Core 1.0.1 1.0.2 delta

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

Bio::Align::Utilities

Place to put various utilities which operate on Bio::Align::AlignI object - for now just 1 method to convert aa alignments to their corresponding DNA alignments much like mrtrans

Can't rely on self methods

No use of self in function

Bio::AlignIO

Added missing supported formats

New suffixes in _guess_format

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::AlignIO::clustalw

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::AlignIO::emboss

Subtle bug in emboss parsing which was adding extra gaps at the beginning of global alignment sequences after parsing

Bio::AlignIO::fasta

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::AlignIO::mega

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::AlignIO::msf

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::AlignIO::nexus

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::AlignIO::pfam

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::AlignIO::phylip

Strip any trailing _'s

Parameterize id_length to avoid hardcoded 10 in the module

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::AlignIO::psi

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::AlignIO::selex

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::Cluster::UniGene

NCBI format changed, module now handles multiple locuslink ids

Documentation changes, next_unigene() should be next_cluster(). ClusterIO now includes Cluster::Unigene, so you don't need to include it in the calling package.

Was calling Bio::Seq::SeqFactory::create_sequence() instead of create()

Bio::Cluster::UniGeneI

NCBI format changed, module now handles multiple locuslink ids

Bio::Cluster::dbSNP

Adding a functional but incomplete dbSNP xml parser. needs docs!

Bio::ClusterIO

Added dbsnp as a valid format

Documentation changes, next_unigene() should be next_cluster(). ClusterIO now includes Cluster::Unigene, so you don't need to include it in the calling package.

Bio::ClusterIO::dbsnp

Adding a functional but incomplete dbSNP xml parser. needs docs!

Fixed an EOF problem

Bio::ClusterIO::unigene

Removed Parse::RecDescent, used regexes instead.

Documentation changes, next_unigene() should be next_cluster(). ClusterIO now includes Cluster::Unigene, so you don't need to include it in the calling package.

Was calling Bio::Cluster::Unigene instead of Bio::Cluster::UniGene

Bio::Coordinate::Collection

First commit of coordinate mapper modules

Mappers in a collection are now sorted

True many-to-many or many-to-one mapping now possible

Bio::Coordinate::ExtrapolatingPair

First commit of coordinate mapper modules

Bio::Coordinate::MapperI

First commit of coordinate mapper modules

Deleted unnecessary methods

Putting back in() and out()

Bio::Coordinate::Pair

First commit of coordinate mapper modules

Fixed coordinate mapping to reverse strand

Added synopsis

Doc fixes

Bio::Coordinate::Result

First commit of coordinate mapper modules

Bio::Coordinate::Result::Gap

First commit of coordinate mapper modules

Bio::Coordinate::Result::Match

First commit of coordinate mapper modules

Bio::DB::Biblio::biofetch

One too many printings of the content str

Bio::DB::Biblio::soap

Fixed: looking for keywords with numeric values

Bio::DB::GFF

Made changes for compatibility with Generic Genome Browser 1.44

Doc type - Bio::DB::Aggregator->Bio::DB::GFF::Aggregator

Changes to Bio::DB::GFF to allow retrieval of segments that do not have genomic coordinates (not listed as features relative to themselves)

Adjusted the dna() method so that it returns full length of the dna if start and end are undefined

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

Made changes for compatibility with Generic Genome Browser 1.44

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

Removed stupid mysql assumptions from the connect() call

Fixed 3-frame translation glyph to accomodate 6-frame translation; improved the "what I wanted, not what I said" behavior of the mysql DBGFF adaptor

Added arrowheads for start codons to three-frame translation, and added settings to change colors and heights

Changes to Bio::DB::GFF to allow retrieval of segments that do not have genomic coordinates (not listed as features relative to themselves)

Adjusted the dna() method so that it returns full length of the dna if start and end are undefined

Adjusted the dna() method so that it returns full length of the dna if start and end are undefined

