Core 1.1.0 1.2.0 delta

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

Bio::Align::AlignI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Align::DNAStatistics

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Align::PairwiseStatistics

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Align::StatisticsI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Align::Utilities

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Removed unused "use Carp" call.

Croak needs Carp

Bio::AlignIO

Doc formatting

Changeover to using Hilmar's _load_module Bio::Root::Root method

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::AlignIO::bl2seq

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::AlignIO::clustalw

Support dynamic line length specification for alignment writing

Doc fix for clarification

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::AlignIO::emboss

Merged bugfix to branch in unlikely event we want to push this out again

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::AlignIO::fasta

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Fixed primary seq seq setting call

Bio::AlignIO::mase

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::AlignIO::mega

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::AlignIO::meme

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::AlignIO::msf

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Parse EMBOSS MSF output which has the alignment position information

Bio::AlignIO::nexus

Allow for empty lines after the matrix line

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::AlignIO::pfam

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::AlignIO::phylip

Doc fix for clarification

Avoid undef $count value

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

New phylip doesn't accept dots, use dashes instead

Code formatting

Allow parsing of more than one alignment entry

Bio::AlignIO::prodom

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::AlignIO::psi

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Deal with changes needed as seen by Issue #1359, mostly this is just a needed map_chars call in StandAloneBlast but have cleaned up the code some in other places

Bio::AlignIO::selex

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::AlignIO::stockholm

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::AnalysisParserI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Doc fix credited to nkuipers

Bio::AnalysisResultI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::AnnotatableI

Final documentation fixes for 1.2

Bio::Annotation

Retired Bio/Annotation.pm. Everything else is minor fixes.

Bio::Annotation::AnnotationFactory

Added a couple of object factories. Fixed Ontology::GOterm to better honor the fact that it inherits off Term (it screwed up parameters). Fixed Unigene member object creation. Fixed Annotation::OntologyTerm (Hilmar, had you written a test you could have avoided this).

Bio::Annotation::Collection

Added Bio::Annotation::OntologyTerm. The rest is insignificant fixes.

Added tagname() to Bio::AnnotationI and adapted the implementing classes to use it. Also, changed Bio::Annotation::Collection to retrieve the key from the object if the key is omitted. Fixed bugs exposed by the removal of Bio::Annotation (it _was_ used in several tests).

Added Bio::SeqFeature::AnnotationAdaptor and its test. Other changes are insignificant.

Added second form of calling to Species::classification() which will potentially bypass all name checks. Added method variant() to Species. Made Annotation::Collection implement AnnotationI too - this allows for nested annotation. Added Annotation::StructuredValue, which is a lightweight way of representing structured simple values. Fixed the swissprot parser to take advantage of these changes, retain the structure of the GN line's content, and parse the species correctly. Added a number of tests for the new stuff and for the previous problems.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Fully moved most of the extended UniGene properties into the annotation collection. Fixed a bug in Annotation::Collection. All tests pass.

Added blast_sequence to Bio::Perl for newbies wanting to "just blast"

Bio::Annotation::Comment

Added tagname() to Bio::AnnotationI and adapted the implementing classes to use it. Also, changed Bio::Annotation::Collection to retrieve the key from the object if the key is omitted. Fixed bugs exposed by the removal of Bio::Annotation (it _was_ used in several tests).

Fixed order of inheritance.

Bio::Annotation::DBLink

SequenceFactoryI wasn't inheriting from ObjectFactoryI. Fixed. DBLink is now IdentifiableI. Otherwise minor things.

Added tagname() to Bio::AnnotationI and adapted the implementing classes to use it. Also, changed Bio::Annotation::Collection to retrieve the key from the object if the key is omitted. Fixed bugs exposed by the removal of Bio::Annotation (it _was_ used in several tests).

Cosmetic and doc fixes. Changed the new get/set method template to the style suggested by Tim Bunce. Be careful: this by default will set to undef if you pass undef.

Fixed namespace_string() in IdentifiableI. Added recognition of parameters for IdentifiableI properties passed to DBLink. Promoted is_remote() to LocationI.

Bio::Annotation::OntologyTerm

Added Bio::Annotation::OntologyTerm. The rest is insignificant fixes.

Added tagname() to Bio::AnnotationI and adapted the implementing classes to use it. Also, changed Bio::Annotation::Collection to retrieve the key from the object if the key is omitted. Fixed bugs exposed by the removal of Bio::Annotation (it _was_ used in several tests).

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added a couple of object factories. Fixed Ontology::GOterm to better honor the fact that it inherits off Term (it screwed up parameters). Fixed Unigene member object creation. Fixed Annotation::OntologyTerm (Hilmar, had you written a test you could have avoided this).

Bio::Annotation::Reference

Retired Bio/Annotation.pm. Everything else is minor fixes.

Added tagname() to Bio::AnnotationI and adapted the implementing classes to use it. Also, changed Bio::Annotation::Collection to retrieve the key from the object if the key is omitted. Fixed bugs exposed by the removal of Bio::Annotation (it _was_ used in several tests).

Fixed order of inheritance.

Bio::Annotation::SimpleValue

Added Bio::Annotation::OntologyTerm. The rest is insignificant fixes.

Added tagname() to Bio::AnnotationI and adapted the implementing classes to use it. Also, changed Bio::Annotation::Collection to retrieve the key from the object if the key is omitted. Fixed bugs exposed by the removal of Bio::Annotation (it _was_ used in several tests).

Too many copy+pastes (dup tagname function)

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added a couple of object factories. Fixed Ontology::GOterm to better honor the fact that it inherits off Term (it screwed up parameters). Fixed Unigene member object creation. Fixed Annotation::OntologyTerm (Hilmar, had you written a test you could have avoided this).

Bio::Annotation::StructuredValue

Added second form of calling to Species::classification() which will potentially bypass all name checks. Added method variant() to Species. Made Annotation::Collection implement AnnotationI too - this allows for nested annotation. Added Annotation::StructuredValue, which is a lightweight way of representing structured simple values. Fixed the swissprot parser to take advantage of these changes, retain the structure of the GN line's content, and parse the species correctly. Added a number of tests for the new stuff and for the previous problems.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Annotation::TypeManager

Added Bio::Annotation::OntologyTerm. The rest is insignificant fixes.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::AnnotationCollectionI

Added Bio::SeqFeature::AnnotationAdaptor and its test. Other changes are insignificant.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::AnnotationI

Added tagname() to Bio::AnnotationI and adapted the implementing classes to use it. Also, changed Bio::Annotation::Collection to retrieve the key from the object if the key is omitted. Fixed bugs exposed by the removal of Bio::Annotation (it _was_ used in several tests).

Added second form of calling to Species::classification() which will potentially bypass all name checks. Added method variant() to Species. Made Annotation::Collection implement AnnotationI too - this allows for nested annotation. Added Annotation::StructuredValue, which is a lightweight way of representing structured simple values. Fixed the swissprot parser to take advantage of these changes, retain the structure of the GN line's content, and parse the species correctly. Added a number of tests for the new stuff and for the previous problems.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Assembly::Contig

Initial comment

Bio::Assembly::ContigAnalysis

Initial comment

Synopsis was mispelled and added small code formatting

Bio::Assembly::IO

Initial comment

Bio::Assembly::IO::ace

Initial commit

Bio::Assembly::IO::phrap

Initial commit

Bio::Assembly::Scaffold

Initial comment

Added Bio::AnnotationI and have it implemented by Bio::Seq, SeqFeature::Generic, and Cluster::UniGene. The rest is minor documentation fixes.

Bio::Assembly::ScaffoldI

Initial comment

Added Bio::AnnotationI and have it implemented by Bio::Seq, SeqFeature::Generic, and Cluster::UniGene. The rest is minor documentation fixes.

Bio::Biblio

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::Article

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::BiblioBase

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::Book

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::BookArticle

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::IO

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::IO::medline2ref

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::IO::medlinexml

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::IO::pubmed2ref

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::IO::pubmedxml

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::Journal

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::JournalArticle

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::MedlineArticle

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::MedlineBook

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::MedlineBookArticle

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::MedlineJournal

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::MedlineJournalArticle

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::Organisation

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::Patent

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::Person

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::Proceeding

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::Provider

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::PubmedArticle

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::PubmedBookArticle

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::PubmedJournalArticle

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::Ref

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::Service

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::TechReport

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::Thesis

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Biblio::WebResource

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Cluster::ClusterFactory

Added species() to Cluster::UniGene and interface. Added species recognition from unigene ID. Added Cluster::ClusterFactory and its utilization to ClusterIO and unigene.

Added a couple of object factories. Fixed Ontology::GOterm to better honor the fact that it inherits off Term (it screwed up parameters). Fixed Unigene member object creation. Fixed Annotation::OntologyTerm (Hilmar, had you written a test you could have avoided this).

Bio::Cluster::FamilyI

SequenceFamily representing a family of sequences

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Tidied up Cluster interfaces. Changed Cluster::UniGene to implement ClusterI, IdentifiableI, and DescribableI. Added display_id to ClusterI. Removed members() from ClusterI. Added namespace and authority defaults to Cluster::UniGene.

Bio::Cluster::SequenceFamily

SequenceFamily representing a family of sequences

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Tidied up Cluster interfaces. Changed Cluster::UniGene to implement ClusterI, IdentifiableI, and DescribableI. Added display_id to ClusterI. Removed members() from ClusterI. Added namespace and authority defaults to Cluster::UniGene.

Support perl 5.005

Bio::Cluster::UniGene

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Tidied up Cluster interfaces. Changed Cluster::UniGene to implement ClusterI, IdentifiableI, and DescribableI. Added display_id to ClusterI. Removed members() from ClusterI. Added namespace and authority defaults to Cluster::UniGene.

First step towards migrating most properties into the AnnotationCollectionI framework.

Fully moved most of the extended UniGene properties into the annotation collection. Fixed a bug in Annotation::Collection. All tests pass.

Added species() to Cluster::UniGene and interface. Added species recognition from unigene ID. Added Cluster::ClusterFactory and its utilization to ClusterIO and unigene.

Added a couple of object factories. Fixed Ontology::GOterm to better honor the fact that it inherits off Term (it screwed up parameters). Fixed Unigene member object creation. Fixed Annotation::OntologyTerm (Hilmar, had you written a test you could have avoided this).

Added Bio::AnnotationI and have it implemented by Bio::Seq, SeqFeature::Generic, and Cluster::UniGene. The rest is minor documentation fixes.

Fixed a bug report about Root::new() complaining about uneven number of parameters for hash initialization.

Support perl 5.005

Make work with perl 5.005

Remove undef warning

Bio::Cluster::UniGeneI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Tidied up Cluster interfaces. Changed Cluster::UniGene to implement ClusterI, IdentifiableI, and DescribableI. Added display_id to ClusterI. Removed members() from ClusterI. Added namespace and authority defaults to Cluster::UniGene.

Added species() to Cluster::UniGene and interface. Added species recognition from unigene ID. Added Cluster::ClusterFactory and its utilization to ClusterIO and unigene.

Bio::ClusterI

First attempt at a cluster interface

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Tidied up Cluster interfaces. Changed Cluster::UniGene to implement ClusterI, IdentifiableI, and DescribableI. Added display_id to ClusterI. Removed members() from ClusterI. Added namespace and authority defaults to Cluster::UniGene.

Bio::ClusterIO

Use _load_module to load dynamically

Based on the fall-out from swissprot->biosql, some more fixes to sanely get the species parsed. Should be OK now ...

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added species() to Cluster::UniGene and interface. Added species recognition from unigene ID. Added Cluster::ClusterFactory and its utilization to ClusterIO and unigene.

Added recognition of all IdentifiableI parameters to PrimarySeq. Added object_factory() as an alias for <type>_factory methods in several places.

Bio::ClusterIO::dbsnp

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::ClusterIO::unigene

Added Dm as a possible organism.

Start of regularising across perl versions unigene regex fixes

Fixed unigene regexs now

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Tidied up Cluster interfaces. Changed Cluster::UniGene to implement ClusterI, IdentifiableI, and DescribableI. Added display_id to ClusterI. Removed members() from ClusterI. Added namespace and authority defaults to Cluster::UniGene.

Added species() to Cluster::UniGene and interface. Added species recognition from unigene ID. Added Cluster::ClusterFactory and its utilization to ClusterIO and unigene.

Added a couple of object factories. Fixed Ontology::GOterm to better honor the fact that it inherits off Term (it screwed up parameters). Fixed Unigene member object creation. Fixed Annotation::OntologyTerm (Hilmar, had you written a test you could have avoided this).

Bio::Coordinate::Chain

Initial commit of the module chaining mappers

Bio::Coordinate::Collection

Added missing includes

Changed privated method _sort() into public: sort()

Implement schwartzian transformation in sort

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added method mappers() to add a prepared array of Mappers

Bio::Coordinate::Result is now a Bio::Location::SplitLocationI. Numerous fixes and tweeks. Saner way of handling gene->cds mapping.

Cleaning up. Fixing GeneMapper::exons bug which changed seq_id of the argument object

Bio::Coordinate::ExtrapolatingPair

Added missing includes

Now handles mapping between opposite directions. Non-zero numbering temporarily disabled.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Coordinate::Result is now a Bio::Location::SplitLocationI. Numerous fixes and tweeks. Saner way of handling gene->cds mapping.

Bio::Coordinate::GeneMapper

Initial commit

Under development

Almost complete rewrite of GeneMapper. Now with real life test data

Was not 'use'ing Bio::Location::Simple

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Move path finding logic into Bio::Coordinate::Graph

Code optimizations, internal changes

Added nozero() which allows the use of coordinate systems without zero (-1 preceds 1) in input and/or output coordinates.

Missing use stmts, Issue #1339

Issue #1341

Bio::Coordinate::Result is now a Bio::Location::SplitLocationI. Numerous fixes and tweeks. Saner way of handling gene->cds mapping.

Cleaning up. Fixing GeneMapper::exons bug which changed seq_id of the argument object

Doc fix a little - exons requires a array not array ref

Bio::Coordinate::Graph

Abstraction of finding shortest paths between gene coordinate systems. This grap is a DAG.

Fix for Graph returning wrong path under perl < 5.8

Bio::Coordinate::MapperI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Coordinate::Result is now a Bio::Location::SplitLocationI. Numerous fixes and tweeks. Saner way of handling gene->cds mapping.

Bio::Coordinate::Pair

Added missing includes

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Code optimizations, internal changes

Bio::Coordinate::Result is now a Bio::Location::SplitLocationI. Numerous fixes and tweeks. Saner way of handling gene->cds mapping.

Cleaning up. Fixing GeneMapper::exons bug which changed seq_id of the argument object

Bio::Coordinate::Result

Silencing spurious warnings

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Coordinate::Result is now a Bio::Location::SplitLocationI. Numerous fixes and tweeks. Saner way of handling gene->cds mapping.

