Core 1.5.1 1.5.2 delta

These are detailed notes on changes made between bioperl-release-1-5-1 and bioperl-release-1-5-2. The main new features are explained in more friendly prose here.

Bio::Align::DNAStatistics

Fix Issue #1991: lower case nucleotides do not work

Email obscuring

Changed die() to __PACKAGE__->throw()

Dnds_pattern_number basically counts the number of codons that have no gaps in the sequence -- patterns in the PAML lingo

Bio::AlignIO

Forgot to commit this; added metafasta to _guess_format

Add xmfa write_aln() method, stk and xmfa file extensions for guessing format

Bio::AlignIO::arp

Simple ARP parser

Bio::AlignIO::bl2seq

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::AlignIO::clustalw

Issue #2000; need to change AlignIO::fasta next_aln to make it more like AlignIO::clustalw, but works for now

Issue #2042; added warnings for duplicate sequences

Issue #2042; fixed unit'd value in numeric == bug

Fix extra Issue #2042

Throw when unable to deal with file, not just warn

Bio::AlignIO::fasta

Start and End refer to length of sequence without gaps

Specify a width in an alignment writing and use regexp to format instead of while loop

Per Albert

Issue #1958; made '?' ambiguous to prevent removal from sequences (was adding trailing gaps)

Issue #2000; need to change AlignIO::fasta next_aln to make it more like AlignIO::clustalw, but works for now

Issue #2000; got rid of sequence validation and substitution (which caused nasty unwarned deletions); sequence validation done in PrimarySeq!

Bio::AlignIO::meme

Version numbers can be non-numeric, corrected throw detection

Meme converts ambiguity codes and its own inserted gaps to X, and allows dash gaps, regex fixed to handle

Bio::AlignIO::metafasta

Need to 'use' module for using module

Issue #2016 : several fixes to accomodate changes in handling meta data. Reverted redundant fix in SimpleAlign; removed relevant tests in SimpleAlign.t

Remove extraneous use statement

Bio::AlignIO::nexus

Don't single quote wrap every id, only those which need it. MrBayes doesn't like it

Bio::AlignIO::phylip

Allow linewrap for phylip sequential

Space

Simplify covoluted logic

Bio::AlignIO::psi

Print last column

Bio::AlignIO::stockholm

Add experimental stockholm write_aln() support

Add sequence-based meta output

Remove old initialization parameter; will add builder later

Add alignment meta string output

Additional fun stuff; write_aln() test added; may move tests to separate test suite (lots of them)

Using DBLinks for database refs

Remove extraneous debugging staatements

Small fixes for AnnotationFactory

Bio::AlignIO::xmfa

First pass at xmfa parser (next_aln() implemented only)

Add xmfa write_aln() method, stk and xmfa file extensions for guessing format

Bio::AnnotatableI

Correct

Bio::Annotation::AnnotationFactory

Add Bio::Annotation::Target to guessed types. Doc fixes: type is guessed, there is no default value

Ticky-tack changes

Bio::Annotation::Collection

Issue #1923

Issue #1922

Bio::Annotation::DBLink

Improved NAME, SYNOPSIS, DESCRIPTION docs

Bio::Annotation::OntologyTerm

Don't use the identifier for as_text() - it's optional, and not in the same alternate key as name. Instead, let's add is_obsolete(), which is in the same alternate key as name, and hence contributes to distinguishing one term from another.

Ticky-tack changes

Bio::Annotation::Reference

Add support for consortiums (CONSRTM) - Issue #2006

Issue #2020

Made pubmed more of an equal alternative to medline

Bio::Annotation::SimpleValue

Fix to allow 0 values despite operator overload (Paul Mooney)

Bio::Annotation::Target

Adding short description

Bio::Assembly::Contig

Issue #2064

Bio::Assembly::IO::ace

Issue #2031; added ace format tests to Assembly.t

Use throw_not_implemented() instead

Bio::Assembly::IO::phrap

Use throw_not_implemented() instead

Bio::Assembly::Scaffold

Issue #2048; need to take a closer look at test suite, skips a lot of tests

Bio::Cluster::SequenceFamily

Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.

Bio::ClusterIO::dbsnp

Issue #2018, patched parser to accept new dbSNP XML, a lot of tags are not recognised and processed

Bio::CodonUsage::IO

More detail

Strip trailing space from species name, fixes t/DBCUTG.t

Bio::DB::Biblio::biofetch

Issue #2083. Add default retrieval type and use it during initialization.

Predeclared $TMP so it doesn't masks earlier use in same sub

Bio::DB::BioFetch

Handle ebi database name change for swall to uniprot

Improve error message by reporting $base

Bio::DB::CUTG

More detail

Throw on server error, skip on test

Bio::DB::DBFetch

Issue #2083. Add format= to URL.

Predeclared $F so it doesn't masks earlier declaration in same scope

Bio::DB::EUtilities

Initial EUtilities commit; test and test modules on the way...

Make get_db_refs a little more forgiving for arrays

Cleaning up; need to make the cookie and elinkset data accessors better, but for now...

More error fixes

Changed the way get_db_ids works

EInfo stuff

Fixed problems with cookies

Fixed retmode issue; added keep_cookies method (for repeated queries using same cookie); minor fixes

Small issue fixed for retmode; separate methods from parameters

Removed extra debugging statement, Doh!

Small fixes

Small update, weirdness with elink.

Small fixes; working on tests and HOWTO

Cleaning up the API a bit

Small fixes picked up during tests

Update, bugs fixes for tests

EUtilties fixes, additional tests

Change use var to our; comment out Dumper lines

Setting DB from cookie is bad for elink; it should be dbfrom

Fixes to get EGQuery working correctly

Bio::DB::EUtilities::Cookie

Cookie not cookie (this is not a plugin)

Updates to elink, methods and so on

Cleaning up; need to make the cookie and elinkset data accessors better, but for now...

Cleaning up the API a bit

EUtilties fixes, additional tests

Adding short description

Bio::DB::EUtilities::DocSum

Add simple docsum container object for esummary

Adding methods to DocSum and esummary (still experimental)

Fixes for tests

Bio::DB::EUtilities::ElinkData

Updates to elink, methods and so on

Cleaning up; need to make the cookie and elinkset data accessors better, but for now...

Oops! Found a few mistakes...

EInfo stuff

Small fix for odd linksets with no return data

A bt more lenient for empty linksets

Small fixes

Small update, weirdness with elink.

Cleaning up the API a bit

Update, bugs fixes for tests

EUtilties fixes, additional tests

Change use var to our; comment out Dumper lines

Bio::DB::EUtilities::ElinkScores

Object to deal with relevancy scores (storing internally was getting too complicated(

Remove ElinkScores (name changed to ElinkData)

Bio::DB::EUtilities::cookie

Initial EUtilities commit; test and test modules on the way...

Renaming cookie

Bio::DB::EUtilities::efetch

Initial EUtilities commit; test and test modules on the way...

Small issue fixed for retmode; separate methods from parameters

Change use var to our; comment out Dumper lines

Bio::DB::EUtilities::egquery

Initial EUtilities commit; test and test modules on the way...

Minor updates

Change use var to our; comment out Dumper lines

Bio::DB::EUtilities::einfo

Initial EUtilities commit; test and test modules on the way...

EInfo stuff

Cleaning up the API a bit

Update, bugs fixes for tests

Change use var to our; comment out Dumper lines

Bio::DB::EUtilities::elink

Initial EUtilities commit; test and test modules on the way...

Minor updates

Updates to elink, methods and so on

Cleaning up; need to make the cookie and elinkset data accessors better, but for now...

Oops! Found a few mistakes...

More error fixes

Fixed problems with cookies

Fixed retmode issue; added keep_cookies method (for repeated queries using same cookie); minor fixes

Small fix for odd linksets with no return data

Small update, weirdness with elink.

Small fixes; working on tests and HOWTO

EUtilties fixes, additional tests

Change use var to our; comment out Dumper lines

Changed or removed VERSION

Oops!

Bio::DB::EUtilities::epost

Initial EUtilities commit; test and test modules on the way...

Fixed problems with cookies

Fixed retmode issue; added keep_cookies method (for repeated queries using same cookie); minor fixes

Change use var to our; comment out Dumper lines

Oops!

Bio::DB::EUtilities::esearch

Initial EUtilities commit; test and test modules on the way...

More error fixes

Changed the way get_db_ids works

Fixed retmode issue; added keep_cookies method (for repeated queries using same cookie); minor fixes

Cleaning up the API a bit

Small fixes picked up during tests

Not description, term

Change use var to our; comment out Dumper lines

Force IDs to be an array at all times

Fixes to get EGQuery working correctly

Bio::DB::EUtilities::esummary

Initial EUtilities commit; test and test modules on the way...

Change use var to our; comment out Dumper lines

Add simple docsum container object for esummary

Adding methods to DocSum and esummary (still experimental)

Fixes for tests

Bio::DB::EntrezGene

Add EntrezGene.pm

Seems that this is required by SeqIO/entrezgene

Doc corrections

More detail on ids

More detail

Email changed

Bio::DB::Expression

Adding support to screenscrape ncbi GEO

Bio::DB::Expression::geo

Adding support to screenscrape ncbi GEO

Updates to parsing code and lazy loading of object attributes

Removed redundant "if $self->verbose" suffix from "$self->debug()" calls

No setting of own $VERSION

Bio::DB::Fasta

Edits

Add to example

Additional suffixes

Add is_circular()

Fixed Issue #2045

Accepted Charles Tilford's patch for fasta files > 4 GB in length

Bio::DB::Flat

Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.

Bio::DB::Flat::BinarySearch

Issue #1840

Issue #1917

Adding short description

Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.

Bio::DB::GDB

Throw, not die

Made (env_proxy => 1) the default for LWP::UserAgent instantiations

Throw on server error

Bio::DB::GFF

Bio::DB::GFF was *unable* to parse GFF3 files; fixed this bad bug

Added regression tests for gff3 support

Lincoln's fix of bug that was introduced prior to 1.5.1 release (fix onto branch)

Removed unsigned from the fdata table so that start and end coordinates can take on negative values

Set gff3_flag properly

Fix gff3_flag full variable name

Fixed gff3 name munging flag

GFF3 processing is a little better now

Remove extra quote

Fix the file handles

Added the method, delete_fattribute_to_feature().

Bio::DB::GFF::Adaptor::berkeleydb

Fixed problem related to aliases not being searched in get_feature_by_name()

Throw, not die

Make synopsis runnable, since this is needed on initial creation

Changing search_notes method to allow wild cards to be passed in

Fixed misalignment of reversec dna glyph and rescued missing grid lines that occur near ends of panel

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

Fixed problem related to aliases not being searched in get_feature_by_name()

Changing search_notes method to allow wild cards to be passed in

Escaped embedded _ and % characters in strings that will be used with the LIKE operator

Goal: delete fattribute_to_feature rows when deleting features. Modified _delete_feature() to use _delete_fattribute_to_feature() to delete fattribute_to_feature values which had been ignored up to this point. Added _delete_fattribute_to_feature() which will remove values from the fattribute_to_feature table. Modified _delete_group() to use the delete_feature method rather than implement that functionality again. This might take a little more time but makes sense for code upkeep. The _delete_fattribute_to_feature() method could potentially check for orphaned fattribute rows and remove them.

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

Removed unsigned from the fdata table so that start and end coordinates can take on negative values

Throw, not die

Moving result filtering from gbrowse to mysql adaptor (where it belongs, so that anybody who uses this method will actually get the results they are expecting).

A few more tweaks to the search_notes methods

Changes to make storable in GFF3 databases

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

Changing search_notes method to allow wild cards to be passed in

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

Throw, not die

Changing search_notes method to allow wild cards to be passed in

Meant to strip the wild cards

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

Throw, not die

Sped up case insensitive name searching in postgres

Added documentation and a commented out version of the search_notes method; this is in preparation of commiting another pg adaptor that implements a fast full text search

Making feature name (gname) and ref seq (fref) searching case insensitive. Class names are not case insensitive though; should they be?

A few more case insensitive fixes

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

New postgres GFF adaptor: makes use of TSearch2 for fast, full text searching of note attributes

Adding a few doc items

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

Bio::DB::GFF was *unable* to parse GFF3 files; fixed this bad bug

Lincoln's fix of bug that was introduced prior to 1.5.1 release (fix onto branch)

Fixed inconsistent behavior wrt "attributes()" and "abs_stop()" both of which are deprecated

Changing search_notes method to allow wild cards to be passed in

A few more tweaks to the search_notes methods

Fixed logic bug in dna retrieval

Bio::DB::GFF::Feature

Fixed an issue in which the gff string will print out "." when the start or end coordinates are zero

Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down

Fixed problem with segments glyph not showing target DNA / multiple alignments due to Bio::DB::GFF::Feature API change

Bio::DB::GFF::RelSegment

Fixed inconsistent behavior wrt "attributes()" and "abs_stop()" both of which are deprecated

Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down

Bio::DB::GFF::Segment

Added draw_dna and draw_protein options to the generic glyph

Bio::DB::GenBank

Issue #1405

Added more (better!) warnings, docs on complexity

Added batch retrieval via epost; only accessible using get_seq_stream using GI's at the moment

Make 'gbwithparts' the default format; added default_format (wasn't picking up $DEFAULTFORMAT from the BEGIN block for some reason).

Bio::DB::GenPept

Added batch retrieval via epost; only accessible using get_seq_stream using GI's at the moment

Bio::DB::GenericWebDBI

Initial EUtilities commit; test and test modules on the way...

Fixed retmode issue; added keep_cookies method (for repeated queries using same cookie); minor fixes

Pass to SUPER::proxy (Issue #2109)

Bio::DB::LocationI

Add Location and Reference RandomAccessI-like interfaces, SeqFeatureI-like one to be added

Bio::DB::MANIFEST

No purpose

No purpose

Bio::DB::Makefile.PL

No purpose

No purpose

Bio::DB::MeSH

Fix for multi-line

Convert 'print' to $self->debug/warn as appropriate. Refactored duplicate hard-coded URLs into a subroutine.

