonomy

Added taxonomy database interface (API subject to change some)

Bio::DB::Taxonomy::entrez

Entrez driver to Taxonomy DB

Bio::DB::WebDBSeqI

Added the dbfetch script

Not very pretty fix to eliminate empty lines returned and keep seqio happy

Removing gimmicks, bug fixed neatly by fasta module commit

Bio::DB::XEMBL

Added some more verbiage to OBDA HOWTO

Added some OBDA documentation plus flat file index load script

Bio::DasI

Interface for Das.pm, was the sole interface for a lot of things; now isa thin addition to Bio::DB::SegmentProviderI and Bio::DB::AggregatingFeatureProviderI

Bio::Factory::AnalysisI

Added interfaces AnalysisI and Factory::AnalysisI; the rest goes to Bio::Tools::Run in bioperl-run

Bio::Factory::EMBOSS

Moving to bioperl-run CVS module

Bio::Factory::ObjectFactory

Added factories for relationships and terms (the latter aren't used at this time because none of the engine implementations create term objects).

Migrated one more serious of changes and fixes to the ontology modules to the branch.

Bio::Factory::SeqAnalysisParserFactory

Copied method docs from superclass

Bio::GloballyIdentifiableI

New interfaces; initial docs are in the cvs add.

Bio::Graphics

Cleared up RangeI confusion in synopsis

Bio::Graphics::ConfiguratorI

New interfaces; initial docs are in the cvs add.

Merged speculative changes to bio::graphics into main trunk; regression tests 2&3 will fail; need to be fixed

Bio::Graphics::Feature

Added a redgreen gradient glyph suitable for representing microarray data in genomic context

Bio::Graphics::FeatureFile

Added a redgreen gradient glyph suitable for representing microarray data in genomic context

Made redgreen_box glyph work nicely with feature file

Made Bio::Graphics::FeatureFile compatible with Bio::SeqFeature::Generic

Added web-based feature renderer to script repository; expanded FeatureFile format so that the same feature can appear in multiple tracks

Bio::Graphics::Glyph

Added option for sorting features by name

Fixing obscure bugs in bio::graphics; one change will break regression tests 1-3 temporarily

Merged speculative changes to bio::graphics into main trunk; regression tests 2&3 will fail; need to be fixed

Fixed uc/lc bug in aggregator names; added ability to specify BioGraphics fonts as strings

Added flip parameter to biographics for drawing in minus strand coordinates

Bio::Graphics::Glyph::Factory

Added flip parameter to biographics for drawing in minus strand coordinates

Bio::Graphics::Glyph::arrow

Added flip parameter to biographics for drawing in minus strand coordinates

Bio::Graphics::Glyph::cds

Added sixframe option to cds glyph

Debugging sixframe option

Debugging sixframe option

Bio::Graphics::Glyph::dna

Checked in changes to dna.pm to allow to work with vanilla Bio::SeqFeatureI objects (rather than broken Bio::DB::GFF::Features).

Merged speculative changes to bio::graphics into main trunk; regression tests 2&3 will fail; need to be fixed

Added some more verbiage to OBDA HOWTO

Bio::Graphics::Glyph::extending_arrow

Deprecated extending_arrow; will send message to Shengqiang asking to fix

Merged speculative changes to bio::graphics into main trunk; regression tests 2&3 will fail; need to be fixed

Bio::Graphics::Glyph::generic

Fixed display_name() seqid() discrepancy

Fixed uc/lc bug in aggregator names; added ability to specify BioGraphics fonts as strings

Added flip parameter to biographics for drawing in minus strand coordinates

Bio::Graphics::Glyph::graded_segments

Added a redgreen gradient glyph suitable for representing microarray data in genomic context

Bio::Graphics::Glyph::redgreen_box

Added a redgreen gradient glyph suitable for representing microarray data in genomic context

Made redgreen_box glyph work nicely with feature file

Bio::Graphics::Glyph::transcript

Added flip parameter to biographics for drawing in minus strand coordinates

Bio::Graphics::Glyph::transcript2

Added flip parameter to biographics for drawing in minus strand coordinates

Bio::Graphics::Glyph::xyplot

Added the xyplot glyph

Bio::Graphics::Panel

Fixed Biographics crash when using a v1.2 Bio::Seq as the coordinate system for a panel

Fixed error in calculation of starting coordinate when passing a segment to Panel

Cleared up RangeI confusion in synopsis

Fixing obscure bugs in bio::graphics; one change will break regression tests 1-3 temporarily

Merged speculative changes to bio::graphics into main trunk; regression tests 2&3 will fail; need to be fixed

Bio::graphics fixes for cases in which the subfeatures do not reach the end of the feature, and the end of the feature is >= the border of the panel

Added a redgreen gradient glyph suitable for representing microarray data in genomic context

Added the xyplot glyph

Added flip parameter to biographics for drawing in minus strand coordinates

Added public method for mapping feature coordinates into pixel coordinates

Bio::Graphics::RendererI

New interfaces; initial docs are in the cvs add.

Merged speculative changes to bio::graphics into main trunk; regression tests 2&3 will fail; need to be fixed

Bio::IdCollectionI

Documentation changes only; changed IdentifiableI to LocallyIdentifiableI

Bio::Index::EMBL

Fixing Issue #1413

Fixing Issue #1413

Bio::LocallyIdentifiableI

New interfaces; initial docs are in the cvs add.

Bio::LocatableSeq

- silence spurious warnings in location_from_column() - correct trunc() documentation: arguments are column locatation not residues - fix trunc() for returned start positions - override revcom from Bio::PrimarySeqI to include start, end and strand

Fixes from HEAD

Bio::Location::Atomic

A bugfix in Atomic when a necessary Location class had not been use'd/require'd

Bio::Location::Simple

Modifications for GFF3

Merged my changes with Chris M's; not tested

Unecessary use stmt

Bio::Matrix::PhylipDist

Remove the _parse function -- avaiable through Bio::Tools::Phylo::Phylip::ProtDist

Removed _parse method - this is part of Tool::Phylo::Phylip::PhyloDist now

Bio::Ontology::GOterm

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.

Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Migrated one more serious of changes and fixes to the ontology modules to the branch.

Bio::Ontology::InterProTerm

Initial revision of SimpleOntologyEngine implementation of OntologyEngineI and the InterPro XML parser.

Commiting the latest changes to InterProParser, SimpleOntologyEngine and their respective test files.

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Bio::Ontology::Ontology

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.

Migrating one round of fixes and enhancements to the ontology modules to the branch.

Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.

Added factories for relationships and terms (the latter aren't used at this time because none of the engine implementations create term objects).

Migrated one more serious of changes and fixes to the ontology modules to the branch.

Bio::Ontology::OntologyEngineI

Added and updated a good deal of documentation. Fixed a bug in SimpleGOEngine.

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.

Migrating one round of fixes and enhancements to the ontology modules to the branch.

Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.

Added factories for relationships and terms (the latter aren't used at this time because none of the engine implementations create term objects).

Migrated one more serious of changes and fixes to the ontology modules to the branch.

Bio::Ontology::OntologyI

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.

Migrating one round of fixes and enhancements to the ontology modules to the branch.

Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.

Migrated one more serious of changes and fixes to the ontology modules to the branch.

Bio::Ontology::OntologyStore

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Migrated one more serious of changes and fixes to the ontology modules to the branch.

Bio::Ontology::Path

Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.

Migrating one round of fixes and enhancements to the ontology modules to the branch.

Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.

Migrated one more serious of changes and fixes to the ontology modules to the branch.

Bio::Ontology::PathI

Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.

Migrating one round of fixes and enhancements to the ontology modules to the branch.

Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.

Migrated one more serious of changes and fixes to the ontology modules to the branch.

Bio::Ontology::Relationship

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.

Migrating one round of fixes and enhancements to the ontology modules to the branch.

Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.

Migrated one more serious of changes and fixes to the ontology modules to the branch.

Bio::Ontology::RelationshipFactory

Forgot to commit the factory for relationships.

Migrated one more serious of changes and fixes to the ontology modules to the branch.

Bio::Ontology::RelationshipI

Added and updated a good deal of documentation. Fixed a bug in SimpleGOEngine.

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.

Migrated one more serious of changes and fixes to the ontology modules to the branch.

Bio::Ontology::RelationshipType

Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.

Migrating one round of fixes and enhancements to the ontology modules to the branch.

Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.

Migrated one more serious of changes and fixes to the ontology modules to the branch.

Bio::Ontology::SimpleGOEngine

Added and updated a good deal of documentation. Fixed a bug in SimpleGOEngine.

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.

Few fixes to remove assumptions on precise format of identifier. Added extensive tests for Sequence Ontology, which at the same time tests the SimpleGOEngine. All tests pass.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.

Migrating one round of fixes and enhancements to the ontology modules to the branch.

Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.

Added factories for relationships and terms (the latter aren't used at this time because none of the engine implementations create term objects).

Migrated one more serious of changes and fixes to the ontology modules to the branch.

Bio::Ontology::SimpleOntologyEngine

Initial revision of SimpleOntologyEngine implementation of OntologyEngineI and the InterPro XML parser.

Commiting the latest changes to InterProParser, SimpleOntologyEngine and their respective test files.

Removing terms that are repeated in the lists returned by get_ancestor_terms and get_descendant_terms.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.

Migrating one round of fixes and enhancements to the ontology modules to the branch.

Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.

Added factories for relationships and terms (the latter aren't used at this time because none of the engine implementations create term objects).

Migrated one more serious of changes and fixes to the ontology modules to the branch.

Bio::Ontology::Term

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.

Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Bio::Ontology::TermFactory

Made fixes to GFF3 added SO validator for GFF3

Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Added factories for relationships and terms (the latter aren't used at this time because none of the engine implementations create term objects).

Migrated one more serious of changes and fixes to the ontology modules to the branch.

Bio::Ontology::TermI

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Migrated one more serious of changes and fixes to the ontology modules to the branch.

Bio::OntologyIO

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.

Added the additional formats that are supported.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Bio::OntologyIO::Handlers::InterProHandler

Initial revision of SimpleOntologyEngine implementation of OntologyEngineI and the InterPro XML parser.

Get rid of unitialized variable errors

Commiting the latest changes to InterProParser, SimpleOntologyEngine and their respective test files.

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.

Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.

Migrated one more serious of changes and fixes to the ontology modules to the branch.

Bio::OntologyIO::InterProParser

Initial revision of SimpleOntologyEngine implementation of OntologyEngineI and the InterPro XML parser.

Commiting the latest changes to InterProParser, SimpleOntologyEngine and their respective test files.

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.

Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Bio::OntologyIO::dagflat

Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.

Few fixes to remove assumptions on precise format of identifier. Added extensive tests for Sequence Ontology, which at the same time tests the SimpleGOEngine. All tests pass.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.

Migrated one more serious of changes and fixes to the ontology modules to the branch.

Bio::OntologyIO::goflat

Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Bio::OntologyIO::simpleGOparser

Made fixes to GFF3 added SO validator for GFF3

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.

Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Bio::OntologyIO::soflat

Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Bio::PopGen::Genotype

Initial population objects -- statistical tests to come

Update the docs

Handle missing data and allele frequency counts correctly for this now

Slighlty more compact code for matching blank alleles

Cache allele blank status

Bio::PopGen::GenotypeI

Initial population objects -- statistical tests to come

Bio::PopGen::IO

Parser driver and single csv parser for allele based-data

Bio::PopGen::IO::csv

Parser driver and single csv parser for allele based-data

Assume population is made up everyone in the file (in the absence of any more information in a .csv file)

Bio::PopGen::Individual

Initial population objects -- statistical tests to come

Update docs

Change API to be lowercase for arrays of strings

Handle case when we accidently pass in a Marker not a string

Bio::PopGen::IndividualI

Initial population objects -- statistical tests to come

Change API to be lowercase for arrays of strings

Bio::PopGen::Marker

Initial population objects -- statistical tests to come

Handle missing data and allele frequency counts correctly for this now

Bio::PopGen::MarkerI

Initial population objects -- statistical tests to come

Bio::PopGen::PopStats

First implementation of Fst (to be tested still)

Handle missing data and allele frequency counts correctly for this now

Fix bugs found when re-evaluating equations

Bio::PopGen::Population

Initial population objects -- statistical tests to come

Update the docs

Handle missing data and allele frequency counts correctly for this now

Add the ability to get the unique list of marker names from the population

Fix bug in homozygote count

Bio::PopGen::PopulationI

Initial population objects -- statistical tests to come

Update the docs

Add the ability to get the unique list of marker names from the population

Bio::PrimarySeq

Let's not talk about moltype's at all. And in throw() let's call the values returned by alphabet() 'alphabet'. Also, I think the doc in validate_seq is incorrect, there is no ref() call, all it's doing is looking for non-alphabetic characters.

