Core 0.7.0 0.7.1 delta

These are detailed notes on changes made between release-0-7-0 and release-0-7-1.

Bio::AlignIO

Made code in SYNOPSIS cut and runnable

Made code in SYNOPSIS cut and runnable

Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.

Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.

Added initial versions for PHYLIP and NEXUS AlignIO modules, and test data files for each

Bio::AlignIO::bl2seq

Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.

Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.

Bio::AlignIO::clustalw

Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.

Bio::AlignIO::fasta

Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.

Bio::AlignIO::mase

Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.

Was including gap characters into end() of the LocatebleSeq.

Was including gap characters into end() of the LocatebleSeq.

Bio::AlignIO::meme

An AlignIO module that reads the "alignment" sections of MEME output files (must be version 3.0 or greater.)

Bio::AlignIO::msf

Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.

Next_aln() got into endless loop added empty lines to output for readability

Next_aln() got into endless loop added empty lines to output for readability aligned sequence names to left in the output according to custom

Output was printing type P, now it prints N if the first sequence is nucleotides

Bio::AlignIO::nexus

Added initial versions for PHYLIP and NEXUS AlignIO modules, and test data files for each

Bio::AlignIO::pfam

Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.

Bio::AlignIO::phylip

Added initial versions for PHYLIP and NEXUS AlignIO modules, and test data files for each

Bio::AlignIO::prodom

Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.

Bio::AlignIO::selex

Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.

Bio::AlignIO::stockholm

Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.

Fix a bug in reading in multiline sequences

Fix a bug in reading in multiline sequences

Bio::Annotation

Made code in SYNOPSIS cut and runnable

Made code in SYNOPSIS cut and runnable

Bio::Annotation::DBLink

Bug #912 fixed -- added documentation

Bio::DB::EMBL

Initial commmit, retrieve EMBL entries over the Web

Moved from emblfetch to more general dbfetch script

Bio::DB::Fasta

Added Bio::DB::Fasta which provides fast indexed access to a directory of Fasta files

Removing perl >= 5.6.0 directives Lincoln was using

Updated to inherit from Bio::DB::SeqI and use RootI throw instead of croakadded method documentation to some methods

Fixed divide by zero errors when indexing empty fasta files

$_ is always null does not need to be part of the calculation

Bio::DB::GDB

Tests pass even when IO::String is not installed

Bio::DB::GenBank

Added documentation about what to do for NT contigs.

Merging changes/fixes from branch-07.

Minor doc fix

Doc formatting

Bio::DB::GenPept

Doc fix

Doc fix

Bio::DB::NCBIHelper

Added documentation about the URLs used.

Merging changes/fixes from branch-07.

Bio::DB::RandomAccessI

Doc formatting

Bio::DB::SeqI

Mailing list update

Mailing list update - purge references to bielefeld list

Bio::DB::SwissProt

Bio::DB::SwissProt updates to point to batch retrieval script and more correctly call these scripts. Batch mode now supported and tested DB.t

Bio::DB::SwissProt updates migrated to branch after testing on main trunk

Added other method documentation

Added Heikki's ebi dbfetch URL for retrieving swissprot entries from a remote web db

Added Heikki's ebi dbfetch URL for retrieving swissprot entries added doc needed for 0.7.1 release

Bio::DB::Universal

Added universal db - as suggested by lincoln

Bio::DB::WebDBSeqI

Bio::DB::SwissProt updates to point to batch retrieval script and more correctly call these scripts. Batch mode now supported and tested DB.t

Bio::DB::SwissProt updates migrated to branch after testing on main trunk

Fixed bug #958

Fixed bug #958

Bio::Index::EMBL

Doc fixes

Doc fixes

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Index::Fasta

Doc fixes

Doc fixes

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Index::GenBank

Doc fixes

Doc fixes

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Index::SwissPfam

Doc fixes

Doc fixes

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Index::Swissprot

Doc fixes

Doc fixes

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::LiveSeq::AARange

Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.