Seq_id returns now a sane value

Bio::Coordinate::Result::Gap

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Coordinate::Result::Match

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Coordinate::Utils

Initial commit, only method is from_align which can handle only pairwire alignments

Bio::DB::Ace

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::DB::Biblio::biofetch

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::DB::Biblio::soap

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::DB::BiblioI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::DB::BioFetch

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added a new class representing a query on a Bio::DB database. The class can accept a query string and other arguments (mindate, maxdate) and then be used directly to retrieve count match or ID list, or indirectly by passing to Bio::DB::* access object. Implemented a "pipeline" fetch that is memory and speed efficient relative to io_string and tempfile. Not tested: ability to upload a list of IDs via query interface.

Bio::DB::DBFetch

Wrong modules name standard comments

Rolled back out BEGIN to INIT changes -- possibly needs more work...

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added a new class representing a query on a Bio::DB database. The class can accept a query string and other arguments (mindate, maxdate) and then be used directly to retrieve count match or ID list, or indirectly by passing to Bio::DB::* access object. Implemented a "pipeline" fetch that is memory and speed efficient relative to io_string and tempfile. Not tested: ability to upload a list of IDs via query interface.

Fixed that Bio::DB::Flat::BDB handling of secondary namespaces, and added a workaround to EMBL web fetcher to avoid crashing when EMBL server gives extra blank line(s) at beginning of content

Bio::DB::EMBL

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Allowed description to be set to undef.

Documentation fixes for Bio::DB::GenBank

Bio::DB::Failover

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::DB::Fasta

Used not defined on value rather than exists to work around sun solaris default AnyDBM_File install

Bio::DB::FileCache

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Cut paste runnable

Bio::DB::Flat

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Fixed that Bio::DB::Flat::BDB handling of secondary namespaces, and added a workaround to EMBL web fetcher to avoid crashing when EMBL server gives extra blank line(s) at beginning of content

Bio::DB::Flat::BDB

Added missing documentation. Fixed missing arrows on transcript glyphs.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

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

Added missing documentation. Fixed missing arrows on transcript glyphs.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

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

Added missing documentation. Fixed missing arrows on transcript glyphs.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::DB::Flat::OBDAIndex

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Laura Clarke's fix of an OBDAIndex bug -- caused module to return WRONG sequence rather than empty when id not found

Bio::DB::GDB

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::DB::GFF

Folded in Aaron Mackey's patches for sort order of glyphs. feature_by_name() method in Bio::DB::GFF now searches Aliases

Bio::DB::GFF hierarchy now correctly inherits from Bio::DasI hierarchy

Relaxed group parsing in Bio::DB::GFF to read the format produced by bioperl GFF formatter

Put eval{} blocks around all the places in bio::graphics where a callback is invoked; this prevents callbacks from making the whole thing crash

Removed unused "use Carp" call.

Adjusted parsing of Target in Bio::DB::GFF so that the tstart and tend are correctly assigned even when the target sequence is a digit.

Refactored acedb code so that it no longer is tangled with relational code

Regularized method names in bio::db::gff and removed some unused methods and variables; also fixed a few warnings

Bio::DB::GFF::Adaptor::ace

Refactored acedb code so that it no longer is tangled with relational code

Bio::DB::GFF::Adaptor::biofetch

Modified embl loading code to accomodate removal of Bio::RangeI from Bio::Seq

Added proxy configuration to Bio::DB::GFF biofetch adaptor

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

Folded in Aaron Mackey's patches for sort order of glyphs. feature_by_name() method in Bio::DB::GFF now searches Aliases

Added a new database adaptor 'dbi::oracleopt' for an Oracle database Modified Files: Bio/DB/GFF/Adaptor/dbi.pm Bio/DB/GFF/Adaptor/dbi/caching_handle.pm Bio/DB/GFF/Adaptor/dbi/mysql.pm Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm Added Files: Bio/DB/GFF/Adaptor/dbi/oracleopt.pm

Reorganization of dbi.pm,mysql.pm and oracle.pm - all the general database stauff moved to dbi.pm and mysql.pm and mysqlopt.pm were combined. the oracle adaptor has changed to oracle (from oracleopt that used to inherit from mysqlopt).

Consolidation of mysql and oracle adaptors

Deal with empty dna string as empty string rather than undef to avoid warnings

Moved hacky acedb stuff out of dbi.pm and into its own subclass

Fix for Issue #1356

Fixed missing chunk size bug reported by jason stajich

Bio::DB::GFF::Adaptor::dbi::caching_handle

Added a new database adaptor 'dbi::oracleopt' for an Oracle database Modified Files: Bio/DB/GFF/Adaptor/dbi.pm Bio/DB/GFF/Adaptor/dbi/caching_handle.pm Bio/DB/GFF/Adaptor/dbi/mysql.pm Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm Added Files: Bio/DB/GFF/Adaptor/dbi/oracleopt.pm

Bio::DB::GFF::Adaptor::dbi::iterator

Added missing documentation. Fixed missing arrows on transcript glyphs.

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

Made the wildcard searching sensitive to aliases and fixed inability to escape wildcard characters

Folded in Aaron Mackey's patches for sort order of glyphs. feature_by_name() method in Bio::DB::GFF now searches Aliases

Fixed strand so that dot is acceptable

Added a new database adaptor 'dbi::oracleopt' for an Oracle database Modified Files: Bio/DB/GFF/Adaptor/dbi.pm Bio/DB/GFF/Adaptor/dbi/caching_handle.pm Bio/DB/GFF/Adaptor/dbi/mysql.pm Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm Added Files: Bio/DB/GFF/Adaptor/dbi/oracleopt.pm

Mysql tables now created with "type=MyISAM". this allows tablesize to exceed the 2GB limit.

Reorganization of dbi.pm,mysql.pm and oracle.pm - all the general database stauff moved to dbi.pm and mysql.pm and mysqlopt.pm were combined. the oracle adaptor has changed to oracle (from oracleopt that used to inherit from mysqlopt).

Consolidation of mysql and oracle adaptors

fgroup.gname is now binary. some ucsc features are cased, which was causing the bulk loader to puke.

Fixed missing chunk size bug reported by jason stajich

Bio::DB::GFF::Adaptor::dbi::mysqlace

Moved hacky acedb stuff out of dbi.pm and into its own subclass

Refactored acedb code so that it no longer is tangled with relational code

Bio::DB::GFF::Adaptor::dbi::mysqlopt

Folded in Aaron Mackey's patches for sort order of glyphs. feature_by_name() method in Bio::DB::GFF now searches Aliases

Added a new database adaptor 'dbi::oracleopt' for an Oracle database Modified Files: Bio/DB/GFF/Adaptor/dbi.pm Bio/DB/GFF/Adaptor/dbi/caching_handle.pm Bio/DB/GFF/Adaptor/dbi/mysql.pm Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm Added Files: Bio/DB/GFF/Adaptor/dbi/oracleopt.pm

Mysql tables now created with "type=MyISAM". this allows tablesize to exceed the 2GB limit.

Reorganization of dbi.pm,mysql.pm and oracle.pm - all the general database stauff moved to dbi.pm and mysql.pm and mysqlopt.pm were combined. the oracle adaptor has changed to oracle (from oracleopt that used to inherit from mysqlopt).

Consolidation of mysql and oracle adaptors

Bio::DB::GFF::Adaptor::dbi::oracle

Oracle adaptor was chenged to ingerit from dbi.pm instead of from oracleopt.pm it's name was changed to oracle instead of oracleopt.pm .

Consolidation of mysql and oracle adaptors

Bio::DB::GFF::Adaptor::dbi::oracleace

Refactored acedb code so that it no longer is tangled with relational code

Bio::DB::GFF::Adaptor::dbi::oracleopt

Added a new database adaptor 'dbi::oracleopt' for an Oracle database Modified Files: Bio/DB/GFF/Adaptor/dbi.pm Bio/DB/GFF/Adaptor/dbi/caching_handle.pm Bio/DB/GFF/Adaptor/dbi/mysql.pm Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm Added Files: Bio/DB/GFF/Adaptor/dbi/oracleopt.pm

Reorganization of dbi.pm,mysql.pm and oracle.pm - all the general database stauff moved to dbi.pm and mysql.pm and mysqlopt.pm were combined. the oracle adaptor has changed to oracle (from oracleopt that used to inherit from mysqlopt).

Oracle adaptor was chenged to ingerit from dbi.pm instead of from oracleopt.pm it's name was changed to oracle instead of oracleopt.pm .

Bio::DB::GFF::Adaptor::memory

Removed warnings from in-memory GFF db

Bio::DB::GFF::Adaptor::memory_iterator

Added missing documentation. Fixed missing arrows on transcript glyphs.

Bio::DB::GFF::Aggregator

Modified gff aggregators so that they do not aggregate features that are on different segments!

Regularized method names in bio::db::gff and removed some unused methods and variables; also fixed a few warnings

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

Adding aggregators for data from UCSC. features were downloaded from ucsc with biodas, exported from biodas as gff, and loaded into a Bio::DB::GFF database with no modifications. the aggregators work for me, more to come.

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

Adding aggregators for data from UCSC. features were downloaded from ucsc with biodas, exported from biodas as gff, and loaded into a Bio::DB::GFF database with no modifications. the aggregators work for me, more to come.

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

Adding aggregators for data from UCSC. features were downloaded from ucsc with biodas, exported from biodas as gff, and loaded into a Bio::DB::GFF database with no modifications. the aggregators work for me, more to come.

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

Adding aggregators for data from UCSC. features were downloaded from ucsc with biodas, exported from biodas as gff, and loaded into a Bio::DB::GFF database with no modifications. the aggregators work for me, more to come.

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

Adding aggregators for data from UCSC. features were downloaded from ucsc with biodas, exported from biodas as gff, and loaded into a Bio::DB::GFF database with no modifications. the aggregators work for me, more to come.

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

Adding aggregators for data from UCSC. features were downloaded from ucsc with biodas, exported from biodas as gff, and loaded into a Bio::DB::GFF database with no modifications. the aggregators work for me, more to come.

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

Adding aggregators for data from UCSC. features were downloaded from ucsc with biodas, exported from biodas as gff, and loaded into a Bio::DB::GFF database with no modifications. the aggregators work for me, more to come.

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

Adding aggregators for data from UCSC. features were downloaded from ucsc with biodas, exported from biodas as gff, and loaded into a Bio::DB::GFF database with no modifications. the aggregators work for me, more to come.

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

Aggregator for ucsc unigene features

Bio::DB::GFF::Feature

Schwartzian transformation sort applied

Make Bio::DB::GFF fully implement Bio::SeqFeatureI interface, and move it from IS-A location to HAS-A location (with Lincoln's blessing) It already implemented HAS-A, but I think it is confusing for it to have a location() method and also BE a location. The problems arise because it previously didn't fully implement Bio::LocationI and this caused SeqFeatureI::spliced_seq to fail, the current implementation works for my local GBrowse setup and for my direct access Bio::DB::GFF scripts

Modified gff aggregators so that they do not aggregate features that are on different segments!

Insure that absolute is passed down to children

Support new Bio::SeqFeatureI interface method "get_all_tags" by aliasing it

Regularized method names in bio::db::gff and removed some unused methods and variables; also fixed a few warnings

Added documentation to the segments glyph and made it work correctly with Bio::SearchIO interface

Bio::DB::GFF::Homol

Segments glyph now semantically morphs to show multiple alignments at high mag

Bio::DB::GFF::RelSegment

1) fixed Bio::DasI in light of experiences getting gbrowse to run on top of BioSQL 2) in the process found and fixed some inconsistencies in Bio::DB::GFF 3) also found and fixed some bugs in the graphics layer

Fixed a bug in RelSegment that caused segments to be wildly awry when strict bounds checking turned on and the subsegment requested was outside the bounds of the containing segment

Bio::DB::GFF::Segment

Bio::DB::GFF hierarchy now correctly inherits from Bio::DasI hierarchy

Regularized method names in bio::db::gff and removed some unused methods and variables; also fixed a few warnings

Bio::DB::GFF::Typename

Bio::DB::GFF hierarchy now correctly inherits from Bio::DasI hierarchy

Bio::DB::GFF::Util::Binning

Added missing documentation. Fixed missing arrows on transcript glyphs.

Bio::DB::GFF::Util::Rearrange

Added missing documentation. Fixed missing arrows on transcript glyphs.

Bio::DB::GenBank

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added a new class representing a query on a Bio::DB database. The class can accept a query string and other arguments (mindate, maxdate) and then be used directly to retrieve count match or ID list, or indirectly by passing to Bio::DB::* access object. Implemented a "pipeline" fetch that is memory and speed efficient relative to io_string and tempfile. Not tested: ability to upload a list of IDs via query interface.

Documentation fixes for Bio::DB::GenBank

Bio::DB::GenPept

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added a new class representing a query on a Bio::DB database. The class can accept a query string and other arguments (mindate, maxdate) and then be used directly to retrieve count match or ID list, or indirectly by passing to Bio::DB::* access object. Implemented a "pipeline" fetch that is memory and speed efficient relative to io_string and tempfile. Not tested: ability to upload a list of IDs via query interface.

Bio::DB::InMemoryCache

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::DB::NCBIHelper

Fixing Issue #1257

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

In preparation for queryi implementation, removed 10k restriction on batch requests

Added a new class representing a query on a Bio::DB database. The class can accept a query string and other arguments (mindate, maxdate) and then be used directly to retrieve count match or ID list, or indirectly by passing to Bio::DB::* access object. Implemented a "pipeline" fetch that is memory and speed efficient relative to io_string and tempfile. Not tested: ability to upload a list of IDs via query interface.

Added a "delay policy" to web-based db fetches and implemented NCBI requested 3s delay -- have fun

Bad bad bad implementation of getting all the contigs for CON files, should work now - testing re bug #977

Doc fix - s/Seq/Stream/ for some docs, code formatting

Bio::DB::Query::GenBank

Simple query interface for Entrez

Added a new class representing a query on a Bio::DB database. The class can accept a query string and other arguments (mindate, maxdate) and then be used directly to retrieve count match or ID list, or indirectly by passing to Bio::DB::* access object. Implemented a "pipeline" fetch that is memory and speed efficient relative to io_string and tempfile. Not tested: ability to upload a list of IDs via query interface.

Bio::DB::Query::GenBank now correctly handles an explicitly uploaded list of GIs, locus numbers or accessions. For the record, there is an inaccuracy in the eutils documentation. The tools do not recognize a composite database named "sequences," but require that "protein", "nucleotide" or "genome" be requested explicitly. Also epost is not very useful since it does not indicate how many of the requested IDs were valid.

Fixed GenBank.pm helper to avoid using indirect method call syntax

Bio::DB::Query::WebQuery

Simple query interface for Entrez

Added a new class representing a query on a Bio::DB database. The class can accept a query string and other arguments (mindate, maxdate) and then be used directly to retrieve count match or ID list, or indirectly by passing to Bio::DB::* access object. Implemented a "pipeline" fetch that is memory and speed efficient relative to io_string and tempfile. Not tested: ability to upload a list of IDs via query interface.

