Core 0.9.3 1.0.0 delta

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These are detailed notes on changes made between release-0-9-3 and bioperl-release-1-0-0.

Bio::Align::AlignI
An interface for describing alignments
Doc changes
Allow subselection of sequences in alignment to be non continuous
Bio::AlignIO
Added support for mega
Bio::AlignIO::clustalw
Force clustal lines to line up even if names exceed 22 chars
Insure that object is an AlignI
Bio::AlignIO::emboss
Insure that object is an AlignI
Updated emboss parsing to work with EMBOSS 2.2.0 alignment output
Handle case where sequence name is longer than emboss outputs
Sparse alignment test
Sparse alignment test -- Issue #1120
Handle global alignments properly by extending gaps leading and trailing gaps
Merge changes from branch-- better emboss alignment parsing
Handle EMBOSS 1.5 alignment files
Bio::AlignIO::fasta
Insure that object is an AlignI
Bio::AlignIO::mega
Added MEGA handling
Corrected so that seqname is always shortened
Bio::AlignIO::meme
Doc update
Bio::AlignIO::msf
Insure that object is an AlignI
Bio::AlignIO::nexus
Use the displayname methods to remove the /num-num for clustalw and phylip output
Insure that object is an AlignI
Bio::AlignIO::phylip
Use the displayname methods to remove the /num-num for clustalw and phylip output
Fixes to Issue #1065
Fixed (again) display name in write_aln()
Redundant display name
Bio::AlignIO::psi
Added psi module for writing psiblast profile alignments -- see Issue #1119
Added psi module for writing psiblast profile alignments -- see Issue #1119 -- onto branch
Bio::AnalysisParserI
Remove Root::Interface go to RootI
Bio::Annotation::Collection
Added more method doc and added ability to initialize SimpleValue with the -value param in the contructor
Bio::Annotation::SimpleValue
Added more method doc and added ability to initialize SimpleValue with the -value param in the contructor
Bio::Biblio
Bibliography query modules added
Soap.pm moved from Factory to DB
Changing pattern for get/set method in biblio objects
Changes in web-service interface and in documentation
Bio::Biblio::Article
Initial commit of Bibligraphic classes
New Biblio objects and XML parsing MEDLINE citations
Removing interfaces from biblio objects
New MEDLINE-specific Biblio objects
Changes in web-service interface and in documentation
Bio::Biblio::BiblioBase
More biblio objects
Changing pattern for get/set method in biblio objects
Several new methods in Ref.pm
Changes in web-service interface and in documentation
Bio::Biblio::Book
Initial commit of Bibligraphic classes
New Biblio objects and XML parsing MEDLINE citations
Removing interfaces from biblio objects
New MEDLINE-specific Biblio objects
Bio::Biblio::BookArticle
Initial commit of Bibligraphic classes
New Biblio objects and XML parsing MEDLINE citations
New MEDLINE-specific Biblio objects
Bio::Biblio::IO
New Biblio objects and XML parsing MEDLINE citations
Use newFH
Changes in web-service interface and in documentation
Bio::Biblio::IO::medline2ref
New Biblio objects and XML parsing MEDLINE citations
Defined() on hashes and arrays is depreciated, removed
Changing pattern for get/set method in biblio objects
Removing interfaces from biblio objects
New MEDLINE-specific Biblio objects
Several new methods in Ref.pm
Changes in web-service interface and in documentation
Bio::Biblio::IO::medlinexml
New Biblio objects and XML parsing MEDLINE citations
Bio::Biblio::Journal
Initial commit of Bibligraphic classes
New Biblio objects and XML parsing MEDLINE citations
Removing interfaces from biblio objects
New MEDLINE-specific Biblio objects
Bio::Biblio::JournalArticle
Initial commit of Bibligraphic classes
New Biblio objects and XML parsing MEDLINE citations
Removing interfaces from biblio objects
New MEDLINE-specific Biblio objects
Changes in web-service interface and in documentation
Bio::Biblio::JournalI
New Biblio objects and XML parsing MEDLINE citations
Removing interfaces from biblio objects
Bio::Biblio::MedlineArticle
New MEDLINE-specific Biblio objects
Changes in web-service interface and in documentation
Bio::Biblio::MedlineBook
New MEDLINE-specific Biblio objects
Changes in web-service interface and in documentation
Bio::Biblio::MedlineBookArticle
New MEDLINE-specific Biblio objects
Changes in web-service interface and in documentation
Bio::Biblio::MedlineJournal
New MEDLINE-specific Biblio objects
Bio::Biblio::MedlineJournalArticle
New MEDLINE-specific Biblio objects
Changes in web-service interface and in documentation
Bio::Biblio::Organisation
Initial commit of Bibligraphic classes
New Biblio objects and XML parsing MEDLINE citations
Removing interfaces from biblio objects
New MEDLINE-specific Biblio objects
Changes in web-service interface and in documentation
Bio::Biblio::Patent
Initial commit of Bibligraphic classes
New Biblio objects and XML parsing MEDLINE citations
Removing interfaces from biblio objects
New MEDLINE-specific Biblio objects
Changes in web-service interface and in documentation
Bio::Biblio::Person
Initial commit of Bibligraphic classes
New Biblio objects and XML parsing MEDLINE citations
Removing interfaces from biblio objects
New MEDLINE-specific Biblio objects
Changes in web-service interface and in documentation
Bio::Biblio::Proceeding
Initial commit of Bibligraphic classes
New Biblio objects and XML parsing MEDLINE citations
Removing interfaces from biblio objects
Changes in web-service interface and in documentation
Bio::Biblio::Provider
Removing interfaces from biblio objects
Changes in web-service interface and in documentation
