Core 1.0.2 1.1.0 delta

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

Bio::Align::DNAStatistics

Descriptions and more importantly words of warning

Bio::Align::Utilities

Doc fix

Bio::AlignIO::phylip

Provide linebreaks for molphy format

Bio::Cluster::UniGene

Methods now return undef instead of stringified hash ref when no value is present

Added MGI method for use with mouse unigene data files.

Bio::Cluster::UniGeneI

Added MGI method for use with mouse unigene data files.

Bio::ClusterIO::dbsnp

Fixed an AUTOLOAD bug

Bio::ClusterIO::unigene

Fixed bug which caused regexes to be precompiled twice.

Bio::DB::Fasta

PrimarySeq::Fasta needs to implement the method 'desc'

Bio::DB::GFF

Changed redundant definition of display_name() to description() so that code matches docs

Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?

Updates & improvements to the glyphs. Added missing methods to Bio::DasI.

Migrating fix 1.52.2.5 to trunk.

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

Changed redundant definition of display_name() to description() so that code matches docs

Handle case of password but no username

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

Changed redundant definition of display_name() to description() so that code matches docs

Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?

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

Fixed problems with merged_segments() subroutine which became apparent when EST alignments got messier; added a pleasantly simple histogram routine to the GFF database

Bio::DB::GFF::Aggregator

Changed redundant definition of display_name() to description() so that code matches docs

Bio::DB::GFF::Aggregator::alignment

Changed redundant definition of display_name() to description() so that code matches docs

Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?

Bio::DB::GFF::Aggregator::clone

Changed redundant definition of display_name() to description() so that code matches docs

Bio::DB::GFF::Aggregator::transcript

Changed redundant definition of display_name() to description() so that code matches docs

Bio::DB::GFF::Feature

Fixed problems with merged_segments() subroutine which became apparent when EST alignments got messier; added a pleasantly simple histogram routine to the GFF database

Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?

Updates & improvements to the glyphs. Added missing methods to Bio::DasI.

Bio::DB::GFF::RelSegment

Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?

Improved semantics of abs_start() and abs_end() calls for gadfly compatibility

Bio::DB::GFF::Segment

Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?

Improved semantics of abs_start() and abs_end() calls for gadfly compatibility

Cleaned up biographics keyhandling; added a -desc argument to the bio::graphics::feature object

Bio::DasI

This will go away eventuall - SeqFeature::CollectionI to replace eventually

Updates & improvements to the glyphs. Added missing methods to Bio::DasI.

Bio::DescribableI

First commits of describable and identifiable interfaces - primaryseqI modified

Small mostly cosmetic changes (like, added $ID$ line etc).

Changed redundant definition of display_name() to description() so that code matches docs

Bio::Factory::EMBOSS

Double quote to see the variable's value

Bio::Factory::FTLocationFactory

Added Bio::Factory::LocationFactoryI with one method (so far) from_string(). Added implementation for Genbank-compatible feature table location strings, which is a complete rewrite of the location parsing code. Also, added test LocationFactory.t. Tests pass.

Adapted FTHelper and the parsers for genbank, embl, and swissprot to utilize the new LocationFactoryI framework for location parsing. All tests pass, which is no guarantee for complete coverage of location string space.

Bio::Factory::LocationFactoryI

Added Bio::Factory::LocationFactoryI with one method (so far) from_string(). Added implementation for Genbank-compatible feature table location strings, which is a complete rewrite of the location parsing code. Also, added test LocationFactory.t. Tests pass.

Bio::Factory::SequenceFactoryI

Documentation fixes

Bio::Graphics::Feature

Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?

Updates & improvements to the glyphs. Added missing methods to Bio::DasI.

Cleaned up biographics keyhandling; added a -desc argument to the bio::graphics::feature object

Bio::Graphics::FeatureFile

Cleaned up biographics keyhandling; added a -desc argument to the bio::graphics::feature object

Bio::Graphics::Glyph

Changed redundant definition of display_name() to description() so that code matches docs

Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?

Bio::Graphics::Glyph::cds

Updates & improvements to the glyphs. Added missing methods to Bio::DasI.

Bio::Graphics::Glyph::diamond

Changed redundant definition of display_name() to description() so that code matches docs

Bio::Graphics::Glyph::dna

Updates & improvements to the glyphs. Added missing methods to Bio::DasI.