Bio::DB::NCBIHelper

Issue #1405

Add format 'gbwithparts' for contig retrieval, and postprocess_data fix for contig assembly (now directly from NCBI instead of bioperl-ish build)

Get rid of potential circular ref from last fix

Issue #1405 (fixed 'strand' issue)

Moved Bio::DB::GenBank-specific params (seq_start, seq_stop, strand, complexity, no_redirect) to NCBIHelper for now; disabled complexity parameter for the time being

Added complexity tag for Bio::DB::GenBank

Added more (better!) warnings, docs on complexity

Added batch retrieval via epost; only accessible using get_seq_stream using GI's at the moment

Make postprocess_data NOOP (removed warnings); use format 'gbwithparts' to get contig files with features or 'fasta' for full sequences alone

Use $self->warn, not warn, for GenBank warnings

Changed or removed VERSION

Bio::DB::Query::GenBank

Use $self->warn, not warn, for GenBank warnings

Bio::DB::ReferenceI

Add Location and Reference RandomAccessI-like interfaces, SeqFeatureI-like one to be added

Bio::DB::Registry

Wiki address

Issue #2012 patch applied, tests pass

This warning shouldn't require a verbosity > 0, otherwise code can fail with no feedback at all

Make it clear we're using globals, declare them up top, and break up overly large main function into logical parts

Allow non-alphabetic chars in database names

Don't lc() the values taken from OBDA registry files

Corrected warning to not include the thing it was warning did not exist!

Bio::DB::SeqFeature

Renamed Bio::DB::SeqFeature::LazyTableFeature to Bio::DB::SeqFeature

More documentation

Fix for Issue #1830

Added more documentation to the GFF3 loader

Added methods to SeqFeature::Segment so that it acts more like a SeqFeature; fixed normalized subfeatures so that they remember what Store they come from, allowing them to fetch their underlying dna/protein and other cute tricks

Accelerate loading performance for humungous multisegmented features

Added a temporary "broken" adaptor to test radical modifications to the DBI::mysql adaptor

Fixed a bug in bio::db::seqfeature which prevented it from producing correct split locations

Fixed boundaries of parent target (in an alignment) to span boundaries of child targets

Fixed bugs: 1) load_id() again returns the load ID as documented; 2) get_SeqFeatures(@typelist) works with children that are inline, not just stored in normalized fashion

Bio::DB::SeqFeature::LazyFeature

Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects

Refactored redundant code; ready to doc

Began documentation for Bio::DB::SeqFeature::Store

Renamed Bio::DB::SeqFeature::LazyTableFeature to Bio::DB::SeqFeature

Renamed Bio::DB::SeqFeature::LazyFeature to Bio::DB::SeqFeature::NormalizedFeature

Bio::DB::SeqFeature::LazyTableFeature

Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects

Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down

Refactored redundant code; ready to doc

Finished documentation for Bio::DB::SeqFeature::Store; Removed Bio::DB::SeqFeature::Store::Cacher because its functionality has been folded into Bio::DB::SeqFeature::Store

Renamed Bio::DB::SeqFeature::LazyTableFeature to Bio::DB::SeqFeature

Bio::DB::SeqFeature::NormalizedFeature

Renamed Bio::DB::SeqFeature::LazyFeature to Bio::DB::SeqFeature::NormalizedFeature

More documentation

Fix for Issue #1830

Added documentation to Bio::DB::SeqFeature; fixed minor bugs in Bio::Graphics

Added more documentation to the GFF3 loader

Fixed syntax errors introduced by recent documentation!

Added a GFF3/SO-compatible gene glyph and made it possible to move labels to the left-hand side of the feature

Tweaking interface to work properly with gbrowse

Added methods to SeqFeature::Segment so that it acts more like a SeqFeature; fixed normalized subfeatures so that they remember what Store they come from, allowing them to fetch their underlying dna/protein and other cute tricks

Updated segments glyph so that it does not assume that features use aggregators

A number of bug fixes and features enhancements to support forthcoming gbrowse release

Various small fixes

Hacky workaround to compensate for the fact that some Bio::DasI adaptors reutrn a string for seq() and others return Bio::PrimarySeq

Added regression tests for Bio::DB::SeqFeature::Store (memory,bdb + mysql)

Fixed boundaries of parent target (in an alignment) to span boundaries of child targets

Fixed bugs: 1) load_id() again returns the load ID as documented; 2) get_SeqFeatures(@typelist) works with children that are inline, not just stored in normalized fashion

Output of gff3_string() method now matches input to GFF3 loader

##Index-subfeatures meta command now case-insensitive; fixed issue with gff3 dumping not matching ID and Parent fields correctly

Never dump load_id and parent_id attributes -- these will cause confusion down the line

Fixed mixing of numeric and symbolic strand notations

Fixed handling of GFF3 printing so that the GFF3 output file matches the input file.

Bio::DB::SeqFeature::NormalizedFeatureI

Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects

Added more documentation to the GFF3 loader

Bio::DB::SeqFeature::NormalizedTableFeatureI

Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects

Added more documentation to the GFF3 loader

Bio::DB::SeqFeature::Segment

Oops, need this file to work

Refactored redundant code; ready to doc

Renamed Bio::DB::SeqFeature::LazyTableFeature to Bio::DB::SeqFeature

Added a GFF3/SO-compatible gene glyph and made it possible to move labels to the left-hand side of the feature

Tweaking interface to work properly with gbrowse

Added methods to SeqFeature::Segment so that it acts more like a SeqFeature; fixed normalized subfeatures so that they remember what Store they come from, allowing them to fetch their underlying dna/protein and other cute tricks

Updated segments glyph so that it does not assume that features use aggregators

A number of bug fixes and features enhancements to support forthcoming gbrowse release

Various small fixes

Added in-memory adaptor - seems to work fine with gbrowse

Segment->features() now behaves properly when given a list (not an array ref) of feature types

Fixed problem that was causing Bio::DB::SeqFeature::Store->segments() to return multiple segments of identical length

Added methods needed by BatchDumper.pm module of gbrowse

Created a fallback overload to avoid cmp functions failing mysteriously

Created a fallback overload to avoid cmp functions failing mysteriously

Bio::DB::SeqFeature::Store

Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects

Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down

Refactored redundant code; ready to doc

Began documentation for Bio::DB::SeqFeature::Store

Fixed a problem with combined attribute/location queries, but made query ugly

Added more documentation

Added LRU caching to the scheme

Finished documentation for Bio::DB::SeqFeature::Store; Removed Bio::DB::SeqFeature::Store::Cacher because its functionality has been folded into Bio::DB::SeqFeature::Store

Renamed Bio::DB::SeqFeature::LazyTableFeature to Bio::DB::SeqFeature

More documentation

Fix for Issue #1830

Added more documentation to the GFF3 loader

Added a GFF3/SO-compatible gene glyph and made it possible to move labels to the left-hand side of the feature

Tweaking interface to work properly with gbrowse

Added methods to SeqFeature::Segment so that it acts more like a SeqFeature; fixed normalized subfeatures so that they remember what Store they come from, allowing them to fetch their underlying dna/protein and other cute tricks

Fixed a bug which prevented the search_notes() feature from returning any results

Added in-memory adaptor - seems to work fine with gbrowse

Berkeleydb adaptor is functional; added compress option to reduce database size

Full tie() interface supported

Added a temporary "broken" adaptor to test radical modifications to the DBI::mysql adaptor

Fixed problem that was causing Bio::DB::SeqFeature::Store->segments() to return multiple segments of identical length

Added regression tests for Bio::DB::SeqFeature::Store (memory,bdb + mysql)

Added Bio::DB::SeqFeature::Store can now create Bio::PrimarySeq objects directly when requested

Use Storable::nfreeze rather than Storable::freeze for saving feature data to allow freeze/thaw across platforms (e.g. x86 / SPARC / PPC). [malcook]

Should now be able to serialize & deserialize features that contain CODE references, such as Bio::Root::Root cleanup procedures

Bio::Graphics::Glyph::Segments -- improved realignment and display of gaps; Bio::DB::SeqFeature::Store -- handle features that contain CODE references

Bio::DB::SeqFeature::Store::Cacher

Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects

Finished documentation for Bio::DB::SeqFeature::Store; Removed Bio::DB::SeqFeature::Store::Cacher because its functionality has been folded into Bio::DB::SeqFeature::Store

Bio::DB::SeqFeature::Store::DBI::Iterator

Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects

Bio::DB::SeqFeature::Store::DBI::broken

Added a temporary "broken" adaptor to test radical modifications to the DBI::mysql adaptor

Removed DBI::broken adaptor because it is now working and code transferred to DBI::mysql

Bio::DB::SeqFeature::Store::DBI::mysql

Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects

Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down

Began documentation for Bio::DB::SeqFeature::Store

Fixed a problem with combined attribute/location queries, but made query ugly

Added more documentation

Finished documentation for Bio::DB::SeqFeature::Store; Removed Bio::DB::SeqFeature::Store::Cacher because its functionality has been folded into Bio::DB::SeqFeature::Store

Fix for Issue #1830

Some, but not all, documentation for mysql adaptor

Fixed syntax errors introduced by recent documentation!

Added a GFF3/SO-compatible gene glyph and made it possible to move labels to the left-hand side of the feature

Tweaking interface to work properly with gbrowse

Fixed a bug which prevented the search_notes() feature from returning any results

Various small fixes

Added in-memory adaptor - seems to work fine with gbrowse

Berkeleydb implementation now working; not extensively tested

Accelerate loading performance for humungous multisegmented features

Fixed exception that occured when loading a FASTA file only

Setting -vertical_spacing to zero now suppresses span lines

Performance improvements to DBI::mysql adaptor; ALL PREVIOUS DATABASE LOADS ARE INVALID AND WILL HAVE TO BE RELOADED

Removed annoying debugging messages

Added regression tests for Bio::DB::SeqFeature::Store (memory,bdb + mysql)

Target attributes now automatically become display names; replaced "or die" with "throw"

Insure that STH is finish-ed before returing from these functions

Accepted Jason's changes to quelch statement handler still active warnings

Bio::DB::SeqFeature::Store::GFF3Loader

Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects

Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down

Refactored redundant code; ready to doc

Began documentation for Bio::DB::SeqFeature::Store

Renamed Bio::DB::SeqFeature::LazyTableFeature to Bio::DB::SeqFeature

Added more documentation to the GFF3 loader

Some, but not all, documentation for mysql adaptor

Tweaking interface to work properly with gbrowse

Added draw_dna and draw_protein options to the generic glyph

Added documentation to the gene glyph and made "gray" a synonym for "grey" in the Bio::Graphics::Panel color list

Added in-memory adaptor - seems to work fine with gbrowse

Implementation of Bio::DB::SeqFeature::Store in BerkeleyDB databases; syntax checked but not tested in any other way

Full tie() interface supported

Accelerate loading performance for humungous multisegmented features

Setting -vertical_spacing to zero now suppresses span lines

Added regression tests for Bio::DB::SeqFeature::Store (memory,bdb + mysql)

Test GFF3 file now passes validation tests at http://dev.wormbase.org/db/validate_gff3/validate_gff3_online

Target attributes now automatically become display names; replaced "or die" with "throw"

Fixed boundaries of parent target (in an alignment) to span boundaries of child targets

Target coordinates work properly now

Fixed bugs: 1) load_id() again returns the load ID as documented; 2) get_SeqFeatures(@typelist) works with children that are inline, not just stored in normalized fashion

##Index-subfeatures meta command now case-insensitive; fixed issue with gff3 dumping not matching ID and Parent fields correctly

Replaced complex CGI::Util::escape routine with a simpler one that respects + characters

Bio::DB::SeqFeature::Store::bdb

Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects

Finished documentation for Bio::DB::SeqFeature::Store; Removed Bio::DB::SeqFeature::Store::Cacher because its functionality has been folded into Bio::DB::SeqFeature::Store

Added in-memory adaptor - seems to work fine with gbrowse

Adding short description

Bio::DB::SeqFeature::Store::berkeleydb

Implementation of Bio::DB::SeqFeature::Store in BerkeleyDB databases; syntax checked but not tested in any other way

Berkeleydb adaptor is functional; added compress option to reduce database size

Berkeleydb implementation now working; not extensively tested

Added missing search_by_attribute() functionality

Full tie() interface supported

Added regression tests for Bio::DB::SeqFeature::Store (memory,bdb + mysql)

Target attributes now automatically become display names; replaced "or die" with "throw"

Fix BioDBSeqfeature bug; passes tests, but still have temp file problems...

Saved too early; added regex for win32

Fixed bug which caused the Bio::DB::SeqFeature::berkeleydb regression test to fail with a "./features.idx not found" error

Fixed bug which caused the Bio::DB::SeqFeature::berkeleydb regression test to fail with a "./features.idx not found" error

Bio::DB::SeqFeature::Store::memory

Added in-memory adaptor - seems to work fine with gbrowse

Implementation of Bio::DB::SeqFeature::Store in BerkeleyDB databases; syntax checked but not tested in any other way

Berkeleydb implementation now working; not extensively tested

Added missing search_by_attribute() functionality

Full tie() interface supported

Added regression tests for Bio::DB::SeqFeature::Store (memory,bdb + mysql)

Target attributes now automatically become display names; replaced "or die" with "throw"

Target coordinates work properly now

Bio::DB::SeqHound

Made (env_proxy => 1) the default for LWP::UserAgent instantiations

_init_SeqHound returns FALSE on failure, removed uninformative warning and plain print statement, added informative warning

Converted hidden 'log file name' to class variable and use $self->debug instead of 'print STDERR';

Do not alter users verbosity

Bio::DB::SeqI

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::DB::SeqVersion

Add DB::SeqVersion files. These serve to query NCBI's Revision History page but they could probably be modified to accomodate other databases without too much difficulty.