Bio::Biblio::ProviderI
Initial commit of Bibligraphic classes
New Biblio objects and XML parsing MEDLINE citations
Removing interfaces from biblio objects
Bio::Biblio::PubmedArticle
Changes in web-service interface and in documentation
Bio::Biblio::PubmedBookArticle
Changes in web-service interface and in documentation
Bio::Biblio::PubmedJournalArticle
Changes in web-service interface and in documentation
Bio::Biblio::Ref
Removing interfaces from biblio objects
New MEDLINE-specific Biblio objects
Several new methods in Ref.pm
Changes in web-service interface and in documentation
Bio::Biblio::RefI
Initial commit of Bibligraphic classes
Un-indented lines with L<> tags
New Biblio objects and XML parsing MEDLINE citations
Removing interfaces from biblio objects
Bio::Biblio::Service
Initial commit of Bibligraphic classes
New Biblio objects and XML parsing MEDLINE citations
Removing interfaces from biblio objects
Changes in web-service interface and in documentation
Bio::Biblio::TechReport
Initial commit of Bibligraphic classes
New Biblio objects and XML parsing MEDLINE citations
Removing interfaces from biblio objects
Changes in web-service interface and in documentation
Bio::Biblio::Thesis
Initial commit of Bibligraphic classes
New Biblio objects and XML parsing MEDLINE citations
Removing interfaces from biblio objects
Changes in web-service interface and in documentation
Bio::Biblio::WebResource
Initial commit of Bibligraphic classes
New Biblio objects and XML parsing MEDLINE citations
Removing interfaces from biblio objects
New MEDLINE-specific Biblio objects
Changes in web-service interface and in documentation
Bio::DB::Biblio::biofetch
Medline access using BioFetch, batch access fails on XML::Parser error
Batch mode fixed in biofetch.pm
Martin's changes from the trunk merged over
Changed WebDBSeqI derived method name get_Stream_by_batch() into Biblio method get_all()
Changed WebDBSeqI derived method name get_Stream_by_batch() into Biblio method get_all()
Bio::DB::Biblio::soap
Soap.pm moved from Factory to DB
Changes in web-service interface and in documentation
Bio::DB::BiblioI
Soap.pm moved from Factory to DB
Cleanup interfaces some - need to rework these eventually
Merged interface cleanup changes to trunk from branch
Bio::DB::BioFetch
The Bio::DB::GFF "note" table is now a special case of a more general attribute table. This is falling into the tag/value trap, but it is sufficient to meet the goal of this module, which is to represent GFF files in a fast searchable format.
Installed Bio::DB::BioFetch module and regression tests. Improved binning of Bio::DB::GFF, leading to slight improvement of performance.
Registry in perl working for biosql and biofetch, moved to new_from_registry methods
Support for multiple databases, added SWALL
- added RefSeq - FASTA format batch retrieval fails
Format/module problems solved!
Cleanup interfaces some - need to rework these eventually
Merged interface cleanup changes to trunk from branch
Bio::DB::DBFetch
Cleanup interfaces some - need to rework these eventually
Bio::DB::EMBL
RefSeq accession numbers are redirected from EMBL and GenBank database calls
Protect isa checks and pass verbose status to instantiated objects
Testing RefSeq $newdb variable first
Synopsis clean up
Bio::DB::Failover
Added Registry and Failover classes
Refactored Registry to work with failover mechanism
Update registry and docs
Update registry to have services and better docs
Bio::DB::Fasta
A minor clarification
Added berkeeley flatfiles
Fixed Bio::DB::Fasta
Added more options to sequence feature renderer
Bio::DB::FileCache
FileCache is on-disk cache
Added Bio::Graphics module
Added feature renderer script and squashed a few rendering bugs in Bio::Graphics.
Bio::DB::Flat
Bio::DB::Flat creates indexed flat files depending on their indexing type and content format.
Bio::DB::Flat creates indexed flat files depending on their indexing type and content format.
Fixed Bio::DB::Fasta
Bio::DB::Flat::BDB
Added berkeeley flatfiles
Bio::DB::Flat creates indexed flat files depending on their indexing type and content format.
Bio::DB::Flat creates indexed flat files depending on their indexing type and content format.
Bio::DB::Flat::BDB::EMBL
Added berkeeley flatfiles
Bio::DB::Flat creates indexed flat files depending on their indexing type and content format.
Bio::DB::Flat::BDB::Fasta
Added berkeeley flatfiles
Bio::DB::Flat creates indexed flat files depending on their indexing type and content format.
Bio::DB::Flat::BDB::embl
Bio::DB::Flat creates indexed flat files depending on their indexing type and content format.
Bio::DB::Flat creates indexed flat files depending on their indexing type and content format.
Bio::DB::Flat::BDB::fasta
Bio::DB::Flat creates indexed flat files depending on their indexing type and content format.
Bio::DB::Flat::OBDAIndex
Flat file indexer with binary search. Able to be creaqted from registry. Patterns for 3 formats exist swissprot,embl and fasta
Fixed nasty filehandle bug
Removed debug line
Removed yet more debug
Documentation fix for index reading
Get_Seq_by_acc checks if the primary key is ACC otherwise goes to secondary index
Merged michele's changes to the branch from the trunk
Fixed unclosed L<> tag
Fixed unclosed L<> tag
Bio::DB::GFF
Variety of fixes to Bio::DB::GFF.
GFF bulk loader now bulk-loads FASTA files. Better documentation of --upgrade option.
Factored out argument munging in segment() call, and added back a stub for abs_segment() for backward compatibility.
I'm about to replace the notes with a more general attribute mechanism
Added attribute searching.