Changed IdentifiableI to GloballyIdentifiableI

Bio::PrimarySeqI

Fixed logic error regarding initiator codon test. Was throwing when it should have been warning and vice versa.

Made LocallyIdentifiable

Value of verbose() is passed on to new sequence objects created by trunc(), revcom() and translate

Fixes from HEAD

Bio::Range

Added seq_id() and updated some docs

Small bugfix

Bio::RangeI

Added seq_id() and updated some docs

In equals(), no longer throws an exception if the other object is undef or not-a-rangeI. Now it just says no, those are not equal.

Bio::RelRange

Initial checkin for Bio::RelRangeI, a Bio::RangeI with additional methods to support shifting between relative and absolute views.

Added the (EXPORT_OKed) utility function absSeqId() for finding the root seq_id for any Bio::RangeI object, even non-Bio::RelRangeI objects.

Minor updates

Lotsa nice new stuff, plus some bugfixes. New stuff includes orientation_policy and better absolutification.

Bio::RelRangeI

Initial checkin for Bio::RelRangeI, a Bio::RangeI with additional methods to support shifting between relative and absolute views.

Minor updates

Lotsa nice new stuff, plus some bugfixes. New stuff includes orientation_policy and better absolutification.

Bio::Root::HTTPget

Support proxy variables in the object

Bio::Root::IO

Issue #1379, can now read from stdin and filelist

Added documentation.

Mode() under linux was always returning 'r'

Mode() under linux was always returning 'r' moved doc fixes and additions from HEAD

Bio::Root::RootI

Initial global BioPerl versioning scheme

Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.

Bio::Root::Version

Initial global BioPerl versioning scheme

Bio::Search::HSP::BlastHSP

Copied the hack in strand() to start() and end()

Bio::Search::HSP::FastaHSP

Fix broken seq_str and added the seq() function which will return a Bio::Seq object for query or hitThanks to Brian O for testing this out better

Specifics of get_aln to Fasta are applied from trunk

Bio::Search::HSP::GenericHSP

Changes to parse megablast

Added megablast blast-like report parsing code

Fix broken seq_str and added the seq() function which will return a Bio::Seq object for query or hitThanks to Brian O for testing this out better

Fix Issue #1381 - seq_inds now returns integers and returns all the proper values for the 'conserved' field - support the new 'conserved-not-identical' value

Seq_inds fix merged from main trunk

Fasta start/end starts with 0, hack is to just accept these numbers for now, a +1 needs to happen somewhere

Use regexps to match algorithms now so things are more compact and handle PSITBLASTN

Add sub cigar_string in GenericHSP

Merge changes from the trunk which use regexp for the algorithm matching

Bio::Search::HSP::HSPFactory

Fix broken seq_str and added the seq() function which will return a Bio::Seq object for query or hitThanks to Brian O for testing this out better

Bio::Search::HSP::HSPI

Fix broken seq_str and added the seq() function which will return a Bio::Seq object for query or hitThanks to Brian O for testing this out better

Slightly more intelligent regexps and fix seq creation

Bug fix - seq_str was not acting properly, added documentation

Some code cleanup made during code audit of Ben B's question

Handle list context properly

Expect is an alias for evalue

Bio::Search::Hit::GenericHit

Some code cleanup made during code audit of Ben B's question

Make debug stmts silent without verbose = 1

Missing s/Blast/Search/

Missing s/Blast/Search/

Doc formatting

Bio::Search::Hit::HitI

Alias for some method names of Steve that are in the XXTable writers

Bio::Search::Result::GenericResult

Remove overloaded operator to_string

Bio::Search::SearchUtils

Some code cleanup made during code audit of Ben B's question

Make debug stmts silent without verbose = 1

Handle more algorithms properly

Stupid bug - has mistyped the hash key with a variable name

Stupid bug - has mistyped the hash key with a variable name

Bio::SearchIO::SearchResultEventBuilder

Insure algorithm value is passed down

Added megablast blast-like report parsing code

Bio::SearchIO::Writer::TextResultWriter

Fixing bug reported by Eric Just

Fixing bug reported by Eric Just

Bio::SearchIO::blast

Changes to parse megablast

Added megablast blast-like report parsing code

Slightly more restrictive regexp to insure we're really matching on the right event class

Merged the more restrictive regexp to the branch

Fix Issue #1378 thanks to Simon Andrews -- GCG blast parsing was broken

Fix Issue #1378 thanks to Simon Andrews -- GCG blast parsing was broken

Handle PSITBLASTN parsing

Handle PSITBLASTN correctly by also using regexp later on

Handle PSITBLASTN

Bio::SearchIO::exonerate

Changes based on code from Gene Cutler at Tularik. I also added hit_length and query_length support since I realized these are encoded in cigar string as well

Fix off-by one errors in exonerate parsing - merge from the main trunk, hopefully everything really works, need one more round of testing perhaps

Undo changes, query length and hit length are not actually available from the sugar/cigar output

Undo changes, query length and hit length are not actually available from the sugar/cigar output

Bio::SearchIO::fasta

Fixed parsing for older fasta v3.2

Added megablast blast-like report parsing code

Bio::SearchIO::hmmer

Handle pesky - ----- - lines in hmmer reports

Catch the error and give more information about how this condition could occur

Catch the error and give more information about how this condition could occur

Bug fix merged from trunk to branch

Make it a debug stmt only

Ugh - bug in parsing multiple domains - forgot to finish the HSP

Ugh - bug in parsing multiple domains - forgot to finish the HSP

Bio::SearchIO::megablast

Changes to parse megablast

Bio::Seq

Ouch! And I've been telling people to read this!