Email changed

Remove unused regexp capture

Use clearer lc() instead of "\L"

Remove unused global variable $MODVERSION

Migrated to Bio::WebAgent from Bio::HTTPGet and added more error checking; now works with authenticating proxies. Partial fix to Issue #2110.

Bio::DB::SeqVersion::gi

How was this deleted from CVS?

Remove unused global variable $ua.

Remove unused global variable $MODVERSION

Removed redundant "if $self->verbose" suffix from "$self->debug()" calls

Migrated to Bio::WebAgent from Bio::HTTPGet and added more error checking; now works with authenticating proxies. Partial fix to Issue #2110.

Bio::DB::SwissProt

Changed EBI default database to UniProtKB

Bio::DB::Taxonomy

Taxa->taxon

Doc fixes, and as per addendum to Issue #2047

Documentation clarification, significantly, get_Taxonomy_Node returns a Bio::Taxonomy::Node, not a Taxon

Bio::Taxonomy overhaul, see Issue #2061

Can now recursively fetch all descendents

Bio::DB::Taxonomy::entrez

As per Issue #2047

Doc fixes, and as per addendum to Issue #2047

Documentation clarification, significantly, get_Taxonomy_Node returns a Bio::Taxonomy::Node, not a Taxon

Bio::Taxonomy overhaul, see Issue #2061

Now a Bio::WebAgent instead of a Bio::Root::HTTPget, allowing proxys to work

Possible fix for Issue #1938: ncbi_taxid() is no longer a direct synonym of id(), only returning if ncbi_taxid had been set

Bio::DB::Taxonomy::flatfile

As per Issue #2047

Doc fixes, and as per addendum to Issue #2047

Documentation clarification, significantly, get_Taxonomy_Node returns a Bio::Taxonomy::Node, not a Taxon

Bio::Taxonomy overhaul, see Issue #2061

Return immediately from get_taxon if supplied a taxonid no in db

Return immediately from get_taxon if supplied a taxonid no in db

Possible fix for Issue #1938: ncbi_taxid() is no longer a direct synonym of id(), only returning if ncbi_taxid had been set

Bio::DB::Taxonomy::list

Bio::Taxonomy overhaul, see Issue #2061

Improved throw messages, can handle consecutive nodes with the same name in the same supplied lineage

Corrected detection of most appropriate throw message

Put the bad lineage and throw in the correct place. there is still a memory leak problem

Possible fix for Issue #1938: ncbi_taxid() is no longer a direct synonym of id(), only returning if ncbi_taxid had been set

Bio::DB::WebDBSeqI

Issue #1405

Removed old email bug reporting address.

Made (env_proxy => 1) the default for LWP::UserAgent instantiations

Issue #1405 (fixed 'strand' issue)

Moved Bio::DB::GenBank-specific params (seq_start, seq_stop, strand, complexity, no_redirect) to NCBIHelper for now; disabled complexity parameter for the time being

Added complexity tag for Bio::DB::GenBank

Added more (better!) warnings, docs on complexity

Use $self->isa, not m//

STREAM could fall out of scope, closing filehandle in returned SeqIO, preventing sequence reads; should be fixed

Issue #2104, may be rolled back if tests on other OS's do not pass

Replaced '/dev/null' with File::Spec->devnull

Bio::Expression::Contact

Adding support to screenscrape ncbi GEO

Updates to parsing code and lazy loading of object attributes

Fixed broken _initialize() docs.

Bio::Expression::DataSet

Adding support to screenscrape ncbi GEO

Fixed broken _initialize() docs.

Bio::Expression::Platform

Adding support to screenscrape ncbi GEO

Updates to parsing code and lazy loading of object attributes

Fixed _initialize() docs

Bio::Expression::Sample

Adding support to screenscrape ncbi GEO

Fixed broken _initialize() docs.

Bio::Factory::DriverFactory

Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.

Bio::Factory::FTLocationFactory

Issue #1754, Florian enhancement to include UNCERTAIN values. Patch did not go in cleanly, needed to hand-coded. Documentation changed

Fixed spacing for future bugfix

Refactored from_string() for full recursion, get rid of $`, $&, $' (bad!!!)

Reverting this back to 1.22, and turning off debugging

Refactored code now passes all tests; let others try it out

Bio::FeatureIO

Syntactic changes to code and documentation needed to compsenate for what seemed to be quick cutting and pasting from the SeqIO module.

Fixed the (presumably untested) tied hash interface which was using code cut&pasted from SeqIO, calling next_seq and write_seq instead of next_feature and write_feature

Added .ptt to _guess_format()

Bio::FeatureIO::bed

Use $feature->end instead of $feature->stop to avoid error: Can't locate object method "stop" via package "Bio::SeqFeature::Annotated" at ..//Bio/FeatureIO/bed.pm line 163.

Improved NAME, SYNOPSIS, DESCRIPTION docs

Bio::FeatureIO::gff

Adding support for Derives_from tag, which is relatively new to the GFF3 spec

Allow Bio::FeatureIO::gff to return the cigar string as a SimpleValue; modified tests to bring in a gff line with a Gap attribute to test that it successfully parses that attribute.

Fixing Target attribute string parsing. Previously, valid postitive strand '+'s were being dropped. Valid strings include: Target=AB1234+1+199 and Target=AB1234 1 199 + but not Target=AB1234+1+199++ because that just plain looks silly. If anyone (ie, Lincoln) complains, I may reconsider this position.

Minor fixes for writing gff3

Cleaning up a mess cause by me editting and commit an old version of this file

Issue #2071

Added a nasty message and a throw if someone violates the GFF3 spec with their tags (before the data was being silently thrown away; which would you prefer?)

Improved NAME, SYNOPSIS, DESCRIPTION docs

Thought I committed this a few months ago; minor addition to add Index tag to the list a acceptable reserved tags

Comment fix

Bio::FeatureIO::interpro

Improved NAME, SYNOPSIS, DESCRIPTION docs

Bio::FeatureIO::ptt

Added read support for NCBI "PTT" protein table feature files.

Return from next_feature early if not in reading mode

Bio::Graph::Edge

Remove duplicate files

Add back Graph files after clean-up

Bio::Graph::IO

Remove duplicate files

Add back Graph files after clean-up

Bio::Graph::IO::dip

Remove duplicate files

Add back Graph files after clean-up

Bio::Graph::IO::psi_xml

HPRD PSI XML has no fullName, use shortLabel for description instead

Remove debugging code

psi_xml graph now destroyed properly

Duplicate lines

Remove duplicate files

Add back Graph files after clean-up

Make friendlier with new Bio::Species

Adding short description

Removed 'Bio::Root::Object' from base class list; all t/protgraph.t tests pass.

Bio::Graph::ProteinGraph

Remove duplicate files

Add back Graph files after clean-up

Bio::Graph::SimpleGraph

Remove duplicate files

Add back Graph files after clean-up

Adding short description

Bio::Graph::SimpleGraph::Traversal

Remove duplicate files

Add back Graph files after clean-up

Adding short description

Bio::Graphics

Fixed synopsis so that it works!

Bio::Graphics::Feature

Made Bio::Graphics::Feature more SeqFeature-compliant

Documented that maxfeature must be a power of 10

Fixed inconsistent behavior wrt "attributes()" and "abs_stop()" both of which are deprecated

Changes to make storable in GFF3 databases

Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down

Refactored redundant code; ready to doc

Bio::Graphics::FeatureBase

Refactored redundant code; ready to doc

Began documentation for Bio::DB::SeqFeature::Store

Fixed dna and cds glyphs so that letters are correctly aligned to right side of base tick when in flip orientation

Tweaking interface to work properly with gbrowse

Updated segments glyph so that it does not assume that features use aggregators

A number of bug fixes and features enhancements to support forthcoming gbrowse release

Major performance increases on xyplot; fixed(?) the cds/translation glyph disconnect

Added documentation to the gene glyph and made "gray" a synonym for "grey" in the Bio::Graphics::Panel color list

Various small fixes

Added in-memory adaptor - seems to work fine with gbrowse

Fix possible uninitialized value in numeric comparisons

Added methods needed by BatchDumper.pm module of gbrowse

Target coordinates work properly now

Output of gff3_string() method now matches input to GFF3 loader

Sigh; yet another problem with GFF3 dumping squashed

Added version flag for gff3 dumping

Fixed handling of GFF3 printing so that the GFF3 output file matches the input file.

Fixed handling of GFF3 writing so that the formatting of features tied together by a single shared ID is not transformed into a object with a parent and multiple children

Quenched "masks earlier declaration" warning

Created a fallback overload to avoid cmp functions failing mysteriously

Bio::Graphics::FeatureFile

Fixed bad interactions between FeatureFile and Bio::DB::GFF

Made FeatureFile work better with gff3 inputs

Changing search_notes method to allow wild cards to be passed in

Added sanity checks to featurefile parsing

Made featurefile robust against bad input data

Added documentation to Bio::DB::SeqFeature; fixed minor bugs in Bio::Graphics

Fix possible uninitialized value in numeric comparisons

Made the API to get the box around the track keys more like the regular boxes() API

Supressed "uninitialized value in hash element" warning

Changed parser to avoid breaking when lines have trailing comments: bgcolor = blue # my favorite color

Cganhed regex to spare hex colors from comment deletion

Bio::Graphics::Glyph

Fixed problem related to aliases not being searched in get_feature_by_name()

Changes to make storable in GFF3 databases

Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down

Removing a stray warn

Removed merged_segments() detection from glyph class because this was causing problems drawing ideograms

Adding an option to limit the number of subfeatures to get (useful when using chado and there are many levels and you only want one)

Added a GFF3/SO-compatible gene glyph and made it possible to move labels to the left-hand side of the feature

Updated segments glyph so that it does not assume that features use aggregators

Cleaned up interaction between padding and label position; however, three-part features (e.g. gene) are still adding an extra "additional_arrow_width" amount of left padding, which causes slightly inefficient padding.

A number of bug fixes and features enhancements to support forthcoming gbrowse release

Added draw_dna and draw_protein options to the generic glyph

Removed code that was causing noticeable performance losses

Major performance increases on xyplot; fixed(?) the cds/translation glyph disconnect

Adding an option to allow ignoring a subpart when drawing a glyph

Fixed more bugs in the cds glyph

Added documentation to the gene glyph and made "gray" a synonym for "grey" in the Bio::Graphics::Panel color list

Modifying the ignore subpart option to allow a space delimited list

Performance increases (maybe 1.5x) for gene glyph

Found and fixed place where padding of subparts were being counted twice

Setting -vertical_spacing to zero now suppresses span lines

Slight performance improvement on box calculations

Removed a restriction that was causing introns not to be drawn correctly when transcript too close to edge of panel

If the left and right borders of a box are on the same pixels, then move right border one pixel to right -- this fixes problems with imagemaps under IE

Restored the previous behavior of -box_subparts=>1 so that the subparts AND the whole feature are appropriately boxed

Generalized -box_subparts so that you can control the level of recursion exactly

Removed stray debugging statement

Allow codon table option to be either "codontable" or "geneticcode" for compatibility with the gbrowse Protein dumper

Test GFF3 file now passes validation tests at http://dev.wormbase.org/db/validate_gff3/validate_gff3_online

Fixed a bug in bio::db::seqfeature which prevented it from producing correct split locations

Added documentation about the new maxdepth() method to bio::graphics::glyph and friends

Replaced die() with throw()

If aligned segment is off at start or end, dash characters now added

If aligned segment is off at start or end, dash characters now added

Fixed aggregation issue

Fixed aggregation issue

Bio::Graphics::Glyph: fixed handling of aggregated features so that subfeatures will be recursed into by default; redgreen_box: made behave more like heterogeneous segments when color_subparts option turned on; xyplot.pm: fixed coordinates issue that caused the contents of all plots to be drawn at the same y offset

Bio::Graphics::Glyph: fixed handling of aggregated features so that subfeatures will be recursed into by default; redgreen_box: made behave more like heterogeneous segments when color_subparts option turned on; xyplot.pm: fixed coordinates issue that caused the contents of all plots to be drawn at the same y offset

Added a -filter callback to selectively display features

Added a -filter callback to selectively display features

Fixed minor bug which caused some features drawn with the "box" glyph to have an unexpected height

Fixed minor bug which caused some features drawn with the "box" glyph to have an unexpected height

Speculative change to fix behavior when zoomed way in on introns

Removed debugging warning

Removed debugging warning

Bio::Graphics::Glyph::Factory

Major performance increases on xyplot; fixed(?) the cds/translation glyph disconnect

Performance increases (maybe 1.5x) for gene glyph

Replaced die() with throw()

Bio::Graphics::Glyph::anchored_arrow

Exceedingly small logic error that blocked display of arrow for features extending off left of panel

Bio::Graphics::Glyph::arrow

Changed draw() to draw_component() for several glyphs in order to make them more easily subclassable

Removed unsigned from the fdata table so that start and end coordinates can take on negative values

Added a -label_intervals option to the arrow glyph

Workaround for roundoff errors in tick position calculation that cause major and minor ticks to sometimes not match by a pixel

Adding short description

Bio::Graphics::Glyph::box

Speculative change to fix behavior when zoomed way in on introns

Removed debugging warning

Bio::Graphics::Glyph::cds

Fixed dna and cds glyphs so that letters are correctly aligned to right side of base tick when in flip orientation

Fixed inconsistent representations of reading frame in dna, cds and translation glyphs

Added draw_dna and draw_protein options to the generic glyph

Cds and translation glyph working correctly forward and reverse strand, flipped and unflipped; all colors, translations and frame positions now consistent

Fixed more bugs in the cds glyph

Fixed bug that caused stray lines to be displayed when applying the filled arrow to a very narrow feature

Removing a redundant line

Added documentation to the gene glyph and made "gray" a synonym for "grey" in the Bio::Graphics::Panel color list

Hacky workaround to compensate for the fact that some Bio::DasI adaptors reutrn a string for seq() and others return Bio::PrimarySeq

Added a temporary "broken" adaptor to test radical modifications to the DBI::mysql adaptor

No setting of own $VERSION

Bio::Graphics::Glyph::dna

Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down

Dramatically simplified the logic of drawing minus strand DNA. LS must have been crazy when he wrote the original version

Fixed misalignment of reversec dna glyph and rescued missing grid lines that occur near ends of panel

Added draw_dna and draw_protein options to the generic glyph

Dna glyph wasn't observing flip flag when strand==0

Avoid gc window division by zero on small regions; fixed alignment glyph so that special case is for bio::db::gff::feature, not other way around

Bio::Graphics::Glyph::ex

Adding short description

Bio::Graphics::Glyph::flag

Adding short description

Bio::Graphics::Glyph::gene

Added a GFF3/SO-compatible gene glyph and made it possible to move labels to the left-hand side of the feature

Cleaned up interaction between padding and label position; however, three-part features (e.g. gene) are still adding an extra "additional_arrow_width" amount of left padding, which causes slightly inefficient padding.