Copying over LiveSeq-wide warning system from main trunk

Merged forgotten carp() -> $self->warn() migration.

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Refixed $VERSION

Bio::LiveSeq::Chain

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::LiveSeq::ChainI

Moving from carp to LiveSeq-wide warn

Moving from carp to LiveSeq-wide warn

Update mailing list even on those modules that are deprecated

Mailing list update - purge references to bielefeld list

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Refixed $VERSION

Bio::LiveSeq::DNA

Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.

Copying over LiveSeq-wide warning system from main trunk

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Refixed $VERSION

Bio::LiveSeq::Exon

Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.

Copying over LiveSeq-wide warning system from main trunk

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Refixed $VERSION

Bio::LiveSeq::Gene

Doc change and adding global (= gene wide) method verbose to Gene

Doc changes from 07 branch

Doc change and adding global (= gene wide) method verbose to Gene

Moving from carp to LiveSeq-wide warn

Moving from carp to LiveSeq-wide warn

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Refixed $VERSION

Bio::LiveSeq::IO::BioPerl

Added support for Bio::DB::EMBL's "get_Seq_by_id" so that an EMBL entry can be fetched through the web instead than read from a file.

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Refixed $VERSION

Bio::LiveSeq::IO::Loader

Added support for Bio::DB::EMBL's "get_Seq_by_id" so that an EMBL entry can be fetched through the web instead than read from a file.

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Refixed $VERSION

Bio::LiveSeq::IO::SRS

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::LiveSeq::Intron

Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.

Copying over LiveSeq-wide warning system from main trunk

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Refixed $VERSION

Bio::LiveSeq::Mutator

Fixed value of AAChange::end for inframe indels on codon pos 1

Fixed value of AAChange::end for inframe indels on codon pos 1

Added third coordinate system: 'gene'. Changes in methods numbering and change_gene.

Added third coordinate system: 'gene'. Changes in methods numbering and change_gene.

Numerous fixes for complex mutations, exon and intron numbers are now reported, distance from intron/exon boundary is shown...

Numerous fixes for complex mutations, exon and intron numbers are now reported, distance from intron/exon boundary is shown...

Fixed genomic gene based coordinate system

Fixed genomic gene based coordinate system

Moving from carp to LiveSeq-wide warn

Moving from carp to LiveSeq-wide warn

Fixed polypeptide mutated allele for frameshifs

Fixed polypeptide mutated allele for frameshifs

New method change_gene_with_alignment()

Escape '+', validate pos and len

Bio::LiveSeq::Mutation was not 'use'd

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::LiveSeq::Prim_Transcript

Removed unused 'use Carp'

Removed unused 'use Carp'

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Refixed $VERSION

Bio::LiveSeq::Range

Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.

Copying over LiveSeq-wide warning system from main trunk

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Refixed $VERSION

Bio::LiveSeq::Repeat_Region

Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.

Copying over LiveSeq-wide warning system from main trunk

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Refixed $VERSION

Bio::LiveSeq::Repeat_Unit

Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.

Copying over LiveSeq-wide warning system from main trunk

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Refixed $VERSION

Bio::LiveSeq::SeqI

Commented out a repeated printed warning

Commented out a repeatedly printed warning

Started the process of changing all "carp" warnings into $self->warn and $self->throw, with customizable verbosity level, inherited from SeqIO.

Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.

Doc change and adding global (= gene wide) method verbose to Gene

Doc changes from 07 branch

Doc change and adding global (= gene wide) method verbose to Gene

Moving from carp to LiveSeq-wide warn

Moving from carp to LiveSeq-wide warn

Update mailing list even on those modules that are deprecated

Mailing list update - purge references to bielefeld list

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Refixed $VERSION

Bio::LiveSeq::Transcript

Commented out a verbose warning

Started the process of changing all "carp" warnings into $self->warn and $self->throw, with customizable verbosity level, inherited from SeqIO.

Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.

Copying over LiveSeq-wide warning system from main trunk

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Refixed $VERSION

Bio::LiveSeq::Translation

Commented out verbose warning

Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.

Copying over LiveSeq-wide warning system from main trunk

Removed redundant inheritance from Bio::LiveSeq::SeqI

Removed redundant inheritance from Bio::LiveSeq::SeqI

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Refixed $VERSION

Bio::LocatableSeq

Changed inheritance to Bio::PrimarySeq.

Changed inheritance to PrimarySeq.

Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.

Added a test for sequence length into end(). If start() and $seq() are defined it calculates the expected end value and overrides the given value if necessary and prints a warning. (lots of them from current test data! ) This a work in progress! Also included are two new experimental methods no_gaps() for counting the number of internal gaps in the alignment column_from_residue_number() which is migrated here from SimpleAlign

Better error message when end() is tried to set into a value not supported by sequence

Bio::Location::Fuzzy

Applying Steve L.'s patch to silence perl on some systems.

Made code in SYNOPSIS cut and runnable

Made code in SYNOPSIS cut and runnable

Bio::Location::Simple

Seq_id initializable in new args

Seqid initialization in new

Made code in SYNOPSIS cut and runnable

Made code in SYNOPSIS cut and runnable

Added is_remote method to Simple Locations, which makes life easier for bioperl-db system. Also, changed sub_Location method for Split Locations, now only ordered if the order paramter is defined, to get EMBL dumping to print them in the same way they were parsed in

Merged heikki's location fixes to branch

Bug #970

Fixed bug #970

Update mailing list even on those modules that are deprecated

Bio::Location::Split

Better parse/writing of locations listed on different sequences. I think that location parsing is still a bit inflexible and we probably can't really parse nested sub_locations (splits of splits) which would violate the dogfoodability of bioperl, perhaps we have to go to a different parsing scheme for the next version

Made code in SYNOPSIS cut and runnable

Made code in SYNOPSIS cut and runnable

Added is_remote method to Simple Locations, which makes life easier for bioperl-db system. Also, changed sub_Location method for Split Locations, now only ordered if the order paramter is defined, to get EMBL dumping to print them in the same way they were parsed in

Handle undefined order parameter as a '0'

Merged heikki's location fixes to branch

Bio::PrimarySeq

Seq method failed when resetting its value to because _guess_type method throws an exception.

Seq method failed when resetting its value to because _guess_type method throws an exception.

Added validate_seq() and made seq() call it for validation.

Added validate_seq(). (Merge from main trunk.)

Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.

Validate_seq() accepts '?' characters into sequence

Bio::PrimarySeqI

Added validate_seq().

Removed validate_seq().

Translate() rewrite, ~4x faster. Suggested by Amir Karger

Bio::Root::Err

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Root::IO

Bug #903 fixed

Attempt at migrating rmtree in to IO.pm -- need to be sure that this will work in case of static obj call

Proper calling of package method

Fixed Issue #0503

Prevent a recursion loop from happening in older perl

Use syntax for perl 5.004 class method calling and dirs are removed

Handle dos linefeeds

Doc fix, unnecessary argument removed

Bio::Root::IOManager

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Root::Object

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Root::RootI

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Root::Utilities

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Root::Vector

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Root::Xref

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Search::Hit::HitI

Update mailing list even on those modules that are deprecated

Bio::Seq

Added implementation of validate_seq().

Added flush_SeqFeatures().

Mailing list update - purge references to bielefeld list

Mailing list update, doc formatting

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Set $VERSION to 0.9

Refixed $VERSION

Bio::Seq::LargePrimarySeq

Make sure initialize_io is called to insure tempfile cleanup

Bio::Seq::RichSeq

Underscoralize hash keys

Leading underscores for data keys in $self hash

Bio::SeqFeature::Exon

Added feature types Exon, Intron, UTR5, UTR3, Promoter, and PolyA. These all inherit from SeqFeature::Generic, but report themselves as the appropriate type when queried with an isa. They are absolutely bare bones at the moment, but there is lots of space for fleshing them out with additional methods and properties.