Changed IdentifiableI to GloballyIdentifiableI

Bio::Seq::QualI

Minor doc fixes

Bio::Seq::RichSeq

Fixed the locuslink parser. Refactored RichSeq to delegate dates, secondary accessions, and keywords to the annotation bundle.

Fixed instantiation to recognize array ref for -keywords.

Fix Issue #1382; Improve keywords parsing, multiline keywords and seconardy accessions

Sync'ed RichSeqI with the implementation. RichSeq provides backward compatibility to the old API. Fixed doc bug in SimpleValue.

Now a GloballyIdentifiableI

Bio::Seq::RichSeqI

Sync'ed RichSeqI with the implementation. RichSeq provides backward compatibility to the old API. Fixed doc bug in SimpleValue.

Bio::Seq::SeqWithQuality

Minor doc fixes

Bio::Seq::SequenceTrace

Complete SequenceTrace.pm models a sequence trace as found in an scf file (check the staden docs for more information on this). TraceI was my starting point. scf.pm has been completely rewritten to take advantage of the new object and to make it, well, better. All methods are now decoupled and references to hashes are passed around instead of the self references. Methods to synthesize synthetic traces have been moved to SequenceTrace.pm Tests illustrate what I intend to do with these modules. Hope that helps, Chad Matsalla

Minor doc fixes

Bio::Seq::TraceI

Complete SequenceTrace.pm models a sequence trace as found in an scf file (check the staden docs for more information on this). TraceI was my starting point. scf.pm has been completely rewritten to take advantage of the new object and to make it, well, better. All methods are now decoupled and references to hashes are passed around instead of the self references. Methods to synthesize synthetic traces have been moved to SequenceTrace.pm Tests illustrate what I intend to do with these modules. Hope that helps, Chad Matsalla

Bio::SeqFeature::AggregatorI

Factory for grouping features into components of a containing feature.

More collection consolodation updates.

Bio::SeqFeature::Collection

Get rid of warnings on OSF1

Plane changes: Implemented Lincoln's idea of serializing feature objects in the collection via Storable, this allows collection reuse from different programs. 2 api changes, init params -file and -keep replace the previous -usefile (which was a tempfile)

Bio::SeqFeature::CollectionI

Removed -category option from features()

Further enrichments

Minor updates

Bio::SeqFeature::CollectionProviderI

New interfaces; initial docs are in the cvs add.

Removed -category option from get_collection()

Further enhancements to get_collection(), plus added types() to retrieve the possible types provided, plus added parent_collection_provider() to return the 'factory', and a factory() method aliased to it.

Minor updates

Merged my changes with Chris M's; not tested

Bio::SeqFeature::Computation

Updates because Generic is now a Bio::SeqFeature::SimpleSegment

Bio::SeqFeature::FeaturePair

Updates because Generic is now a Bio::SeqFeature::SimpleSegment

Merged my changes with Chris M's; not tested

Bio::SeqFeature::Gene::Transcript

Fixed bugs in adding exons

Bio::SeqFeature::Generic

Added speculative code for multiple alternative feature locations

Support for soon-to-be-proposed GFF3 format

Added option for sorting features by name

Modifications for GFF3

Made fixes to GFF3 added SO validator for GFF3

Made SeqFeatureI a Bio::SeqFeature::CollectionI and a Bio::LocallyIdentifiableI. Also added the type() method for keeping a Bio::SeqFeature::TypeI (and then type_string and primary_tag are defined in relation to type()).

Now a Bio::SeqFeature::SimpleSegment

More collection consolodation updates.

Bio::SeqFeature::IteratorI

New interface; initial docs are in the cvs add.

Documentation changes

Bio::SeqFeature::PositionProxy

Updated for the changes to SeqFeatureI, plus changed it to use AUTOLOAD for proxy delegation.

Bio::SeqFeature::SegmentI

New interfaces; initial docs are in the cvs add.

Minor updates

Bio::SeqFeature::SimpleCollection

Initial checkin. Note that the present features() implementation is severely crippled.

Minor updates

More collection consolodation updates.

Bio::SeqFeature::SimpleCollectionProvider

Initial checkin. Note that get_collection() has yet to be implemented.

Note that the present get_collection() implementation is severely crippled.

Implementation of enhancements to get_collection()

Minor updates

More collection consolodation updates.

Bio::SeqFeature::SimpleIterator

A simple implementation of the Bio::SeqFeature::IteratorI interface. An iterator over Bio::SeqFeatureI objects.

Minor updates

Bio::SeqFeature::SimpleSegment

A simple implementation of a Bio::SeqFeature::CollectionI that is also a Bio::RelRangeI. Implemented as a Bio::SeqFeature::SimpleCollection that is also a Bio::RelRange.

More collection consolodation updates.

Bio::SeqFeature::SimpleType

A simple implementation of the Bio::SeqFeature::TypeI interface. A feature type.

Bio::SeqFeature::TypeI

New interface; initial docs are in the cvs add.

Fixes & updates; minor

Bio::SeqFeatureI

Fix to spliced_seq on branch; will also commit on head

Added speculative code for multiple alternative feature locations

Made fixes to GFF3 added SO validator for GFF3

Made SeqFeatureI a Bio::SeqFeature::CollectionI and a Bio::LocallyIdentifiableI. Also added the type() method for keeping a Bio::SeqFeature::TypeI (and then type_string and primary_tag are defined in relation to type()).

Now a Bio::SeqFeature::SegmentI

Copied a little code from the non-freaky branch to fix a bug (in spliced_seq())

Bio::SeqIO

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Bio::SeqIO::bsml

Fixed Issue #1367, SeqFactory migrated to method create() from create_sequence()

(branch) fixed Issue #1367, SeqFactory migrated to method create() from create_sequence()

Bio::SeqIO::embl

Fix Issue #1393; multiple keywords handled okay, swiss and embl more robust now I hope

Bio::SeqIO::fasta

Changes to handle Issue #1403

Allow fasta-formatted sequence files to have leading whitespace before first entry

Migrated Jason's (see log/diff for 1.42) and Aaron's fix (allow empty lines before the first entry (see 1.43).

