Core 1.1.0 1.2.0 delta

From BioPerl
Jump to: navigation, search

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/...
Personal tools
Namespaces
Variants
Actions
Main Links
documentation
community
development
Toolbox