The Bio::DB::GFF "note" table is now a special case of a more general attribute table. This is falling into the tag/value trap, but it is sufficient to meet the goal of this module, which is to represent GFF files in a fast searchable format.
Installed Bio::DB::BioFetch module and regression tests. Improved binning of Bio::DB::GFF, leading to slight improvement of performance.
Got Bio::DB::GFF to work properly under 5.005_03
Made bounds checking optional
Started to add the Bio::DasI interface -- not complete
Bio::DB::GFF::Adaptor::dbi
Variety of fixes to Bio::DB::GFF.
Upped length limit on reference sequence name
I'm about to replace the notes with a more general attribute mechanism
Added attribute searching.
Started to add the Bio::DasI interface -- not complete
Bio::DB::GFF::Adaptor::dbi::caching_handle
Variety of fixes to Bio::DB::GFF.
Protect the disconnect in case dbh is not initialized
Protect dbh calls when dbh is not defined
Bio::DB::GFF::Adaptor::dbi::mysql
Variety of fixes to Bio::DB::GFF.
Upped length limit on reference sequence name
I'm about to replace the notes with a more general attribute mechanism
Added attribute searching.
The Bio::DB::GFF "note" table is now a special case of a more general attribute table. This is falling into the tag/value trap, but it is sufficient to meet the goal of this module, which is to represent GFF files in a fast searchable format.
Updated the GFF loader --update option
Installed Bio::DB::BioFetch module and regression tests. Improved binning of Bio::DB::GFF, leading to slight improvement of performance.
New truncation routines broke Bio::DB::GFF regression tests, now fixed
Bio::DB::GFF::Adaptor::dbi::mysqlopt
Variety of fixes to Bio::DB::GFF.
GFF bulk loader now bulk-loads FASTA files. Better documentation of --upgrade option.
Upped length limit on reference sequence name
I'm about to replace the notes with a more general attribute mechanism
Added attribute searching.
Installed Bio::DB::BioFetch module and regression tests. Improved binning of Bio::DB::GFF, leading to slight improvement of performance.
Robustified the gff->acedb connection to survive acedb timeouts
Bio::DB::GFF::Adaptor::memory
Works up to test 80
Folded in changes to in-memory GFF database, but only works up to test 62
Bio::DB::GFF::Aggregator
Added attribute searching.
The Bio::DB::GFF "note" table is now a special case of a more general attribute table. This is falling into the tag/value trap, but it is sufficient to meet the goal of this module, which is to represent GFF files in a fast searchable format.
Bio::DB::GFF::Aggregator::clone
The Bio::DB::GFF "note" table is now a special case of a more general attribute table. This is falling into the tag/value trap, but it is sufficient to meet the goal of this module, which is to represent GFF files in a fast searchable format.
Bio::DB::GFF::Aggregator::transcript
I'm about to replace the notes with a more general attribute mechanism
Bio::DB::GFF::Feature
I'm about to replace the notes with a more general attribute mechanism
Added attribute searching.
Updated the GFF loader --update option
Started to add the Bio::DasI interface -- not complete
Bio::DB::GFF::RelSegment
Variety of fixes to Bio::DB::GFF.
I'm about to replace the notes with a more general attribute mechanism
Added attribute searching.
Installed Bio::DB::BioFetch module and regression tests. Improved binning of Bio::DB::GFF, leading to slight improvement of performance.
New truncation routines broke Bio::DB::GFF regression tests, now fixed
Fixed an error in the calculation of intersection and union in Bio::DB::RelSegment
Made bounds checking optional
Bio::DB::GFF::Segment
New truncation routines broke Bio::DB::GFF regression tests, now fixed
Fixed an error in the calculation of intersection and union in Bio::DB::RelSegment
Bio::DB::GFF::Util::Binning
Installed Bio::DB::BioFetch module and regression tests. Improved binning of Bio::DB::GFF, leading to slight improvement of performance.
Bio::DB::GenBank
Fixed multi-seq retrieval with standard entrez script (which is encouraged by NCBI) by determining a '+' character can combines multiple accessions in a queryFixed problems with parsing out the appropriate data between the <pre> blocksAdded some more documentationNCBI Batch Entrez is still a problem because it does not return non-HTML data and - only a table of links to the data based on a set of accessionsWe need to investigate the limits of the GET queries with the NCBI standard entrez CGI and provide documentation warning users and/or provide a wrapper to chain together queries.
Bio::DB::GenPept
Fixed multi-seq retrieval with standard entrez script (which is encouraged by NCBI) by determining a '+' character can combines multiple accessions in a queryFixed problems with parsing out the appropriate data between the <pre> blocksAdded some more documentationNCBI Batch Entrez is still a problem because it does not return non-HTML data and - only a table of links to the data based on a set of accessionsWe need to investigate the limits of the GET queries with the NCBI standard entrez CGI and provide documentation warning users and/or provide a wrapper to chain together queries.
Bio::DB::InMemoryCache
In memory cache for random access databases
Fixes to InMemoryCache...
Bio::DB::NCBIHelper
Fixed multi-seq retrieval with standard entrez script (which is encouraged by NCBI) by determining a '+' character can combines multiple accessions in a queryFixed problems with parsing out the appropriate data between the <pre> blocksAdded some more documentationNCBI Batch Entrez is still a problem because it does not return non-HTML data and - only a table of links to the data based on a set of accessionsWe need to investigate the limits of the GET queries with the NCBI standard entrez CGI and provide documentation warning users and/or provide a wrapper to chain together queries.