Get rid of warnings on some empty sequence cases

Make empty sequences not complain

Make warnings go away for empty sequences

Bio::SeqIO::genbank

Fixes Issue #1326

Fixes Issue #1326 on branch-1-2

Applied Peter Chines' patch to genbank.pm to handle entries without sequence.

Fix Issue #1382; Improve keywords parsing, multiline keywords and seconardy accessions

Migrated fix to deal with entries without sequence.

Issue #1382; Also fixed multi-line Accessions and definitions and keywords parsing

Fix small bug introduced in fixing

Fix Issue #1393; multiple keywords handled okay, swiss and embl more robust now I hope

Add trailing period

Fix periods - Issue #1395) on the branch

Fix periods - Issue #1395) - even if user has added the last keyword with a trailing '.'

Bio::SeqIO::locuslink

Fixed a bug in the LL parser.

Propagated fix to the branch.

Fixed the locuslink parser. Refactored RichSeq to delegate dates, secondary accessions, and keywords to the annotation bundle.

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.

Bio::SeqIO::raw

Issue #1377

Issue #1377

Bio::SeqIO::scf

Bio/SeqIO/scf.pm: fix for incorrect extraction of trace data from 8-bit-encoded SCF files. Added a perl emulation of a signed/unsigned cast that is implicit in the c-implementation of the code. Works correctly now.

Bio/SeqIO/scf.pm: added slightly faster version of the trace double delta code

Complete SequenceTrace.pm models a sequence trace as found in an scf file (check the staden docs for more information on this). TraceI was my starting point. scf.pm has been completely rewritten to take advantage of the new object and to make it, well, better. All methods are now decoupled and references to hashes are passed around instead of the self references. Methods to synthesize synthetic traces have been moved to SequenceTrace.pm Tests illustrate what I intend to do with these modules. Hope that helps, Chad Matsalla

Bio::SeqIO::swiss

Issue #1387

Issue #1387

Use get_keywords api and send in pre-parsed keywords when initializing a richseq object so to eventually phase out the expected keyword separator for all formats

Fix Issue #1393; multiple keywords handled okay, swiss and embl more robust now I hope

Bio::SeqIO::swissprot

Added Bio::SeqIO::swissprot for the purposes of OBDA naming compatibility; this is just a subclass of Bio::SeqIO::swiss and doesnt add new functionality

Check in reasonable howtos for database access and flat databases

Bio::SimpleAlign

Added remove gaps methods

Bio::Species

Code cleanup

Use underscores in data field names

Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.

Removed left-over print statement.

Bio::Tools::BPbl2seq

Fix problems with BPbl2seq when parsing blastn reports because we can't detect which blast program was used -- force user to provide this information

Bio::Tools::BPlite

Fix applied for Issue #1216 supplied by Sami Ashour

Fix applied for Issue #1216 supplied by Sami Ashour

Bug fixes provided Paracel developers to parse BTK formats

Changes for Paracel BTK Genewise output -- contributed by Sami Ashour

Paracel BTK parsing supported as provided by Sami Ashour

Bio::Tools::BPlite::HSP

Bug fixes provided Paracel developers to parse BTK formats

Paracel BTK parsing supported as provided by Sami Ashour

Bio::Tools::BPlite::Sbjct

Bug fixes provided Paracel developers to parse BTK formats

Changes for Paracel BTK Genewise output -- contributed by Sami Ashour

Paracel BTK parsing supported as provided by Sami Ashour

Bio::Tools::Blat

Parser for Blat

Bio::Tools::GFF

Added speculative code for multiple alternative feature locations

Support for soon-to-be-proposed GFF3 format

Modifications for GFF3

Made fixes to GFF3 added SO validator for GFF3

Merged my changes with Chris M's; not tested

This had been checked in with a bunch of cvs conflict garbage. Removed that and synced it as best I could with the apparent intention. Added feat->ensure_orientation() because the start and end positions might be reversed.

Bio::Tools::Genewise

Added setting exon coding flag true

Bio::Tools::HMMER::Results

Issue #1177

Merging fix for Issue #1177 to branch

Bio::Tools::Hmmpfam

Change to seq_id from seqname

Bio::Tools::IUPAC

Type -> alphabet in new() documentation

Bio::Tools::Lagan

Added Lagan.pm in

Moving into bioperl-run. Note: name change: Bio::Tools::Lagan -> Bio::Tools::Run::Lagan

Bio::Tools::OddCodes

Warn if used on nucleotide sequence

Bio::Tools::Phylo::PAML

Return at least something for get_seqs when parsing yn00

Oops remove unecessary parameter passing

Deal with slightly different format and the NOTE: information

Bio::Tools::Phylo::Phylip::ProtDist

Fix to support parsing multi-line protdist files

Handle case where distance is -1.000 for the wraparound line

Removed _parse method - this is part of Tool::Phylo::Phylip::PhyloDist now

Bio::Tools::Prediction::Gene

Support primary_tag argument as well as primary

Bio::Tools::Promoterwise

Jet lag commits

Bio::Tools::Pseudowise

Eliminate WrapperBase non-needed include

Bio::Tools::Run::StandAloneBlast

Fixing Issue #1168

Fixing Issue #1168

Need to implement program method (or alias the method) in the class, also implementing program_dir and program_name -- a little more complicated since there is not a 1-1 correspondance of module to program here

Fixed small bug in StandAloneBlast when using with BPbl2seq

Migrate changes from trunk to branch -- includes fix for Issue #1406

Fixed unclosed filehandle bug

Reinstated tempfile in constructor

Explicitly close a filehandle rather than assigning it to undef which will keep it open

Tempfile creation should be correct and not cause out tempfile handle problems

Bio::Tools::Run::WrapperBase

Adding to the branch - migrating from bioperl-run

Moving executable mathod to WrapperBase

Remove alias, which was giving StandAloneBlast problems

Migrate changes from trunk to branch -- includes fix for Issue #1406

Doc fix to cleanup()

Removing "use warnings" which < 5.6 perls do not know

Default wrapperbase behavior should be to clean up after oneself

Bio::Tools::SeqStats

SeqStat was not able to handle RNA RichSeqs from databases. get_mol_wt() and count_monomers() now converts T->U internally.

