Core 0.9.3 1.0.0 delta

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...