Added an index to the attribute_value field, causing vast improvement in performance on alias searches

Added an index to the attribute_value field, causing vast improvement in performance on alias searches

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

Adjusted the dna() method so that it returns full length of the dna if start and end are undefined

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

Made changes for compatibility with Generic Genome Browser 1.44

Adjusted the dna() method so that it returns full length of the dna if start and end are undefined

Adjusted the dna() method so that it returns full length of the dna if start and end are undefined

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

Made changes for compatibility with Generic Genome Browser 1.44

Adjusted the dna() method so that it returns full length of the dna if start and end are undefined

Bio::DB::GFF::Feature

Made changes for compatibility with Generic Genome Browser 1.44

Adding SeqFeatureI method seqname which points to the hashkey 'sourceseq'

Adjusted the dna() method so that it returns full length of the dna if start and end are undefined

Bio::DB::GFF::RelSegment

Made changes for compatibility with Generic Genome Browser 1.44

Return from overlaps/contains when item is not a RelSegment

Return from overlaps/contains when item is not a RelSegment

Changes to Bio::DB::GFF to allow retrieval of segments that do not have genomic coordinates (not listed as features relative to themselves)

Adjusted the dna() method so that it returns full length of the dna if start and end are undefined

Bio::DB::GFF::Segment

Segment implements SeqI now

Bio::DB::GenBank

Migrate to Eutils

Bio::DB::GenPept

Migrate to Eutils

Bio::DB::NCBIHelper

Migrate to Eutils

Bio::DB::RefSeq

Support embl-> embl

Bio::DB::WebDBSeqI

Migrate to Eutils

Quieter warnings - they show up in the 'throw' which can be trapped

Bio::Factory::EMBOSS

Added ACD parsing and modified EMBOSS modules to check parameters if verbose() is set over zero

Bio::Factory::ObjectFactoryI

New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects

Bio::Factory::Pise

Added id

Bio::Factory::SequenceFactoryI

Move to more general factory type

Bio::Graphics::Feature

Made changes for compatibility with Generic Genome Browser 1.44

Added a decent 6-frame translation glyph

Added spliced cds and 3-frame translation glyphs

Bio::Graphics::FeatureFile

Made changes for compatibility with Generic Genome Browser 1.44

Added regression tests and more documentation for Bio::Graphics. Also made the Bio::Graphics::Panel::bump method more flexible by allowing EnsEMBL-style simple bumping.

Added regression tests and more documentation for Bio::Graphics. Also made the Bio::Graphics::Panel::bump method more flexible by allowing EnsEMBL-style simple bumping.

Better bump control in the render() call

Better bump control in the render() call

Reenabled ability of feature2label to detect type/subtype relationships

Folded recent bug fixes from release branch into dev branch

POX fixes

Updated Bio::Graphics::FeatureFile to allow glyph-specific settings in configuration files to be set programmatically. For example: [named genes] glyph = arrow fgcolor = blue height = sub { shift->source eq 'GenBank' ? 20 : 10 } The power of perl. You can't help loving it.

Added spliced cds and 3-frame translation glyphs

Bio::Graphics::Glyph

Added regression tests and more documentation for Bio::Graphics. Also made the Bio::Graphics::Panel::bump method more flexible by allowing EnsEMBL-style simple bumping.

Added regression tests and more documentation for Bio::Graphics. Also made the Bio::Graphics::Panel::bump method more flexible by allowing EnsEMBL-style simple bumping.