Bio::DB::Query::GenBank now correctly handles an explicitly uploaded list of GIs, locus numbers or accessions. For the record, there is an inaccuracy in the eutils documentation. The tools do not recognize a composite database named "sequences," but require that "protein", "nucleotide" or "genome" be requested explicitly. Also epost is not very useful since it does not indicate how many of the requested IDs were valid.

Explicit check for windows systems.

Bio::DB::QueryI

Simple query interface for Entrez

Bio::DB::RandomAccessI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::DB::RefSeq

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::DB::Registry

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::DB::SeqI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::DB::SwissProt

Default is now US

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::DB::Universal

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::DB::UpdateableSeqI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::DB::WebDBSeqI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Issue #1334, proxy user/pass authentication through separate UserAgent method

Added a new class representing a query on a Bio::DB database. The class can accept a query string and other arguments (mindate, maxdate) and then be used directly to retrieve count match or ID list, or indirectly by passing to Bio::DB::* access object. Implemented a "pipeline" fetch that is memory and speed efficient relative to io_string and tempfile. Not tested: ability to upload a list of IDs via query interface.

Added a "delay policy" to web-based db fetches and implemented NCBI requested 3s delay -- have fun

Documentation fixes for Bio::DB::GenBank

Modified Bio::DB::WebDBQueryI to work properly on windows systems (hopefully)

Fixed missing first residue in cds translations

Explicit check for windows systems.

Some testing revealed that local $/ was not necessarily staying local... causing Bio::SeqIO to barf. Should be in order now

Better workaround for mswin machines

Properly throw an error when no sequences are retrieved for a query -- cannot distinguish between errors and non-connections though at this point, but this makes t/Perl.t now properly run when network is disconnected [during an ice storm]

Bio::DB::XEMBL

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::DB::XEMBLService

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::DBLinkContainerI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Das::FeatureTypeI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added Bio::AnnotationI and have it implemented by Bio::Seq, SeqFeature::Generic, and Cluster::UniGene. The rest is minor documentation fixes.

Bio::Das::SegmentI

1) fixed Bio::DasI in light of experiences getting gbrowse to run on top of BioSQL 2) in the process found and fixed some inconsistencies in Bio::DB::GFF 3) also found and fixed some bugs in the graphics layer

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Regularized method names in bio::db::gff and removed some unused methods and variables; also fixed a few warnings

Bio::DasI

Bio::DB::GFF hierarchy now correctly inherits from Bio::DasI hierarchy

1) fixed Bio::DasI in light of experiences getting gbrowse to run on top of BioSQL 2) in the process found and fixed some inconsistencies in Bio::DB::GFF 3) also found and fixed some bugs in the graphics layer

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added Bio::AnnotationI and have it implemented by Bio::Seq, SeqFeature::Generic, and Cluster::UniGene. The rest is minor documentation fixes.

Bio::DescribableI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Tidied up Cluster interfaces. Changed Cluster::UniGene to implement ClusterI, IdentifiableI, and DescribableI. Added display_id to ClusterI. Removed members() from ClusterI. Added namespace and authority defaults to Cluster::UniGene.

Bio::Event::EventGeneratorI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Event::EventHandlerI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Expression::FeatureI

Renaming to align bioperl expression classes with MGED.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Cleaning implementation out of interface class.

Bio::Expression::FeatureSet

This was previously Microarray::Probeset, moving to align with MGED conventions

Cleaned out some microarray references. just a thought... shouldn't this be inheriting from a ClusterI class? Why don't we have one?

FeatureSet needs to be able to be treated as a Feature itself, as it can be considered a composite Feature. It now ISA FeatureI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Adding a is_qc method for affy QC probesets.

Bio::Expression::ProbeI

Adding a ProbeI class. This is going to be used for the Bio::Expression::Microarray::Probe class.

Added sanity check to prevent recursive calls on descendent nodes that may not be NodeI compliant.

No longer inheritting from RootI

Changing value()'s error message when non numeric data is passed in.

Renaming and moving some B::E::M::ProbeI methods to B::E::ProbeI. adding perldocs.

Renaming to align bioperl expression classes with MGED.

Cleaning implementation out of interface class.

Probei isa featurei, nothing more. i'm trying to conform with mged here, but i can see people wanting to use 'probe' at some point in the future. if not, we just cvs rm it.

Bio::Factory::ApplicationFactoryI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Factory::BlastHitFactory

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Using the correct constructor arguments for passing name of query and hit sequences to the HSP object. No functional impact, just allows for more informative exception messages.

Migrating fix 1.5.2.1 to the main trunk.

Bio::Factory::BlastResultFactory

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Factory::DriverFactory

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Factory::EMBOSS

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Factory::FTLocationFactory

Handle whitespace and parentheses better in FT handling; not sure how this got broken, but I saw a bunch of gross warnings during testing; small regexp-compilation optimization in tight loop

Almost revoked the changes to FTLocationFactory, tests pass again. Also, fixed setting the seq in EncodedSeq such that the alphabet is preserved no matter what.

Fixed up my earlier botched attempt to make the FT helper code warnings-free

Added capability to deal with locations enclosed in parentheses, like (102..202), or J00194:(100..202). Also added corresponding tests.

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Factory::HitFactoryI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Factory::LocationFactoryI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Factory::MapFactoryI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Factory::ObjectBuilderI

Intermediate commit of ObjectBuilderI and its implementation. Not ready yet, do not use.

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Factory::ObjectFactoryI

Added alias accession for accession_number, with deprecation warning.

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Factory::Pise

Bioperl Pise: moving Bio::Factory::Pise to bioperl-run

Bio::Factory::ResultFactoryI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Factory::SeqAnalysisParserFactory

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Factory::SeqAnalysisParserFactoryI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Factory::SequenceFactoryI

SequenceFactoryI wasn't inheriting from ObjectFactoryI. Fixed. DBLink is now IdentifiableI. Otherwise minor things.

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Factory::SequenceProcessorI

Interface and base implementation, first revision. Tested, works.

Bio::Factory::SequenceStreamI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Factory::TreeFactoryI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::FeatureHolderI

Added FeatureHolderI. Migrated SeqI, Seq, SeqFeatureI, and SeqFeature::Generic to the FeatureHolderI method definitions.

Small doc fix.

Bio::Graphics::Feature

Fixed problems that cds glyph had when representing single-cds features

Added incomplete graphics HOWTO

Accepted -seqname argument for compatibility with Bio::SeqFeature::Generic

1) fixed Bio::DasI in light of experiences getting gbrowse to run on top of BioSQL 2) in the process found and fixed some inconsistencies in Bio::DB::GFF 3) also found and fixed some bugs in the graphics layer

Pad_left() and pad_right() methods no longer crash if the target feature does not have a hit() method

Bio::Graphics::FeatureFile

1) fixed Bio::DasI in light of experiences getting gbrowse to run on top of BioSQL 2) in the process found and fixed some inconsistencies in Bio::DB::GFF 3) also found and fixed some bugs in the graphics layer

Fix to Bio::Graphics::FeatureFile to support internationalization semantics

Put eval{} blocks around all the places in bio::graphics where a callback is invoked; this prevents callbacks from making the whole thing crash

Added $segstart and $segend options to link patterns

Fixed bug in Bio::Graphics::FeatureFile that prevents # comments from being properly interpreted in callbacks

Bio::Graphics::Glyph

Folded in Aaron Mackey's patches for sort order of glyphs. feature_by_name() method in Bio::DB::GFF now searches Aliases

Fixed biographics regression test failure due to bump changes.

Got the reciprocal synteny display working

1) fixed Bio::DasI in light of experiences getting gbrowse to run on top of BioSQL 2) in the process found and fixed some inconsistencies in Bio::DB::GFF 3) also found and fixed some bugs in the graphics layer

Added Aaron Mackey's new bump_limit option

First cut at fast layout algorithm for the glyphs; sort by attribute is now working without big speed hit

Additional documentation added to Bio::Graphics glyphs

Added missing documentation. Fixed missing arrows on transcript glyphs.

Schwartzian transformation sort applied

Fixed a bug that caused the feature labels to disappear when features were grouped

Fix to Bio::Graphics::FeatureFile to support internationalization semantics

Removed the "fast but inefficient" bumping mechanism because the efficient one is also fast now

Fixed the graphics howto to accomodate changed Bio::RichSeq API; added a workaround for broken colorClosest() call in libgd 2.04

Bio::Graphics::Glyph::Factory

Added missing documentation. Fixed missing arrows on transcript glyphs.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Put eval{} blocks around all the places in bio::graphics where a callback is invoked; this prevents callbacks from making the whole thing crash

Bio::Graphics::Glyph::arrow

First cut at fast layout algorithm for the glyphs; sort by attribute is now working without big speed hit

Fixed the abbreviation Kbp (wrong) to kbp (right).

Added more regression tests to biographics.t

Bio::Graphics::Glyph::cds

Fixed problems that cds glyph had when representing single-cds features

Fixed multiple places where perl 5.00503 complained about inability to subscript a qw() list

Fixed problems with internal features bumping in cds, segments and graded_segments glyphs

1) fixed Bio::DasI in light of experiences getting gbrowse to run on top of BioSQL 2) in the process found and fixed some inconsistencies in Bio::DB::GFF 3) also found and fixed some bugs in the graphics layer

CDS sequences on reverse strand that extend past the right-end of the window weren't being drawn (code assumed all sequences were 'printed' left-to-right; fixed, at the cost of a small optimization

Schwartzian transformation sort applied

Fixed missing first residue in cds translations

Worked out some problems involving the ragged ends option; added more documentation to segments glyph

Bio::Graphics::Glyph::diamond

Missing a use stmt

Bio::Graphics::Glyph::dna

Fixed multiple places where perl 5.00503 complained about inability to subscript a qw() list

Fixed off by one error in DNA display

Segments glyph now semantically morphs to show multiple alignments at high mag

Worked out some problems involving the ragged ends option; added more documentation to segments glyph

Bio::Graphics::Glyph::dot

Fixed bug in the dot glyph that prevented label from appearing

Bio::Graphics::Glyph::generic

1) fixed Bio::DasI in light of experiences getting gbrowse to run on top of BioSQL 2) in the process found and fixed some inconsistencies in Bio::DB::GFF 3) also found and fixed some bugs in the graphics layer

Removed the "fast but inefficient" bumping mechanism because the efficient one is also fast now

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Fixed the graphics howto to accomodate changed Bio::RichSeq API; added a workaround for broken colorClosest() call in libgd 2.04

Segments glyph now semantically morphs to show multiple alignments at high mag

Bio::Graphics::Glyph::graded_segments

Added a patch from Aaron Mackey to handle graded alignments when the alignment has no subparts

Added Aaron Mackeys hue limit modified

Added incomplete graphics HOWTO

Fixed problems with internal features bumping in cds, segments and graded_segments glyphs

Additional documentation added to Bio::Graphics glyphs

Fixed the graphics howto to accomodate changed Bio::RichSeq API; added a workaround for broken colorClosest() call in libgd 2.04

Fixed inheritance so that graded_segments and heterogeneous_segments also display DNA at high mag when option is activated

Bio::Graphics::Glyph::group

Fixed blatant error in group bumping behavior

Removed the "fast but inefficient" bumping mechanism because the efficient one is also fast now

Improved slight misalignment of base-level multiple alignments, but there are still aesthetic problems

Bio::Graphics::Glyph::heterogeneous_segments

Fixed problems with internal features bumping in cds, segments and graded_segments glyphs

Fixed inheritance so that graded_segments and heterogeneous_segments also display DNA at high mag when option is activated

Bio::Graphics::Glyph::segments

Fixed problems with internal features bumping in cds, segments and graded_segments glyphs

Additional documentation added to Bio::Graphics glyphs

Added missing documentation. Fixed missing arrows on transcript glyphs.

Removed the "fast but inefficient" bumping mechanism because the efficient one is also fast now

Segments glyph now semantically morphs to show multiple alignments at high mag

Segments now can be configured to show a little bit of the nonalighing overlap at the ends via the ragged_ends option

Added documentation to the segments glyph and made it work correctly with Bio::SearchIO interface

Worked out some problems involving the ragged ends option; added more documentation to segments glyph

Fixed inheritance so that graded_segments and heterogeneous_segments also display DNA at high mag when option is activated

Improved slight misalignment of base-level multiple alignments, but there are still aesthetic problems

Pad_left() and pad_right() methods no longer crash if the target feature does not have a hit() method

Bio::Graphics::Glyph::transcript2

1) fixed Bio::DasI in light of experiences getting gbrowse to run on top of BioSQL 2) in the process found and fixed some inconsistencies in Bio::DB::GFF 3) also found and fixed some bugs in the graphics layer

Additional documentation added to Bio::Graphics glyphs

Added missing documentation. Fixed missing arrows on transcript glyphs.

Bio::Graphics::Glyph::translation

Fixed multiple places where perl 5.00503 complained about inability to subscript a qw() list

Bio::Graphics::Panel

Got the reciprocal synteny display working

Documentation fixes for Bio::Graphics::Panel

More debugging code to track down obscure error in GD graphics layer

Fix to Bio::Graphics::FeatureFile to support internationalization semantics

Removed the "fast but inefficient" bumping mechanism because the efficient one is also fast now

Removed unused "use Carp" call.

Fixed the graphics howto to accomodate changed Bio::RichSeq API; added a workaround for broken colorClosest() call in libgd 2.04

Made workaround more efficient

Adding missing accessor documentation for Panel

Can now provide a hashref as the -glyph argument to add_track(), as stated by the documentation

Provided additional documentation of how to use callbacks with -bump

Improved slight misalignment of base-level multiple alignments, but there are still aesthetic problems

Scale is actually now off by one, but I dont want to redo all regression tests

Bio::IdCollectionI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::IdentifiableI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Fixed namespace_string() in IdentifiableI. Added recognition of parameters for IdentifiableI properties passed to DBLink. Promoted is_remote() to LocationI.

Bio::Index::Abstract

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Fix Issue #1355

Bio::Index::AbstractSeq

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Index::Blast

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Index::EMBL

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Index::Fasta

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Index::Fastq

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Index::GenBank

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Index::SwissPfam

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Index::Swissprot

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::LiveSeq::ChainI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::LiveSeq::Mutation

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::LiveSeq::Mutator

Fixed mutated aa sequence in compex inframe mutations

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::LiveSeq::SeqI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::LiveSeq::Transcript

Silenced a couple of noncritical warnings

Bio::LiveSeq::Translation

Silenced a couple of noncritical warnings

Bio::LocatableSeq

Initial commit of Bio::Seq::EncodedSeq and corresponding required patches to make LocatableSeq work (and to get PrimarySeq to quit calling guess_alphabet so willy nilly)

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Location::Atomic

Minor bugs fixed. A searchio bug still outstanding. I think heikki broke the seqio->location dumping stuff and need to talk to him

You should not try to check $start and $end here for being numeric - derived classed may (and in fact do) accept non-numeric arguments, which are then parsed to be numeric.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Location::AvWithinCoordPolicy

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Location::CoordinatePolicyI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Location::Fuzzy

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Location::FuzzyLocationI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Location::NarrowestCoordPolicy

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Location::Simple

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Location::Split

Doc fixes

Schwartzian transformation sort applied

Fix mistype of => to , in this schwartzian transform

Handle undefined locations, that may come in to split locations, more gracefully (those may represent a parsing bug which need to be looked at/tested for). Found while parsing whole genome genbank files from NCBI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Doc fix in Location::Split. Fixed FTHelper to set location seq ids throughout the sub-locations.