This is on Marks orders to fix a cvs problem

Rewrote my Exon object to be compatible with Hilmars GeneStrucuture objects, but without the restrictions on the generic feature tags. Initial tests have been successful, but I havent used GeneStructure objects enough to know how to test it rigorously. Some of the code is copied directly from Hilmars Exon object. Hilmar, can you do this testing when you get back?

Bio::SeqFeature::Gene::GeneStructure

Fixed a bug reported by Mark W.

Fixed a bug reported by Mark W.

Bio::SeqFeature::Gene::Transcript

Fixed bug reported by Mark W.

Fixed a bug reported by Mark W.

Bio::SeqFeature::Generic

Bug #947 fixed

Bug #970

Fixed bug #970

Fixed bug #947 on 0.7 branch

Changed Bio::SeqFeature::Generic so that it does not require new() to init data structures in the new object

Bio::SeqFeature::Intron

Added feature types Exon, Intron, UTR5, UTR3, Promoter, and PolyA. These all inherit from SeqFeature::Generic, but report themselves as the appropriate type when queried with an isa. They are absolutely bare bones at the moment, but there is lots of space for fleshing them out with additional methods and properties.

Features now initialized with a SUPER::new call, and removed Exon.pm because Hilmar as a much better one.

Bio::SeqFeature::PolyA

Added feature types Exon, Intron, UTR5, UTR3, Promoter, and PolyA. These all inherit from SeqFeature::Generic, but report themselves as the appropriate type when queried with an isa. They are absolutely bare bones at the moment, but there is lots of space for fleshing them out with additional methods and properties.

Features now initialized with a SUPER::new call, and removed Exon.pm because Hilmar as a much better one.

Bio::SeqFeature::Promoter

Added feature types Exon, Intron, UTR5, UTR3, Promoter, and PolyA. These all inherit from SeqFeature::Generic, but report themselves as the appropriate type when queried with an isa. They are absolutely bare bones at the moment, but there is lots of space for fleshing them out with additional methods and properties.

Features now initialized with a SUPER::new call, and removed Exon.pm because Hilmar as a much better one.

Bio::SeqFeature::UTR3

Added feature types Exon, Intron, UTR5, UTR3, Promoter, and PolyA. These all inherit from SeqFeature::Generic, but report themselves as the appropriate type when queried with an isa. They are absolutely bare bones at the moment, but there is lots of space for fleshing them out with additional methods and properties.

Features now initialized with a SUPER::new call, and removed Exon.pm because Hilmar as a much better one.

Bio::SeqFeature::UTR5

Added feature types Exon, Intron, UTR5, UTR3, Promoter, and PolyA. These all inherit from SeqFeature::Generic, but report themselves as the appropriate type when queried with an isa. They are absolutely bare bones at the moment, but there is lots of space for fleshing them out with additional methods and properties.

Features now initialized with a SUPER::new call, and removed Exon.pm because Hilmar as a much better one.

Bio::SeqIO

Doc update: example on how to do SeqIO into a string

Doc update: example on how to do SeqIO into a string

Bio::SeqIO::FTHelper

Better parse/writing of locations listed on different sequences. I think that location parsing is still a bit inflexible and we probably can't really parse nested sub_locations (splits of splits) which would violate the dogfoodability of bioperl, perhaps we have to go to a different parsing scheme for the next version

Commented out debugging line printing "dogfood location is..." :-)

Bug #930 parsing complement(join(...)) FT lines

Bug #930 protecting case when seqfeature is undef-ed (not really a safe way to do things...) when line is unparseable