Algorithm improvements to bump algorithm give 5x speedup for complex images

Algorithm improvements to bump algorithm give 5x speedup for complex images

The group glyph will now refuse to do simple bumping because it is unattractive

Improved behavior of segmented glyphs when they go off the edges

Improved behavior of segmented glyphs when they go off the edges

Cleaned up the boundaries of graphic elements so that adjacent features exactly abut at the nucleotide level (this problem always occurs when numbering nucleotides rather than numbering spaces between nucleotides)

Off-by-one error in glyph coordinates -- only apparent at nucleotide-level resolution

Added 6-frame translation and cds glyphs

Added spliced cds and 3-frame translation glyphs

Bio::Graphics::Glyph::Factory

Added 6-frame translation and cds glyphs

Added spliced cds and 3-frame translation glyphs

Bio::Graphics::Glyph::alignment

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::anchored_arrow

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::arrow

Made changes for compatibility with Generic Genome Browser 1.44

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::box

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::cds

Updated Bio::Graphics::FeatureFile to allow glyph-specific settings in configuration files to be set programmatically. For example: [named genes] glyph = arrow fgcolor = blue height = sub { shift->source eq 'GenBank' ? 20 : 10 } The power of perl. You can't help loving it.

Added spliced cds and 3-frame translation glyphs

Fixed a problem in cds glyph that caused first methionine to be skipped on forward cds

Added arrowheads for start codons to three-frame translation, and added settings to change colors and heights

Added arrowheads for start codons to three-frame translation, and added settings to change colors and heights

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::crossbox

Made changes for compatibility with Generic Genome Browser 1.44

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::diamond

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::dna

Rename s/Ace::Graphics/Bio::Graphics/ where applicable

Made changes for compatibility with Generic Genome Browser 1.44

Updated regression tests to accomodate earlier changes to Glyph coordinate mapping

Added a decent 6-frame translation glyph

Added 6-frame translation and cds glyphs

Added spliced cds and 3-frame translation glyphs

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::dot

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::ellipse

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::ex

Made changes for compatibility with Generic Genome Browser 1.44

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::extending_arrow

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::generic

Made changes for compatibility with Generic Genome Browser 1.44

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::graded_segments

Made changes for compatibility with Generic Genome Browser 1.44

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::group

The group glyph will now refuse to do simple bumping because it is unattractive

The group glyph will now refuse to do simple bumping because it is unattractive

Bio::Graphics::Glyph::heterogeneous_segments

Made changes for compatibility with Generic Genome Browser 1.44

Added 6-frame translation and cds glyphs

Added spliced cds and 3-frame translation glyphs

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::line

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::oval

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::pinsertion

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::primers

Made changes for compatibility with Generic Genome Browser 1.44

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::rndrect

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::ruler_arrow

Rename s/Ace::Graphics/Bio::Graphics/ where applicable

Made changes for compatibility with Generic Genome Browser 1.44

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::segmented_keyglyph

Made changes for compatibility with Generic Genome Browser 1.44

Added spliced cds and 3-frame translation glyphs

Added arrowheads for start codons to three-frame translation, and added settings to change colors and heights

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::segments

Added 6-frame translation and cds glyphs

Added spliced cds and 3-frame translation glyphs

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::span

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::toomany

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::track

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::transcript

Made changes for compatibility with Generic Genome Browser 1.44

Added spliced cds and 3-frame translation glyphs

Added arrowheads for start codons to three-frame translation, and added settings to change colors and heights

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::transcript2

Made changes for compatibility with Generic Genome Browser 1.44

Added spliced cds and 3-frame translation glyphs

Added arrowheads for start codons to three-frame translation, and added settings to change colors and heights

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::translation

Updated Bio::Graphics::FeatureFile to allow glyph-specific settings in configuration files to be set programmatically. For example: [named genes] glyph = arrow fgcolor = blue height = sub { shift->source eq 'GenBank' ? 20 : 10 } The power of perl. You can't help loving it.

Added spliced cds and 3-frame translation glyphs

Fixed 3-frame translation glyph to accomodate 6-frame translation; improved the "what I wanted, not what I said" behavior of the mysql DBGFF adaptor

Added arrowheads for start codons to three-frame translation, and added settings to change colors and heights

Added arrowheads for start codons to three-frame translation, and added settings to change colors and heights

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::triangle

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Glyph::wormbase_transcript

Removed wormbase_transcript.pm glyph; this is properly part of gbrowse

Bio::Graphics::Panel

Added the much-requested color_name_to_rgb() method

Added the much-requested color_name_to_rgb() method

Added regression tests and more documentation for Bio::Graphics. Also made the Bio::Graphics::Panel::bump method more flexible by allowing EnsEMBL-style simple bumping.