RefSeq accession numbers are redirected from EMBL and GenBank database calls
Protect isa checks and pass verbose status to instantiated objects
Cleanup interfaces some - need to rework these eventually
Merged interface cleanup changes to trunk from branch
Bio::DB::RandomAccessI
Added berkeeley flatfiles
Cleanup interfaces some - need to rework these eventually
Merged interface cleanup changes to trunk from branch
Bio::DB::RefSeq
Synopsis is now runnable
Bio::DB::Registry
Added Registry and Failover classes
On the way to sanity in Registry, works now with simple bioperldb implementation
Not assuming biodbname is the same as the db name in ini file
Registry in perl working for biosql and biofetch, moved to new_from_registry methods
Ignore spaces in value parsing
HTTPGet.pm now has a getFH() method that returns a raw socket handle Registry.pm can now successfully use HTTPGet.pm to fetch and read the fallback registry file from the web. Still more work needed but this is the basic stuff. -CDagdigian
added a services method that returns an array of services found in the registry file. -CDagdigian
Refactored Registry to work with failover mechanism
Added flat file entry to Registry.pm
Update registry and docs
Update registry to have services and better docs
Bio::DB::SwissProt
Added US Expasy mirror
Bio::DB::WebDBSeqI
Fixed multi-seq retrieval with standard entrez script (which is encouraged by NCBI) by determining a '+' character can combines multiple accessions in a queryFixed problems with parsing out the appropriate data between the <pre> blocksAdded some more documentationNCBI Batch Entrez is still a problem because it does not return non-HTML data and - only a table of links to the data based on a set of accessionsWe need to investigate the limits of the GET queries with the NCBI standard entrez CGI and provide documentation warning users and/or provide a wrapper to chain together queries.
Installed Bio::DB::BioFetch module and regression tests. Improved binning of Bio::DB::GFF, leading to slight improvement of performance.
Cleanup interfaces some - need to rework these eventually
Merged interface cleanup changes to trunk from branch
Bio::DB::XEMBL
Added Bio::DB::XEMBL accessor, for use with the published XEMBL SOAP interface (see http://www.ebi.ac.uk/xembl/).
Bio::DB::XEMBLService
Added Bio::DB::XEMBL accessor, for use with the published XEMBL SOAP interface (see http://www.ebi.ac.uk/xembl/).
Bio::DasI
Started to add the Bio::DasI interface -- not complete
Doc changes
Bio::DasSegmentI
Bio::DB::Flat creates indexed flat files depending on their indexing type and content format.
Doc changes
Bio::Event::EventGeneratorI
Document methods better
Bio::Event::EventHandlerI
Document methods better
Bio::Factory::ApplicationFactoryI
Remove Root::Interface go to RootI
Bio::Factory::BiblioI
Bibliography query modules added
Soap.pm moved from Factory to DB
Bio::Factory::EMBOSS
Fix to remove hanging on Darwin
Bio::Factory::HitFactoryI
Remove Root::Interface go to RootI
Bio::Factory::ResultFactoryI
Remove Root::Interface go to RootI
Bio::Graphics
Added Bio::Graphics module
Added feature renderer script and squashed a few rendering bugs in Bio::Graphics.
Bio::Graphics::Feature
Added Bio::Graphics module
Added feature renderer script and squashed a few rendering bugs in Bio::Graphics.
Inherit from SeqFeatureI
Added DESTROY method to prevent RootI deprecation messages
Bio::Graphics::FeatureFile
Added Bio::Graphics module
Bio::Graphics::Glyph
Added Bio::Graphics module
Added feature renderer script and squashed a few rendering bugs in Bio::Graphics.
Fixed boundary conditions that popped up when viewing sequence features that are completely outside displayed range
Performance improvements in arrow glyph
Bio::Graphics::Glyph::Factory
Added Bio::Graphics module
Added feature renderer script and squashed a few rendering bugs in Bio::Graphics.
Fixed boundary conditions that popped up when viewing sequence features that are completely outside displayed range
Bio::Graphics::Glyph::alignment
Added Bio::Graphics module
Bio::Graphics::Glyph::anchored_arrow
Added Bio::Graphics module
Bio::Graphics::Glyph::arrow
Added Bio::Graphics module
Performance improvements in arrow glyph
Bio::Graphics::Glyph::box
Added Bio::Graphics module
Bio::Graphics::Glyph::crossbox
Added Bio::Graphics module
Bio::Graphics::Glyph::diamond
Added Bio::Graphics module
Bio::Graphics::Glyph::dna
Added Bio::Graphics module
Performance improvements in arrow glyph
Bio::Graphics::Glyph::dot
Added Bio::Graphics module
Bio::Graphics::Glyph::ellipse
Added Bio::Graphics module
Bio::Graphics::Glyph::ex
Added Bio::Graphics module
Bio::Graphics::Glyph::extending_arrow
Added Bio::Graphics module
Bio::Graphics::Glyph::generic
Added Bio::Graphics module
Added feature renderer script and squashed a few rendering bugs in Bio::Graphics.
Bio::Graphics::Glyph::graded_segments
Added Bio::Graphics module
Bio::Graphics::Glyph::group
Added Bio::Graphics module
Added feature renderer script and squashed a few rendering bugs in Bio::Graphics.
Fixed boundary conditions that popped up when viewing sequence features that are completely outside displayed range
Bio::Graphics::Glyph::line
Added Bio::Graphics module
Bio::Graphics::Glyph::oval
Added Bio::Graphics module
Bio::Graphics::Glyph::pinsertion
Added Bio::Graphics module
Bio::Graphics::Glyph::primers
Added Bio::Graphics module
Bio::Graphics::Glyph::rndrect
Added Bio::Graphics module
Bio::Graphics::Glyph::ruler_arrow
Added Bio::Graphics module
Bio::Graphics::Glyph::segmented_keyglyph
Added Bio::Graphics module
Bio::Graphics::Glyph::segments
Added Bio::Graphics module
Added feature renderer script and squashed a few rendering bugs in Bio::Graphics.