Fixed a number of Issue #1357 (GI number storage doc).

Bio::Location::SplitLocationI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Location::WidestCoordPolicy

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::LocationI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Fixed namespace_string() in IdentifiableI. Added recognition of parameters for IdentifiableI properties passed to DBLink. Promoted is_remote() to LocationI.

Bio::Map::CytoMap

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Map::CytoMarker

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Map::CytoPosition

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Map::LinkageMap

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Map::LinkagePosition

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Map::MapI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Map::MappableI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Map::Marker

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Map::MarkerI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Map::Microsatellite

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Map::OrderedPosition

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Map::OrderedPositionWithDistance

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Map::Position

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Map::PositionI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Map::SimpleMap

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::MapIO

Use _load_module to load dynamically

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::MapIO::mapmaker

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Matrix::PhylipDist

Object to represent phylip distance matrices, a MatrixI to come

Allow creation from parser

Bio::Ontology::GOterm

Added Files: Bio/Ontology/GOterm.pm Bio/Ontology/TermI.pm t/GOterm.t ----------------------------------------------------------------------

Modified Files: Bio/Ontology/GOterm.pm Bio/Ontology/TermI.pm t/GOterm.t Added Files: Bio/Ontology/Term.pm

Modified Files: Bio/Ontology/GOterm.pm Bio/Ontology/Term.pm Bio/Ontology/TermI.pm t/GOterm.t Added Files: t/Term.t

Fixed setters such that setting to an empty string results in setting to undef.

Avoid uninit warnings on perl 5.005 -- is something else going on though as these fields are undef, need better tests perhaps?

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added a couple of object factories. Fixed Ontology::GOterm to better honor the fact that it inherits off Term (it screwed up parameters). Fixed Unigene member object creation. Fixed Annotation::OntologyTerm (Hilmar, had you written a test you could have avoided this).

Fixed a number of Issue #1357 (GI number storage doc).

Bio::Ontology::RelationshipType

Added CONTAINS and FOUND_IN RelationshipTypes.

Bio::Ontology::SimpleGOEngine

Applied proper case to names. Moved the parser to the IO directory, after creating it.

Bio::Ontology::Term

Modified Files: Bio/Ontology/GOterm.pm Bio/Ontology/TermI.pm t/GOterm.t Added Files: Bio/Ontology/Term.pm

Retired Bio/Annotation.pm. Everything else is minor fixes.

Modified Files: Bio/Ontology/GOterm.pm Bio/Ontology/Term.pm Bio/Ontology/TermI.pm t/GOterm.t Added Files: t/Term.t

Fixed setters such that setting to an empty string results in setting to undef.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added a couple of object factories. Fixed Ontology::GOterm to better honor the fact that it inherits off Term (it screwed up parameters). Fixed Unigene member object creation. Fixed Annotation::OntologyTerm (Hilmar, had you written a test you could have avoided this).

Bio::Ontology::TermFactory

Added a couple of object factories. Fixed Ontology::GOterm to better honor the fact that it inherits off Term (it screwed up parameters). Fixed Unigene member object creation. Fixed Annotation::OntologyTerm (Hilmar, had you written a test you could have avoided this).

Bio::Ontology::TermI

Added Files: Bio/Ontology/GOterm.pm Bio/Ontology/TermI.pm t/GOterm.t ----------------------------------------------------------------------

Modified Files: Bio/Ontology/GOterm.pm Bio/Ontology/TermI.pm t/GOterm.t Added Files: Bio/Ontology/Term.pm

Retired Bio/Annotation.pm. Everything else is minor fixes.

Modified Files: Bio/Ontology/GOterm.pm Bio/Ontology/Term.pm Bio/Ontology/TermI.pm t/GOterm.t Added Files: t/Term.t

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Ontology::simpleGOengine

Applied proper case to names. Moved the parser to the IO directory, after creating it.

Bio::Ontology::simpleGOparser

Applied proper case to names. Moved the parser to the IO directory, after creating it.

Bio::OntologyIO::simpleGOparser

Applied proper case to names. Moved the parser to the IO directory, after creating it.

Added FeatureHolderI. Migrated SeqI, Seq, SeqFeatureI, and SeqFeature::Generic to the FeatureHolderI method definitions.

Bio::Perl

Added translate and translate_as_string helper functions to Bio::Perl

Reverse_complement functionality into bioperl

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added blast_sequence to Bio::Perl for newbies wanting to "just blast"

Output_format in SearchIO... we dont have this quite right and Bio::Perl write_blast now put in

Fixed seq documentation

Export all methods as suggested by Issue #1313. Also added Bio::DB::GenPept as an available database as well

Documentation fixes and tweaks

Bio::Phenotype::Correlate

Added Files: Bio/Phenotype/Correlate.pm Bio/Phenotype/Measure.pm Bio/Phenotype/PhenotypeI.pm Bio/Phenotype/OMIM/MiniMIMentry.pm Bio/Phenotype/OMIM/OMIMentry.pm Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm Bio/Phenotype/OMIM/OMIMparser.pm t/Correlate.t t/Measure.t t/MiniMIMentry.t t/OMIMentry.t t/OMIMentryAllelicVariant.t ----------------------------------------------------------------------

Modified Files: Bio/Phenotype/Correlate.pm Bio/Phenotype/Measure.pm Bio/Phenotype/PhenotypeI.pm Bio/Phenotype/OMIM/MiniMIMentry.pm Bio/Phenotype/OMIM/OMIMentry.pm Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm Bio/Phenotype/OMIM/OMIMparser.pm Bio/Tools/ECnumber.pm t/OMIMentryAllelicVariant.t Added Files: t/OMIMparser.t t/data/omim_genemap_test t/data/omim_text_test ----------------------------------------------------------------------

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Phenotype::Measure

Added Files: Bio/Phenotype/Correlate.pm Bio/Phenotype/Measure.pm Bio/Phenotype/PhenotypeI.pm Bio/Phenotype/OMIM/MiniMIMentry.pm Bio/Phenotype/OMIM/OMIMentry.pm Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm Bio/Phenotype/OMIM/OMIMparser.pm t/Correlate.t t/Measure.t t/MiniMIMentry.t t/OMIMentry.t t/OMIMentryAllelicVariant.t ----------------------------------------------------------------------

Modified Files: Bio/Phenotype/Correlate.pm Bio/Phenotype/Measure.pm Bio/Phenotype/PhenotypeI.pm Bio/Phenotype/OMIM/MiniMIMentry.pm Bio/Phenotype/OMIM/OMIMentry.pm Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm Bio/Phenotype/OMIM/OMIMparser.pm Bio/Tools/ECnumber.pm t/OMIMentryAllelicVariant.t Added Files: t/OMIMparser.t t/data/omim_genemap_test t/data/omim_text_test ----------------------------------------------------------------------

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Phenotype::OMIM::MiniMIMentry

Added Files: Bio/Phenotype/Correlate.pm Bio/Phenotype/Measure.pm Bio/Phenotype/PhenotypeI.pm Bio/Phenotype/OMIM/MiniMIMentry.pm Bio/Phenotype/OMIM/OMIMentry.pm Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm Bio/Phenotype/OMIM/OMIMparser.pm t/Correlate.t t/Measure.t t/MiniMIMentry.t t/OMIMentry.t t/OMIMentryAllelicVariant.t ----------------------------------------------------------------------

Modified Files: Bio/Phenotype/Correlate.pm Bio/Phenotype/Measure.pm Bio/Phenotype/PhenotypeI.pm Bio/Phenotype/OMIM/MiniMIMentry.pm Bio/Phenotype/OMIM/OMIMentry.pm Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm Bio/Phenotype/OMIM/OMIMparser.pm Bio/Tools/ECnumber.pm t/OMIMentryAllelicVariant.t Added Files: t/OMIMparser.t t/data/omim_genemap_test t/data/omim_text_test ----------------------------------------------------------------------

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Phenotype::OMIM::OMIMentry

Added Files: Bio/Phenotype/Correlate.pm Bio/Phenotype/Measure.pm Bio/Phenotype/PhenotypeI.pm Bio/Phenotype/OMIM/MiniMIMentry.pm Bio/Phenotype/OMIM/OMIMentry.pm Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm Bio/Phenotype/OMIM/OMIMparser.pm t/Correlate.t t/Measure.t t/MiniMIMentry.t t/OMIMentry.t t/OMIMentryAllelicVariant.t ----------------------------------------------------------------------

Modified Files: Bio/Phenotype/Correlate.pm Bio/Phenotype/Measure.pm Bio/Phenotype/PhenotypeI.pm Bio/Phenotype/OMIM/MiniMIMentry.pm Bio/Phenotype/OMIM/OMIMentry.pm Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm Bio/Phenotype/OMIM/OMIMparser.pm Bio/Tools/ECnumber.pm t/OMIMentryAllelicVariant.t Added Files: t/OMIMparser.t t/data/omim_genemap_test t/data/omim_text_test ----------------------------------------------------------------------

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Phenotype::OMIM::OMIMentryAllelicVariant

Added Files: Bio/Phenotype/Correlate.pm Bio/Phenotype/Measure.pm Bio/Phenotype/PhenotypeI.pm Bio/Phenotype/OMIM/MiniMIMentry.pm Bio/Phenotype/OMIM/OMIMentry.pm Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm Bio/Phenotype/OMIM/OMIMparser.pm t/Correlate.t t/Measure.t t/MiniMIMentry.t t/OMIMentry.t t/OMIMentryAllelicVariant.t ----------------------------------------------------------------------

Modified Files: Bio/Phenotype/Correlate.pm Bio/Phenotype/Measure.pm Bio/Phenotype/PhenotypeI.pm Bio/Phenotype/OMIM/MiniMIMentry.pm Bio/Phenotype/OMIM/OMIMentry.pm Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm Bio/Phenotype/OMIM/OMIMparser.pm Bio/Tools/ECnumber.pm t/OMIMentryAllelicVariant.t Added Files: t/OMIMparser.t t/data/omim_genemap_test t/data/omim_text_test ----------------------------------------------------------------------

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Phenotype::OMIM::OMIMparser

Added Files: Bio/Phenotype/Correlate.pm Bio/Phenotype/Measure.pm Bio/Phenotype/PhenotypeI.pm Bio/Phenotype/OMIM/MiniMIMentry.pm Bio/Phenotype/OMIM/OMIMentry.pm Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm Bio/Phenotype/OMIM/OMIMparser.pm t/Correlate.t t/Measure.t t/MiniMIMentry.t t/OMIMentry.t t/OMIMentryAllelicVariant.t ----------------------------------------------------------------------

Modified Files: Bio/Phenotype/Correlate.pm Bio/Phenotype/Measure.pm Bio/Phenotype/PhenotypeI.pm Bio/Phenotype/OMIM/MiniMIMentry.pm Bio/Phenotype/OMIM/OMIMentry.pm Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm Bio/Phenotype/OMIM/OMIMparser.pm Bio/Tools/ECnumber.pm t/OMIMentryAllelicVariant.t Added Files: t/OMIMparser.t t/data/omim_genemap_test t/data/omim_text_test ----------------------------------------------------------------------

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Modidified example slightly.

Bio::Phenotype::Phenotype

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Phenotype::PhenotypeI

Added Files: Bio/Phenotype/Correlate.pm Bio/Phenotype/Measure.pm Bio/Phenotype/PhenotypeI.pm Bio/Phenotype/OMIM/MiniMIMentry.pm Bio/Phenotype/OMIM/OMIMentry.pm Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm Bio/Phenotype/OMIM/OMIMparser.pm t/Correlate.t t/Measure.t t/MiniMIMentry.t t/OMIMentry.t t/OMIMentryAllelicVariant.t ----------------------------------------------------------------------

Modified Files: Bio/Phenotype/Correlate.pm Bio/Phenotype/Measure.pm Bio/Phenotype/PhenotypeI.pm Bio/Phenotype/OMIM/MiniMIMentry.pm Bio/Phenotype/OMIM/OMIMentry.pm Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm Bio/Phenotype/OMIM/OMIMparser.pm Bio/Tools/ECnumber.pm t/OMIMentryAllelicVariant.t Added Files: t/OMIMparser.t t/data/omim_genemap_test t/data/omim_text_test ----------------------------------------------------------------------

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::PrimarySeq

Added translate and translate_as_string helper functions to Bio::Perl

Simplified and cleaned up subseq().

Made seq() take an (optional) alphabet argument, so as to override any (incorrect) automatic guessing

Separated IdentifiableI and DescribableI from PrimarySeqI. Made both PrimarySeq and Seq fully comply with both interfaces. Added tests to test for IdentifiableI and DescribableI compliance.

Initial commit of Bio::Seq::EncodedSeq and corresponding required patches to make LocatableSeq work (and to get PrimarySeq to quit calling guess_alphabet so willy nilly)

Added alias accession for accession_number, with deprecation warning.

Fixed messed up decision whether or not to guess the alphabet. Restructured the code and added comments, so intentions maybe are clearer now.

SequenceFactoryI wasn't inheriting from ObjectFactoryI. Fixed. DBLink is now IdentifiableI. Otherwise minor things.

Removed unnecessary BEGIN block to initialize global, static %valid_type

Root/RootI changes - sliming the create path and new ref_to_seq constructor pattern

Speed ups for fasta file parsing

Small fixes. Added -namespace as parameter to Bio::PrimarySeq constructor.

Flush moved up into Root/IO to allow perl 5.5 work around

Added documentation to SeqBuilder. Unified and fixed all delegation calls in Seq not to prescribe the number of arguments and to allow passing undef. Changed PrimarySeq::length to possibly be a real attribute.

Added check to PrimarySeq::length that throws an exception if someone lies about the length. Fixed Issue #1317.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Tidied up Cluster interfaces. Changed Cluster::UniGene to implement ClusterI, IdentifiableI, and DescribableI. Added display_id to ClusterI. Removed members() from ClusterI. Added namespace and authority defaults to Cluster::UniGene.

Added recognition of all IdentifiableI parameters to PrimarySeq. Added object_factory() as an alias for <type>_factory methods in several places.

Allowed description to be set to undef.

Fixed seq documentation

Fixed primary seq seq setting call

Fixed docs (little) wrt primary_id; fasta parser; swissprot output on fuzzies

Final documentation fixes for 1.2

Bio::PrimarySeqI

Separated IdentifiableI and DescribableI from PrimarySeqI. Made both PrimarySeq and Seq fully comply with both interfaces. Added tests to test for IdentifiableI and DescribableI compliance.