Bio::Graphics::Glyph::generic

Changed label() code so that display_id() is preferred over the seqname()

Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?

Updates & improvements to the glyphs. Added missing methods to Bio::DasI.

Bio::Graphics::Glyph::graded_segments

Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?

Bio::Graphics::Glyph::translation

Updates & improvements to the glyphs. Added missing methods to Bio::DasI.

Bio::Graphics::Glyph::triangle

Changed redundant definition of display_name() to description() so that code matches docs

Bio::Graphics::Panel

Fixed stupid error in which pad_left was used instead of pad_right, rendering pad_right unusable

Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?

Updates & improvements to the glyphs. Added missing methods to Bio::DasI.

Cleaned up biographics keyhandling; added a -desc argument to the bio::graphics::feature object

Bio::IdCollectionI

The IdCollectionI interface supports objects with multiple ids

Bio::IdentifiableI

First commits of describable and identifiable interfaces - primaryseqI modified

Small mostly cosmetic changes (like, added $ID$ line etc).

Changed redundant definition of display_name() to description() so that code matches docs

Bio::Location::Fuzzy

Added Bio::Factory::LocationFactoryI with one method (so far) from_string(). Added implementation for Genbank-compatible feature table location strings, which is a complete rewrite of the location parsing code. Also, added test LocationFactory.t. Tests pass.

Bio::Location::Simple

Added Bio::Factory::LocationFactoryI with one method (so far) from_string(). Added implementation for Genbank-compatible feature table location strings, which is a complete rewrite of the location parsing code. Also, added test LocationFactory.t. Tests pass.

Bio::Location::Split

Undo commented region so that we fix reported FThelper writing problem

Added Bio::Factory::LocationFactoryI with one method (so far) from_string(). Added implementation for Genbank-compatible feature table location strings, which is a complete rewrite of the location parsing code. Also, added test LocationFactory.t. Tests pass.

Adapted FTHelper and the parsers for genbank, embl, and swissprot to utilize the new LocationFactoryI framework for location parsing. All tests pass, which is no guarantee for complete coverage of location string space.

Need to check is_remote() before propagating strand to a subloc.

Bio::LocationI

Added Bio::Factory::LocationFactoryI with one method (so far) from_string(). Added implementation for Genbank-compatible feature table location strings, which is a complete rewrite of the location parsing code. Also, added test LocationFactory.t. Tests pass.

Bio::PrimarySeq

First commits of describable and identifiable interfaces - primaryseqI modified

Bio::PrimarySeqI

First commits of describable and identifiable interfaces - primaryseqI modified

Support desc and description per the identifier interface

Bio::Root::Err

Http://bio.perl.org/Core/Examples no longer exists, the scripts are in examples/

Bio::Root::IO

No msgs on undefined CLEANUP

Bio::Root::Root

Added _load_module().

Propagated Lincoln's untainting fix to SeqIO module loading. _load_module() now throws an exception if name not legal.

Bio::Root::RootI

Migrating commit 1.47.2.7 on branch-1-0-0 to trunk

Bio::Root::Vector

Http://bio.perl.org/Core/Examples no longer exists, the scripts are in examples/

Bio::Search::HSP::BlastHSP

The regexp in _set_seq inserted an extra space on the end of each alignment line. In _set_residues(), these lines get concatenated together but the blank space still remains between each line. This screws up the generation of the $identicalList_query, $identicalList_sbjct, etc., because the characters in the query and sbjct sequences (with spaces) don't line up with the match line sequence (which, because it's parsed differently doesn't have the spaces). I was getting incorrect seq_inds() coordinates because of this.

The regexp in _set_seq inserted an extra space on the end of each alignment line. In _set_residues(), these lines get concatenated together but the blank space still remains between each line. This screws up the generation of the $identicalList_query, $identicalList_sbjct, etc., because the characters in the query and sbjct sequences (with spaces) don't line up with the match line sequence (which, because it's parsed differently doesn't have the spaces). I was getting incorrect seq_inds() coordinates because of this.