Added regression tests and more documentation for Bio::Graphics. Also made the Bio::Graphics::Panel::bump method more flexible by allowing EnsEMBL-style simple bumping.

Added 6-frame translation and cds glyphs

Added spliced cds and 3-frame translation glyphs

Complete documentation of all glyphs

Complete documentation of all glyphs

Bio::Graphics::Util

Updated Bio::Graphics::FeatureFile to allow glyph-specific settings in configuration files to be set programmatically. For example: [named genes] glyph = arrow fgcolor = blue height = sub { shift->source eq 'GenBank' ? 20 : 10 } The power of perl. You can't help loving it.

Added spliced cds and 3-frame translation glyphs

Bio::Index::Blast

For best results "use strict"

Bio::Index::EMBL

For best results "use strict"

Bio::Index::Fasta

For best results "use strict"

Bio::Index::Fastq

For best results "use strict"

Bio::Index::GenBank

For best results "use strict"

Bio::Index::SwissPfam

For best results "use strict"

Bio::Index::Swissprot

For best results "use strict"

Bio::LocatableSeq

Refactoring Locations so that 22^23 is valid for Bio::Location::Simple. Fuzzy throws an error if given this location.

Updated to full name of parameter as required

Bio::Location::Atomic

This is the old Simple.pm

Added each_Location() to Location/Atomic.pm and removed it from Simple.pm (it inherits from Atomic). This also fixes Fuzzy.pm since that one also inherits from Atomic.

Bio::Location::Fuzzy

Changed 'loc_type' into 'location_type' everywhere

Changed 'loc_type' into 'location_type' everywhere

Refactoring Locations so that 22^23 is valid for Bio::Location::Simple. Fuzzy throws an error if given this location.

Doc fix and update

Make sure SEQ_ID method exists for fuzzy

Undo braindead duplicate parameter parsing -- read the inheritance first jason!

Bio::Location::Simple

Doc fixes. cleaner default value setting for strand()

Doc fixes. cleaner default value setting for strand()

Allowed setting seq_id() in the contructor

Enabled setting seq_id in the constructor

Refactoring Locations so that 22^23 is valid for Bio::Location::Simple. Fuzzy throws an error if given this location.

Fixed setting location_type('\^')

Removed a debugging statement

Fixed location_type() when given '^' as an argument

Addition of method each_Location(), which will return an array of locations for either a Simple or Split locations. Called on Simple, it will just return itself in a one-element array. Called on Split, will return an array with all sub_Locations (recursively checked).

Added each_Location() to Location/Atomic.pm and removed it from Simple.pm (it inherits from Atomic). This also fixes Fuzzy.pm since that one also inherits from Atomic.

Bio::Location::Split

Allowed setting seq_id() in the contructor

Enabled setting seq_id in the constructor

Refactoring Locations so that 22^23 is valid for Bio::Location::Simple. Fuzzy throws an error if given this location.

Addition of method each_Location(), which will return an array of locations for either a Simple or Split locations. Called on Simple, it will just return itself in a one-element array. Called on Split, will return an array with all sub_Locations (recursively checked).

Doc fix and update

Cleanup params

Bio::LocationI

Addition of method each_Location(), which will return an array of locations for either a Simple or Split locations. Called on Simple, it will just return itself in a one-element array. Called on Split, will return an array with all sub_Locations (recursively checked).