Added draw_dna and draw_protein options to the generic glyph

Fixed bug that caused stray lines to be displayed when applying the filled arrow to a very narrow feature

Added documentation to the gene glyph and made "gray" a synonym for "grey" in the Bio::Graphics::Panel color list

Added in-memory adaptor - seems to work fine with gbrowse

Adding a sub_part option to the gene glyph, to allow specifying exons be used to build transcripts.

Performance increases (maybe 1.5x) for gene glyph

Found and fixed place where padding of subparts were being counted twice

Setting -vertical_spacing to zero now suppresses span lines

Bio::Graphics::Glyph::generic

Dramatically simplified the logic of drawing minus strand DNA. LS must have been crazy when he wrote the original version

Added a GFF3/SO-compatible gene glyph and made it possible to move labels to the left-hand side of the feature

Cleaned up interaction between padding and label position; however, three-part features (e.g. gene) are still adding an extra "additional_arrow_width" amount of left padding, which causes slightly inefficient padding.

A number of bug fixes and features enhancements to support forthcoming gbrowse release

Added draw_dna and draw_protein options to the generic glyph

Hacky workaround to compensate for the fact that some Bio::DasI adaptors reutrn a string for seq() and others return Bio::PrimarySeq

Found and fixed place where padding of subparts were being counted twice

Added a temporary "broken" adaptor to test radical modifications to the DBI::mysql adaptor

Fixed problem with segments glyph not showing target DNA / multiple alignments due to Bio::DB::GFF::Feature API change

Sorted out confusion between -canonical_strand and -true_target

Added documentation about the new maxdepth() method to bio::graphics::glyph and friends

Fixed minor bug which caused some features drawn with the "box" glyph to have an unexpected height

Fixed minor bug which caused some features drawn with the "box" glyph to have an unexpected height

Speculative change to fix behavior when zoomed way in on introns

Removed debugging warning

Bio::Graphics::Glyph::group

Cleaned up interaction between padding and label position; however, three-part features (e.g. gene) are still adding an extra "additional_arrow_width" amount of left padding, which causes slightly inefficient padding.

Bio::Graphics::Glyph::heterogeneous_segments

Heterogeneous segments glyph was invoking the graded_segments draw() method, thereby wiping out its calculation of part colors

The -merge_parts option was preventing heterogeneous segments from drawing properly

Bio::Graphics::Glyph::image

Added a glyph that will paste photographic images onto the sequence display

Made (env_proxy => 1) the default for LWP::UserAgent instantiations

Setting -vertical_spacing to zero now suppresses span lines

Replaced die() with throw()

Bio::Graphics::Glyph::lightning

Added an option to make the lightning bolt point upward

Bio::Graphics::Glyph::line

Changed draw() to draw_component() for several glyphs in order to make them more easily subclassable

Bio::Graphics::Glyph::merge_parts

Adding short description

Bio::Graphics::Glyph::primers

Changed draw() to draw_component() for several glyphs in order to make them more easily subclassable

Added option to control line thickness

Bio::Graphics::Glyph::processed_transcript

Folded in Don Gilbert\'s patch that prevents exons from getting clipped to oblivion

Added documentation to the gene glyph and made "gray" a synonym for "grey" in the Bio::Graphics::Panel color list

Setting -vertical_spacing to zero now suppresses span lines

Bio::Graphics::Glyph::protein

Initial Kyte-Doolittle hydropathy plot glyph

Now it works, enjoy

Bio::Graphics::Glyph::redgreen_box

Bio::Graphics::Glyph: fixed handling of aggregated features so that subfeatures will be recursed into by default; redgreen_box: made behave more like heterogeneous segments when color_subparts option turned on; xyplot.pm: fixed coordinates issue that caused the contents of all plots to be drawn at the same y offset

Bio::Graphics::Glyph: fixed handling of aggregated features so that subfeatures will be recursed into by default; redgreen_box: made behave more like heterogeneous segments when color_subparts option turned on; xyplot.pm: fixed coordinates issue that caused the contents of all plots to be drawn at the same y offset

Bio::Graphics::Glyph::ruler_arrow

Adding short description

Bio::Graphics::Glyph::segments

Cleaned up interaction between padding and label position; however, three-part features (e.g. gene) are still adding an extra "additional_arrow_width" amount of left padding, which causes slightly inefficient padding.

A number of bug fixes and features enhancements to support forthcoming gbrowse release

Added draw_dna and draw_protein options to the generic glyph

Fixed problem with segments glyph not showing target DNA / multiple alignments due to Bio::DB::GFF::Feature API change

Sorted out confusion between -canonical_strand and -true_target

Workaround for chado adaptor

Added documentation about the new maxdepth() method to bio::graphics::glyph and friends

Improved the way that mismatched bases are drawn. New option -mismatch_color

Fixed boundaries of parent target (in an alignment) to span boundaries of child targets

Avoid gc window division by zero on small regions; fixed alignment glyph so that special case is for bio::db::gff::feature, not other way around

Added protein alignments to segments glyph (experimental)

Realign=1 now forces realignment with dynamic programming aligner; slows it down some, but results are more satisfactory

Bio::Graphics::Glyph::Segments -- improved realignment and display of gaps; Bio::DB::SeqFeature::Store -- handle features that contain CODE references

If aligned segment is off at start or end, dash characters now added

If aligned segment is off at start or end, dash characters now added

Created a fallback overload to avoid cmp functions failing mysteriously

Multiple alignments now accomodate a data bug in which target start < end

Multiple alignments now accomodate a data bug in which target start < end

Bio::Graphics::Glyph::so_transcript

No setting of own $VERSION

Bio::Graphics::Glyph::three_letters

Adding short description

Bio::Graphics::Glyph::transcript

Added a GFF3/SO-compatible gene glyph and made it possible to move labels to the left-hand side of the feature

Cleaned up interaction between padding and label position; however, three-part features (e.g. gene) are still adding an extra "additional_arrow_width" amount of left padding, which causes slightly inefficient padding.

Added draw_dna and draw_protein options to the generic glyph

Setting -vertical_spacing to zero now suppresses span lines

Bio::Graphics::Glyph::transcript2

Fixed problem related to aliases not being searched in get_feature_by_name()

Removed stray debugging statement

Added a GFF3/SO-compatible gene glyph and made it possible to move labels to the left-hand side of the feature

Cleaned up interaction between padding and label position; however, three-part features (e.g. gene) are still adding an extra "additional_arrow_width" amount of left padding, which causes slightly inefficient padding.

Added draw_dna and draw_protein options to the generic glyph

Setting -vertical_spacing to zero now suppresses span lines

Bio::Graphics::Glyph::translation

Fixed dna and cds glyphs so that letters are correctly aligned to right side of base tick when in flip orientation

Fixed inconsistent representations of reading frame in dna, cds and translation glyphs

Added methods to SeqFeature::Segment so that it acts more like a SeqFeature; fixed normalized subfeatures so that they remember what Store they come from, allowing them to fetch their underlying dna/protein and other cute tricks

Removed stray debugging message in translation glyph

Added draw_dna and draw_protein options to the generic glyph

Removed code that was causing noticeable performance losses

Major performance increases on xyplot; fixed(?) the cds/translation glyph disconnect

Fixed logic bug in dna retrieval

Removing a stray debugging statement

Maybe fixed reverse complement - needs testing

Cds and translation glyph working correctly forward and reverse strand, flipped and unflipped; all colors, translations and frame positions now consistent

Fixed more bugs in the cds glyph

Hacky workaround to compensate for the fact that some Bio::DasI adaptors reutrn a string for seq() and others return Bio::PrimarySeq

Fix to stop drawing translation key glyphs 'beneath' from crashing the panel

Allow codon table option to be either "codontable" or "geneticcode" for compatibility with the gbrowse Protein dumper

No setting of own $VERSION

Bio::Graphics::Glyph::xyplot

Fix for Issue #1830

Cleaned up interaction between padding and label position; however, three-part features (e.g. gene) are still adding an extra "additional_arrow_width" amount of left padding, which causes slightly inefficient padding.

Removed code that was causing noticeable performance losses

Major performance increases on xyplot; fixed(?) the cds/translation glyph disconnect

Bio::Graphics::Glyph: fixed handling of aggregated features so that subfeatures will be recursed into by default; redgreen_box: made behave more like heterogeneous segments when color_subparts option turned on; xyplot.pm: fixed coordinates issue that caused the contents of all plots to be drawn at the same y offset

Bio::Graphics::Glyph: fixed handling of aggregated features so that subfeatures will be recursed into by default; redgreen_box: made behave more like heterogeneous segments when color_subparts option turned on; xyplot.pm: fixed coordinates issue that caused the contents of all plots to be drawn at the same y offset

Bio::Graphics::Panel

Fixed sort_order documentation

Bio::DB::GFF was *unable* to parse GFF3 files; fixed this bad bug

Removed unsigned from the fdata table so that start and end coordinates can take on negative values

Updating version in Panel for GBrowse patch awareness

Bumping api version for gbrowse

Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down

Fixed misalignment of reversec dna glyph and rescued missing grid lines that occur near ends of panel

Ripped out thread sharing stuff, which isn't working

Fixed inconsistent representations of reading frame in dna, cds and translation glyphs

Fixed more bugs in the cds glyph

Added documentation to the gene glyph and made "gray" a synonym for "grey" in the Bio::Graphics::Panel color list

Fixed problem in which full color range was not utilized in truecolor images

Bumping biographics api version in prep for a gbrowse release

Added a method for getting the rectangles around the track labels

Made the API to get the box around the track keys more like the regular boxes() API

Generalized -box_subparts so that you can control the level of recursion exactly

Replaced die() with throw()

Added option to extend grid into pad top and pad bottom regions; this is useful when placing images top to bottom

Added option to extend grid into pad top and pad bottom regions; this is useful when placing images top to bottom

Added a -filter callback to selectively display features

Added a -filter callback to selectively display features

Bio::Graphics::Pictogram

Adding short description

Bio::Graphics::Util

Fixed inconsistent representations of reading frame in dna, cds and translation glyphs

Adding short description

Bio::Index::Abstract

Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Removed redundant "if $self->verbose" suffix from "$self->debug()" calls

Replaced warn "" with $self->warn("")

Changed warn() to debug() as more appropriate.

Bio::Index::AbstractSeq

Issue #1989 - don't reset the primary_id if it is a GI number

Issue #2049; committed patches from Robert Buels - need to add warnings for nonexistent IDs

Doc fix

Bio::Index::Blast

Throw, not die

Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}

Fixed uninitialized value in join or string emerging from test script

No setting of own $VERSION

Bio::Index::EMBL

Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}

Bio::Index::Fasta

Refer to online Bioperl Tutorial

Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}

Bio::Index::Fastq

Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}

Bio::Index::GenBank

Remove redundancy in collection accession numbers

Prevents indexing of the same sequence by the same id more than once

Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}

Bio::Index::Hmmer

Throw, not die

Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}

No setting of own $VERSION

Bio::Index::Qual

Refer to online Bioperl Tutorial

Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}

Bio::Index::SwissPfam

Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}

Bio::Index::Swissprot

New address

Make it a bit clearer that there are 2 scripts here

Prevents indexing of the same sequence by the same id more than once

Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}

Email changed

Bio::LiveSeq::IO::Loader

Removed unused and outdated Bio::LiveSeq::IO::SRS class from the distribution

Bio::LiveSeq::IO::README

Removed unused and outdated Bio::LiveSeq::IO::SRS class from the distribution

Bio::LiveSeq::IO::SRS

Removed unused and outdated Bio::LiveSeq::IO::SRS class from the distribution

Bio::LiveSeq::Mutator

Issue #1701

Bio::Location::Atomic

Convert use vars to our; small Issue #2101- can't treat remote locations differently with strand()

Bio::Location::Fuzzy

Issue #1754, Florian enhancement to include UNCERTAIN values. Patch went in cleanly, documentation changed

Realign synopsis code

Bug 992

Convert use vars to our; small Issue #2101- can't treat remote locations differently with strand()

Bio::Location::FuzzyLocationI

Convert use vars to our; small Issue #2101- can't treat remote locations differently with strand()

Bio::Location::Simple

Convert use vars to our; small Issue #2101- can't treat remote locations differently with strand()

Bio::Location::Split

Change to_FTstring to work even if the split location contain only a single sublocation. Previously, it did not correctly complement in this case. In general practice split locations won't only contain a single sublocation, unless you write code that treats all features added to a sequence 'equally' and thus adds them all as Split features.

Obfuscation is fun

Issue #2008

Added comments pertaining to Issue #1952; need to work out what's going wrong here

Convert use vars to our; small Issue #2101- can't treat remote locations differently with strand()

Issue #2101 (tentative fix)

Updating from HEAD (Issue #2101)

Remove redundant sub_Location_by_order()

Bio::Map::Clone

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

Bio::Map::Contig

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

Bio::Map::CytoMap

First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

Bio::Map::CytoMarker

As per Issue #2028

Doc update and use tidy; CytoPosition no longer a Bio::Variation::VariantI

First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

Bio::Map::CytoPosition

Removed questionable 'undef' r-value on my() array assignment.