Initial commit of Bio::Seq::EncodedSeq and corresponding required patches to make LocatableSeq work (and to get PrimarySeq to quit calling guess_alphabet so willy nilly)

Give slightly more informative error message

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Trailing ] in the err msg

Fixed seq documentation

Fixed docs (little) wrt primary_id; fasta parser; swissprot output on fuzzies

Bio::Range

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::RangeI

Respect the API and return start,end,strand when wantarray()

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

If $other is not defined would die without showing you the stack trace

Fixed setting seq_id to top location.

Bio::Root::Err

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Root::HTTPget

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Root::IO

Minor bugs fixed. A searchio bug still outstanding. I think heikki broke the seqio->location dumping stuff and need to talk to him

Spaces

Made Text::Shellwords description in Makefile.PL more accurate/descriptive. made changes to Root::IO::_readline to accept a paremeter which prevents \r\n stripping of input.

Changed -strip=>0 option to _readline to be -raw=>1. this should evaluate faster for the common scenario.

Flush moved up into Root/IO to allow perl 5.5 work around

Added mode() to Root::IO that allows the readability/writeability of the filehandle to be determined. added t/RootIO.t to test mode().

Mode() was having some problems. calling fdopen() on the existing file descriptor was causing it to go stale. now we POSIX::dup() the descriptor, and make the fdopen() calls on the dup.

Added more tests for the mode() function. altered behavior of _pushback() to store buffer as an array. this allows _pushback to accept multiple lines as opposed to one line. added tests for new _pushback() as well.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Insure than an executable is +x

Bio::Root::IOManager

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Root::Object

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Root::Root

Fixed a couple of small omissions.

Fixes small bug (missing 'use' statement).

BEGIN -> INIT changes, a slightly optimized _rearrange; may now see some warnings about odd number of elements in hash assignment; IMO, these are programming errors and shouldn't be hidden. I've left the vestiges of the former _rearrange code in place but commented out; if everyone is OK with these patches, I'll later clean it up a bit

Rolled back out BEGIN to INIT changes -- possibly needs more work...

_cleanup_methods assumes $self is a hashref, and accesses it directly; this does not work if $self is some other ref (as seems to be the case when I ran make test - some "cannot coerce array into hash" errors). added ref check to make sure we are really a hashref

Fix logic in test for underlying object type

Root/RootI changes - sliming the create path and new ref_to_seq constructor pattern

Tim bunces speed ups. Very nice...

Moved debug() from RootI to Root and allowed an array of strings which are concatenated. Fixed the bug introduced into Variation::IO. Fixed swissprot parser not to set primary_id if XXX_XXXX scheme (otherwise it is set to the same value as display_id, which is unchanged to before). Fixed swissprot parser to deal with multiple species (OS lines). This can only be a temporary fix, as information is essentially lost. Added test entry to swiss.dat, and tests to SeqIO.t. All tests pass.

Throw() gave a string concatenation warning if no string was given as an argument. It is now possible, although, not recommended, to call throw without arguments (mainly for debugging purposes).

Removed unused "use Carp" call.

Fixed a bug report about Root::new() complaining about uneven number of parameters for hash initialization.

Flipped over DESTROY method, which is implementation specific to Root from RootI. Jason - are you ok with this?

Bio::Root::RootI

BEGIN -> INIT changes, a slightly optimized _rearrange; may now see some warnings about odd number of elements in hash assignment; IMO, these are programming errors and shouldn't be hidden. I've left the vestiges of the former _rearrange code in place but commented out; if everyone is OK with these patches, I'll later clean it up a bit

Added tim bunces fix - old one still in there so we can flip flop easily, but I will eventuaaly remove it

Rolled back out BEGIN to INIT changes -- possibly needs more work...

Root/RootI changes - sliming the create path and new ref_to_seq constructor pattern

Moved debug() from RootI to Root and allowed an array of strings which are concatenated. Fixed the bug introduced into Variation::IO. Fixed swissprot parser not to set primary_id if XXX_XXXX scheme (otherwise it is set to the same value as display_id, which is unchanged to before). Fixed swissprot parser to deal with multiple species (OS lines). This can only be a temporary fix, as information is essentially lost. Added test entry to swiss.dat, and tests to SeqIO.t. All tests pass.

Fix Issue #1343 for now, although if there is a perf hit will want to make the documentation say explicitly that uppercase are required

Since the odd-numbered elements bug in _rearrange calls seems to be pervasive, we silently fix it

A little more resilence to perl 5.0004. Not that we can maintain this

Flipped over DESTROY method, which is implementation specific to Root from RootI. Jason - are you ok with this?

Bio::Root::Utilities

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Root::Vector

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Root::Xref

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Search::BlastUtils

Add revision info

Use the algorithm method instead

Major bug fix: tile_hsps() now takes into account HSP strand and frame information when creating contigs. Formerly, tile_hsps() and _adjust_contigs() were blind to strand/frame data. HSPs on different frames and strand within a hit were incorrectly being tiled together. This affected the accuracy of BlastHit (but *not* BlastHSP) methods such as: length_aln, frac_conserved, frac_identical, start, end, range, gaps, num_unaligned_query/hit for blast reports of flavors BLASTX, TBLASTN, and TBLASTX. In practice however, blast reports with significant HSPs on different strands/frames are unusual, so I don't suspect this bug had much of an impact. The situation that revealed this bug involved a blastx analysis against a SP-TrEMBL database containing protein sequences with ALU contamination. In this case the HSPs had numerous in-frame stops. TODO: Consider adding a method to BlastHit and/or BlastHSP that reports the number of in-frame stops.

Migrating fix 1.4.2.1 to the main trunk.

Removed unused "use Carp" call.

Bio::Search::DatabaseI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Search::GenericDatabase

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Search::HSP::BlastHSP

Removed reference to UnivAln

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

* Propagating frame info to the query and hit Similarity objects constructed by new() (required for HSP tiling). * Added names of query and hit sequences within throw messages to make them more informative. (new internal method _id_str);

Migrating fix 1.11.2.4 to the main trunk.

Support the API - bits was getting overridden by inheritance of SimilarityPair

Insure that start/end/strand are pulled out properly when building the feature pair

Bio::Search::HSP::FastaHSP

Object to put Fasta-specific state (sw-score only at this point)

Properly init values

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Search::HSP::GenericHSP

Use the algorithm method not report_type

Tighten logic slightly

Support rank for Hit and Hsp

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Made -seqname for SeqFeature::Generic deprecated.

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Evalue is now an alias of significance because we are supporting both methods (Similiarity inheritance) they shouldn't be stored in separate slots then.

Added methods to support functionality provided by BlastHSP.pm: n(), range()

Small changes to keep up with adding exonerate

Use SearchUtils, BlastUtils will be deprecated. Also support sbjct,subject,hit as aliases of each other

Bio::Search::HSP::HMMERHSP

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Search::HSP::HSPFactory

Properly do the type dynamic searching

Proper loading of modules with eval blocks at runtime

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Search::HSP::HSPI

Copied interface changes from Steve's implementations - need to be refactored more

Small fixes for non-BLAST searching: added 'list' option to HSPI strand sub; required BlastUtils in GenericHit so that tile_hsp() could be used

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added methods to support functionality provided by BlastHSP.pm: n(), range()

Bio::Search::HSP::WABAHSP

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Search::Hit::BlastHit

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

* frame() and strand() now invoke tile_hsps() so that they can report the frame and strand data for the best HSP, as determined during HSP tiling (if there are >1 HSPs). Formerly, strand() reported a value such as "-1/1" if there were HSPs on multiple strands. However, now that strand and frame is properly being accounted for during HSP tiling, it makes more sense for strand() to return the strand data for the best HSP after tiling. If you really want to know about hits on opposite strands, you should be iterating through the HSPs using methods on the HSP objects. A possible use case where knowing whether a hit has HSPs on both strands would be when filtering via SearchIO for hits with this property. However, in this case it would be better to have a dedicated method such as $hit->hsps_on_both_strands(). Similarly for frame. This could be provided if there is interest. * Added note about whether or not to perform HSP tiling for seq_inds().

Migrating fix 1.9.2.2 to the main trunk.

Bio::Search::Hit::Fasta

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Search::Hit::GenericHit

Comment

Support rank for Hit and Hsp

Small fixes for non-BLAST searching: added 'list' option to HSPI strand sub; required BlastUtils in GenericHit so that tile_hsp() could be used

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Add interfaces to get the locus from the Display_id, and to to get each_accession_number from the description of the hit.

Bio::Search::Hit::HMMERHit

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Search::Hit::HitFactory

Proper loading of modules with eval blocks at runtime

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Search::Hit::HitI

Copied interface changes from Steve's implementations - need to be refactored more

Support rank for Hit and Hsp

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Add interfaces to get the locus from the Display_id, and to to get each_accession_number from the decription of the hit.

- Added new methods to conform to API required for HSP tiling: tiled_hsps(), strand(), frame(), matches().

Bio::Search::Processor

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Search::Result::BlastResult

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added method impls to conform to ResultI.pm. Now works with HTMLResultWriter.

Replaced ResultI conformance methods with versions from branch-1-0-0. They're still no-ops, but more correct no-ops.

Fix double copies of method to remove some warnings (although expect to deprecate module eventually)

Shift not pop to get the hits in order

Code reformatting in bits

Bio::Search::Result::GenericResult

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Changed program_reference() to algorithm_reference() which is now part of ResultI.

Added support for program_version() for backward compatibility. Delegates to algorithm_version().

- Added methods required for PSI-Blast support and other features in BlastResult.pm: no_hits_found(), set_no_hits_found(), iterations(), psiblast(), to_string(). - Added a use overload pointer to to_string(). May be controversial but seems handy. Opinions welcome.

Bio::Search::Result::HMMERResult

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Search::Result::ResultFactory

Proper loading of modules with eval blocks at runtime

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Search::Result::ResultI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

- Added methods required for PSI-Blast support and other features in BlastResult.pm: no_hits_found(), set_no_hits_found(), iterations(), psiblast().

Bio::Search::Result::WABAResult

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Search::SearchUtils

Genericized version of BlastUtils.pm that uses method calls instead of direct data member access. Conforms to HitI and HSPI, though it's using new, undocumented setting abilities of the interface methods.

Respect standard HSPI methods gaps() and strand() return types

Bio::SearchDist

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SearchIO

Changeover to using Hilmar's _load_module Bio::Root::Root method

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added result_count() to SearchIO and impls to blast.pm, blastxml.pm. Renamed report_count() in psiblast.pm to keep to consistent terminology.

Output_format in SearchIO... we dont have this quite right and Bio::Perl write_blast now put in

Handle the closing of reports and the calling of end_report when handle is closed or object is destroyed

Add handler for exonerate

Bio::SearchIO::EventHandlerI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SearchIO::FastHitEventBuilder

Added documentation about how to use this object

Support rank for Hit and Hsp

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SearchIO::SearchResultEventBuilder

Handle special cases b/c of newer NCBI Blast XML format

Support rank for Hit and Hsp

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Small changes to keep up with adding exonerate

Avoid undef warnings when no alignment sequence

Bio::SearchIO::SearchWriterI

Filters for Hits,HSPs,and Results so that writers can show subset of the data

Not a required method

Bio::SearchIO::Writer::HSPTableWriter

Intermediate changes to support hsps()

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Filters for Hits,HSPs,and Results so that writers can show subset of the data

Bio::SearchIO::Writer::HTMLResultWriter

Issue #1239 although I do prefer insuring that a number is printed here

Handle conversion of NCBIXML -> HTML where bitscore and significance is not list (pull from HSP)

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

missing space

- Using the now standard result->algorithm_reference instead of program_reference(). - Checking if the result can('rewind') before calling it to support impls that can't rewind.

Filters for Hits,HSPs,and Results so that writers can show subset of the data

Bio::SearchIO::Writer::HitTableWriter

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added frame to the column map.

Migrated fix 1.6.2.3 to the main trunk. NOTE: This module not functional on the main trunk. It's producing the "all zeros" bug, indicating (most likely) that some method call within the generated function call is bogus. Need to look into this...

Made the score column use the more standard raw_score method.

Filters for Hits,HSPs,and Results so that writers can show subset of the data

Get rid of undefined warnings (which may be useful, but one will see zeros in the table)

Bio::SearchIO::Writer::ResultTableWriter

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Fixed the "all zeros" bug which was due to trouble with the eval call within the function generated by _set_row_data_func(). This is now equivalent to the branch-1-0-0 version. Not sure how they got out of sync.

Changed a debug() call to throw() within _set_row_data_func(). This should reduce the occurrence of those opaque "all zeros" bugs.

Filters for Hits,HSPs,and Results so that writers can show subset of the data

Bio::SearchIO::Writer::TextResultWriter

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Filters for Hits,HSPs,and Results so that writers can show subset of the data

Work on hit object

Bio::SearchIO::blast

Handle subset queried databases

Handle 'letters; record X' as well as 'letters)'

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added result_count() to SearchIO and impls to blast.pm, blastxml.pm. Renamed report_count() in psiblast.pm to keep to consistent terminology.

Fixes for Issue #1335 - blastcl3 report parsing

Change the accession number parsing to get the accession number. Was sometimes pulling out the locus numbe instead. Used info from ftp://ftp.ncbi.nih.gov/blast/db/README as guide.

Parse BLAT NCBI-like BLAST report

Added report_count() for backward compatibility. Delegates to result_count(), which is now preferred.

Filters for Hits,HSPs,and Results so that writers can show subset of the data

Bio::SearchIO::blastxml

Handle special cases b/c of newer NCBI Blast XML format

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added result_count() to SearchIO and impls to blast.pm, blastxml.pm. Renamed report_count() in psiblast.pm to keep to consistent terminology.

Bio::SearchIO::chado

Inital commit of chado modules - so far, write only

Bio::SearchIO::chadosxpr

Inital commit of chado modules - so far, write only

Bio::SearchIO::exonerate

Exonerate parsing

Cigar string is 0 based - we convert to 1 based for consistency with rest of bioperl

Properly parse out HSPs from Cigar lines and avoid touching align HSP stuff which is not really parseable according to Guy's

Bio::SearchIO::fasta

Update SearchIO::fasta to modern fasta34 output; paves the way for both mlib query-isa-library and pvm/mpi-formatted output. Also incorporated knowledge of -m 9 tabular output, which will substitute for hsp data when no alignments are shown (-d 0). Combined, this makes SearchIO::fasta usable for the Pearson lab, and more likely to see action 'in the wild'

Object to put Fasta-specific state (sw-score only at this point)

Fixed hit-vs-query strandedness/frame issues, and cleaned up descriptions with embedded hit_len's as well; all SearchIO.t tests pass

More fixes for mlib/pvm-style multiple-query output files

Slightly more sane way of doing the description rebuild

Fixed up test and description trailing whitespace removed

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Logic to handle mlib output which does not repeat the FASTA line

Need to keep lastline as object state

Apply Aaron's patch which superceeds my initial fix with mlib parsing

Fix frame regexp logic

Handle case when there is no description

Tiny tiny optimization tweak

Filters for Hits,HSPs,and Results so that writers can show subset of the data

Bio::SearchIO::hmmer

Parse alignments from hmmsearch

Fix so that can either parse hmmsearch which does or does not have alignments, whew! -- more testing needed to be sure all values are transfered correctly in the right order

Parse hmmsearch and hmmpfam full alignment and just model/domain info

Better process weirdly wrapped alignment lines

Applied patches to fix problem for multi domained hits thanks to Alex Zelensky

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

HMMPFAM parsing now handles multiple domain hits -- note the Hits are returned in order sorted by location not e-value, will need to add a convience method for people to get it sorted in different way.This code also handles the RF xxxx lines and - -------- - lines in a report

Parse multi-report PVM reports

Fix again - now process HMMPfam properly

Filters for Hits,HSPs,and Results so that writers can show subset of the data

Deal with the occasional hmmpfam PVM hiccup where trailing \ is left off

Bio::SearchIO::psiblast

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added result_count() to SearchIO and impls to blast.pm, blastxml.pm. Renamed report_count() in psiblast.pm to keep to consistent terminology.