Fixed boundary conditions that popped up when viewing sequence features that are completely outside displayed range
Bio::Graphics::Glyph::span
Added Bio::Graphics module
Bio::Graphics::Glyph::toomany
Added Bio::Graphics module
Bio::Graphics::Glyph::track
Added Bio::Graphics module
Bio::Graphics::Glyph::transcript
Added Bio::Graphics module
Added feature renderer script and squashed a few rendering bugs in Bio::Graphics.
Fixed boundary conditions that popped up when viewing sequence features that are completely outside displayed range
Bio::Graphics::Glyph::transcript2
Added Bio::Graphics module
Added feature renderer script and squashed a few rendering bugs in Bio::Graphics.
Fixed boundary conditions that popped up when viewing sequence features that are completely outside displayed range
Bio::Graphics::Glyph::triangle
Added Bio::Graphics module
Bio::Graphics::Glyph::wormbase_transcript
Added Bio::Graphics module
Bio::Graphics::Panel
Added Bio::Graphics module
Added feature renderer script and squashed a few rendering bugs in Bio::Graphics.
Fixed boundary conditions that popped up when viewing sequence features that are completely outside displayed range
Performance improvements in arrow glyph
Bio::LiveSeq::IO::README
Short explanation of different ways of retrieving gene and sequences into Bio::LiveSeq
Short explanation of different ways of retrieving gene and sequences into Bio::LiveSeq
Added note about srsperl.pm
Added note about srsperl.pm
Bio::LocatableSeq
End() warns when it readjusts its value only if has been set verbose() > 0
Runnable synopsis
Bio::Location::Simple
Refseq.t handles lack of IO::String gracefully
Embl/genbank parsing improved by 36secs (now) vs 55(secs) previously. The cost is now spread across a number of points in the FTHelper system --- for any more speed well need some gutting/replacing
Catch verbose flag since we're not doing chained new for optimization
Bio::Location::Split
Applied suggested fix for Issue #1074
Added feature renderer script and squashed a few rendering bugs in Bio::Graphics.
Bio::Map::CytoMap
Classes for storing and comparing cytogenetic bands
Bio::Map::CytoMarker
Classes for storing and comparing cytogenetic bands
Cleaned inheritance
Bio::Map::CytoPosition
Classes for storing and comparing cytogenetic bands
Cleaned inheritance
Bio::Map::LinkageMap
Major rewrite of Bio::Map classes
Bio::Map::LinkagePosition
Major rewrite of Bio::Map classes
Bio::Map::MappableI
Migrated from _abstract to throw_not_implemented
Bio::Map::Marker
Major rewrite of Bio::Map classes
Fixed small bug Heikki had with -POSITION
Forgot to assign map data to the Marker object in the constructor
Bio::Map::MarkerI
Major rewrite of Bio::Map classes
Migrated from _abstract to throw_not_implemented
Doc cleanup
Got all tests to pass
Bio::Map::Microsatellite
Major rewrite of Bio::Map classes
Bio::Map::OrderedPosition
Major rewrite of Bio::Map classes
Bio::Map::OrderedPositionWithDistance
Cleaned inheritance
Bio::Map::Position
Major rewrite of Bio::Map classes
Bio::Map::PositionI
Major rewrite of Bio::Map classes
Bio::Map::SimpleMap
Major rewrite of Bio::Map classes
Bio::MapIO::mapmaker
Major rewrite of Bio::Map classes
Bio::PrimarySeq
Handle with error msg when start/end are undefined in subseq
Remove deprecated methods (getseq, ary, out_fasta, setseq, type, seq_len,str)
Bio::PrimarySeqI
Trunc supports Location objects
Remove deprecated methods (getseq, ary, out_fasta, setseq, type, seq_len,str)
Cleaned Carp dependencies from code - no more confess() Bio::Root::RootI has throw() and throw_not_implemented() so removed all can('throw') can('throw_not_implemented') bits.
Cleaned Carp dependencies from code - no more confess() Bio::Root::RootI has throw() and throw_not_implemented() so removed all can('throw') can('throw_not_implemented') bits.
Bio::Range
Moved SYNOPSIS before DESCRIPTION
Moved SYNOPSIS before DESCRIPTION
Bio::RangeI
Fixing strong and weak logical operators bug
Fixed nasty RangeI bug in branch as well
Fixed overlap_extent to use new intersection API
Remove Root::Interface go to RootI
Synopsis
Synopsis
Bio::Root::HTTPget
HTTPGet.pm now has a getFH() method that returns a raw socket handle Registry.pm can now successfully use HTTPGet.pm to fetch and read the fallback registry file from the web. Still more work needed but this is the basic stuff. -CDagdigian
Bio::Root::Interface
Now integrated within RootI.
Bio::Root::Root
Allow global setting of verbosity flag with the $DEBUG class variable
Update release version and allow global DEBUG flag
Bio::Root::RootI
RootI --- rolled out buggy Error.pm chaining. embl.pm - smarter about accessions
Bio::DB::Flat creates indexed flat files depending on their indexing type and content format.
Parameterized the args in the throw() call within throw_not_implemented to throw an exception of type Bio::Root::NotImplemented.