Fixed bug #952

Removed debugging print statement

Added is_remote method to Simple Locations, which makes life easier for bioperl-db system. Also, changed sub_Location method for Split Locations, now only ordered if the order paramter is defined, to get EMBL dumping to print them in the same way they were parsed in

Merged FTHelper fixes for remote locations to branch

Protect against non SeqFeature::Generic features when writing a sequence out score and frame are not part of SeqFeatureI

Protect against non SeqFeature::Generic features when writing a sequence out score and frame are not part of SeqFeatureI

Fix for bug #965

Bug #965 test and fix

Commented out subseqfeature locations FT string printing, Jason to check

Removed STDERR

Minor missing things for the release

Bio::SeqIO::embl

Added guessing of seq->molecule based on seq->primary_seq->moltype and viceversa assigning of seq->primary_seq->moltype based on seq->molecule, purely for EMBL dumping purposes

Silly me... XXX is an EMBl thing, not a bioperl acceptmoltype

More strict embl writing

More strict embl writing,support for PUBMED

PubMed support, accesion versioon printing correctly

Bio::SeqIO::fasta

Added Alignment output for psiblast searches

Use display_id() for printing identifier

Use display_id() for printing identifier

Index.t changes

Bio::SeqIO::game

Bug #912 fixed -- added documentation

Bio::SeqIO::game::featureHandler

Bug #912 fixed -- added documentation

Bio::SeqIO::game::idHandler

Bug #912 fixed -- added documentation

Added RootI inheritance

Bio::SeqIO::game::seqHandler

Bug #912 fixed -- added documentation

Bio::SeqIO::genbank

Applied fixes submitted by Malcolm Cook <Malcolm.Cook@ppgx.com>.

Merged fixes suggested by Malcolm Cook.

Bug #956

Bug #956

Bug #950, stricter genbank formatting support for MEDLINE/PUBMED parsing & writing

Bug #950, strict writing of genbank format added support for MEDLINE and PUBMED parsing/writing as part of references

Die calls converted to throw calls

Bio::SeqIO::pir

Remove pir from 0.7 branch since it does not work

Bio::SeqIO::scf

Replaced STDIN by $fh in new() (bug report #920).

Bio::SeqIO::swiss

Fixes from emmanuel for more detailed swissprot format

Fixes from emmanuel for more detailed swissprot format - main trunk

Corrected _crc64 method which was wrong!!!

Corrected _crc64 method

Bug #946 - fixed regex per bug when parsing TrEMBL swissprot. This occurs becuase TrEMBL lists the id on the ID line as just an accession while SwissProt has ID_DIVISION

Migrated fix for bug #946 to branch

Doc fix

Better protecting of ! Bio::Seq::RichSeqI sequences being printed Handle all gene names through each_gene_name rather than deprecated gene_name

Better protecting of non Bio::Seq::RichSeqI sequences being printed Handle all gene names through each_gene_name rather than deprecated gene_name and join with the proper 'OR ' syntax

JitterIssue #2001

JitterIssue #2001

Bio::SimpleAlign

Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.

New method: slice()

Column_from_residue_number() uses now identically named method in LocatableSeq get_seq_by_pos() Gets one sequence based on its position in the alignment select() creates a new alignment from a continuous range of sequences dot() remaps residue columns to "dot" notation. output only!

Fixed a bug percentage_identity()

Minor formatting and underscoring of private data variables

Underscoralize private data variables because I'm a picky mofo

Reorganized methods into logical categories

Attribute setting methods missing_char(), unknown_char(), match_char(), gap_char() work now.

Removed unknown_char(). I do not know where I got that from. missing_char() does the same thing

Bio::Tools::BPbl2seq

Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.

Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.