Added report_count() for backward compatibility. Delegates to result_count(), which is now preferred.

Code reformatting in bits

Bio::SearchIO::waba

Set the HSPfactory properly -- should do an ISA test eventually as well

WABA is 0 based, we are 1 based

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Filters for Hits,HSPs,and Results so that writers can show subset of the data

Small changes to keep up with adding exonerate

Bio::Seq

Separated IdentifiableI and DescribableI from PrimarySeqI. Made both PrimarySeq and Seq fully comply with both interfaces. Added tests to test for IdentifiableI and DescribableI compliance.

Added alias accession for accession_number, with deprecation warning.

Small potential perf boost by doing lazy instantiation of seqfeature collection

Promoted seq(), entire_seq(), seqname(), and attach_seq() to SeqFeatureI. Made flush_XXXX and remove_tag adhere to the new convention for array flush. Renamed bulkset() to set_attributes() and have it called by new().

Added documentation to SeqFeatureI::attach_seq. Also, removed the checks in Seq.pm and Generic.pm for $feat->can('attach_seq') (features now always 'can' attach a seq).

Speed ups for fasta file parsing

Tim bunces speed ups. Very nice...

Fixed bugs introduced into Bio::Seq (does it really cost that much time to create an anonymous array?). Updated the last entry in test.genbank data file to conform to the location string standard (NCBI had changed that a while ago).

Enforced type-checking in Seq::annotation(). Fixed test accordingly.

Moved debug() from RootI to Root and allowed an array of strings which are concatenated. Fixed the bug introduced into Variation::IO. Fixed swissprot parser not to set primary_id if XXX_XXXX scheme (otherwise it is set to the same value as display_id, which is unchanged to before). Fixed swissprot parser to deal with multiple species (OS lines). This can only be a temporary fix, as information is essentially lost. Added test entry to swiss.dat, and tests to SeqIO.t. All tests pass.

Made genbank and embl to force the species classification array. Added to genbank the capability to possibly set the species NCBI taxon id from the 'source' feature. Added tests for this. The rest is doc fixes.

Added documentation to SeqBuilder. Unified and fixed all delegation calls in Seq not to prescribe the number of arguments and to allow passing undef. Changed PrimarySeq::length to possibly be a real attribute.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Removed useless inheritance from Bio::RangeI as well as methods start(), end() and strand().

Added Bio::AnnotationI and have it implemented by Bio::Seq, SeqFeature::Generic, and Cluster::UniGene. The rest is minor documentation fixes.

Added FeatureHolderI. Migrated SeqI, Seq, SeqFeatureI, and SeqFeature::Generic to the FeatureHolderI method definitions.

Allowed description to be set to undef.

Fixed seq documentation

Fixed docs (little) wrt primary_id; fasta parser; swissprot output on fuzzies

Final documentation fixes for 1.2

Bio::Seq::BaseSeqProcessor

Interface and base implementation, first revision. Tested, works.

Added recognition of all IdentifiableI parameters to PrimarySeq. Added object_factory() as an alias for <type>_factory methods in several places.

Bio::Seq::EncodedSeq

Initial commit of Bio::Seq::EncodedSeq and corresponding required patches to make LocatableSeq work (and to get PrimarySeq to quit calling guess_alphabet so willy nilly)

Almost revoked the changes to FTLocationFactory, tests pass again. Also, fixed setting the seq in EncodedSeq such that the alphabet is preserved no matter what.

Make EncodedSeq warnings-free again

Start of regularising across perl versions unigene regex fixes

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Seq::LargePrimarySeq

Strand is only considered rev if it is defined and < 0

Insure filename is defined and exists before calling unlink

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Seq::LargeSeq

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Seq::PrimaryQual

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Seq::PrimedSeq

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Using a hash as a reference is deprecated. Silenced verbose tests. Tests were run from blib directories

Removed unused "use Carp" call.

Bio::Seq::QualI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Seq::RichSeq

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added Bio::AnnotationI and have it implemented by Bio::Seq, SeqFeature::Generic, and Cluster::UniGene. The rest is minor documentation fixes.

Bio::Seq::RichSeqI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Seq::SeqBuilder

Intermediate commit of ObjectBuilderI and its implementation. Not ready yet, do not use.

Implemented SeqBuilder. Adopted in the genbank parser. Added test, all pass.

Added documentation to SeqBuilder. Unified and fixed all delegation calls in Seq not to prescribe the number of arguments and to allow passing undef. Changed PrimarySeq::length to possibly be a real attribute.

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Seq::SeqFactory

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added species() to Cluster::UniGene and interface. Added species recognition from unigene ID. Added Cluster::ClusterFactory and its utilization to ClusterIO and unigene.

Bio::Seq::SeqFastaSpeedFactory

Speed ups for fasta file parsing

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Fixed the bug Mat Wiepert reported: fasta seqs lost their primary id.

Bio::Seq::SeqWithQuality

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

First commit of an interface for dealing with sequence traces and a module that uses this interface. This is a rough commit- I will make sure that all tests pass within an hour. Chad Matsalla

Bio::Seq::SequenceTrace

First commit of an interface for dealing with sequence traces and a module that uses this interface. This is a rough commit- I will make sure that all tests pass within an hour. Chad Matsalla

Bio::Seq::TraceI

First commit of an interface for dealing with sequence traces and a module that uses this interface. This is a rough commit- I will make sure that all tests pass within an hour. Chad Matsalla

Bio::SeqAnalysisParserI

Get the actual object when calling the method

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqFeature::AnnotationAdaptor

Added Bio::SeqFeature::AnnotationAdaptor and its test. Other changes are insignificant.

Added tagvalue_object_factory().

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added Bio::AnnotationI and have it implemented by Bio::Seq, SeqFeature::Generic, and Cluster::UniGene. The rest is minor documentation fixes.

Bio::SeqFeature::Collection

New API features to remove features from collection

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Seqfeature collection Issue #1318 potential fix

Properly push onto list only values which are defined avoiding those which have been cleaned up -- still testing proper deletion of features

Bio::SeqFeature::CollectionI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqFeature::Computation

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqFeature::FeaturePair

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Bio::SeqFeature::Gene::Exon

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqFeature::Gene::ExonI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqFeature::Gene::GeneStructure

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqFeature::Gene::GeneStructureI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqFeature::Gene::Intron

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqFeature::Gene::NC_Feature

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqFeature::Gene::Poly_A_site

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqFeature::Gene::Promoter

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqFeature::Gene::Transcript

Schwartzian transformation sort applied

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Set the features array to empty by default

Fixed Issue #1321 (intron start/ends screwed up on negative strand transcripts). Confirmation from Jason pending since fixing this reversed a change he had introduced into the sorting behaviour.

Bio::SeqFeature::Gene::TranscriptI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqFeature::Gene::UTR

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqFeature::Generic

Minor bugs fixed. A searchio bug still outstanding. I think heikki broke the seqio->location dumping stuff and need to talk to him

1) fixed Bio::DasI in light of experiences getting gbrowse to run on top of BioSQL 2) in the process found and fixed some inconsistencies in Bio::DB::GFF 3) also found and fixed some bugs in the graphics layer

Bio::Annotation::Collection instead of Bio::Annotation

Promoted seq(), entire_seq(), seqname(), and attach_seq() to SeqFeatureI. Made flush_XXXX and remove_tag adhere to the new convention for array flush. Renamed bulkset() to set_attributes() and have it called by new().

Added documentation to SeqFeatureI::attach_seq. Also, removed the checks in Seq.pm and Generic.pm for $feat->can('attach_seq') (features now always 'can' attach a seq).

Added Bio::SeqFeature::AnnotationAdaptor and its test. Other changes are insignificant.

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Added check to PrimarySeq::length that throws an exception if someone lies about the length. Fixed Issue #1317.

Made -seqname for SeqFeature::Generic deprecated.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Update documentation

Added Bio::AnnotationI and have it implemented by Bio::Seq, SeqFeature::Generic, and Cluster::UniGene. The rest is minor documentation fixes.

Added FeatureHolderI. Migrated SeqI, Seq, SeqFeatureI, and SeqFeature::Generic to the FeatureHolderI method definitions.

Make 'new' backward-compatibly accept primary_tag and source_tag as new arguments.

Bio::SeqFeature::PositionProxy

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqFeature::Primer

Added tagname() to Bio::AnnotationI and adapted the implementing classes to use it. Also, changed Bio::Annotation::Collection to retrieve the key from the object if the key is omitted. Fixed bugs exposed by the removal of Bio::Annotation (it _was_ used in several tests).

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Using a hash as a reference is deprecated. Silenced verbose tests. Tests were run from blib directories

Bio::SeqFeature::Similarity

Use Annotation::Collection interface

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Check if value is defined not evalued to true otherwise we drop cases where significance is '0'

Bio::SeqFeature::SimilarityPair

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Made -seqname for SeqFeature::Generic deprecated.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Support the aliasing of sbjct for subject

Bio::SeqFeatureI

Added spliced_seq and test... on train so hard to test remote locations

Reverse complement method is revcom not complement

Promoted seq(), entire_seq(), seqname(), and attach_seq() to SeqFeatureI. Made flush_XXXX and remove_tag adhere to the new convention for array flush. Renamed bulkset() to set_attributes() and have it called by new().

Added documentation to SeqFeatureI::attach_seq. Also, removed the checks in Seq.pm and Generic.pm for $feat->can('attach_seq') (features now always 'can' attach a seq).

Handle revstrand features for splicing better (missing ->revcom->seq() was ->revcom())

Properly splice sequence on rev strand by sorting list (yes Tim, I used a Schwartzian transformation ;) -- not sure it will work if we had the unlikely (but possible) case of mixed strand features, perhaps if they are mixed we revert to the input order?

Deal with case of zero strand (peptides)

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Spliced seq handles Bio::Das::SegmentI objects (special casing it for now due to different interpretations) -- still need to have called abosolute beforehand or else it won't get rev strand features properly

Added FeatureHolderI. Migrated SeqI, Seq, SeqFeatureI, and SeqFeature::Generic to the FeatureHolderI method definitions.

Insure that Bio::Seq is 'used' since we instantiate a new Bio::Seq object in spliced_seq

Bio::SeqI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added Bio::AnnotationI and have it implemented by Bio::Seq, SeqFeature::Generic, and Cluster::UniGene. The rest is minor documentation fixes.

Added FeatureHolderI. Migrated SeqI, Seq, SeqFeatureI, and SeqFeature::Generic to the FeatureHolderI method definitions.

Fixed seq documentation

Bio::SeqIO

Tim bunces speed ups. Very nice...

Implemented SeqBuilder. Adopted in the genbank parser. Added test, all pass.

Made genbank and embl to force the species classification array. Added to genbank the capability to possibly set the species NCBI taxon id from the 'source' feature. Added tests for this. The rest is doc fixes.

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added recognition of all IdentifiableI parameters to PrimarySeq. Added object_factory() as an alias for <type>_factory methods in several places.

Bio::SeqIO::FTHelper

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Doc fix in Location::Split. Fixed FTHelper to set location seq ids throughout the sub-locations.

Fixed setting seq_id to top location.

Bio::SeqIO::MultiFile

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqIO::abi

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqIO::ace

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Support multiple sequences writing in function call and function API documentation is up to date

Bio::SeqIO::alf

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqIO::bsml

Remove Annotation reference, add Collection,Comment,Reference,DBlink use stmts

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqIO::chado

Inital commit of chado modules - so far, write only

Bio::SeqIO::chadoitext

Inital commit of chado modules - so far, write only

Bio::SeqIO::chadosxpr

Inital commit of chado modules - so far, write only

Bio::SeqIO::chadoxml

Inital commit of chado modules - so far, write only

Bio::SeqIO::ctf

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqIO::embl

Remove Annotation reference, add Collection,Comment,Reference,DBlink use stmts

Enforced type-checking in Seq::annotation(). Fixed test accordingly.

Flush moved up into Root/IO to allow perl 5.5 work around

Made genbank and embl to force the species classification array. Added to genbank the capability to possibly set the species NCBI taxon id from the 'source' feature. Added tests for this. The rest is doc fixes.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Issue #1332 fixed

Support multiple sequences writing in function call and function API documentation is up to date

Fixed version parsing in genbank and in embl. Believe it or not, but this was neither working in genbank nor tested for. I also added the version being set as -version (previously it was -seq_version only).

Get rid of warning messages due to unitialized values

Some descriptions of what are the keys used to extract fields from Bio::Annotation::Collection objects when writing out embl/genbank/swiss rich sequence files

Bio::SeqIO::exp

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqIO::fasta

Root/RootI changes - sliming the create path and new ref_to_seq constructor pattern

Rolling back SeqIO speed fix... doesnt work as planned!

Speed ups for fasta file parsing

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Support multiple sequences as input when writing -- insure that seq is defined though

Fixed docs (little) wrt primary_id; fasta parser; swissprot output on fuzzies

Bio::SeqIO::fastq

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqIO::game

Flush moved up into Root/IO to allow perl 5.5 work around

Use named parameters

Bio::SeqIO::gcg

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Support multiple sequences as input when writing -- insure that seq is defined though

Bio::SeqIO::genbank

Handle misformatted locus lines better - was overwriting defaulted 'name' field

Separated IdentifiableI and DescribableI from PrimarySeqI. Made both PrimarySeq and Seq fully comply with both interfaces. Added tests to test for IdentifiableI and DescribableI compliance.

Handle whitespace and parentheses better in FT handling; not sure how this got broken, but I saw a bunch of gross warnings during testing; small regexp-compilation optimization in tight loop

Made Classification parsing looser, simply looking for words

Remove Annotation reference, add Collection,Comment,Reference,DBlink use stmts

Enforced type-checking in Seq::annotation(). Fixed test accordingly.

Flush moved up into Root/IO to allow perl 5.5 work around

Implemented SeqBuilder. Adopted in the genbank parser. Added test, all pass.