Replaced die() with throw()

As per Issue #2028

Doc update and use tidy; CytoPosition no longer a Bio::Variation::VariantI

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

You can no longer set numeric

Bio::Map::EntityI

Bio::Map objects are now EntityIs

Corrected inheritance and new() args for PositionHandler and Mappable

The core Map modules can now cope with relative positions

Bio::Map::FPCMarker

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

New tests and bugfixes from Will Nelson

Bio::Map::LinkageMap

First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

Bio::Map::LinkagePosition

First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

Bio::Map::MapI

First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

Corrected inheritance and new() args for PositionHandler and Mappable

The core Map modules can now cope with relative positions

Minor tweaks. Mappables are now AnnotatableIs

Do not directly return a sort

Precompute sort values when they involve subroutine calls for efficiency and to avoid bugs

Major bug fixes and API change for overlap-related methods

Bio::Map::Mappable

First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

Corrected inheritance and new() args for PositionHandler and Mappable

The core Map modules can now cope with relative positions

Minor tweaks. Mappables are now AnnotatableIs

Accept and handle -name and -id

Precompute sort values when they involve subroutine calls for efficiency and to avoid bugs

Major bug fixes and API change for overlap-related methods

Speed up and bugfixes for disconnected_*

Bio::Map::MappableI

First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

Corrected inheritance and new() args for PositionHandler and Mappable

The core Map modules can now cope with relative positions

Minor tweaks. Mappables are now AnnotatableIs

Do not directly return a sort, option for unsorted position retrieval

Precompute sort values when they involve subroutine calls for efficiency and to avoid bugs

Bio::Map::Marker

Issue #1998 : Added Sendu Bala's Bio::Map modifications and tests

Added CVS tag

As per Issue #2028

First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

The core Map modules can now cope with relative positions

Minor tweaks. Mappables are now AnnotatableIs

Bio::Map::MarkerI

First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

The core Map modules can now cope with relative positions

Minor tweaks. Mappables are now AnnotatableIs

Bio::Map::Microsatellite

First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

Bio::Map::OrderedPosition

First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

Corrected inheritance and new() args for PositionHandler and Mappable

The core Map modules can now cope with relative positions

Bio::Map::OrderedPositionWithDistance

First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

Bio::Map::Physical

Cleanup doc versus implementation consistency

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

New tests and bugfixes from Will Nelson

Bio::Map::Position

Issue #1998 : Added Sendu Bala's Bio::Map modifications and tests

As per Issue #2028

First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

The core Map modules can now cope with relative positions

Length() now settable, new absolute_relative method, tweaks and bug fixes

Major bug fixes and API change for overlap-related methods

Bio::Map::PositionHandler

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

Corrected inheritance and new() args for PositionHandler and Mappable

The core Map modules can now cope with relative positions

Bug fix for purging when position supplied

Bio::Map::PositionHandlerI

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

The core Map modules can now cope with relative positions

Bio::Map::PositionI

Issue #1998 : Added Sendu Bala's Bio::Map modifications and tests

First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

Corrected inheritance and new() args for PositionHandler and Mappable

The core Map modules can now cope with relative positions

Precompute sort values when they involve subroutine calls for efficiency and to avoid bugs

Major bug fixes and API change for overlap-related methods

Speed up and bugfixes for disconnected_*

Bio::Map::Relative

The core Map modules can now cope with relative positions

Minor tweaks. Mappables are now AnnotatableIs

Bio::Map::RelativeI

The core Map modules can now cope with relative positions

Minor tweaks. Mappables are now AnnotatableIs

Bio::Map::SimpleMap

First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works

Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules

Corrected inheritance and new() args for PositionHandler and Mappable

The core Map modules can now cope with relative positions

Minor tweaks. Mappables are now AnnotatableIs

Do not directly return a sort

Precompute sort values when they involve subroutine calls for efficiency and to avoid bugs

Bio::MapIO::fpc

Issue #1952

New tests and bugfixes from Will Nelson

Bio::MapIO::mapmaker

Fixed missing marker, Issue #1890, but additional work may be necessary, depending on how the module is used

Multiple maps

Bio::Matrix::Generic

Fix remove_column

Correct name

Synopsis snafu

Bio::Matrix::PSM::IO::mast

Gao Ge Issue #1900

Gao Ge Issue #1901

Issue #1905 + plus additional checks

Edits

Handle nuc DB and protein motif query+frames

Bio::Matrix::PSM::IO::masta

Correction for 0 in SiteMatrix not required and invalid; resulted in wrong frequencies, IUPAC, consensus and regex. Now all fixed, and tests corrected to expect the correct answers

Bio::Matrix::PSM::IO::transfac

Actually get the dbid when parsing references

Bio::Matrix::PSM::InstanceSite

Gao Ge Issue #1901

Added frame, which may be necessary if the motif was protein, but the DB is nucleic acid

Bio::Matrix::PSM::ProtMatrix

Throw, not die

Bio::Matrix::PSM::SiteMatrix

Throw, not die

Bug: chop chokes so split is better here, bug found by Elodie Portales, UBC

Correction for 0 in SiteMatrix not required and invalid; resulted in wrong frequencies, IUPAC, consensus and regex. Now all fixed, and tests corrected to expect the correct answers

Option to do pseudocount correction, threshold for IUPAC, test expectations updated with new behaviour in mind

Improved docs to explain the consensus-related methods, changed default significance level of IUPAC method to 95%, allowed changing of the thresholds of consensus() and IUPAC() to be independant of each other

Added sites(), a method to get/set one of the attributes you can set in new()

Regexp methods now output regexps that will match sequences with ambiguity codes in them, and also now works when the regexp is supposed to include an N; sequence_match_weight now works with mixed-case input sequences and warns about inputs with ambiguity codes

Bio::Matrix::PSM::SiteMatrixI

Made (more) consistent with SiteMatrix.pm

Bio::Ontology::DocumentRegistry

Fixing URL for so ontology files due to SourceForge's server reorg

Bio::Ontology::OBOEngine

Adding OBO-format ontology parser by Sohel Merchant.

MIgrated all the methods from SimpleGOEngine to this module.

New method: find_similar_terms() that finds term instances where name or synonym or part of one matches the query

Find_similar_terms(): documentaion updated. Note that the argument is a term, not names parameters

New method find_identically_named_terms(), there are now three methods for searching on ontology with a term object

Bio::Ontology::OBOterm

Adding OBO-format ontology parser by Sohel Merchant.

Moved the has_dblink method to Term object

Bio::Ontology::Ontology

Must have get_relationship_type - API demands it.

Adding OBO-format ontology parser by Sohel Merchant.

Made synopsis runnable: Bio::Ontology::Term needs an identifier or you can add only one term inot an ontology (with an empty but unique identifier!)

Find_similar_terms(): documentaion updated. Note that the argument is a term, not names parameters

New method find_identically_named_terms(), there are now three methods for searching an ontology with a term object

Bio::Ontology::SimpleGOEngine

Moved all the methods to Bio::Ontology::OBOEngine

Bio::Ontology::SimpleOntologyEngine

Find_similar_terms(): documentaion updated. Note that the argument is a term, not names parameters

Bio::Ontology::Term

Added the method has_dblink() from OBOterm object

Removed 'use Bio::Root::Object' artifact.

Bio::Ontology::Xref

Adding OBO-format ontology parser by Sohel Merchant.

No message

Bio::OntologyIO

Adding OBO-format ontology parser by Sohel Merchant.

Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler

Adding short description

Bio::OntologyIO::dagflat

Susbtituted all the references to SimpleGOEngine by OBOEngine

Do not cross-reference a term back to itself

Bio::OntologyIO::obo

Adding OBO-format ontology parser by Sohel Merchant.

Removed unnecessary 'undef' assignments.

Fix warnings popping up on 'make test'

Bio::OntologyIO::simplehierarchy

Susbtituted all the references to SimpleGOEngine by OBOEngine

Bio::Phenotype::Correlate

Removed "use Bio::Root::Object" artifact; all tests pass.

Bio::Phenotype::Measure

Removed "use Bio::Root::Object" relic; all tests pass.

Bio::Phenotype::OMIM::MiniMIMentry

Removed "use Bio::Root::Object" artifact; all tests pass.

Bio::Phenotype::OMIM::OMIMentryAllelicVariant

Removed "use Bio::Root::Object" artifact; all tests pass.

Bio::Phenotype::OMIM::OMIMparser

Issue #1951

$self->throw, not die

Bio::PopGen::IO::hapmap

Switch to $self->throw_not_implemented();

Replace warn() with explicit $self->warn()

Bio::PopGen::Marker

Corrected confusing grammar/tense in throw() message for parameter type-checking.

Bio::PopGen::Simulation::Coalescent

Throw, not die

Bio::PopGen::Statistics

Make sure haploid pop is called when calculating sample size for theta

Jason gets bad marks in spelling.

Added F* which was present but not listed here

Bio::PrimarySeq

When reporting the pattern mismatch, list it out with commas separating, previously just reporting the length of the array (number of mismatched bases)

Issue #2000; need to change AlignIO::fasta next_aln to make it more like AlignIO::clustalw, but works for now

Issue #2000; got rid of sequence validation and substitution (which caused nasty unwarned deletions); sequence validation done in PrimarySeq!

Seq() does not take named parameters

For wrong input to subseq(), no undefined variables in warn message, return undef

Bio::PrimarySeqI

Better way to pass alternative initation codon to translate()

Add -offset parameter to translate() for fuzzy locations

Bio::PullParserI

New PullParserI and hmmer parser

Documentation clarification, warn that rewind does not work in sequential_read mode, make that mode default

Compatable with perls older than 5.8

Nicer perl version test

Filehandle was already lexically scoped; avoid redeclaration

Bio::RangeI

Intersection now can take an array ref: slight API change

Mention both args for equals() in its docs

Bio::Restriction::Analysis

Edits

Border condition where a RE cuts at the end of the sequence.

Oops. Forgot to remove the print.

Bio::Restriction::Enzyme

Fixed error when asking for the isoschizomers() of an enzyme that has none.

Border condition where a RE cuts at the end of the sequence.

Issue #2139

Bio::Restriction::EnzymeCollection

Conrad's patch

Bio::Restriction::IO::bairoch

A little rearranging, though bairoch.pm is still broken

Added warning for multicut/multisite enzyme issue (Issue #2010); will resolve hopefully soon

Convert print STDERR to $self->debug and new Class to Class->new

Bio::Restriction::IO::base

A little rearranging, though bairoch.pm is still broken

Bio::Restriction::IO::withrefm

A little rearranging, though bairoch.pm is still broken

Bio::Root::Err

Deprecated and removed these relics

Bio::Root::Global

Deprecated and removed these relics

Bio::Root::HTTPget

As per Issue #2037

Proxy default to environment variable

Proxy fixes

Bio::Root::IO

Issue #2022; speed improvements for Windows parsing; shouldn't affect other OS's

Fix for mode(): do not push back random lines into the buffer, do not leave the filehandle at a random point under Mac OS X

Rewrote mode(), prevents spurious warnings, works on all platforms (?) and with piped input

Bio::Root::IOManager

Deprecated and removed these relics

Bio::Root::Object

Removed references to deprecated/removed Bio::Tools::Blast

Deprecated and removed these relics

Bio::Root::Root

Notes about not starting throw messages with dashes; really its a bug but would be too expensive to fix

Possible fix for Issue #1938

Bio::Root::RootI

Remove cruft from warn(); passes all tests

Notes about not starting throw messages with dashes; really its a bug but would be too expensive to fix

Bio::Root::Storable

Throw, not die

Get rid of $'

Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.

Bio::Root::Utilities

Fixed num2month() returning wrong months, 0/1 array base problem

Made mean_stdev() more robust when data list has less than 2 elements

Bug in std.dev. calculation, was X^2/N-1 should be X^2/(N-1)

* Added file_flavor() -- a simple wrapper around get_newline() that returns the 'flavor' given a filename (unix, dos, mac). * Added require FileHandle at the appropriate spot in create_filehandle() for convenience.

Deprecated and removed these relics

Bio::Root::Vector

Deprecated and removed these relics

Bio::Root::Version

CPAN-compatible version

Our $VERSION (perl 5.6.1-ish)

Quenched "masks earlier declaration" warning

Good style for $VERSION

Version increase for 1.5.2rc4

Version increase for RC5

Bio::Root::Xref

Deprecated and removed these relics

Bio::Search::GenericStatistics

Added available_* methods so GenericResult can delegate, made GenericResult use objects properly

Bio::Search::HSP::GenericHSP

Missing :

General SearchIO speed-up

Issue #2075; I will add tests for these as soon as I can to SearchIO.t

Simplify Issue #2075 fixes; now reports RPS-BLAST type (BLASTP or BLASTX), similar to blastxml; revert changes in BlastResult

Merge Bio::SearchIO speedup from experimental

Fix for Issue #2075

Merge Bio::SearchIO speedup changes from branch-1-5-2

Lazily evaluate feature1 and feature2, not just query and hit

Bio::Search::HSP::HMMERHSP

Spelling correction

Bio::Search::HSP::HSPI

Syncing documents with code for matches method

Off by one error; previously all matches returned could have been wrong!