Bio::Search::HSP::GenericHSP

Changes for WABA parsing and inheritance fixes with SeqFeature::SimilarityPair

Moved some BlastXX methods over

Bio::Search::HSP::WABAHSP

Changes so that WABAs output more-or-less informatively

Bio::Search::Hit::BlastHit

After discussion with steve chervitz, decided that frac_identical and frac_conserved would be better off returning a fraction with 3 digits of precision (rather than 2). I also changed these functions so that the never round up to 100%, in other words, .9997 gets rounded off to .999 rather than 1.000

Bio::Search::Hit::GenericHit

Moved some BlastXX methods over

Bio::SearchIO

Doc bug fixed

Doc bug fixed

Bio::SearchIO::FastHitEventBuilder

Fast Event processor which does not handle HSPs for fast skims

Set query length in the Hit for the sake of logical length code

Bio::SearchIO::SearchResultEventBuilder

Set query length in the Hit for the sake of logical length code

Bio::SearchIO::blast

Support parsing of RPS-BLAST

Remove test for /Score/ in query description parsing to deal with people putting weird things in their blast db descriptions

Bio::SearchIO::blastxml

Set query length in the Hit for the sake of logical length code

Bio::SearchIO::waba

Set reporttype

Bio::Seq

Added mention of LocationI and Location::SplitLocationI

Bio::Seq::PrimedSeq

These are the early versions of this. I am actively working on these at the moment and will be continuing over the next several days.

Substantial revisions in the way things are behaving. This thing is shaping up nicely. Far too many changes to document here. Things that are yet to be done: 1. Implement RangeI methods in SeqFeature::Primer 2. complete tests 3. implement negative testing. "only tests that throw are successful, grasshopper." 4. fix primer3 test so that the stream itself is tested. 5. decide on a proper ID scheme.

Bio::Seq::SeqFactory

Test that type which factory is asked to instantiate is-a Bio::PrimarySeqI

For now allow SeqFactory to accept Bio::Seq::QualI objects as well as Bio::PrimarySeqI types for creation

Bio::SeqFeature::CollectionI

Initial collection interface -- will change

Bio::SeqFeature::Computation

Inheritance fixes -- improvements to computation

Bio::SeqFeature::Generic

Inheritance fixes -- improvements to computation

Repaired spelling error in documentation.

Bio::SeqFeature::Primer

These are the early versions of this. I am actively working on these at the moment and will be continuing over the next several days.

Substantial revisions in the way things are behaving. This thing is shaping up nicely. Far too many changes to document here. Things that are yet to be done: 1. Implement RangeI methods in SeqFeature::Primer 2. complete tests 3. implement negative testing. "only tests that throw are successful, grasshopper." 4. fix primer3 test so that the stream itself is tested. 5. decide on a proper ID scheme.

More fun implementing interfaces. Whoooey, is this a good time.

Altered some of the RangeI-implementing methods in Primer.pm. Discovered a hideous fault in Consed and fixed it. (set_contig_quality doubles quality values if called) Mangled Trim.pm in slight ways to figure out what was broken in Consed. Working on nicer tests for primer3.

Bio::SeqFeature::Similarity

Inheritance fixes -- improvements to computation

Bio::SeqFeature::SimilarityPair

Inheritance fixes -- improvements to computation

Bio::SeqFeatureI

Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?

Repaired spelling error in documentation. ('implementation')

Bio::SeqIO

Small mostly cosmetic changes (like, added $ID$ line etc).

Link to fh

Updates & improvements to the glyphs. Added missing methods to Bio::DasI.

Adapted to use _load_module() in Root.pm.

Adapted FTHelper and the parsers for genbank, embl, and swissprot to utilize the new LocationFactoryI framework for location parsing. All tests pass, which is no guarantee for complete coverage of location string space.

Bio::SeqIO::FTHelper

Added $location->strand setting for sublocations in a split location

Undo chris's changes

Adapted FTHelper and the parsers for genbank, embl, and swissprot to utilize the new LocationFactoryI framework for location parsing. All tests pass, which is no guarantee for complete coverage of location string space.

Bio::SeqIO::bsml

Updates & improvements to the glyphs. Added missing methods to Bio::DasI.

_initialize() got duplicated a while back when SeqFactory methods were added - moved the appropriate code to the right version of _initialize.

Bio::SeqIO::embl

Adapted FTHelper and the parsers for genbank, embl, and swissprot to utilize the new LocationFactoryI framework for location parsing. All tests pass, which is no guarantee for complete coverage of location string space.