Made genbank and embl to force the species classification array. Added to genbank the capability to possibly set the species NCBI taxon id from the 'source' feature. Added tests for this. The rest is doc fixes.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Support multiple sequences writing in function call and function API documentation is up to date

Fixed version parsing in genbank and in embl. Believe it or not, but this was neither working in genbank nor tested for. I also added the version being set as -version (previously it was -seq_version only).

Handle uppercased BP

Insure that separator is "\n"

Some descriptions of what are the keys used to extract fields from Bio::Annotation::Collection objects when writing out embl/genbank/swiss rich sequence files

Fixed a number of Issue #1357 (GI number storage doc).

Fixed Issue #1338 (write_line_GenBank_regex lost information occasionally and silently).

Bio::SeqIO::largefasta

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Fixed more bugs; no real change in the testing status

Bio::SeqIO::locuslink

Committed locuslink parser, sample, and test.

Fixed a number of Issue #1357 (GI number storage doc).

Bio::SeqIO::phd

Flush moved up into Root/IO to allow perl 5.5 work around

Changed the ways in which the ID is established from an existing phd file.

Use the Root level flush instead of filehandle flush

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

I think I made a mistake in committing here. I will go back and make test first.

Nope, make test_consed, test_trim, and test_phd were all fine. Sorry about the previous message. Things I changed in phd.pm : 1. added TRACE_ARRAY_MAX_INDEX default to 10000 2. added a third column to each base line. Representing the trace index, this column will contain 10 because, well, using the module like this: Bio::SeqIO::phd->write_seq(Bio::Seq::SeqWithQUality) means that you obviously don't have the trace index and it was only today that i found that it is required for certain programs. HTH, HAND. Chad Matsalla

Bio::SeqIO::pir

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Support multiple sequences writing in function call and function API documentation is up to date

Bio::SeqIO::pln

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqIO::qual

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Replace %args with @args in write_seq to allow correct handling of single element argument list (e.g. just a qualObj, as opposed to -source=>$qualObj)

Bugfix in write_seq wherein it would chop off the last qual value if it was by itself on the last line.

In Bio::SeqIO::qual::write_seq, changed the check for $source being Bio::Seq::SeqWithQuality or Bio::PrimaryQual from using "ref($source) eq '...'" to using "$source->isa('...')". So objects which inherit from these classes can be written with this module.

Fixed more bugs; no real change in the testing status

Bio::SeqIO::raw

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Support multiple sequences as input when writing -- insure that seq is defined though

Bio::SeqIO::scf

Start of regularising across perl versions unigene regex fixes

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Fixing Issue #1329 as suggested by Tony Cox

- second place where packing was not not correct fixed - Using a hash as a reference is deprecated Tony Cox: - next_seq() was broken because it was not seeking to the correct place in the file to retrieve SCF comments. - Extra debug routine: _dump_comments

Tests failing because a variable was not initialized. Sloppy!

Bio::SeqIO::swiss

Remove Annotation reference, add Collection,Comment,Reference,DBlink use stmts

Added Bio::Annotation::OntologyTerm. The rest is insignificant fixes.

Moved debug() from RootI to Root and allowed an array of strings which are concatenated. Fixed the bug introduced into Variation::IO. Fixed swissprot parser not to set primary_id if XXX_XXXX scheme (otherwise it is set to the same value as display_id, which is unchanged to before). Fixed swissprot parser to deal with multiple species (OS lines). This can only be a temporary fix, as information is essentially lost. Added test entry to swiss.dat, and tests to SeqIO.t. All tests pass.

Added second form of calling to Species::classification() which will potentially bypass all name checks. Added method variant() to Species. Made Annotation::Collection implement AnnotationI too - this allows for nested annotation. Added Annotation::StructuredValue, which is a lightweight way of representing structured simple values. Fixed the swissprot parser to take advantage of these changes, retain the structure of the GN line's content, and parse the species correctly. Added a number of tests for the new stuff and for the previous problems.

Based on the fall-out from swissprot->biosql, some more fixes to sanely get the species parsed. Should be OK now ...

Flush moved up into Root/IO to allow perl 5.5 work around

Fixed write_seq() to terminate species with a dot. Also, adapted to new Species::variant() and different virus parsing. We need to add tests for round-tripping.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Support multiple sequences writing in function call and function API documentation is up to date

Added a new class representing a query on a Bio::DB database. The class can accept a query string and other arguments (mindate, maxdate) and then be used directly to retrieve count match or ID list, or indirectly by passing to Bio::DB::* access object. Implemented a "pipeline" fetch that is memory and speed efficient relative to io_string and tempfile. Not tested: ability to upload a list of IDs via query interface.

Some descriptions of what are the keys used to extract fields from Bio::Annotation::Collection objects when writing out embl/genbank/swiss rich sequence files

Fixed docs (little) wrt primary_id; fasta parser; swissprot output on fuzzies

Bio::SeqIO::ztr

Flush moved up into Root/IO to allow perl 5.5 work around

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::SeqUtils

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Terminator symbols were not included in valid_aa() list causing Bio::Tools::CodonTable::revtranslate to fail. Fixes Issue #1333

Bio::SimpleAlign

Fixed the consensus_string() problem as suggested by David Evans

Changed Allen's email to one he prefers

Added functional purge() from From: Richard Adams

Applied Allen Smith's fix on _consensus_iupac(). It was ignoring ambiguous character R.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Fix bug in sort alphabetically as reported by A.Underwood

Fixed sort_alphabetically() and each_alphabetically() as suggested by Anthony Underwood

Added remove_columns method to allow editing of alignment

Bio::Species

Fixes small bug (missing 'use' statement).

Fixed broken validation of names and species.

Support genus/family names with spaces

Made Classification parsing looser, simply looking for words

Support spaces as well in the name, species should start lowercase but might contain a space or number?

Added missing documentation. Fixed missing arrows on transcript glyphs.

Not sure why this was never caught -- order/families can be extremely wacko. See accession O39869, 'ssRNA positive-strand viruses, no DNA stage' as a phylum. Species validate name accepts .,; now

Added second form of calling to Species::classification() which will potentially bypass all name checks. Added method variant() to Species. Made Annotation::Collection implement AnnotationI too - this allows for nested annotation. Added Annotation::StructuredValue, which is a lightweight way of representing structured simple values. Fixed the swissprot parser to take advantage of these changes, retain the structure of the GN line's content, and parse the species correctly. Added a number of tests for the new stuff and for the previous problems.

Made genbank and embl to force the species classification array. Added to genbank the capability to possibly set the species NCBI taxon id from the 'source' feature. Added tests for this. The rest is doc fixes.

Bio::Structure::Atom

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Structure::Chain

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Structure::Entry

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Structure::IO

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Structure::IO::pdb

Fix for Issue #1187 (multiple chains appearing out of order in record)

Reference use stmt added

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Structure::Model

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Structure::Residue

Test for commit mails

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Structure::SecStr::DSSP::Res

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Structure::SecStr::STRIDE::Res

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Structure::StructureI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Symbol::Alphabet

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Symbol::AlphabetI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Symbol::DNAAlphabet

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Symbol::ProteinAlphabet

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Symbol::Symbol

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Symbol::SymbolI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Taxonomy

The first public viewing of Taxonomy classes, what has been tested seems to work, this is not everything.

Bio::Taxonomy::Taxon

The first public viewing of Taxonomy classes, what has been tested seems to work, this is not everything.

Bio::Taxonomy::Tree

The first public viewing of Taxonomy classes, what has been tested seems to work, this is not everything.

Bio::Tools::Alignment::Consed

Some small changes in what trim_singlets() returns and mostly cosmetic changes in Consed.

Don't try and find exported dumpval since we are using class methods and it doesn't work on Windows

Remove getting exported dumpval method since we use the classmethod anyways and it is broken on windows

Lets just disable doing the verbose - somthing fishy may still be going on as points[0] points[1] is undefined

Altered the ways in which the trim method is called.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Using a hash as a reference is deprecated. Silenced verbose tests. Tests were run from blib directories

Removed unused "use Carp" call.

Minor changes in Trim and modified trim_doublets in Consed.

Ahem, someone switched from returning arrays to return arrayrefs...

I think I made a mistake in committing here. I will go back and make test first.

Added a get_class method. <boggle> Why was that not in here?

Bio::Tools::Alignment::Trim

Some small changes in what trim_singlets() returns and mostly cosmetic changes in Consed.

Significantly modified the trim_singlet routine INCLUDING the signature for this method. Added default windowsizes and phred values for trimming. This thing is being heavily used these days and these changes reflect general maintenance.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Using a hash as a reference is deprecated. Silenced verbose tests. Tests were run from blib directories

Minor changes in Trim and modified trim_doublets in Consed.

Code format + fixed Usage to reflect way one should call the method to recast arrayref as array

I think I made a mistake in committing here. I will go back and make test first.

Bio::Tools::AnalysisResult

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::BPbl2seq

Removed reference to Blast.pm

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::BPlite

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Start of regularising across perl versions unigene regex fixes

Bio::Tools::BPlite::HSP

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::BPlite::Sbjct

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::BPpsilite

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::Blast

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Removed unused "use Carp" call.

Bio::Tools::CodonTable

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::Coil

Parser for coil

Bio::Tools::ECnumber

Added Bio/Tools/ECnumber.pm czmasek@gnf.org 09/04/02

Modified Files: Bio/Tools/ECnumber.pm t/ECnumber.t

Modified Files: Bio/Phenotype/Correlate.pm Bio/Phenotype/Measure.pm Bio/Phenotype/PhenotypeI.pm Bio/Phenotype/OMIM/MiniMIMentry.pm Bio/Phenotype/OMIM/OMIMentry.pm Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm Bio/Phenotype/OMIM/OMIMparser.pm Bio/Tools/ECnumber.pm t/OMIMentryAllelicVariant.t Added Files: t/OMIMparser.t t/data/omim_genemap_test t/data/omim_text_test ----------------------------------------------------------------------

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::EPCR

Made -seqname for SeqFeature::Generic deprecated.

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::ESTScan

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::Eponine

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Made -seqname for SeqFeature::Generic deprecated.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::Est2Genome

An initial hacky pass at Est2Genome parser (which does what >I< need)

Rename function for now

Stupidity comes from copy+paste... need to always return something here othw we get 0

Oops, was not checking correct field for reversed genomic orientation

Tag the field as 'sequence' rather than Quer/Hit

Made -seqname for SeqFeature::Generic deprecated.

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Fix Issue #1332. Handle ?Intron and properly return undef when no more features are found. Still need to implement next_feature so this can fit into the pipeline. Also need it to probably act more like Sim4

Lost the n in Intron - added for completeness

Bio::Tools::FootPrinter

FootPrinter parser

Quieten tests

Fixes, taking into account spaces

Initialize variable to quieten test

Bio::Tools::GFF

Support and array of features not just a single one

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Calling method twice seems silly, do it only once

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Support Birney-GFF (i.e. ending with a // in genewise GFF

Support newFh for GFF streams

S/sequence/feature/

Zero values we getting skipped

Bio::Tools::Gel

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::Genemark

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::Genewise

First addition of Genewise.pm

Refactored genewise parsing

Refactore genewise wrapper. added sypnosis

Made -seqname for SeqFeature::Generic deprecated.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Slight Tweaks for more general parsing -- setting source tags, seqid for the exons and transcripts

Always use local directive when changing the line separator

Use NOT WHITESPACE instead of \w\. to match names of sequences - this allow us to throw things that have _ or : in there

Bio::Tools::Genomewise

Genomewise parsing

Bio::Tools::Genscan

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::Grail

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::HMMER::Domain

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Bio::Tools::HMMER::Results

Schwartzian transformation sort applied

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::HMMER::Set

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::Hmmpfam

Parser for Hmmpfam

Bio::Tools::IUPAC

Make AUTOLOAD DESTROY-safe

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Fix docs on how to instantiate a sequence with alphabet

Bio::Tools::Lucy

Added diff for Lucy source code to the Appendix.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::MZEF

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::OddCodes

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::Phylo::Molphy

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::Phylo::Molphy::Result

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::Phylo::PAML

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Parse YN00 reports

Store version info

Bio::Tools::Phylo::PAML::Result

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Store version info

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

A simple parser that parses multiple protdist matrices

Bio::Tools::Prediction::Exon

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::Prediction::Gene

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::Primer3

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Using a hash as a reference is deprecated. Silenced verbose tests. Tests were run from blib directories

Bio::Tools::Prints

Committing in fixes, unfinished

Added docs

Little changes in the code and the documentation

Made -seqname for SeqFeature::Generic deprecated.

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::Profile

Parser for Profile output

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::Pseudowise

First addition of Pseudowise.pm

Added Synopsis

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::RepeatMasker

Parser for repeatmasker

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::RestrictionEnzyme

Migrated fix 1.23 to branch-1-0-0

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Fix small RE problem where cut sites occur after the requested site

Bio::Tools::Run::README

Added StandAloneBlast and README

Bio::Tools::Run::RemoteBlast

Moving remote blast into core

Bio::Tools::Run::StandAloneBlast

Added StandAloneBlast and README

Bio::Tools::Run::WrapperBase

Programs should support a version number if possible

Correct doc

Force directories to be cleaned up unless save_tempfiles is set -- this is still a bit unstable as it can't be flip flopped around and order matters...

Bio::Tools::Seg

Parser for Seg output file

Parser module for Seg

Made -seqname for SeqFeature::Generic deprecated.

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::SeqAnal

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::SeqPattern

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::SeqStats

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::SeqWords

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::Sigcleave

Fixes bug #948. In the end, I rewrote the module to work more like the EMBOSS sigcleave. It can now take in a Bio::PrimarySeqI objects, in addition to sequence string, as a parameter. Also, procaryotic weight matrix is now built in.

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::Signalp

Parser for signalp

Bio::Tools::Sim4::Exon

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::Sim4::Results

Renamed seqname() to seq_id() and display_id() to display_name() on SeqFeatureI. Changed SeqFeature::Generic accordingly. Changed the names in all modules and tests. Also, started to make array accessors consistent: renamed each_tag_value to get_tag_values() and all_tags to get_all_tags().

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

SYNOPSIS is cut+paste runnable

Bio::Tools::Tmhmm

Parser module for Tmhmm

Made -seqname for SeqFeature::Generic deprecated.

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::WWW

Removed reference to Bio::Tools::Blast

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tools::pSW

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tree::AlleleNode

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tree::Node

Schwartzian transformation sort applied

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Improve the docs and make sure NodeI SYNOPSIS is cut+paste runnable, thanks to Ramiro Barrantes for input and corrections

Bio::Tree::NodeI

Added sanity check to prevent recursive calls on descendent nodes that may not be NodeI compliant.

Quotes missing -- this may need to change back and instead have implementing node just return 0.