Bump the version
Update release version and allow global DEBUG flag
Bio::Search::DatabaseI
Remove Root::Interface go to RootI
Bio::Search::HSP::BlastHSP
Consistently use pvalue not p as method name in HSPs
Remove UnivAln dependancy
Remove UnivAln dependancy -- merge to branch
Bio::Search::HSP::GenericHSP
Use superclass SimilarityPair methods for score and bits and significanceadded get_aln() method which builds a Bio::SimpleAlign object from the HSP
Oops - override SimilarityPair implementation of bits and score, doesn't work here
Fixed Issue #1053
Generate a frame for hit and query where necessarysetup the strand/frame tests more clearly and correct for the fact thatfasta does not report a frame for tfastxy/fastxy reportsMoved implementation of get_aln from interface to generic implementation
Fixed a gap calculation error
Added pvalue as its own field and test for conserved only warns when NOT a BLASTN report
Recalculate how hit and query frac ide is calculated
Added BLASTX back into the mix for query/hit strand setting
Bio::Search::HSP::HSPI
Use superclass SimilarityPair methods for score and bits and significanceadded get_aln() method which builds a Bio::SimpleAlign object from the HSP
Generate a frame for hit and query where necessarysetup the strand/frame tests more clearly and correct for the fact thatfasta does not report a frame for tfastxy/fastxy reportsMoved implementation of get_aln from interface to generic implementation
Redundant line in doc
Consistently use pvalue not p as method name in HSPs
Remove Root::Interface go to RootI
Bio::Search::Hit::GenericHit
Raw score and signif values propiagated to Hit objects
Added rewind method to go back to the first HSP since this is an in-memory implementation
Bio::Search::Hit::HitI
Remove Root::Interface go to RootI
Doc update
Bio::Search::Result::Fasta
Old FASTA object is not used any more
Bio::SearchIO
Change dependancy to the toplevel Event::EventGeneratorI class
Bio::SearchIO::EventGeneratorI
Remove unncessary event generator interface
Bio::SearchIO::SearchResultEventBuilder
Workaround to handle blast 2.1.2 xml which does not contain HSP_align-len
Added support for pvalue in hsp
Raw score and signif values propiagated to Hit objects
Bio::SearchIO::SearchWriterI
Remove Root::Interface go to RootI
Bio::SearchIO::Writer::HTMLResultWriter
HTML writing for Bio::Search results
Added name links to the generated HTML
Bio::SearchIO::Writer::ResultTableWriter
Empty string inits to avoid warn msgs
Bio::SearchIO::blast
Corrected some Issue #1056 for sequence length messages and incorperated Andew Dalke's suggestionsAdded more statistics to the available list
Added better blastn parsing to fix MarkW reported bug (Stranded information) and retrieval of pvalue from wublast reports
Handle multi-line db names
Raw score and signif values propiagated to Hit objects
Fixed Issue #1095
Parsing empty reports okay now - Issue #1063 thx to Jim Diggans
Make query/subject line parsers slightly smarter per bug shown by Matthew Wiepert
Handle old blast 2.0 CPU lines
Tighten up line regex
Bio::SearchIO::blastxml
Workaround to handle blast 2.1.2 xml which does not contain HSP_align-len
Map Statistics dblen to db letter count
Added more documentation, cut-paste runnable synopsis and new method to write data to tempfile for parsing large XML documents (instead of keeping data in memory as per first implementation)
Debugging comments to help in profiling the XML parsing code - beginning of work to handle PSI-BLAST Iterations
Fix logic wrt Time::HiRes debugging
Removed unecessary _mode field
Bio::SearchIO::fasta
Reflect a more specific coding for fastp and fastn type reports so that frame and strands can be better extracted
Fixed to have report type persist when fixed for fasta (fastn or fastp detected)
Renamed statistics from dbnum -> dbentries, dblength -> dbletters
Raw score and signif values propiagated to Hit objects
Bio::Seq
Fixes to InMemoryCache...
Added feature renderer script and squashed a few rendering bugs in Bio::Graphics.
Changes and documentation for 1.0
Remove deprecated methods (getseq, ary, out_fasta, setseq, type, seq_len,str)
Bio::SeqFeature::Generic
Return empty list when tag is not defined
Embl/genbank parsing improved by 36secs (now) vs 55(secs) previously. The cost is now spread across a number of points in the FTHelper system --- for any more speed well need some gutting/replacing
Bio::SeqFeature::PositionProxy
Adding position proxy
Bio::SeqFeature::SimilarityPair
Use Bio::SearchIO not Bio::Tools::Blast
Use Bio::SearchIO not Tools::Blast
Use Bio::SearchIO not Tools::Blast
Bio::SeqIO
Added 'return 'swiss' if /\.(swiss|sp)$/i;', no suffixes for SwissProt files had been entered. Any other SwissProt suffixes?
Added phd suffix for phred in _guess_format, added L<>s, corrected older function names
Bio::SeqIO::FTHelper
Support for 'bond' keyword in FTHelper - Issue #1043
Handle read/write of CONTIG descriptions for NCBI genome files
Bozo! $fth not $self
Embl/genbank parsing improved by 36secs (now) vs 55(secs) previously. The cost is now spread across a number of points in the FTHelper system --- for any more speed well need some gutting/replacing
Added feature renderer script and squashed a few rendering bugs in Bio::Graphics.
Have to set verbosity explicity if not using chained new
Bio::SeqIO::bsml
Added Bio::DB::XEMBL accessor, for use with the published XEMBL SOAP interface (see http://www.ebi.ac.uk/xembl/).
Changed API to better reflect BioPerl conventions. Also modified Annotations to utilize new Annotation::Collection system.
Installed Bio::DB::BioFetch module and regression tests. Improved binning of Bio::DB::GFF, leading to slight improvement of performance.
Bio::SeqIO::embl
Write_seq() now accepts Bio::PrimarySeqI objects warns unless $self->verbose < 0 on Bio::PrimarySeqI and throws on non-seqs
RootI --- rolled out buggy Error.pm chaining. embl.pm - smarter about accessions
Can read/write EMBL Contig files for whole genome
Bio::DB::Flat creates indexed flat files depending on their indexing type and content format.