Bio::PrimarySeq

Issue #1211

Report the offending characters in the throw string

Bio::Range

Minor doc format fixes

Minor doc format fixes

Bio::Root::Err

Fixed name

Bio::Root::Exception

Migrating fix 1.14 to branch-1-0-0

Bio::Root::IO

Made tempfile() respect an (UNLINK => 0) parameter

UNLINK now behaves properly and is tested

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Moved flush trait up to Root::IO

Bio::Root::Root

Modifications to throw() - Better test for key-value pairs and passing original @args through if not. Bio::Root::Exception can deal with raw args now. - Added leading newline to the output string to ensure that the output doesn't start on a partial line.

Migrated changes into branch-1-0-0 from the trunk version 1.12.

Fixed %args in scalar context bug

Fixed my %args || @args fix

Bio::Root::RootI

Modifications to _rearrange(): Added the mod test to ensure we have key-value pairs. Fixes bug where a single string parameter beginning with '-' gets lost. This tends to happen in error messages such as: $obj->throw("-id not defined") Modifications to throw() and warn(): Added leading newline to the output string to ensure that the output doesn't start on a partial line.

Migrated changes in 1.47.2.5 and 1.47.2.4 to the trunk (BIOPERLDEBUG stuff)

Migrated changes from trunk version 1.50

Bio::Search::HSP::BlastHSP

New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects

Bio::Search::HSP::GenericHSP

New method seq_inds as part of migration from BlastHSP to GenericHSP, will also perform properly on FASTA HSPs by trimming the context sequence first

POX fixes

Strip '\' and '/' splicing indicator and remove contextual sequence before building an Align::AlignI object with get_aln

Handle empty sequence names when preping for get_aln

Changes to calculate alignment and HSP trimming better

Trim out the splice chars from fasta HSPs - but trunc both query and sbjct sequence

New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects

Better fasta parsing merged from main trunk

Yet another fix for gawd-awful parsing of FastA

Merged FastA changes from trunk to branch, <whew> think it is right now

Strand and length are now properly matched up to the 'hit'/'subject', 'query', 'total'/'hsp' values through hsp->strand('query') or hsp->length('hit')

Small changes to improve generic nature of these objects

Supidity abounds! left off the lefthand side in eq comparison, wonder why it always true

Bio::Search::HSP::HMMERHSP

New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects

POX fixes

Bio::Search::HSP::HSPFactory

New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects

Bio::Search::HSP::HSPI

New method seq_inds as part of migration from BlastHSP to GenericHSP, will also perform properly on FASTA HSPs by trimming the context sequence first

Override strand method to delegate to query or hit/subject

Override start/end to work with named start/end components params, added tests for these

Small changes to improve generic nature of these objects

Bio::Search::HSP::WABAHSP

Parse waba output as an alignment

Bio::Search::Hit::GenericHit

Iteration supported as a data field

New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects

POX fixes

Bio::Search::Hit::HMMERHit

New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects

POX fixes

Bio::Search::Hit::HitFactory

New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects

Bio::Search::Hit::HitI

Teeny addition to the SYNOPSIS

Small changes to improve generic nature of these objects

Bio::Search::Result::GenericResult

Result can store the lit reference for the algorithm

Bio::Search::Result::HMMERResult

New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects

POX fixes

Bio::Search::Result::ResultFactory

New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects

Bio::Search::Result::WABAResult

Parse waba output as an alignment

Bio::SearchIO::EventHandlerI

Plug in new Result/Hit/HSP factory interface

Bio::SearchIO::SearchResultEventBuilder

Query,name,accession split into separate fields properly

Use object specific tags for the fields so we can strip them out in the event-builder without having to know what the arguments to the object are - this simplifies the event builder

Plug in new Result/Hit/HSP factory interface

Take either specified algorithm_name or the requested type

Bio::SearchIO::Writer::HTMLResultWriter

Fix bugs exposed by double checking

Use object specific tags for the fields so we can strip them out in the event-builder without having to know what the arguments to the object are - this simplifies the event builder

Bio::SearchIO::Writer::TextResultWriter

Dump a text BLAST format report out from a SearchIO object

Use object specific tags for the fields so we can strip them out in the event-builder without having to know what the arguments to the object are - this simplifies the event builder

Bio::SearchIO::blast

Use object specific tags for the fields so we can strip them out in the event-builder without having to know what the arguments to the object are - this simplifies the event builder

Plugin auto-writer

Modified start_element() to prevent lots of uninitialized warnings when type isn't defined.