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Improve the docs and make sure NodeI SYNOPSIS is cut+paste runnable, thanks to Ramiro Barrantes for input and corrections

Bio::Tree::NodeNHX

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Improve the docs and make sure NodeI SYNOPSIS is cut+paste runnable, thanks to Ramiro Barrantes for input and corrections

Bio::Tree::RandomFactory

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Improve the docs and make sure NodeI SYNOPSIS is cut+paste runnable, thanks to Ramiro Barrantes for input and corrections

Bio::Tree::Statistics

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Improve the docs and make sure NodeI SYNOPSIS is cut+paste runnable, thanks to Ramiro Barrantes for input and corrections

Bio::Tree::Tree

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Improve the docs and make sure NodeI SYNOPSIS is cut+paste runnable, thanks to Ramiro Barrantes for input and corrections

Bio::Tree::TreeFunctionsI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Tree::TreeI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Improve the docs and make sure NodeI SYNOPSIS is cut+paste runnable, thanks to Ramiro Barrantes for input and corrections

Bio::TreeIO

Changeover to using Hilmar's _load_module Bio::Root::Root method

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added nhx into _guess_format()

Bio::TreeIO::TreeEventBuilder

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::TreeIO::newick

Tree writing supports a list of trees or just one

Start of regularising across perl versions unigene regex fixes

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::TreeIO::nhx

Tree writing supports a list of trees or just one

Use the Root level flush instead of filehandle flush

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::TreeIO::tabtree

Use the Root level flush instead of filehandle flush

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::UnivAln

This module is no longer supported

Bio::UpdateableSeqI

Replaced bioperl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Variation::AAChange

Fixed trivname() in compex inframe mutations

Fixed again trivname() so that tests pass

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Variation::AAReverseMutate

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Variation::Allele

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Variation::DNAMutation

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Variation::IO

Changeover to using Hilmar's _load_module Bio::Root::Root method

Moved debug() from RootI to Root and allowed an array of strings which are concatenated. Fixed the bug introduced into Variation::IO. Fixed swissprot parser not to set primary_id if XXX_XXXX scheme (otherwise it is set to the same value as display_id, which is unchanged to before). Fixed swissprot parser to deal with multiple species (OS lines). This can only be a temporary fix, as information is essentially lost. Added test entry to swiss.dat, and tests to SeqIO.t. All tests pass.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

No need for PRINT(), it is inherited

Bio::Variation::IO::flat

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Variation::IO::xml

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Variation::RNAChange

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Variation::SNP

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Variation::SeqDiff

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Bio::Variation::VariantI

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

FAQ

Running external programs questions added

Added citation

Documentation fixes and tweaks

LocalConfig.pm

Replaced our with use vars to allow compilation on 5.00503

Makefile.PL

Added requirement for enum.pm

Added PDL requirement for the Affymetrix modules.

Microarray classes are moving to the bioperl-microarray repository, as are the PDL/enum dependencies i just commented in the makefile.

Documentation change, BioGFFDB -> BioDBGFF

Minor bugs fixed. A searchio bug still outstanding. I think heikki broke the seqio->location dumping stuff and need to talk to him

Made Text::Shellwords description in Makefile.PL more accurate/descriptive. made changes to Root::IO::_readline to accept a paremeter which prevents \r\n stripping of input.

Made genbank and embl to force the species classification array. Added to genbank the capability to possibly set the species NCBI taxon id from the 'source' feature. Added tests for this. The rest is doc fixes.

Added Graph::Directed as dependency.

Makefile fix

Fixed more bugs; no real change in the testing status

biodesign.PL

Documentation fixes and tweaks

biodesign.pod

Examples/ is now scripts/

bioperl.PL

Adding links to biodesign and biodatabases

Aggregator for ucsc unigene features

More summary information - start of a module walkthrough, added to the acknowledgements

Documentation fixes and tweaks

Fixed a bad manpage ref to bptutorial.

Oops, missed one.

Final documentation fixes for 1.2

bioperl.lisp

Fixed a couple of small omissions.

SequenceFactoryI wasn't inheriting from ObjectFactoryI. Fixed. DBLink is now IdentifiableI. Otherwise minor things.

Cosmetic and doc fixes. Changed the new get/set method template to the style suggested by Tim Bunce. Be careful: this by default will set to undef if you pass undef.

Added second form of calling to Species::classification() which will potentially bypass all name checks. Added method variant() to Species. Made Annotation::Collection implement AnnotationI too - this allows for nested annotation. Added Annotation::StructuredValue, which is a lightweight way of representing structured simple values. Fixed the swissprot parser to take advantage of these changes, retain the structure of the GN line's content, and parse the species correctly. Added a number of tests for the new stuff and for the previous problems.

Change bug website link

bioperl.pod

Removed all references to Bio::Tools::Blast and BPLite from the examples

bptutorial.pl

Removed all traces of Tools::Blast except for a note that it's deprecated and removed

Removed all references to UnivAln

Examples/ is out, scripts/ is in

Handle case that StandAloneBlast is not in the standard dist anymore

Fixed tutorial, now it compiles

Bptutorial.pl edits for release 1.2

More bptutorial.pl edits for release 1.2

Updates to bptutorial.pl re Annotation objects

More bptutorial edits

Seqfeature API method more sensibly named now, and annotations are referred to the correct place

Fixes to bptutorial.pl so it more gracefully handles misssing modules

More bptutorial edits

Fixed bptutorial bugs

Correct way to test for executable existance

Documentation fixes and tweaks

More modifications to bptutorial.pl

examples/BioPerlBlast.pl

Merging scripts and examples...

examples/aligntutorial.pl

Merging scripts and examples...

examples/biblio.pl

Merging scripts and examples...

examples/biblio_soap.pl

Merging scripts and examples...

examples/biographics/dynamic_glyphs.pl

Fixed biographics regression test failure due to bump changes.

examples/biographics/feature_data.gff

Fixed biographics regression test failure due to bump changes.

examples/biographics/feature_data.txt

Fixed biographics regression test failure due to bump changes.

examples/biographics/lots_of_glyphs.pl

Fixed biographics regression test failure due to bump changes.

examples/blosum62.bla

Merging scripts and examples...

examples/change_gene.pl

Merging scripts and examples...

examples/clustalw.pl

Merging scripts and examples...

examples/gb2features.pl

Merging scripts and examples...

examples/getGenBank.pl

Merging scripts and examples...

examples/gon250.bla

Merging scripts and examples...

examples/gsequence

Merging scripts and examples...

examples/hitdisplay.pl

Merging scripts and examples...

examples/longorf.pl

Merging scripts and examples...

examples/psw.pl

Merging scripts and examples...

examples/remote_blast.pl

Merging scripts and examples...

examples/restriction.pl

Merging scripts and examples...

examples/rev_and_trans.pl

Merging scripts and examples...

examples/run_genscan.pl

Merging scripts and examples...

examples/searchio/psiblast_features.pl

Merging scripts and examples...

examples/seq_pattern.pl

Merging scripts and examples...

examples/simplealign.pl

Merging scripts and examples...

examples/standaloneblast.pl

Merging scripts and examples...

examples/state-machine.pl

Merging scripts and examples...

examples/structure/struct_example1.pl

Merging scripts and examples...

examples/structure/struct_example2.pl

Merging scripts and examples...

examples/test-genscan.pl

Merging scripts and examples...

examples/use_registry.pl

Merging scripts and examples...

scripts/Bio-DB-GFF/README

Moved Bio::DB::GFF support scripts into Bio-DB-GFF

scripts/Bio-DB-GFF/bulk_load_gff.pl

Merging scripts/ and examples/...

Moved Bio::DB::GFF support scripts into Bio-DB-GFF

Put eval{} blocks around all the places in bio::graphics where a callback is invoked; this prevents callbacks from making the whole thing crash

scripts/Bio-DB-GFF/fast_load_gff.pl

Moved Bio::DB::GFF support scripts into Bio-DB-GFF

Put eval{} blocks around all the places in bio::graphics where a callback is invoked; this prevents callbacks from making the whole thing crash

scripts/Bio-DB-GFF/gadfly_to_gff.pl

Merging scripts/ and examples/...

scripts/Bio-DB-GFF/generate_histogram.pl

Added biographics documentation; test data.

scripts/Bio-DB-GFF/load_gff.pl

Merging scripts/ and examples/...

Moved Bio::DB::GFF support scripts into Bio-DB-GFF

scripts/Bio-DB-GFF/process_gadfly.pl

Moved Bio::DB::GFF support scripts into Bio-DB-GFF

scripts/Bio-DB-GFF/process_ncbi_human.pl

Moved Bio::DB::GFF support scripts into Bio-DB-GFF

Resynched these scripts with their gbrowse equivalents

scripts/Bio-DB-GFF/process_sgd.pl

Moved Bio::DB::GFF support scripts into Bio-DB-GFF

Resynched these scripts with their gbrowse equivalents

scripts/Bio-DB-GFF/process_wormbase.pl

Moved Bio::DB::GFF support scripts into Bio-DB-GFF

scripts/Bio-DB-GFF/sgd_to_gff.pl

Merging scripts/ and examples/...

scripts/Bio-DB-GFF/ucsc2gff.pl

This script converts UCSC SQL table dumps into GFF files compatible with Bio::DB::GFF. no warranty this code is bug free. commit early, commit often.

Nci60, unigene, and affy tables were not being gff-ized properly. fixed.

scripts/DB/blast_fetch_local.pl

Slightly more sensible NCBI id parsing for local indexing by the various types of accession numbers

Handle cases [pir,prf] where accession is in fact the last field, added pdb,tpg,prf -- thanks to AMackey. Untested

scripts/DB/dbfetch

Merging scripts/ and examples/...

scripts/DB/flanks.pl

Merging scripts/ and examples/...

scripts/DB/get_seqs.pl

Support genpept

scripts/align_on_codons.pl

Merging scripts/ and examples/...

scripts/biographics/README

Two useful scripts that run on top of Bio::Graphics

scripts/biographics/frend

Two useful scripts that run on top of Bio::Graphics

scripts/biographics/render_sequence.pl

Added incomplete graphics HOWTO

Fixed the graphics howto to accomodate changed Bio::RichSeq API; added a workaround for broken colorClosest() call in libgd 2.04

scripts/bioperl.pl

Merging scripts/ and examples/...

scripts/blast_fetch.pl

Merging scripts/ and examples/...

scripts/blast_fetch_local.pl

Merging scripts/ and examples/...

scripts/bpfetch.pl

Merging scripts/ and examples/...

scripts/bpindex.pl

Merging scripts/ and examples/...

scripts/das/README

Removed the DAS server from the bioperl scripts repository and instead pointed users at www.biodas.org/servers.

scripts/das/das_server

Merging scripts/ and examples/...

scripts/das/das_server.pl

Removed the DAS server from the bioperl scripts repository and instead pointed users at www.biodas.org/servers.

scripts/dbsnp.pl

Merging scripts/ and examples/...

scripts/est_tissue_query.pl

Merging scripts/ and examples/...

scripts/feature_draw.pl

Merging scripts/ and examples/...

scripts/gb_to_gff.pl

Merging scripts/ and examples/...

scripts/generate_random_seq.pl

Merging scripts/ and examples/...

Mini fixes inside scripts

scripts/get_seqs.pl

Merging scripts/ and examples/...

scripts/gff2ps.pl

Merging scripts/ and examples/...

scripts/make_mrna_protein.pl

Merging scripts/ and examples/...

Mini fixes inside scripts

scripts/make_primers.pl

Merging scripts/ and examples/...

scripts/parse_codeml.pl

Merging scripts/ and examples/...

scripts/prosite2perl.pl

Merging scripts/ and examples/...

scripts/render_sequence.pl

Merging scripts/ and examples/...

scripts/revcom_dir.pl

Merging scripts/ and examples/...

scripts/rfetch.pl

Merging scripts/ and examples/...

scripts/searchio/custom_writer.pl

Relocating the SearchIO writer example scripts from examples/ to scripts/. Updated the comments a bit. These versions still use the SearchIO::psiblast parser. Will convert to SearchIO::blast as functionality is ported over.

Changed report_count -> result_count to conform to new method name in SearchIO.pm

scripts/searchio/hitwriter.pl

Relocating the SearchIO writer example scripts from examples/ to scripts/. Updated the comments a bit. These versions still use the SearchIO::psiblast parser. Will convert to SearchIO::blast as functionality is ported over.

Changed report_count -> result_count to conform to new method name in SearchIO.pm

scripts/searchio/hspwriter.pl

Relocating the SearchIO writer example scripts from examples/ to scripts/. Updated the comments a bit. These versions still use the SearchIO::psiblast parser. Will convert to SearchIO::blast as functionality is ported over.

Changed report_count -> result_count to conform to new method name in SearchIO.pm

scripts/searchio/htmlwriter.pl

HTMLResultWriter.pm example. Currently uses psiblast.pm

Changed report_count -> result_count to conform to new method name in SearchIO.pm

scripts/searchio/psiblast_features.pl

Changed report_count -> result_count to conform to new method name in SearchIO.pm

scripts/searchio/rawwriter.pl

Relocating the SearchIO writer example scripts from examples/ to scripts/. Updated the comments a bit. These versions still use the SearchIO::psiblast parser. Will convert to SearchIO::blast as functionality is ported over.

Changed report_count -> result_count to conform to new method name in SearchIO.pm

scripts/searchio/resultwriter.pl

Relocating the SearchIO writer example scripts from examples/ to scripts/. Updated the comments a bit. These versions still use the SearchIO::psiblast parser. Will convert to SearchIO::blast as functionality is ported over.

Removed Error.pm dependency so it's more likely to work out of the box.

Changed report_count -> result_count to conform to new method name in SearchIO.pm

scripts/seq/extract_cds.pl

Example of how to extract CDS sequences

scripts/seq/seqs1.pl

Fixed doc bugs in header comments (main trunk).

scripts/seq/seqs2.pl

Fixed doc bugs in header comments (main trunk).

scripts/seq/seqs3.pl

Fixed doc bugs in header comments (main trunk).

scripts/seq/seqtools.pl

Fixed doc bugs in header comments (main trunk).

scripts/seq_length.pl

Merging scripts/ and examples/...

scripts/seqstats/aacomp.pl

Merging scripts/ and examples/...

scripts/seqstats/chaos_plot.pl

Merging scripts/ and examples/...

scripts/seqstats/gccalc.pl

Merging scripts/ and examples/...

scripts/seqstats/oligo_count.pl

Merging scripts/ and examples/...

scripts/subsequence.cgi

Merging scripts/ and examples/...

scripts/taxa/taxid4species.PLS

Print the TaxIDs for requested organisms, to be integrated into a module some day

Fix type

scripts/tree/blast2tree.pl

Build trees from a blast report: PRELIMINARY script

scripts/tree/paup2phylip.pl

Merging scripts/ and examples/...

scripts/utilities/README

Robust scripts go here

scripts/utilities/bp_mrtrans.PLS

Perl implementation of mrtrans

scripts/utilities/bp_sreformat.PLS

Perl implementation of sreformat

Support for extra features in MSA output

Added doc of new input options

scripts/waba2gff.pl

Merging scripts/ and examples/...