Bio::SeqIO::fasta

Programatically set the sequence width

Bio::SeqIO::genbank

Fixed missing GI bug for buggy records without versions tested on 20,000 sequences

Adapted FTHelper and the parsers for genbank, embl, and swissprot to utilize the new LocationFactoryI framework for location parsing. All tests pass, which is no guarantee for complete coverage of location string space.

Bio::SeqIO::phd

phd.pm was not getting the proper $id. trim.pm was not returning proper trimpoints from trim_singlet() both are 'fixed' now.

These are the early versions of this. I am actively working on these at the moment and will be continuing over the next several days.

Bio::SeqIO::primer3

These are really rough starts for a module that will read primer3 outfiles and return Bio::SeqFeature::Primer objects. I will commit Bio::SeqFeature::Primer later today, I hope. This tests successfully and generally works but really is a work in progress.

These are the early versions of this. I am actively working on these at the moment and will be continuing over the next several days.

Substantial revisions in the way things are behaving. This thing is shaping up nicely. Far too many changes to document here. Things that are yet to be done: 1. Implement RangeI methods in SeqFeature::Primer 2. complete tests 3. implement negative testing. "only tests that throw are successful, grasshopper." 4. fix primer3 test so that the stream itself is tested. 5. decide on a proper ID scheme.

Bio::SeqIO::swiss

The annotation object wasn't being correctly attached to the new seqs.

Adapted FTHelper and the parsers for genbank, embl, and swissprot to utilize the new LocationFactoryI framework for location parsing. All tests pass, which is no guarantee for complete coverage of location string space.

Bio::SimpleAlign

Moved comments to notes so they show up in perldoc

Bio::Structure::Atom

Added methods for segID and saner atomname writing

Bio::Structure::IO::pdb

- segID reading / writing added - better (correct ?) ATOM name writing - sane placement of TER record - fixed bug when writing continuation lines

Bio::Tools::Alignment::Consed

Altered some of the RangeI-implementing methods in Primer.pm. Discovered a hideous fault in Consed and fixed it. (set_contig_quality doubles quality values if called) Mangled Trim.pm in slight ways to figure out what was broken in Consed. Working on nicer tests for primer3.

Bio::Tools::Alignment::Trim

phd.pm was not getting the proper $id. trim.pm was not returning proper trimpoints from trim_singlet() both are 'fixed' now.

Altered some of the RangeI-implementing methods in Primer.pm. Discovered a hideous fault in Consed and fixed it. (set_contig_quality doubles quality values if called) Mangled Trim.pm in slight ways to figure out what was broken in Consed. Working on nicer tests for primer3.

Bio::Tools::BPpsilite

Some updates so the CPAN rendered modules have the correct name

Bio::Tools::Blast

Http://bio.perl.org/Core/Examples no longer exists, the scripts are in examples/

Some updates so the CPAN rendered modules have the correct name

Bio::Tools::GFF

Indented some code

Bio::Tools::Phylo::Molphy

Added Molphy parser (only tested on protml)

Need IO::String

Bio::Tools::Phylo::Molphy::Result

Added Molphy parser (only tested on protml)

Bio::Tools::Phylo::PAML

Implement seqtype CODONML parsing

NG parser more intelligent

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

Implement seqtype CODONML parsing

Bio::Tools::Primer3

Put this in the new place as discussed on Bioperl-l. Added things that broke when it moved from under the umbrella of SeqIO.

Bio::Tools::RestrictionEnzyme

Migrating fix 1.19.2.2 to trunk.

Added Ryan's enzymes

Bio::Tools::Run::WrapperBase

Base for runnable wrappers

Doc fix, default value of for error_string, leading underscore for private data

Cleanup of tempfiles works

Bio::Tools::SeqAnal

Some updates so the CPAN rendered modules have the correct name

Bio::Tools::Sigcleave

Some updates so the CPAN rendered modules have the correct name

Bio::Tools::Sim4::Results

Estisfirst -> estfirst

Bio::Tools::WWW

Some updates so the CPAN rendered modules have the correct name

Bio::Tree::Node

Fixes to ancestor (couldn't set value) and description (_desription -> _desc) subs

Completed depth/breadth 'order' option for get_nodes(); added 'sortby' option for get_Descendents and each_Descendent: takes 'height', 'creation' or coderef to be used for sorting

Bio::Tree::NodeI

Tree builder event handler made aware of nodetype/treetype arguments (to implement a node/tree factory); NHX tree format added; Tree::NodeNHX node type added (for nhx tag storage); TreeEventBuilder made NHX tag aware, and able to handle nonbinary trees; basic testing added.