Complete fix for out by 1 error

Bio::Search::HSP::HmmpfamHSP

New PullParserI and hmmer parser

Use base, not @ISA

Bio::Search::HSP::PullHSPI

New PullParserI and hmmer parser

Bio::Search::Hit::BlastHit

Changed 'require Class' to 'use Class'

Bio::Search::Hit::Fasta

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::Search::Hit::GenericHit

General SearchIO speed-up

Merge Bio::SearchIO speedup from experimental

Merge Bio::SearchIO speedup changes from branch-1-5-2

Changed 'require Class' to 'use Class'

Bio::Search::Hit::HmmpfamHit

New PullParserI and hmmer parser

Bio::Search::Hit::PsiBlastHit

Changed 'require Class' to 'use Class'

Bio::Search::Hit::PullHitI

New PullParserI and hmmer parser

Bio::Search::Iteration::GenericIteration

General SearchIO speed-up

Merge Bio::SearchIO speedup from experimental

Merge Bio::SearchIO speedup changes from branch-1-5-2

Bio::Search::Result::BlastResult

Issue #2075; I will add tests for these as soon as I can to SearchIO.t

Simplify Issue #2075 fixes; now reports RPS-BLAST type (BLASTP or BLASTX), similar to blastxml; revert changes in BlastResult

Bio::Search::Result::GenericResult

General SearchIO speed-up

Added available_* methods so GenericResult can delegate, made GenericResult use objects properly

Merge Bio::SearchIO speedup from experimental

Merge Bio::SearchIO speedup changes from branch-1-5-2

Next_hit, not next_hits

Bio::Search::Result::HmmpfamResult

New PullParserI and hmmer parser

Make evalues play nice under WinXP

Bio::Search::Result::PullResultI

New PullParserI and hmmer parser

Bio::Search::Result::ResultI

Fix error message to accurately report failed condition

Bio::Search::SearchUtils

Tile_hsps() now returns HSP contig data in a two-element array. 0=query contigs, 1=sbjct contigs

Tiling of hsps was broken; now HitI methods frac_aligned_query and frac_aligned_hit will return more sane answers (perhaps even correct ones!)

Fixed uninitialized values introduced in last commit

Spelling error

Calculate identities and conserveds correctly when merging hsps into tiles

Hsp tiling and indentitiy calculation algorithm should now be correct (though there are much simpler, saner ways of doing the same thing...)

Removed debug line

Bio::SearchIO

Wiki address

Bio::SearchIO::EventHandlerI

Moved start_iteration, end_iteration to EventHandlerI; modified SearchIO::blast to play nice when using other event handlers

Bio::SearchIO::FastHitEventBuilder

Allow event handler to work with SearchIO::blast

Moved start_iteration, end_iteration to EventHandlerI; modified SearchIO::blast to play nice when using other event handlers

Make this a bit more flexible. This handler doesn't use HSP's!

Bio::SearchIO::IteratedSearchResultEventBuilder

General SearchIO speed-up

Merge Bio::SearchIO speedup from experimental

Merge Bio::SearchIO speedup changes from branch-1-5-2

Bio::SearchIO::SearchResultEventBuilder

Issue #1986 and allow SREB to be swapped back into IteratedREB

Moved start_iteration, end_iteration to EventHandlerI; modified SearchIO::blast to play nice when using other event handlers

General SearchIO speed-up

Merge Bio::SearchIO speedup from experimental

Merge Bio::SearchIO speedup changes from branch-1-5-2

Bio::SearchIO::Writer::BSMLResultWriter

Improved NAME, SYNOPSIS, DESCRIPTION docs

Bio::SearchIO::Writer::GbrowseGFF

Sped up case insensitive name searching in postgres

Silenced a warning about warn() given an uninitialised argument

Bio::SearchIO::Writer::HTMLResultWriter

Replaced 'print STDERR' with '$self->warn', plus minor formatting.

Add back in $Revision assignment line; this module actually prints it out in the footer of the HTML it produces.

Bio::SearchIO::Writer::HitTableWriter

Add 'rank' and 'num_hits' to column_map

Bio::SearchIO::Writer::ResultTableWriter

Support new column in result table: num_hits

Bio::SearchIO::axt

Issue #1748, set $/ to "\n" and local $_

Add extra comment via Cathy

Bio::SearchIO::blast

Issue #1748, set $/ to "\n" and local $_

Issue #1934; perltidy'd code, workarounds for added/changed text output

Fix for Issue #1985 - difference in blastpgp output from Linux and Windows breaks parsing

Added CVS tag line (wasn't updating)

Issue #1986 and allow SREB to be swapped back into IteratedREB

Moved start_iteration, end_iteration to EventHandlerI; modified SearchIO::blast to play nice when using other event handlers

Small fix to catch optional frame info for RPS-BLAST (BLASTX-like); working on rest of Issue #2075

Issue #2075; I will add tests for these as soon as I can to SearchIO.t

Simplify Issue #2075 fixes; now reports RPS-BLAST type (BLASTP or BLASTX), similar to blastxml; revert changes in BlastResult

Issue #2091 (second bug)

Added comments relevant to Issue #1986

Issue #2108

Deal with WU-BLAST weird case

Removed redundant "if $self->verbose" suffix from "$self->debug()" calls

Issue #2121

Bio::SearchIO::blasttable

Issue #1748, set $/ to "\n" and local $_

Removed ambiguous undef assignment to array

Bio::SearchIO::blastxml

Issue #1748, set $/ to "\n" and local $_

Added SAX2 parsing (switch over to XML::SAX)

Added a bit about using XML::SAX and XML::SAX::ExpatXS

Added warnings for XML::SAX::Expat, which has DTD issues. Still won't play nice!

Oops! Made XML::SAX::Expat the default during testing...

Simplify Issue #2075 fixes; now reports RPS-BLAST type (BLASTP or BLASTX), similar to blastxml; revert changes in BlastResult

Commented out timing debugs to give clean test output

Throw, not warn, since this dies 99% of the time anyway. Make error message more explicit.

Bio::SearchIO::exonerate

Issue #1748, set $/ to "\n" and local $_

Bio::SearchIO::fasta

Issue #1748, set $/ to "\n" and local $_

Wiki address

Bio::SearchIO::hmmer

Issue #1748, set $/ to "\n" and local $_

Repair broken regexp (duplicated \s+ prevented domains with more than 99 instances from being seen); also handle PVM-restartable hmmpfam format (e.g. Query sequence 15:); other tidying

Perltidy'd for personal sanity; working on Issue #2036...

Fix Issue #2036

Removed redundant "if $self->verbose" suffix from "$self->debug()" calls

Bio::SearchIO::hmmer_pull

New PullParserI and hmmer parser

Documentation clarification, warn that rewind does not work in sequential_read mode, make that mode default

Default hmmer_pull piped_behaviour mode now sequential_read

Bio::SearchIO::megablast

Issue #1748, set $/ to "\n" and local $_

Corrected confusing grammar/tense in throw() message for parameter type-checking.

Bio::SearchIO::psl

Issue #1748, set $/ to "\n" and local $_

Fix Issue #1977

Removed ambiguous undef assignment to array.

Bio::SearchIO::sim4

Issue #1748, set $/ to "\n" and local $_

Bio::SearchIO::waba

Issue #1748, set $/ to "\n" and local $_

Bio::SearchIO::wise

Issue #1748, set $/ to "\n" and local $_

Bio::Seq

The API has changed... binomial_name --> binomial

Bio::Seq::BaseSeqProcessor

Corrected write_seq() to it should be (IMHO anyway).

Bio::Seq::Meta

Copy-paste error in synopsis code

Bio::Seq::RichSeq

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::SeqFeature::Annotated

Remove id, test passes.

Emmanuel's suggestion on names

Issue #2026; Robert's enhancements

Fixing a bug that silently converted phases of 0 to null

Bio::SeqFeature::Collection

Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.

Bio::SeqFeature::Gene::NC_Feature

Improved NAME, SYNOPSIS, DESCRIPTION docs

Bio::SeqFeature::Gene::Poly_A_site

Improved NAME, SYNOPSIS, DESCRIPTION docs

Bio::SeqFeature::Gene::Transcript

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::SeqFeature::Generic

Format

Throw, not die

Documented that -primary and -primary_tag contructor keys are synonyms.

Changes to make storable in GFF3 databases

Bio::SeqFeature::SimilarityPair

General SearchIO speed-up

Bio::SeqFeature::Tools::Unflattener

Fixed unflattener for unusual form of genbank record - see new test for details

Issue #1810

Bio::SeqFeatureI

Format

Issue #2039 : changed spliced_seq API, added warning about old API (but having it still work)

Issue #1780 (try to catch mismatched location end/seq length)

Bio::SeqIO

Add suffix for entrezgene

Wiki address

Add a couple more suffixes to fasta

Extend _guess_format to know about 'strider' files

Bio::SeqIO::abi

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::SeqIO::agave

Throw, not die

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::SeqIO::alf

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::SeqIO::bsml

Throw, not die

Bio::SeqIO::bsml_sax

Bio::Taxonomy overhaul, see Issue #2061

Bio::SeqIO::chadoxml

Clarify that this is write-only

Throw, not die

Bio::SeqIO::chaos

Throw, not die

Fixed syntax error (is anybody using this module?).

Replace print STDERR with $self->warn

Bio::SeqIO::ctf

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::SeqIO::embl

Throw, not die

Issue #2056 : Update embl.pm for EMBL sequence format changes

Bio::Taxonomy overhaul, see Issue #2061

Improved species handling; now more likely that output of input OS, OC lines matches input

Removed print line

Issue #2077; make organism name parsing more consistent between GenBank and EMBL formats (Bio::Taxon methods only)

Issue #2077 : split and store dates from versioning info, rebuild on write_seq()

Add warning to check seq quality

Not map(), join(); not unless, if (!defined()). Damian Conway would be proud...

Issue #2087

Throw informative message for OS and OC line problems, prior to handing off to Bio::Species

Do not throw when the next sequence is just a blank line

Improved genus capturing, new-style organism parsing for swiss.pm

Return with no species on failure to parse even the scientific name

Issue #2089

Indenting code and init DBlink all at once

Indent madness merged to trunk

Issue #2130

Issue #2130

Bio::SeqIO::entrezgene

Capture locus synonym data was missing annotation when not an array for gene->db

Speed up parser and suppress some warnings by initializing debug to 'off'

Capture KEGG pathway name

Bit more on what's returned

Handles multiple taxon id/db entries

Some refseqs uncaptured when multiple comment->product levels exist

Revert back to previous revision to avoid bug

Bio::SeqIO::excel

Added SeqIO parsers for column-delimited tables, and as a specialization for Excel workbooks. Includes test files and script.

Id line

Bio::SeqIO::exp

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::SeqIO::fasta

Issue #2022; speed improvements for Windows parsing; shouldn't affect other OS's

Oops; fixed wrong line! Odd that tests didn't pick that up...

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::SeqIO::fastq

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::SeqIO::game::gameWriter

Issue #1954 : patch from Robert Buels, adds <computational_analysis> to output

Get rid of $&

Bio::SeqIO::gcg

Checksum on uppercase sequence; Do not filter sequence, remove only explicitly specified characters

Bio::SeqIO::genbank

Fix Issue #1647

New address

Wiki address

Issue #1925. I fix this thing and it just looks worse and worse, someday...

Added WGS_SCAFLD support for WGS files (was not parsing these)

Fix suggested by Scott Markel (issue with writing GenBank files)

Back out the last changes (fixes for Scott) as they are redundant; Heikki's fix to Bio::Annotation::SimpleValue (1.15) already addressed this issue

Changed the way CONTIG line is handled; passes tests and should fix infinite loop bug

Make it a little easier to get CONTIG info, if needed for Bio::Location objects

Drop debug and reformat indents

Add support for consortiums (CONSRTM) - Issue #2006

Extra check for empty CONSRTM line (per M. Rogoff)

Issue #2020

Do not exceed 80 character line width when printing out long SOURCE lines

Correct handling of genus, species and subspecies in in/out

Bio::Taxonomy overhaul, see Issue #2061

Fixed handling of organism lines split over 2 lines and creation of classification array when multi-word name is split over 2 lines

Parse out organelle, common name, abbr. name (bypassed for now)

Some small common name changes (more to come?)

Issue #2077; make organism name parsing more consistent between GenBank and EMBL formats (Bio::Taxon methods only)

Issue #2062

Improved genus capturing, new-style organism parsing for swiss.pm

Return with no species on failure to parse even the scientific name

Email changed

Replaced /^\Q...\E$/ and /\Q...\E/ code with clearer more efficient 'eq' and 'index()'

Dblink fix to keep version and accession separate

Indentation madness

Indentation madness merged to 1.5.2 branch

Issue #2146

Issue #2124

Issue #2152

Change for block to a map

Bio::SeqIO::interpro

Issue #1908. Also removed use statements for Data::Dumper and XML::DOM::XPath, these modules appear to be unused.

Improved NAME, SYNOPSIS, DESCRIPTION docs

Bio::SeqIO::kegg

Guido's new version

Format

On Fri, 18 Nov 2005, "Greenberg, Simon [PRDUS Non-J&J]" <SGreenb1@prdus.jnj.com> wrote: > Hi Allen, > > I'm trying to implement KEGG parser and found your latest release. > I made some minor changes because not all input files containing some of the > 'key' values:

Fix to return the value rather than a boolean

Bio::SeqIO::largefasta

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::SeqIO::lasergene

Support strider and lasergene formats in seqio. NB: new dependency in strider.pm - Convert::Binary::C

Fixed to actually pass "perl -c", removed cruft, converted die to throw

Repaired module and wrote tests for "Lasergene" sequence format.

Bio::SeqIO::locuslink

Improved NAME, SYNOPSIS, DESCRIPTION docs

Bio::SeqIO::metafasta

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::SeqIO::phd

Added support for reading comments in a phd file. This really needs a "phred_comments" object of some sort so that it will be serializable. Then when java clients get this object they will be able to deserialize it.

Issue #2120

Bio::SeqIO::pln

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::SeqIO::scf

Nancy's patch and some formatting, removing debugging statements

Nancy's patch

Bio::SeqIO::strider

Support strider and lasergene formats in seqio. NB: new dependency in strider.pm - Convert::Binary::C

Replaced die() with $self->throw()

Documentation fix

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::SeqIO::swiss

Issue #2003 : added support for seq_version; see bug report for details

Improved genus capturing, new-style organism parsing for swiss.pm

Return with no species on failure to parse even the scientific name

STANDARD/PRELIMINARY based on SwissProt/TrEMBL

Replaced /^\Q...\E$/ and /\Q...\E/ code with clearer more efficient 'eq' and 'index()'

Simplified dblink parsing and setting, code indenting

Issue #2134

Issue #2134 (change output to conform with rel. 9 ID changes)

Use Comment object

Bio::SeqIO::table

Added SeqIO parsers for column-delimited tables, and as a specialization for Excel workbooks. Includes test files and script.