RNA RichSeq objects from databases whichactually have sequence in DNA alphabet are now accommodated

Bio::Tools::SeqWords

Issue #1403 - removed assumption of DNA alphabet from the word counter

Issue #1403 fixed on the 1.2 branch

Bio::Tools::Sim4::Results

Fix docs - Bio::Tools::Sim4::Results is what should be initialized

Fix docs - Bio::Tools::Sim4::Results is what should be initialized.

Bio::Tools::pICalculator

Added pICalcutor.pm. Standalone module by Mark Southern, I changed new() and the documentation to fit into Bioperl

Removing "use warnings" which < 5.6 perls do not know

Bio::Tree::Node

More appropriate way to set data in get/set methods (so that undefs can be passed in to reset data)

Use object method rather than internal hashkey

Properly remove descendents by eliminating intermediete nodes when they are not needed (recursively as well)

Debugging stmts missing newlines

Mistakenly was using same hashkey on description and descendents -- merging fix from trunk to branch

Bio::Tree::NodeI

Get_all_Descendents is a more explicit name - aliasing get_Descendents as well

Debugging stmts missing newlines

Missing newline

Bio::Tree::TreeFunctionsI

Support rerooting the tree

Remove a node from the tree as a top level method

Bio::TreeIO::TreeEventBuilder

Support passing in verbosity settings to the instatiated objects - useful for debugging

Bio::TreeIO::newick

Fixed bug that messed up nodes with 0 branch lengths

Merge Aaron's bugfix to the branch from the main trunk -- was problem with empty branchlength value

Bio::TreeIO::nhx

Fixed bug that messed up nodes with 0 branch lengths

Merge Aaron's bugfix to the branch from the main trunk -- was problem with empty branchlength value

Bio::Variation::IO::xml

Fix bug with newer IO::String which causes seg fault when closing an IO::String FH

Fix bug with closing filehandle on IO::String with later versions of IO::String

FAQ

Update the blast info

Updated

Makefile.PL

Initial global BioPerl versioning scheme

Removed references to bio*PL files, added doc/makedoc.PL

On the Web or locally

Added description of Data::Stag

Value strings in %packages have specific format, delimited by /

Wants both key and value for PL_FILES

Can't check this but should work

biodatabases.PL

Capitialization of GenBank

Added note on setting env's

Added VERSION, read from bioperl.conf

Missing =cut statements - I think this fixes Issue #1396 but I'm not sure, I can't reproduce this bug

Found and escaped a few more embedded variable names

(hopefully) fixing some interpolation issues with heredocs.

Removing \'s to see if hilmar's make problem is fixed by non-interpolated heredocs

Removed the backslashes and corrected the output stream in bioperl.PL. Enabled use strict.

biodatabases.pod

System works, let's replace version number with ==VERSION==

Add back @@VERSION@@. The programmers all seemed to like '@@', they never told me why. Odd, those...

Added mention of Biosql

Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.

biodesign.PL

Minor changes, some necessary for corresponding HTML versions

Added VERSION, read from bioperl.conf

Missing =cut statements - I think this fixes Issue #1396 but I'm not sure, I can't reproduce this bug

Found and escaped a few more embedded variable names

(hopefully) fixing some interpolation issues with heredocs.

Removed the backslashes and corrected the output stream in bioperl.PL. Enabled use strict.

biodesign.pod

Minor changes, some necessary for corresponding HTML versions

Applied Peter Chines' patch to genbank.pm to handle entries without sequence.

System works, let's replace version number with ==VERSION==

Add back @@VERSION@@. The programmers all seemed to like '@@', they never told me why. Odd, those...

Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.

bioperl.PL

Minor changes, some necessary for corresponding HTML versions

(hopefully) fixing some interpolation issues with heredocs.

Removed the backslashes and corrected the output stream in bioperl.PL. Enabled use strict.

bioperl.lisp

Simple stuff

Added macro for array get/add/remove.

bioperl.pod

Minor changes, some necessary for corresponding HTML versions

Applied Peter Chines' patch to genbank.pm to handle entries without sequence.

System works, let's replace version number with ==VERSION==

Add back @@VERSION@@. The programmers all seemed to like '@@', they never told me why. Odd, those...

Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.

bioscripts.PL

Missing script

Added VERSION, read from bioperl.conf

Added new *PLS scripts - thank you Lincoln, Heikki, Ewan, and Jason

(hopefully) fixing some interpolation issues with heredocs.

Removed the backslashes and corrected the output stream in bioperl.PL. Enabled use strict.

bioscripts.pod

System works, let's replace version number with ==VERSION==

Update

Add back @@VERSION@@. The programmers all seemed to like '@@', they never told me why. Odd, those...

Two worth mentioning

bptutorial.pl

Replace \' with '

Add in software link to clustalw at EBI ftp server as well

README should be INSTALL, minor stuff...

Added additional sequence formats

Link DB section to SeqIO section

Describe all SeqIO formats

Both Bio::Index::Fasta and Bio::DB::Fasta can retrieve substrings of the header as ids - here's how

Fixed bugs in bptutorial option 100 subroutine

Added more on Bio::Index::Fasta, multiple keys per sequence

Insure that tutorial ends with a 1 so that require will play nicely

Documentation updates

Allow the tutorial to be testable and silent when running with -1 as initial argument

Complete this type -> alphabet exercise, hopefully

Added mention of chado

Corrected paths to scripts

Matt's fixes

doc/makedoc.PL

Remove File::Find, use @ARGV

examples/biblio/biblio_soap.pl

Reintroducing biblio scrips into head

examples/bioperl.pl

Moving from scripts/ to examples/

examples/generate_random_seq.pl

Moving from scripts/ to examples/

examples/liveseq/change_gene.pl

Put an old script back as an example

examples/longorf.pl

Moving from scripts/ to examples/

examples/make_mrna_protein.pl

Moving from scripts/ to examples/

examples/rev_and_trans.pl

Moving from scripts/ to examples/

examples/revcom_dir.pl

Moving from scripts/ to examples/

Removing "use warnings" which < 5.6 perls do not know

examples/root/README

README for scripts located in examples/root.