Bio::SearchIO::blastxml

Query,name,accession split into separate fields properly

Use object specific tags for the fields so we can strip them out in the event-builder without having to know what the arguments to the object are - this simplifies the event builder

Bio::SearchIO::fasta

More intelligently handle FASTA 'context' sequence

Use object specific tags for the fields so we can strip them out in the event-builder without having to know what the arguments to the object are - this simplifies the event builder

More robust FastA parsing -- toaddress bug illustrated by Robin Emig

Changes to better parse fasta (merged from trunk)

Better fasta parsing merged from main trunk

Default ID size is actually 6 -- and allow it to be automagically adjusted (not-well-tested)

Yet another fix for gawd-awful parsing of FastA

Merged FastA changes from trunk to branch, <whew> think it is right now

Handle another stupid case

Handle another stupid case

Another bug thanks to Robin Emig's excellent testsuite of FASTA reports

Another bug thanks to Robin Emig's excellent testsuite of FASTA reports

Bio::SearchIO::hmmer

Parse HMMER reports with SearchIO

POX fixes

Bio::SearchIO::psiblast

Add doc for write_result

Bio::SearchIO::waba

Parse waba output as an alignment

Bio::Seq

Expanded doc, more methods are documented now with lovely L<> links

Bio::Seq::SeqFactory

Move to more general factory type

Bio::SeqFeature::Collection

Fixed boundary bug that was exposed on MacOS X, us for loop instead of while to insure initial key value is retrieved. Fun with BDB and DB_File interface

Properly set the tmpname- was getting the filehandle there previously

Added feature_count method to return number of features contained in the collection

Bio::SeqFeature::Computation

Warning when initializing strangely

Bio::SeqFeature::Gene::Transcript

Add_utr and add_exon now return true which makes tests possible

Bio::SeqFeature::SimilarityPair

Undo deprecation of subject() in similarityPair - both hit and subject will work

Bio::SeqI

Expanded doc, more methods are documented now with lovely L<> links

Fix stupid copy+paste error

Bio::SeqIO

Added fastq to valid formats

Added new SeqIO formats supported by the Staden io_lib read library, available in bioperl_ext; Pure perl versions left as an exercize for the reader ;)

Preload staden::read (via eval, so safe if not installed) - not entirely happy about having to do this, but load_format() for the staden::read-using formats doesn't seem to do the trick

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Moved flush trait up to Root::IO

Bio::SeqIO::FTHelper

Refactoring Locations so that 22^23 is valid for Bio::Location::Simple. Fuzzy throws an error if given this location.

Named parameter needs to change from seqid to seq_id

Used named parameter location_type instead of old shorthand loc_type

Bio::SeqIO::abi

Added new SeqIO formats supported by the Staden io_lib read library, available in bioperl_ext; Pure perl versions left as an exercize for the reader ;)

Fixed a few warning-bugs

Made new formats not throw on loading, but usage (allowing future pure Perl methods to work)

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::ace

The method 'create' now since we are dealing with a more generalized factory

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::alf

Added new SeqIO formats supported by the Staden io_lib read library, available in bioperl_ext; Pure perl versions left as an exercize for the reader ;)

Fixed a few warning-bugs

Made new formats not throw on loading, but usage (allowing future pure Perl methods to work)

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::bsml

Bsml module calling a bunch of methods that are not part of primarySeqI or SeqI, so I put an eval{} around them. Also changed molecule() call to alphabet(); this module is still producing a major number of "odd numbered elements in hash assignment" warnings; could someone put it out of its misery?