Embl/genbank parsing improved by 36secs (now) vs 55(secs) previously. The cost is now spread across a number of points in the FTHelper system --- for any more speed well need some gutting/replacing
Have to set verbosity explicity if not using chained new
Bio::SeqIO::genbank
Support for 'bond' keyword in FTHelper - Issue #1043
Handle read/write of CONTIG descriptions for NCBI genome files
Fixes Issue #1091: new genbank LOCUS parsing - reads both old and new LOCUS format with date - writes always out in new format
Fixed Issue #1098 - infinite parse loop on poorly formatted features.
Have to set verbosity explicity if not using chained new
Merged interface cleanup changes to trunk from branch
Protect when genbank file falls off
Bio::SeqIO::pir
No space between id and ';' in pir format
Bio::SeqIO::scf
Minor changes to a couple of functions - get_trace returns a reference to an array rather then a scalar.
Modified the function to retrieve peak indices. Works for v3 and v2 scf. New function forms the basis for a SVG-based sequence trace display perl module.
- Added methods for retrieving base call peak indices. - Corrected error in how trace data was stored (array vs scalar). - Minor doc fixes. - Slightly more elaborate test.
Bio::SeqIO::swiss
Added Species->ncbi_taxa_id() swiss.pm now deals with SP OX lines (ncbi taxa id) added test to deal with OX lines
DB link comments preserved and author,titles are followed by ';'
Bio::SimpleAlign
Escape patterns (metaquote)
Handle gap chars in match stmts new interface dependance for alignments
Avoid divide by zero errors when length is 0
Added method to track source program of an alignment
First stab at cigar line dumping, still needs finishing, but does the basic, rest tomorrow
Allow subselection of sequences in alignment to be non continuous
Removed references to UnivAln
Removed references to UnivAln
Correctly calculate percentage identity
Merge from branch - rewrite of percentage_identity
Use average and overall percentage identity methods
Bio::Species
Spelling. My apologies James, it was late, I was tired and had nothing better to do...
Added Species->ncbi_taxa_id() swiss.pm now deals with SP OX lines (ncbi taxa id) added test to deal with OX lines
Bio::Structure::Entry
Migrated StructureI to the Structure direcetory
Bio::Structure::IO
Documentation update
Bio::Structure::IO::pdb
Migrated StructureI to the Structure direcetory
Documentation update
Bio::Structure::StructureI
Migrated StructureI to the Structure direcetory
Bio::StructureI
Migrated StructureI to the Structure direcetory
Bio::Tools::Blast
Deprecated message for Tools::Blast
Deprecated Bio::Tools::Blast
Bio::Tools::FASTAParser
Replaced by Bio::SearchIO functionality
Bio::Tools::Fasta
Removing old deprecated Fasta parser
Bio::Tools::GFF
Fixed bug that Lincoln noticed in the GFF2 dumping. Tags with null values were not printing a value at all in the attributes section of the GFF line, which is not valid GFF2. Tags with no value now report their value as empty string.
Bio::Tools::RestrictionEnzyme
- Added method _expanded_string() to refactor the expansion of ambiguity codes. - Fixes Issue #1014
Bio::Tools::Run::EMBOSSApplication
Handle cmd line arguments pointing to a Bio::PrimarySeqI object or array or Bio::PrimarySeqI
Added ability to dump alignments as well as sequences when running an EMBOSS application
Bio::Tools::Run::RemoteBlast
Better synopsis and doc update
Merge main trunk changes which include using SearchIO by default and a better SYNOPSIS
Bio::Tools::Run::StandAloneBlast
Find blast executeable in the PATH if possible -- bl2seq might still fail if one does not have .ncbirc set correctly
Use SearchIO not Tools::Blast
Call cleanup upon _setinput call
Io cleanup called at outset of an analyses -- from branch
Merge cleanup io from main trunk
StandAlone tests will detect that data dir is not set and exit test nicely
Remove debug code and tests for blastinstalled more efficiently
Merge changes from branch
Minor documentation fixes
Bio::Tools::SeqPattern
Amino codes B and Z now follow IUPAC rules: B Aspartic Acid, Asparagine Z Glutamic Acid, Glutamine rather than mark hydrophobic/hydrophilic aminos.
Bio::Tools::SwissProtParser
Yes, it does what you guess it does. The data structures returned may need some tweaking.
Started a todo list
Small array problem
Dropping scalar support for now. don't have time to figure it out
Last commit before merging to swiss.pm
Removed swissprot parser
Merge changes from branch
Bio::Tree::PhyloNode
Remove phylonode
Bio::UnivAln
Remove UnivAln from distribution
FAQ
Added beginning of the FAQ
Added section for Sequence utilities and question/answer describing EMBOSS and Bio::Factory::EMBOSS
Added question/answer about motif searching
Added question/answer about MEDLINE, Bio::Biblio
Some more info about pairwise alignments and RefSeq sequences
Makefile.PL
Added module dependency check for SOAP::Lite which is used by Biblio and XEMBLServices -cdagdigian
Now prompt for BioDBGFF on perl Makefile.PL
Changes and documentation for 1.0
Unlink the file if 'n' is chosen in Makefile.PL
Unlink the file if 'n' is chosen in Makefile.PL
Added note on srsperl.pm dependency, made check_package() more robust, added white space to output
Added note on srsperl.pm dependency, made check_package() more robust, added white space to output
Added module dependancy listing to INSTALL and added GD dependancy
Merge from branch
Added storable
biodatabases.pod
Deleted mention of bioperl.idl, added L<>s, editing
Made bounds checking optional
biodesign.pod
Deleted mention of bioperl.idl, added L<>s, editing
Added mention of class diagrams in models/ dir, added a final paragraph
Migrated to Root object and some words about performance
bioperl.lisp
Was still using RootI. Now Root.
bioperl.pod
Describe all scripts in examples/ and scripts/, briefly.