examples/root/exceptions1.pl

Sample scripts demonstrating exception handling.

examples/root/exceptions2.pl

Sample scripts demonstrating exception handling.

examples/root/exceptions3.pl

Sample scripts demonstrating exception handling.

examples/root/exceptions4.pl

Sample scripts demonstrating exception handling.

examples/root/lib/Bio/PrimarySeq.pm

Versions of Bio:: modules that demonstrate how to throw Error.pm-compliant exceptions.

examples/root/lib/Bio/PrimarySeqI.pm

Versions of Bio:: modules that demonstrate how to throw Error.pm-compliant exceptions.

examples/root/lib/Bio/Seq.pm

Versions of Bio:: modules that demonstrate how to throw Error.pm-compliant exceptions.

examples/root/lib/Bio/SeqI.pm

Versions of Bio:: modules that demonstrate how to throw Error.pm-compliant exceptions.

examples/root/lib/Error.pm

Graham Barr's module for fancy exception handling. Including it so the example/root/exceptions* scripts work out of the box.

examples/root/lib/TestInterface.pm

Modules for use with the examples/root exceptions scripts.

examples/root/lib/TestObject.pm

Modules for use with the examples/root exceptions scripts.

examples/searchio/blast_example.pl

Simple SearchIO example for blast

Minor additions...

Cross-reference to SearchIO HOWTO

examples/searchio/custom_writer.pl

Moving scripts from scripts/ to examples/

examples/searchio/hitwriter.pl

Moving scripts from scripts/ to examples/

examples/searchio/hspwriter.pl

Moving scripts from scripts/ to examples/

examples/searchio/htmlwriter.pl

Moving scripts from scripts/ to examples/

examples/searchio/psiblast_features.pl

Moving scripts from scripts/ to examples/

examples/searchio/rawwriter.pl

Moving scripts from scripts/ to examples/

examples/searchio/resultwriter.pl

Moving scripts from scripts/ to examples/

examples/subsequence.cgi

Moving from scripts/ to examples/

models/coordinatemapper.dia

Initial commit

scripts/Bio-DB-GFF/README

Changed to reflect new locations

Correct

scripts/Bio-DB-GFF/bulk_load_gff.PLS

Added GFF loaders in correctly documented .PLS form

scripts/Bio-DB-GFF/bulk_load_gff.pl

A few minor changes to make bulk_load_gff.pl run on Windows: - STDIN used instead of TTY - Backslashes in paths are escaped when needed - Approprate line terminators are used when needed

Stripped annoying DOS line terminators

Added back code inadvertently removed from revision 1.9.

Removed potentially disastrous windows workaround

Added a note to the usage text for Windows users.

Added code to die if using on Windows with out --create.

Changed $^O regex so that Darwin will not be considered a MS OS.

Moving scripts from scripts/ to examples/

scripts/Bio-DB-GFF/fast_load_gff.PLS

Added GFF loaders in correctly documented .PLS form

scripts/Bio-DB-GFF/fast_load_gff.pl

Moving scripts from scripts/ to examples/

scripts/Bio-DB-GFF/generate_histogram.PLS

Certain scripts are being renamed, from *pl to *PLS, so I've removed them, now I'll add them back as *PLS

scripts/Bio-DB-GFF/generate_histogram.pl

Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...

scripts/Bio-DB-GFF/load_gff.PLS

Added GFF loaders in correctly documented .PLS form

scripts/Bio-DB-GFF/load_gff.pl

Moving scripts from scripts/ to examples/

scripts/Bio-DB-GFF/process_gadfly.PLS

Certain scripts are being renamed, from *pl to *PLS, so I've removed them, now I'll add them back as *PLS

scripts/Bio-DB-GFF/process_gadfly.pl

Updated the process_*.pl scripts for gff tweaking

Stupid mistake in gadfly url

Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...

scripts/Bio-DB-GFF/process_ncbi_human.PLS

Certain scripts are being renamed, from *pl to *PLS, so I've removed them, now I'll add them back as *PLS

scripts/Bio-DB-GFF/process_ncbi_human.pl

Updated the process_*.pl scripts for gff tweaking

Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...

scripts/Bio-DB-GFF/process_sgd.PLS

Certain scripts are being renamed, from *pl to *PLS, so I've removed them, now I'll add them back as *PLS

scripts/Bio-DB-GFF/process_sgd.pl

Updated the process_*.pl scripts for gff tweaking

Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...

scripts/Bio-DB-GFF/process_wormbase.PLS

Certain scripts are being renamed, from *pl to *PLS, so I've removed them, now I'll add them back as *PLS

scripts/Bio-DB-GFF/process_wormbase.pl

Updated the process_*.pl scripts for gff tweaking

Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...

scripts/Bio-DB-GFF/ucsc2gff.pl

Moving scripts from scripts/ to examples/

scripts/DB/biofetch_genbank_proxy.PLS

Added the dbfetch script

Fixed bug that caused script to crap out on "default" format

scripts/DB/bioflat_index.pl

Added some OBDA documentation plus flat file index load script

Moving scripts from scripts/ to examples/

scripts/DB/biogetseq

Initial commit of ODBA Registry compliant sequence retrieval script

Added namespace processing

Failing to find sequence handled better

Moved biogetseq to biogetseq.PLS

scripts/DB/biogetseq.PLS

Moved biogetseq to biogetseq.PLS

scripts/DB/blast_fetch.pl

Moving scripts from scripts/ to examples/

scripts/DB/blast_fetch_local.pl

Moving scripts from scripts/ to examples/

scripts/DB/dbfetch.pl

Moving scripts from scripts/ to examples/

scripts/DB/est_tissue_query.pl

Moving scripts from scripts/ to examples/

scripts/DB/flanks.PLS

Putting back the 1.0 bioperl release flanks.pl with a name and new interface and better documentation

Putting back the 1.0 bioperl elease flanks.pl with a name and new interface and better documentation