Id line

Bio::SeqIO::tinyseq

No setting of own $VERSION

Bio::SeqIO::tinyseq::tinyseqHandler

No setting of own $VERSION

Bio::SeqIO::ztr

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::SeqUtils

Added and modified Roy Chaudhuri's cat method for concatenating sequences with features

Fix for some omissions in last commit

Interim procedural solution to sequence evolution simulation

Added trunc_with_features and relevant tests (Roy Chaudhuri, from Issue #2019)

Allow any sort of uc or lc triplet in seq3in()

Issue #2052

Issue #2053

Added additional IUPAC amino acids GenBank is adding starting in October (per Neil Saunders on the mail list)

Replaced print STDERR with $self->debug()

Issue #2145

Bio::SimpleAlign

Modified remove_columns(). Now columns can be removed by property (['weak','mismatch']) or by position ([0,0],[5,10]).

Must sort args, can't assume user enters them in correct order

Edits

Fix cigar_line (it had never been completed in fact), add tests. This is the old-style cigar line, not the exonerate/ENSEMBL-style cigar line.

Edits

New function to get a matrix of where the gaps are in the alignment. test and example code to be added later; also respect gapchar

Fix wrong coordinate

Fix slice() when the slice is a single column, this wasn't working

Add slice() example

Resolving metafasta/SimpleAlign::consensus_string() issues in Issue #2016

Issue #2016 : several fixes to accomodate changes in handling meta data. Reverted redundant fix in SimpleAlign; removed relevant tests in SimpleAlign.t

Issue #1984

Issue #2106

Issue #2099

Email changed

Replaced /^\Q...\E$/ and /\Q...\E/ code with clearer more efficient 'eq' and 'index()'

Implement AnnotatableI (for alignment-specific annotation)

Add experimental stockholm write_aln() support

Add alignment meta string output

Additional fun stuff; write_aln() test added; may move tests to separate test suite (lots of them)

No symbols if no seq

Bio::Species

Additional 'rule' in validate_species_name - not entirely sure that it's possible to validate some of these virus names

Bio::Taxonomy overhaul, see Issue #2061

Put the bad lineage and throw in the correct place. there is still a memory leak problem

Fixes for binomial, species when creating a Bio::Species from a db; merges scientific_name now

Remove debug comments

This fixes Issue #2092. What I don't know is whether this is also the correct behaviour. It turns out that when you're working within bioperl-db you're comparing the node_name to elements of an array where the species name and the genus name are in adjacent elements.

Do not try and shortcut in binomial() to better emulate old usage

Do not call classification() in new unless a classification actually supplied

Possible fix for Issue #1938: ncbi_taxid() is no longer a direct synonym of id(), only returning if ncbi_taxid had been set

Weaken refs to avoid circular references

Get rid of cleanup methods for serialize success

Bio::Structure::Entry

Issue #1893

Add alias for conect()

Issue #1894

Bio::Structure::IO

Removed text which didn't make much sense

Bio::Structure::IO::pdb

Issue #1895

Initialize to suppress a warning

Bio::Structure::SecStr::DSSP::Res

Spelling error

Issue #1966

Bio::Structure::StructureI

Remove duplicated lines

Bio::Symbol::Alphabet

Improved NAME, SYNOPSIS, DESCRIPTION docs

Bio::Symbol::ProteinAlphabet

Yet mores fixes for additional amino acid codes 'U', 'O', 'J'

Bio::Taxon

Bio::Taxonomy overhaul, see Issue #2061

Fixes for binomial, species when creating a Bio::Species from a db; merges scientific_name now

Corrected confusing grammar/tense in throw() message for parameter type-checking.

Possible fix for Issue #1938: ncbi_taxid() is no longer a direct synonym of id(), only returning if ncbi_taxid had been set

Bio::Taxonomy

Bio::Taxonomy overhaul, see Issue #2061

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::Taxonomy::FactoryI

Bio::Taxonomy overhaul, see Issue #2061

Bio::Taxonomy::Node

Added get_Lineage_Nodes

Added get_LCA_Node

As per Issue #2047

Doc fixes, and as per addendum to Issue #2047

Bio::Taxonomy overhaul, see Issue #2061

Bio::Taxonomy::Taxon

Minor code and doc fixes

Bio::Taxonomy doesnt export rank information; dont try and use it to validate in rank()

Bio::Taxonomy overhaul, see Issue #2061

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::Taxonomy::Tree

Minor code and doc fixes

Bio::Taxonomy overhaul, see Issue #2061

Bio::Tools::Alignment::Consed

Throw, not die

Corrected comment URL reference to 'tcgrep'

Replaced UNIX-specific "/" stuff with File::Spec->splitpath

Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.

Bio::Tools::Analysis::DNA::ESEfinder

Made (env_proxy => 1) the default for LWP::UserAgent instantiations

Throw on server error, skip on tests

Throw on all server errors

New WebAgent, not UserAgent

Bio::Tools::Analysis::Protein::ELM

Adding short description

Bio::Tools::Analysis::Protein::GOR4

Behave well on server error

Behave well on server error

Bio::Tools::Analysis::Protein::HNN

Behave well on server error

Behave well on server error

Bio::Tools::Analysis::Protein::Scansite

Corrected URL for MIT's ScanSite web site

Fixed previously mis-deduced part of documentation (via author's other modules)

Bio::Tools::BPbl2seq

Add deprecation warnings

Warn, not warning (duh....)

Bio::Tools::BPlite

Add deprecation warnings

Warn, not warning (duh....)

Fixed formatting of deprecation message.

Bio::Tools::BPlite::Iteration

Replaced /^\Q...\E$/ and /\Q...\E/ code with clearer more efficient 'eq' and 'index()'

Bio::Tools::BPpsilite

Fixed localization problem

Add deprecation warnings

Warn, not warning (duh....)

Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.

Replaced /^\Q...\E$/ and /\Q...\E/ code with clearer more efficient 'eq' and 'index()'

Bio::Tools::Blast

Removing files from CVS HEAD which were scheduled for removal in version 1.1 but were still hanging around.

Bio::Tools::Blat

Adding short description

Bio::Tools::CodonTable

Added Bio::Tools::CodonTable->tables() method and corresponding tests.

Added additional IUPAC amino acids GenBank is adding starting in October (per Neil Saunders on the mail list)

Bio::Tools::Coil

Adding short description

Bio::Tools::ECnumber

Removed "use Bio::Root::Object" relic; all tests pass. It already ISA Bio::Root::Root.

Bio::Tools::EPCR

Support decoding strand supplied when calling e-PCR with decode -option

Avoid adding empty 'Note' tag to feature when $rest only contained e-PCR strand info

Bio::Tools::ERPIN

Initial commit; adding tests to rnamotif.test

Get rid of newline at end of sequence

Minor changes; plan on makeover for these soon (maybe move to SearchIO?)

Minor changes (deal with evalue perliness)

Now with 'our'

Bio::Tools::Fgenesh

Fixed (selected) vestigal cruft wrought by Genscan.pm copy/paste origins of this module: * start/end coordinate swapping is NOT needed for fgenesh (at least in fgenesh v 2.4 in my hands). * analysis_method still 'thought' it was genscan. Not! I'm expect there is other such cruft...

Fixed spelling in comment.

1) small corrections to field to tag mapping from 'PolA' to 'PolyAsite' and 'TSS' to 'Promoter' (which remains incorrect, but at least now maps the correct field) 2) comment out a debugging/trace message

allows >999 predictions to be parsed without error

Bio::Tools::FootPrinter

Improved NAME, SYNOPSIS, DESCRIPTION docs

V2.1 now has header lines - added compatability

Bio::Tools::GFF

Updating the lists of reserved tags (it was REALLY out of date).

Fixing the handling of Targets for GFF3

Adding items to escape in GFF3 attributes per Robert Buels patch

Fix for segments to have a defined length

Bio::Tools::Gel

Updated the synopsis

Bio::Tools::Geneid

Removed redundant "if $self->verbose" suffix from "$self->debug()" calls

Bio::Tools::Genewise

Issue #1980

Issue #1973

Removed redundant "if $self->verbose" suffix from "$self->debug()" calls

Bio::Tools::Genomewise

Removed redundant "if $self->verbose" suffix from "$self->debug()" calls

Bio::Tools::Glimmer

Added support for GlimmerHMM and clarified that module does not support Glimmer2 and Glimmer3.

Bio::Tools::GuessSeqFormat

Throw, not die

Deleting debugging comments

Bio::Tools::HMM

No setting of own $VERSION

Bio::Tools::HMMER::Results

Fixed wrong bugzilla URL.

Replaced Carp::carp with $self->warn()

Bio::Tools::HMMER::Set

Checking URLs

Bio::Tools::Hmmpfam

Adding short description

Bio::Tools::IUPAC

Fixes for new amino acid codes 'J', 'O'

Bio::Tools::Lucy

Removed references to deprecated/removed Bio::Tools::Blast

Bio::Tools::OddCodes

Cleaned up documentation and improved method examples

Throw, not die

Corrected URL for bugzilla (removed "www." prefix)

Bio::Tools::Phylo::Molphy

Improved NAME, SYNOPSIS, DESCRIPTION docs

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

Improved NAME, SYNOPSIS, DESCRIPTION docs

Corrected confusing grammar/tense in throw() message for parameter type-checking.

Bio::Tools::Phylo::PAML

Capturing number of parameters as tree id

Added parsing for beta_w1

Uops -- there was a type in the last commit

Sometimes the omega is too big and there is no space

Treefile is seqfile instead in paml (this is only cosmetic)

PAML 3.15 parsing supported

Issue #1983, parse NEB and BEB sites from PAML 3.15 properly now so that all model reports are parsed

Ryan's version

Ryan Golhar's fixes for 3.15 parsing

Issue #2054

Issue #1883

Issue #2055; committing these in steps in case of rollbacks

Bio::Taxonomy overhaul, see Issue #2061

Issue #2080

Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.

Move get_posteriors comments to TO DO section

More API doc in the SYNOPSIS

Bio::Tools::Phylo::PAML::ModelResult

Issue #1983, parse NEB and BEB sites from PAML 3.15 properly now so that all model reports are parsed

Corrected confusing grammar/tense in throw() message for parameter type-checking.

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

Adding seqfile method -- it may not make sense for this to set, but it makes to get

Corrected confusing grammar/tense in throw() message for parameter type-checking.

Bio::Tools::Phylo::Phylip::ProtDist

Improved NAME, SYNOPSIS, DESCRIPTION docs

Bio::Tools::Primer3

Some hashes were used for temporary storage in next_primer(), removed them for simplicity

Issue #1833

Email changed

Bio::Tools::Promoterwise

Improved NAME, SYNOPSIS, DESCRIPTION docs

Bio::Tools::QRNA

Throw, not die

Bio::Tools::RNAMotif

Initial commit

Changed line endings from Windows to UNIX

Add clean_features method; returns hits based on score, location as Bio::Seqfeature::Collection object

Fixed silly mistake in clean_features.

Fix error in clean_features where last SeqFeature may be left off

Forgot to take out debugging before committing.

Make seqfeature tags more like Bio::Tools::ERPIN

Minor changes; plan on makeover for these soon (maybe move to SearchIO?)

Remove debugging stuff

Now with 'our'

Bio::Tools::RandomDistFunctions

Throw, not die

Bio::Tools::RepeatMasker

Emmanuel Quevillon's reported bug in creating feature2, I also simplified code into 2 new calls

Add Id line

Use internal warn instead of STDERR

Fix RepeatMasking - features were flipped 1/2

Adding short description

Bio::Tools::RestrictionEnzyme

Add DEPRECATED

Module cleanup. Shame I didn't realise it was deprecated until afterwards!

Add deprecation warnings

Warn, not warning (duh....)

Bio::Tools::Run::GenericParameters

Added available_* methods so GenericResult can delegate, made GenericResult use objects properly

Bio::Tools::Run::RemoteBlast

Throw, not die

Further removing myself from direct responsibility... =)

Issue #1935; save XML output

Applied Sendu Bala's patch (Issue #2015)

Issue #2007

Add option to change default URL (highly experimental, emphasis on the 'mental')

Perltidy'd for future work

Save tabular blast output

Avoid UTF-8 warnings

Bio::Tools::Run::StandAloneBlast

Torsten's patch

Documentation and formatting cleanup

Updated valid command line switches for NCBI BLAST tools.

Minor logic and formatting changes.

Added support for "-param" options as well as "param" as per Bioperl Issue #1912

Named parameters in docs

Replaced '/dev/null' with File::Spec->devnull

Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.

Bio::Tools::Run::WrapperBase

Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.

Is an abstract base class, not an interface - use Bio::Root::Root

Bio::Tools::Seg

Issue #1898

Completely re-wrote and documented Seg.pm parser and added sample input and tests.

Bio::Tools::SeqAnal

Removing files from CVS HEAD which were scheduled for removal in version 1.1 but were still hanging around.

Bio::Tools::SeqPattern

Get rid of $`,$&

Bio::Tools::SeqStats

Throw, not die

Added hydropathicity() calculation.

Silence a warning

Bio::Tools::SiRNA::Ruleset::saigo

Repaired mis-use of $self->debug ; all tests pass.

Bio::Tools::SiRNA::Ruleset::tuschl

Get rid of $`,$&

Bio::Tools::Signalp

Adding short description

Bio::Tools::Sim4::Results

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::Tools::Spidey::Results

Throw, not die

Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"

Bio::Tools::Tmhmm

Totally reimplemented TMHMM parser and added previously non-existent tests.

Bio::Tools::WWW

Removing files from CVS HEAD which were scheduled for removal in version 1.1 but were still hanging around.