Missing scripts
Added new scripts, some editing
Added examples/biblio.pl
Added rfetch.pl
Added descriptions of render_sequence.pl, biblio_soap.pl
Minor errors...
Minor errors...
bptutorial.pl
Added info and pointer to Steve Cannon's "Installing Bioperl on OS X" web page. (http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html) -cdagdigian
Added notes on Bundle::BioPerl and easy access to BPlite from StandAloneBlast.
Bptutorial updates for release 1.0
Added some more commentary on the Bio::DB modulesadded BSML entry under the XML sequence parsingadded EMBOSS 'water' as an alternative to the bioperl-ext for getting out smith-waterman alignments using the Bio::AlignIO::emboss alignment readeralso removed reference to Bio::DB::GDB - I think we will probably kill this some day
Looked at the CVS commit log and made sure that the AUTHOR section listed all the people who have contributed to this document. -cdagdigian
Added to bioperl-db section, added L<> and =for html tags such that section names become hyperlinks, added mention of Bio::DB::Fasta
More L<> and for= tags to create hyperlinks
More on DB::GFF
Factory::EMBOSS accepts sequence objects, some editing
Added mention of phd files to SeqWithQuality section, added more formats to III.2.1, made new section IV.5 for GFF and Bio::DB::GFF*
Added XML-DOM and SOAP-Lite to Perl extensions, added clustalw to AlignIO input formats
Edits and minor additions in Bio::DB::GenBank (about RefSeq entries), bioperl-db, and GFF sections
Various minor updates to bptutorial.pl
Added mention of BioFetch, -makeid in Bio::DB::Fasta
Removed reference to UnivAln, added section III.8.4, Bio::Biblio
Removed reference to UnivAln, added section III.8.4, Bio::Biblio
Added mention of needle and water format to AlignIO and EMBOSS sections
Added mention of needle and water format to AlignIO and EMBOSS sections
Minor documentation fixes
Added table of file-format suffixes to section III.2.1
Added table of file-format suffixes to section III.2.1
Added section III.8.5, Bio::Graphics, and minor fixes, L<>s
Added section III.8.5, Bio::Graphics, and minor fixes, L<>s
examples/biblio.pl
Bibliography query modules added
New MEDLINE-specific Biblio objects
examples/biblio_soap.pl
Migrate Martin's test code into an example
Changes in web-service interface and in documentation
Merge martin's changes to branch
Rm comments from test copy-paste
examples/restriction.pl
Added example showing how to cut a seq at runs of N's. Added example trying to create a bogus enzyme. Using PrimarySeq instead of Seq.
examples/run_genscan.pl
This script more suited to examples/ directory...
examples/structure/struct_example1.pl
Two example scripts for the Bio::Structure class
examples/structure/struct_example2.pl
Two example scripts for the Bio::Structure class
examples/use_registry.pl
Registry example
Registry example on branch
models/README
Initial commit
Added dia home page link
models/biblio.dia
Added new modules to model
Store dia files as binary (which is just gzipped xml)
models/bio_liveseq_variation.dia
Store dia files as binary (which is just gzipped xml)
models/bio_map.dia
Diagram of Bio::Map classes
Store dia files as binary (which is just gzipped xml)
models/bioperl.dia
Added new modules to model
Store dia files as binary (which is just gzipped xml)
models/maps_and_markers.dia
Store dia files as binary (which is just gzipped xml)
scripts/Bio-DB-GFF/bulk_load_gff.pl
Renamed Bio::DB::GFF to Bio-DB-GFF
Relaxed restriction on fasta files that they exist
I'm about to replace the notes with a more general attribute mechanism
The Bio::DB::GFF "note" table is now a special case of a more general attribute table. This is falling into the tag/value trap, but it is sufficient to meet the goal of this module, which is to represent GFF files in a fast searchable format.
scripts/Bio-DB-GFF/gadfly_to_gff.pl
Renamed Bio::DB::GFF to Bio-DB-GFF
scripts/Bio-DB-GFF/load_gff.pl
Renamed Bio::DB::GFF to Bio-DB-GFF
The Bio::DB::GFF "note" table is now a special case of a more general attribute table. This is falling into the tag/value trap, but it is sufficient to meet the goal of this module, which is to represent GFF files in a fast searchable format.
scripts/Bio-DB-GFF/sgd_to_gff.pl
Renamed Bio::DB::GFF to Bio-DB-GFF
scripts/DB/dbfetch
Dbfetch version 3.4. - assumes perl 5.6.0 - has code for XEMBL retrieval - follows new BioFetch specs
scripts/DB/flanks.pl
A script for fetching sequences remotely and extracting subsequences around (SNP) positions.
A script for fetching sequences remotely and extracting subsequences around (SNP) positions.
scripts/blast_fetch.pl
Changed to not use Tools::Blast
Changed to not use Tools::Blast
scripts/est_tissue_query.pl
Use Bio::SearchIO instead of BPlite
scripts/render_sequence.pl
Added feature renderer script and squashed a few rendering bugs in Bio::Graphics.
Performance improvements in arrow glyph
Added more options to sequence feature renderer
Minor doc fix
scripts/rfetch.pl
Script which uses the registry to fetch sequences
Simple rfetch updates more options etc...
scripts/run_genscan.pl
This script more suited to examples/ directory...
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