Bio::Tools::BPlite

Doc fixes

Doc fixes

The solution yesterday was a bit too simplistic and failed if you started skimming over reports without ever parsing them by iteratively using the ->_parseHeader call. This is now fixed. In addition, it was necessary to distinguish between an empty Blast result, and the end of the input stream. _parseHeader now returns 0 for an empty Blast result, and -1 for an EOF. The return of 0 is usually not necessary to catch because the call to ->nextSbjct will also return 0 under these circumstances. I also made some changes to the documentation to correct some documented calls to a routine ->sbjct, which is actually ->subject. See the revised Synopsis for an example of usage. Please let me know if my changes are buggering anyone up...

Documentation fixes.

Documentation fixes.

Merged from main trunk the capability to parse multiple reports.

Applied Steve L.'s fix for bug #935.

Merged Steve L.'s fixes from branch (bug #935).

Added Alignment output for psiblast searches

Bio::Tools::BPlite::HSP

JB 949 - Creates too many warnings for blastx report. Future enhancement to BPLite::_parseHeader needed to set report type so that subject strand is used with tblastn and query strand with blastx

JB 949 - Creates too many warnings for blastx report. Future enhancement to BPLite::_parseHeader needed to set report type so that subject strand is used with tblastn and query strand with blastx

Fix small scientific values and validate P as numberic (Blast chooses to be different when reporting small values.)

Fix small scientific values and validate P as numberic (Blast chooses to be different when reporting small values.)

Oops method name was supposed to be percent not P

More stringent P checking, method name corrected, again - we lost percent in previous fixes

Bio::Tools::BPlite::Iteration

Added Alignment output for psiblast searches

Bio::Tools::BPlite::Sbjct

Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.

Bio::Tools::BPpsilite

Remove old doc cruft

Added Alignment output for psiblast searches

Bio::Tools::Blast

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Tools::CodonTable

Translate() rewrite, ~4x faster. Suggested by Amir Karger

Bio::Tools::Fasta

Corrected old mailing lists.

Merging over fixes from branch-07.

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Tools::GFF

Modified the GFF2 parser such that semicolons in the free-text value field of a tag/value pair will not break the parse. It is an ugly hack, and if I ever find time to make it better I promise to go back in and fix it... but it works for now anyway.

Fixed an error reported by Ann Loraine where the GFF attributes parser choked on having a quoted pound sign. It now recognizes quoted pound signs as NOT being the start of the comments field. The first un-quoted pound sign IS considered the start of the comments field. Sorry 'bout that all you who were affected by this.

Silenced perl by properly initializing the infamous loop variable $a. ;)

Merged over some fixes by Mark W. from the main trunk.

Bio::Tools::Genemark

Genemark.hmm eu- and prokaryot (2.2-1.3) parser, a adaptation of Genscan.pm

Small bugfixes + parse out date&matrixfile

Fixed wrong index to determine type of exon.

Updated: recognizes next gene based on gene-number instead of an empty line between two genes

Extacts cds from original sequence now since genemark does not give a predicted cds (my version does not in every case)

Added possibilty to get cds based on original sequence + small bugfixes

Get seqname from seqfile at least for now, Mark F and Jason to hash over details later, this lets test pass in t/Genepred.t

Bio::Tools::Genscan

Added parsing of the matrix name in analysis_subject()

Bio::Tools::Grail

Added Grail skeleton code

Bio::Tools::HMMER::Results

Added updated HMMER files; passes tests

Moved HMMER to main trunk. Fixed 76 --> 77 tests in BPlite

Bio::Tools::Prediction::Exon

Primary tag setting for predicted exon

Undo my bad changes

Bio::Tools::Prediction::Gene

Update mailing list even on those modules that are deprecated

Bio::Tools::RestrictionEnzyme

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Tools::Run::RemoteBlast

Pure perl (via HTTP) Remote blast submission and retrieval -- see test script for example usage

Quieter tests when verbose == 0, use tempfile for HTML -> text cleanup

Fixed tempfile filehandle handling in retrieve_blast().

Updated to use ncbi Blast.cgi script rather than blast.cgi Text formatting done by cgi rather than HTML tag stripping in module code

Status set to invalid on a failed retrieval

Bio::Tools::Run::StandAloneBlast

Io was not initialized, meaning tempfiles were not cleaned up - better argument matching

Intitialize io -- facilitate tempfile cleanup

Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.