Bio::Tools::WebBlat

HTTP::Response, not LWP

Made (env_proxy => 1) the default for LWP::UserAgent instantiations

No setting of own $VERSION

Bio::Tools::dpAlign

Added Ends-Free Alignment support

Fixed a bug that complains when you specify ends-free alignment

Sorry another minor fix

No setting of own $VERSION

Bio::Tools::pICalculator

Throw, not die

Correct URL for description of EMBOSS "iep" program

Adding short description

Bio::Tools::tRNAscanSE

Fix return type - thanks to Ryan Morin @ BCGSC.ca

Bio::Tree::Compatible

Postorder is postorder_traversal

Fixed sub topological_restriction

Bio::Tree::Draw::Cladogram

Added branch coloring

Added label coloring

Revised drawing colored branches

Fixed drawing colored branches

Bio::Tree::Node

Support alpha sorting for node order in each_Descendent

Allow arbitrary code to passed in for sorting

Oops - need to keep mapping, undo stupid change

Undo change to sub height

Bio::Taxonomy overhaul, see Issue #2061

When branch length changes, so does the tree height

Weaken refs to avoid circular references

Bio::Tree::NodeI

Clarify documentation

Rejigger sort order so it doesn't require query to get the height (by default)

Bio::Tree::NodeNHX

Only write NHX block when there is something to write

Bio::Tree::Tree

ID and SCORE are settable at init time

Rejigger sort order so it doesn't require query to get the height (by default)

Bio::Taxonomy overhaul, see Issue #2061

Bio::Tree::TreeFunctionsI

Create nodes of the same type as the existing nodes when re-rooting

Bio::Taxonomy overhaul, see Issue #2061

Issue #2082

Bio::Tree::TreeI

Rejigger sort order so it doesn't require query to get the height (by default)

Bio::Taxonomy overhaul, see Issue #2061

Bio::TreeIO

Allow newline separated clustalW dendogram style output

Bio::TreeIO::cluster

Corrected confusing grammar/tense in throw() message for parameter type-checking.

Issue #2151

Bio::TreeIO::newick

Sort node order so that it can be consistently printed out for same node set

Allow newline separated clustalW dendogram style output

Hackily parse score and associate it with a tree

Bio::TreeIO::nexus

Proper nexus writing, map the names to numbers in the tree writing

Proper nexus writing, map the names to numbers in the tree writing; merge to branch for fun

Bio::TreeIO::nhx

Issue #1823; write internal node ids in nhx format

Allow newline separated clustalW dendogram style output

Bio::Variation::IO::flat

Changed "if not" to "if not defined" for numeric regexp captures

Bio::Variation::VariantI

Use $self->throw_not_implemented();

Bio::WebAgent

Made (env_proxy=>1) the default in the constructor while maintaining ability for user to over-ride it by passing (env_proxy=>0).

Replaced warn() with $self->warn()

New() no longer expects all args are method names, allowing complex inheritance

Fix for last commit

Warning in sleep was only supposed to happen when verbose; changed to debug()

Build.PL

Moved to Module::Build installation system

Removed extraneous comment

Added bioperl.lisp to MANIFEST.SKIP

MANIFEST.SKIP deprecated module Bio/Tools/WebBlat.pm

Corrected comment

New Build.PL system added to branch

Made required pre_reqs from bioperl 1.5.1 requirments in 1.5.2 as well

Nicer BioDBGFF questions

Added dynamic_config, clarified BioDBGFF feedback

Additions to get `perl Build.PL` to complete successfully on Windows with ActivePerl 819 and no DBD::mysql

Fixed bug which caused the Bio::DB::SeqFeature::berkeleydb regression test to fail with a "./features.idx not found" error

Fixed bug which caused the Bio::DB::SeqFeature::berkeleydb regression test to fail with a "./features.idx not found" error

Better auto-feature checking for BioDBGFF test

Better auto-feature checking for BioDBGFF test

No printing undef

Added URI::Escape as an optional pre-req

FAQ

Remove FAQ

Makefile.PL

Removed unused and outdated Bio::LiveSeq::IO::SRS class from the distribution

Note that Set::Scalar is needed by Bio::Tree::Compatible

Comments on Set::Scalar

Added dependency on Convert::Binary::C needed by Bio::SeqIO::strider

Added dependency HTML::Parser > 3.0 for Bio::DB::GDB

Commented out unnecessary 'IO::Scalar' dependency for now non-existent Bio::Tools::Blast::Run::Webblast

Removed the deleted documentation files

Added new dependencies: t/chaosxml...................Data::Stag::Writer t/interpro...................XML::DOM::XPath t/table......................Spreadsheet::ParseExcel

OBOEngine.pm replaces SimpleGOEngine.pm

Rearranged dependencies

Getting rid of tabs!

More ordering

Fixed small formatting error that disabled Makefile

Add XML::Simple

Added regression tests for Bio::DB::SeqFeature::Store (memory,bdb + mysql)

Now uses %packages to create a hash for PREREQ_PM. "perl Makefile.PL" uses this to check for prerequisites and reports any that are missing. In addition, "nmake ppd" will now result in PPD containing all the prerequisites listed in %packages.

Overhauled: use strict; use File::Spec; pre-reqs corrected; bugs fixed; clearer output; delete created files on make clean; reordered for sanity

Removed unnecessary comments

IO::String pre-reqs correction

Another pre-req correction

Corrected install path

Added comment to clarify external dependencies are optional

We need at least v1.01 of Class::AutoClass

Exclusion system to avoid circular dependencies

Nicer messaging for excluded prereqs, forced to ask for 1.0 of Class::AutoClass, not 1.01

Removed unneccessary use

Clearer version checking

Correct strict problem

Some modules don't define VERSION, default to 0

Use single quotes for system calls to prevent interpolation

Need 'use IO::File' statement

Moved to Module::Build installation system

Added Makefile.PL back as a stub that just issues a warning

Warning that Build.PL is preferred

Improved warning message, pre_reqs do not include optional modules

Improved warning message, pre_reqs do not include optional modules

Reverted back to stub for HEAD

ModuleBuildBioperl.pm

Moved to Module::Build installation system

When have ll pre-reqs, dont complain

Nice, CPAN-aware dist names

Nice, CPAN-aware dist names, correction

Nice, CPAN-aware dist names, further correction

New Build.PL system added to branch

CPAN doesn't like RC in middle of version number?

CPAN doesn't like RC in middle of version number?

Dist runs manifest and creates all archive forms

Dist runs manifest and creates all archive forms

CPAN doesn't support optional_features syntax? Include recommends as well...

CPAN doesn't support optional_features syntax? Include recommends as well...

Removed duplicated methods

Offer to install optional deps

Comment clarification

Improved module install question, corrected comments, added bootstrap to install Module::Build

No need for print_build_script() override, add self to INC just in case

Generalized checking types, added excludes_os type

Fixed interactive script installation, allowed install of .pl files

Fix strange stringify bug

Update fix from HEAD

Explicitly require v0.2805 of Module::Build since some earlier versions do not have Module::Build::Notes

bptutorial.pl

Correct URL

Correct URL

Correct translate() docs

Better way to pass alternative initation codon to translate()

Wiki addresses

No more BPLite

Created a dummy entry for run_test number 7, modified list of all tests to ignore test no 7

Fixed formatting and URL's

Fixed remote blast tutorial (was using BPLite, maybe?)

RemoteBlasts are not performed with StandAloneBlast!

Change input file for Structure tutorial

Remove bptutorial.pl, the tutorial is now in the Wiki.

Was removed from HEAD

doc/Deobfuscator/Build.PL

Deobfuscator 1st check-in

doc/Deobfuscator/Changes

Deobfuscator 1st check-in

Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.

NEW: -s <version_string> option now can be passed to deob_index.pl to store a version string in packages.db which deob_interface.cgi can read and show.

doc/Deobfuscator/LICENSE

Deobfuscator 1st check-in

doc/Deobfuscator/MANIFEST

Deobfuscator 1st check-in

Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.

doc/Deobfuscator/META.yml

Deobfuscator 1st check-in

Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.

doc/Deobfuscator/Makefile.PL

Deobfuscator 1st check-in

doc/Deobfuscator/README

Deobfuscator 1st check-in

Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.

doc/Deobfuscator/bin/deob_index.pl

Deobfuscator 1st check-in

Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.

Deob_index.pl now accepts relative paths for BioPerl lib dir and output dir

NEW: -s <version_string> option now can be passed to deob_index.pl to store a version string in packages.db which deob_interface.cgi can read and show.

Updating USAGE

doc/Deobfuscator/cgi-bin/deob_detail.cgi

Deobfuscator 1st check-in

Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.

doc/Deobfuscator/cgi-bin/deob_flowchart.png

Deobfuscator 1st check-in

doc/Deobfuscator/cgi-bin/deob_help.html

Deobfuscator 1st check-in

Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.

doc/Deobfuscator/cgi-bin/deob_interface.cgi

Deobfuscator 1st check-in

Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.

NEW: -s <version_string> option now can be passed to deob_index.pl to store a version string in packages.db which deob_interface.cgi can read and show.

doc/Deobfuscator/excluded_modules.txt

Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.

doc/Deobfuscator/lib/Deobfuscator.pm

Deobfuscator 1st check-in

Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.

doc/Deobfuscator/t/00.load.t

Deobfuscator 1st check-in

doc/Deobfuscator/t/pod.t

Deobfuscator 1st check-in

doc/README

Add README

examples/Bio-DB-GFF/load_ucsc.pl

Issue #2060

examples/root/README

Inclusion of Error.pm causes CPAN indexing failure, removed

Inclusion of Error.pm causes CPAN indexing failure, removed

examples/root/lib/Error.pm

Inclusion of Error.pm causes CPAN indexing failure, removed

Inclusion of Error.pm causes CPAN indexing failure, removed

examples/tools/extract_genes.pl

Add script that extracts genes

Better docs

A bit more

examples/tools/run_primer3.pl

Add example script

Change email

examples/tools/standaloneblast.pl

Removed code referring to BPLite, but script still does not work

maintenance/README

Added list of dependencies

maintenance/check_NAME.pl

Removed cut-paste cruft and added count summary.

maintenance/check_URLs.pl

Fix regexp to also clean URLs ending with ")."

Improved removal of non-URL punctuation at end of embedded URLs

maintenance/cvs2cl_by_file.pl

Hack version of cvs2cl.pl that is file-centric, useful for doing Change Log updates

Highlight bug fixes, skip trivial commits

maintenance/modules.pl

Throw, not die

Better "untested" functionality

Improve untested() to take into account syntax to import methods, e.g. use Bio::Align::Utilities qw(aa_to_dna_aln bootstrap_replicates);

maintenance/ncbi_blast_switches.pl

Maintenance Perl script to summarize the command line switches of the NCBI BLAST tools, so updating the @PARAMS in StandAloneBlast.pm is easier and more accurate.

maintenance/symlink_script.pl

Moved to Module::Build installation system

Newline after printing message

Newline after printing message

New Build.PL system added to branch

maintenance/symlink_scripts.PLS

Moved to Module::Build installation system

scripts/Bio-DB-GFF/bulk_load_gff.PLS

Documented that maxfeature must be a power of 10

Added an "analyze" step after loading data - should make queries faster

Added albert smith's fix to mixed gff2/gff3 file loading

Made the bulk and fast loaders reset gff3 tag each time a ##gff-version comment is found

Fixed case-sensitive confusion in the two bulk loaders

Got rid of extraneous debugging message

Added a setting for temporary directory

Fixed syntax error and added temporary directory error reporting to fast loader

Removing postgres password flag (-W doesn't work the way I thought it does)

Fast and bulk loaders no longer leave temporary fasta files lying around

scripts/Bio-DB-GFF/fast_load_gff.PLS

Documented that maxfeature must be a power of 10

Added an "analyze" step after loading data - should make queries faster

Added albert smith's fix to mixed gff2/gff3 file loading

Fixed invalid check for mysql version

Made the bulk and fast loaders reset gff3 tag each time a ##gff-version comment is found

Fixed case-sensitive confusion in the two bulk loaders

Fixed syntax error and added temporary directory error reporting to fast loader

Fast and bulk loaders no longer leave temporary fasta files lying around

I believe I've fixed a bug in the fast loader that caused it to miss some existing types in the database, and possibly fixed an similar bug with groups.

scripts/Bio-DB-GFF/load_gff.PLS

Documented that maxfeature must be a power of 10

Allow shorthand u and p

scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS

Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects

Finished documentation for Bio::DB::SeqFeature::Store; Removed Bio::DB::SeqFeature::Store::Cacher because its functionality has been folded into Bio::DB::SeqFeature::Store

Fixed dna and cds glyphs so that letters are correctly aligned to right side of base tick when in flip orientation

Some, but not all, documentation for mysql adaptor

Tweaking interface to work properly with gbrowse

Berkeleydb adaptor is functional; added compress option to reduce database size

Setting -vertical_spacing to zero now suppresses span lines

Remove unecessary use lib

scripts/DB/biofetch_genbank_proxy.PLS

Scripts are installed as .pl files, instructions made to match

scripts/DB/bioflat_index.PLS

Scripts are installed as .pl files, instructions made to match

scripts/README

Removed ^M chars

scripts/install_bioperl_scripts.pl

Redundant

No purpose

scripts/searchio/parse_hmmsearch.PLS

Add Mauricio's script

scripts/seq/seqconvert.PLS

Added some newer SeqIO formats to known_formats array

scripts/taxa/local_taxonomydb_query.PLS

API changed and this is no longer a Taxonomy::Node but a Bio::Taxon object with different methods

scripts/taxa/taxonomy2tree.PLS

Add Gabriel's script

Added contraction of simple paths

Bio::Taxonomy overhaul, see Issue #2061

scripts/utilities/bp_sreformat.PLS

Issue #2073

scripts/utilities/mutate.PLS

New address

Change email

scripts/utilities/pairwise_kaks.PLS

Ryan's fix to deal with inclusion of internal stops in target sequences

scripts/utilities/remote_blast.PLS

New method names

Evan's version

scripts/utilities/search2gff.PLS

Added a whole number of additions, like --addid, --parent, --onehsp, and options for controlling the score, location, and method of a feature.