Doc fixes

scripts/DB/gb2features.pl

Moving scripts from scripts/ to examples/

scripts/DB/getGenBank.pl

Moving scripts from scripts/ to examples/

scripts/DB/get_seqs.pl

Moving scripts from scripts/ to examples/

scripts/DB/rfetch.pl

Moving scripts from scripts/ to examples/

scripts/DB/use_registry.pl

Moving scripts from scripts/ to examples/

scripts/biblio/biblio.PLS

Reintroducing biblio scrips into head

scripts/biblio/biblio.pl

Moving from scripts/ to examples/

scripts/biblio/biblio_examples.pl

Some simple queries using Bio::Biblio

Moving from scripts/ to examples/

scripts/biblio/biblio_soap.pl

Moving scripts from scripts/ to examples/

scripts/biographics/README

Redundant directory with scripts/graphics

scripts/biographics/frend

Redundant directory with scripts/graphics

scripts/biographics/render_sequence.pl

Redundant directory with scripts/graphics

scripts/bioperl.pl

Moving from scripts/ to examples/

scripts/generate_random_seq.pl

Moving from scripts/ to examples/

scripts/graphics/README

Moved from biographics

Changed to reflect new locations

Correct

scripts/graphics/feature_draw.PLS

Certain scripts are being renamed, from *pl to *PLS, so I've removed them, now I'll add them back as *PLS

scripts/graphics/feature_draw.pl

Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...

scripts/graphics/frend

Moved from biographics

Moving scripts

scripts/graphics/frend.PLS

Added web-based feature renderer to script repository; expanded FeatureFile format so that the same feature can appear in multiple tracks

scripts/graphics/render_sequence.pl

Moved from biographics

Changed display_name to display_id to accomodate some changes in Bio::SeqFeatureI

Fixed RangeI problem

Moving scripts

scripts/index/bpfetch.PLS

Certain scripts are being renamed, from *pl to *PLS, so I've removed them, now I'll add them back as *PLS

Moved branch fixes over .PLS in index directory

scripts/index/bpfetch.pl

Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...

Fixed bpindex for genbank

scripts/index/bpindex.PLS

Certain scripts are being renamed, from *pl to *PLS, so I've removed them, now I'll add them back as *PLS

Moved branch fixes over .PLS in index directory

scripts/index/bpindex.pl

Added ability to index Genbank and SwissPfam

Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...

Fixed bpindex for genbank

scripts/longorf.pl

Moving from scripts/ to examples/

scripts/make_mrna_protein.pl

Moving from scripts/ to examples/

scripts/make_primers.pl

Moving scripts from scripts/ to examples/

scripts/rev_and_trans.pl

Moving from scripts/ to examples/

scripts/revcom_dir.pl

Moving from scripts/ to examples/

Replacing 'use warnings' with -w

scripts/searchio/custom_writer.pl

Moving scripts from scripts/ to examples/

scripts/searchio/hitwriter.pl

Moving scripts from scripts/ to examples/

scripts/searchio/hspwriter.pl

Moving scripts from scripts/ to examples/

scripts/searchio/htmlwriter.pl

Moving scripts from scripts/ to examples/

scripts/searchio/psiblast_features.pl

Moving scripts from scripts/ to examples/

scripts/searchio/rawwriter.pl

Moving scripts from scripts/ to examples/

scripts/searchio/resultwriter.pl

Moving scripts from scripts/ to examples/

scripts/searchio/waba2gff.pl

Moving scripts from scripts/ to examples/

scripts/seq/extract_cds.pl

Moving scripts from scripts/ to examples/

scripts/seq/extract_feature_seq.PLS

More general implementation to extract features and properly name the sequence that is extracted

scripts/seq/id.list

Moving scripts from scripts/ to examples/

scripts/seq/seq.fasta.gz

Moving scripts from scripts/ to examples/

scripts/seq/seq1.fasta

Moving scripts from scripts/ to examples/

scripts/seq/seq2.fasta

Moving scripts from scripts/ to examples/

scripts/seq/seqs1.pl

Moving scripts from scripts/ to examples/

scripts/seq/seqs2.pl

Moving scripts from scripts/ to examples/

scripts/seq/seqs3.pl

Moving scripts from scripts/ to examples/

scripts/seq/seqtools.pl

Moving scripts from scripts/ to examples/

scripts/seq_length.pl

Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...

scripts/seqstats/aacomp.pl

Moving scripts from scripts/ to examples/

scripts/seqstats/chaos_plot.PLS

Reworking old scripts into new standard

Doc update

scripts/seqstats/chaos_plot.pl

Moving scripts from scripts/ to examples/

scripts/seqstats/gccalc.pl

Moving scripts from scripts/ to examples/

scripts/seqstats/oligo_count.pl

Moving scripts from scripts/ to examples/

scripts/subsequence.cgi

Moving from scripts/ to examples/

scripts/tree/blast2tree.PLS

Certain scripts are being renamed, from *pl to *PLS, so I've removed them, now I'll add them back as *PLS

scripts/tree/blast2tree.pl

Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...

scripts/tree/paup2phylip.pl

Moving scripts from scripts/ to examples/

scripts/utilities/bp_mrtrans.PLS

Removing "use warnings" which < 5.6 perls do not know

scripts/utilities/bp_nrdb.PLS

Nrdb makes a sequence unique database -- still needs some thorough debugging

Added some perldoc and fleshed out cmd line arguments -- still need a bit more testing

scripts/utilities/dbsplit.PLS

Simple script to split database into chunks

Make sure scount gets reset to 0

Use prefix to get current count

scripts/utilities/pairwise_kaks.PLS

Utility script to run PAML on cDNA sequences

Missing bug URL

Add some percent identity information

Simple script to split database into chunks

Should be perl 5.8.0 compliant

scripts/utilities/remote_blast.PLS

No sense in having both a tools/ and a utilities/ directory

scripts/utilities/search2tribe.PLS

A script to turn SearchIO-parseable reports into a Tribe matrix

Use tabs, it is simplier

scripts/utilities/seq_length.PLS

No sense in having both a tools/ and a utilities/ directory

scripts/validate_gff_via_ontology.pl

Made fixes to GFF3 added SO validator for GFF3