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::ctf

Added new SeqIO formats supported by the Staden io_lib read library, available in bioperl_ext; Pure perl versions left as an exercize for the reader ;)

Fixed a few warning-bugs

Made new formats not throw on loading, but usage (allowing future pure Perl methods to work)

Messed up the SeqFactory settings - reset

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::embl

The method 'create' now since we are dealing with a more generalized factory

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::exp

Added new SeqIO formats supported by the Staden io_lib read library, available in bioperl_ext; Pure perl versions left as an exercize for the reader ;)

Fixed a few warning-bugs

Made new formats not throw on loading, but usage (allowing future pure Perl methods to work)

Messed up the SeqFactory settings - reset

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::fasta

The method 'create' now since we are dealing with a more generalized factory

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::fastq

The method 'create' now since we are dealing with a more generalized factory

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::game

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::game::seqHandler

The method 'create' now since we are dealing with a more generalized factory

Bio::SeqIO::gcg

Removed upper-casing of sequence.

The method 'create' now since we are dealing with a more generalized factory

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::genbank

The method 'create' now since we are dealing with a more generalized factory

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::largefasta

The method 'create' now since we are dealing with a more generalized factory

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::phd

The method 'create' now since we are dealing with a more generalized factory

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::pir

The method 'create' now since we are dealing with a more generalized factory

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::pln

Added new SeqIO formats supported by the Staden io_lib read library, available in bioperl_ext; Pure perl versions left as an exercize for the reader ;)

Fixed a few warning-bugs

Made new formats not throw on loading, but usage (allowing future pure Perl methods to work)

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::qual

The method 'create' now since we are dealing with a more generalized factory

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::raw

The method 'create' now since we are dealing with a more generalized factory

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::scf

The method 'create' now since we are dealing with a more generalized factory

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::swiss

The method 'create' now since we are dealing with a more generalized factory

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SeqIO::ztr

Added new SeqIO formats supported by the Staden io_lib read library, available in bioperl_ext; Pure perl versions left as an exercize for the reader ;)

Fixed a few warning-bugs

Made new formats not throw on loading, but usage (allowing future pure Perl methods to work)

Messed up the SeqFactory settings - reset

Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::SimpleAlign

Handle missing ids a bit more gracefully

Bio::Tools::Blast

Doc fix

Bio::Tools::Eponine

wrapper for Eponine - a mammalian TSS predictor(written by Thomas Down - Sanger)

parser for Eponine..updated description. (wrapper on it's way)

Bio::Tools::HMMER::Results

Remove debugging

Bio::Tools::HMMER::Set

Insure that each added domain is unique

Insure that each added domain is unique

Bio::Tools::Phylo::PAML

Added ISA for AnalysisResultI

Initial parsing setup; everything should work (but return empty objects)

Fixed bug with io not being initialized

Get the ISA correct

Bio::Tools::Phylo::PAML::Codeml

Bare bones object for Aaron and Jason to expand

Proposed usage documented in the SYNOPSIS - open for discussion, of course

PAML parser and result objects

Bio::Tools::Phylo::PAML::Result

PAML parser and result objects

Initial parsing setup; everything should work (but return empty objects)

Fixed bug with io not being initialized

Bio::Tools::Run::EMBOSSApplication

Added ACD parsing and modified EMBOSS modules to check parameters if verbose() is set over zero

Removed Run wrappers -- they are in bioperl-run repository

Bio::Tools::Run::EMBOSSacd

Added ACD parsing and modified EMBOSS modules to check parameters if verbose() is set over zero