Bio::Tools::SeqAnal

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Tools::SeqPattern

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Tools::SeqStats

Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.

Bio::Tools::Sigcleave

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Tools::WWW

Corrected mailing lists.

Merging over fixes from branch-07.

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Tools::pSW

Corrected MailList.*s*html link.

Merging over fixes from branch-07.

Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.

Bio::UnivAln

Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Variation::AAChange

Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation

Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Variation::AAReverseMutate

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Variation::Allele

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Variation::DNAMutation

Separator was missing from systematic name when mutation was 'complex' Fixed sysname method.

Separator was missing from systematic name when mutation was 'complex' Fixed sysname method.

Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation

Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Variation::IO

Removed redundant 'use Symbol'

Removed redundant 'use Symbol'

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Variation::IO::flat

Fixed Variation::IO::flat insertion locations from "55^55" into "54^55"

Fixed Variation::IO::flat insertion locations from "55^55" into "54^55"

Distance from region edge handled now

Distance from region edge handled now

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Variation::IO::xml

Distance from region edge handled now

Distance from region edge handled now

The xml output now separates each label inside individual element tags rather than pooling all into one.

The xml output now separates labels inot individual tags rather than pooling them into one.

Swapped the order of two elements for consistent output. \nBackward compatibel change

Swapped the order of two elements for consistent output. \nBackward compatibel change

XML::Writer was complaining about empty attribute values. Lesson: always run tests with -w!

XML::Writer was complaining about empty attribute values. Lesson: always run tests with -w!

Moved from XML::Node to XML::Twig in XML parsing

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Variation::RNAChange

Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation

Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Variation::SeqDiff

Fixed method alignment for nontranslated locations

Fixed method alignment for nontranslated locations

Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation

Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Bio::Variation::VariantI

Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation

Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation

$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)

Makefile.PL

Moved from XML::Node to XML::Twig in XML parsing

Updated MANIFEST and MANIFEST.skip to reflect new files in this distro. Also updated Makefile.PL to change the distro version number to 0.7.1pre --Chris Dagdigian

Update version to 0.7.1 for release

bioperl.lisp

Updated to new Bio::Root::RootI system

Dos2unix and better formatting for us emacs users

bptutorial.pl

Moved from XML::Node to XML::Twig in XML parsing

Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.

examples/clustalw.pl

Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.

examples/hitdisplay.pl

Bug #915 verifies that Bio::Tk::HitDisplay is actually installed before running script

Bug #915 verifiesthat Bio::Tk::HitDisplay is actually installed before running script

examples/psw.pl

Updated psw.pl to work with AlignIO.pm

Merged Peter S.'s fixes on the main trunk.

examples/remote_blast.pl

Example of how to use Bio::Tool::Run::RemoteBlast

Doc fix

examples/simplealign.pl

Updated simplealign.pl to work with AlignIO.pm

Merged Peter S.'s changes on the main trunk.

examples/standaloneblast.pl

Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.

examples/test-genscan.pl

Bug #917

Bug #917

Bug #917 - s/poly_A_sites/poly_A_site/

models/bio_liveseq_variation.dia

Bio::LiveSeq and Bio::Variation diagrams with methods

models/bioperl.dia

Initial commit of bioperl UML -- we can tag it to specify version

Added Bio::Variation UML

Added package for Bio::LiveSeq

scripts/DB/dbfetch

Initial version

Fixed polypeptide mutated allele for frameshifs

scripts/bpfetch.pl

Mailing list doc update

Added support for DB::EMBL and fixed mailing list doc info

scripts/bpindex.pl

Mailing list doc update

Added support for DB::EMBL and fixed mailing list doc info

scripts/gb_to_gff.pl

Turn a genbank file into a gff file suitable for gff2ps