Completed depth/breadth 'order' option for get_nodes(); added 'sortby' option for get_Descendents and each_Descendent: takes 'height', 'creation' or coderef to be used for sorting

Placeholder warnings about height() method yielding incorrect answers for anything but binary trees ... will fixup after discussions at BOSC

Bio::Tree::NodeNHX

Add to repository

Quote hash keys for backward compatibility

Bio::Tree::Tree

Tree builder event handler made aware of nodetype/treetype arguments (to implement a node/tree factory); NHX tree format added; Tree::NodeNHX node type added (for nhx tag storage); TreeEventBuilder made NHX tag aware, and able to handle nonbinary trees; basic testing added.

Completed depth/breadth 'order' option for get_nodes(); added 'sortby' option for get_Descendents and each_Descendent: takes 'height', 'creation' or coderef to be used for sorting

New functions - split to new module (monophyly test and find_node)

Added score and id capability

Placeholder warnings about height() method yielding incorrect answers for anything but binary trees ... will fixup after discussions at BOSC

Bio::Tree::TreeFunctionsI

New functions - split to new module (monophyly test and find_node)

Fixed is_monophyletic thx to Justin Reese

Test of paraphyly added

Bio::Tree::TreeI

Added score and id capability

Placeholder warnings about height() method yielding incorrect answers for anything but binary trees ... will fixup after discussions at BOSC

Bio::TreeIO

Tree builder event handler made aware of nodetype/treetype arguments (to implement a node/tree factory); NHX tree format added; Tree::NodeNHX node type added (for nhx tag storage); TreeEventBuilder made NHX tag aware, and able to handle nonbinary trees; basic testing added.

Bio::TreeIO::TreeEventBuilder

Tree builder event handler made aware of nodetype/treetype arguments (to implement a node/tree factory); NHX tree format added; Tree::NodeNHX node type added (for nhx tag storage); TreeEventBuilder made NHX tag aware, and able to handle nonbinary trees; basic testing added.

Bio::TreeIO::nhx

Tree builder event handler made aware of nodetype/treetype arguments (to implement a node/tree factory); NHX tree format added; Tree::NodeNHX node type added (for nhx tag storage); TreeEventBuilder made NHX tag aware, and able to handle nonbinary trees; basic testing added.

Bio::TreeIO::tabtree

Made tabtree.pm know about nonbinary trees ...

Bio::Variation::SNP

Fixed an AUTOLOAD bug

FAQ

How do I parse CDS join() statements in Genbank or EMBL...

Motifs and agrep, minor changes

Makefile.PL

ExtUtils::MakeMaker provides a prompt function

1.1 release version for makefile

biodesign.pod

Mention howto, minor changes

bioperl.lisp

Small mostly cosmetic changes (like, added $ID$ line etc).

Added Bio::Factory::LocationFactoryI with one method (so far) from_string(). Added implementation for Genbank-compatible feature table location strings, which is a complete rewrite of the location parsing code. Also, added test LocationFactory.t. Tests pass.

bioperl.pod

Added waba2gff.pl

Added script parse_codeml.pl

Dan's script...

Added description of longorf.pl

New revcom_dir location

bptutorial.pl

SearchIO supports RPS-BLAST, minor changes

Added mention of LocationI and Location::SplitLocationI

Added example for changing CGI parameter using RemoteBlast

Space before comma allows URL to work

examples/gb2features.pl

Dan's script...

examples/longorf.pl

Dan's script...

Minor changes

Minor change

scripts/feature_draw.pl

Cleaned up biographics keyhandling; added a -desc argument to the bio::graphics::feature object

scripts/parse_codeml.pl

Example of parsing codeml results

Print some more info

scripts/render_sequence.pl

Cleaned up biographics keyhandling; added a -desc argument to the bio::graphics::feature object

scripts/revcom_dir.pl

New location

scripts/waba2gff.pl

Convert raw waba to one type of GFF (not necessarily sanger output from WABA storage)

Support infile passing on cmd line with no argument