Removed Run wrappers -- they are in bioperl-run repository

Bio::Tools::Run::Genscan

Wrapper for Genscan executable

POX fixes

Removed Genscan from main - moved to bioperl-run

Bio::Tools::Run::PiseApplication

Removed Run wrappers -- they are in bioperl-run repository

Bio::Tools::Run::PiseJob

Removed Run wrappers -- they are in bioperl-run repository

Bio::Tools::Run::PiseJobParser

Removed Run wrappers -- they are in bioperl-run repository

Bio::Tools::Run::Pseudowise

Removed Run wrappers -- they are in bioperl-run repository

Bio::Tools::Run::RemoteBlast

Removed Run wrappers -- they are in bioperl-run repository

Bio::Tools::Run::RepeatMasker

Use the determined path to RP when attempting to find the version

Doc fix

POX fixes

Removed Run wrappers -- they are in bioperl-run repository

Bio::Tools::Run::StandAloneBlast

Removed Run wrappers -- they are in bioperl-run repository

Bio::Tools::Run::TribeMCL

Wrapper for tribemcl program for protein family clustering using markov flow simulation based on blast scores

Modified the way input is fed.

Removed Run wrappers -- they are in bioperl-run repository

Bio::Tools::SeqAnal

Doc fix

Bio::Tools::SeqPattern

Doc fix

Http://bioperl.org/Core/Examples no longer exists

Bio::Tools::Sigcleave

Doc fix

Bio::Tools::WWW

Doc fix

Bio::Tools::pSW

Noted protein-only. Removed IN_DEVELOPMENT comment

Bio::Tree::Node

Changes to fix problems described by Howard Ross including reading/writing newick format without branch lengths and storing nodes in proper read-in order (for clarity).

Eliminate stupid double-recursion when getting nodes in-order based on height in tree, this fixes Issue #1218 reported by Howard Ross

Eliminate stupid double-recursion when getting nodes in-order based on height in tree, this fixes Issue #1218 reported by Howard Ross

Bio::Tree::NodeI

Changes to fix problems described by Howard Ross including reading/writing newick format without branch lengths and storing nodes in proper read-in order (for clarity).

Eliminate stupid double-recursion when getting nodes in-order based on height in tree, this fixes Issue #1218 reported by Howard Ross

Eliminate stupid double-recursion when getting nodes in-order based on height in tree, this fixes Issue #1218 reported by Howard Ross

Bio::Tree::Tree

Changes to fix problems described by Howard Ross including reading/writing newick format without branch lengths and storing nodes in proper read-in order (for clarity).

Bio::TreeIO

Verbosity persists with the event based tree builder too

Bio::TreeIO::TreeEventBuilder

Changes to fix problems described by Howard Ross including reading/writing newick format without branch lengths and storing nodes in proper read-in order (for clarity).

Bio::TreeIO::newick

Changes to fix problems described by Howard Ross including reading/writing newick format without branch lengths and storing nodes in proper read-in order (for clarity).

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::TreeIO::tabtree

New output only module for displaying a tree as an ASCII drawing

POX fixes

Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO

Bio::Variation::SNP

Adding a functional but incomplete dbSNP xml parser. needs docs!

Forgot to SNP to inherit from Allele, cleaned up test file, added more tests.

More docs

Bio::Variation::VariantI

Doc fix

Doc fix

FAQ

Generated FAQ update with new questions baout features and annotations

Added mention of NP_

Makefile.PL

Added BioGraphics dependency to Text::Shellwords

Added DIR option to WriteMakefile for future need

bioperl.pod

Added mention of BioPerlBlast.pl

Added mention of dbsnp.pl and feature_draw.pl

bptutorial.pl

Note on -readmethod and RemoteBlast

Revcom->trunc() becomes trunc()->revcom

Georg's suggestions

Added mention of HMMER parsing by SearchIO

Added phylip to AlignIO's I/O list

Updated supported AlignIO formats, updated EMBOSS sections, minor stuff...

For best results "use strict" with Bio::Index

examples/BioPerlBlast.pl

Script from Simon Chan

scripts/bpindex.pl

Uncomment "use strict", script works

scripts/feature_draw.pl

Added regression tests and more documentation for Bio::Graphics. Also made the Bio::Graphics::Panel::bump method more flexible by allowing EnsEMBL-style simple bumping.

Added regression tests and more documentation for Bio::Graphics. Also made the Bio::Graphics::Panel::bump method more flexible by allowing EnsEMBL-style simple bumping.