Core 0.6.2 0.7.0 delta

These are detailed notes on changes made between release-06-2 and release-0-7-0.

Bio::AlignIO

Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)

RootI compliance and some documentation reformatting

Quoted unquoted string literals used as hash keys.

Changed to new RootI chained new structure

Cleanup to support 5.00404

Corrected error in documentation (SYNOPSIS)

Bio::AlignIO::bl2seq

Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)

RootI compliance

Quoted unquoted string literals used as hash keys.

Changed to new RootI chained new structure

Cleanup to support 5.00404

BPlite changes to make BPlite a SeqAnalysisParserI object BPbl2seq now requires named input parameter (no longer can just pass in filehandle reference, must pass in -fh => $filehandle) Assundry changes made to related files to handle these changes

Bio::AlignIO::clustalw

Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)

RootI compliance

Changed to new RootI chained new structure

Fixed clustalw alignIO module to honor input file order

Bio::AlignIO::fasta

Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)

RootI compliance

Changed to new RootI chained new structure

Bio::AlignIO::mase

Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)

RootI compliance

Changed to new RootI chained new structure

Bio::AlignIO::msf

Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)

RootI compliance

Changed to new RootI chained new structure

Changed code needing a checksum to use SeqIO::gcg->GCG_checksum().

Bio::AlignIO::pfam

Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)

RootI compliance

Changed to new RootI chained new structure

Bio::AlignIO::prodom

Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)

RootI compliance

Changed to new RootI chained new structure

Bio::AlignIO::selex

Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)

RootI compliance

Changed to new RootI chained new structure

Bio::AlignIO::stockholm

Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)

RootI compliance

Changed to new RootI chained new structure

Cleanup to support 5.00404

Bio::Annotation

Got annotation objects up to 0.7 spec. Made tests more robust to non present modules

Changed to new RootI chained new structure

Corrected syntax error in documentation (SYNOPSIS)

Corrected documentation (SYNOPSIS) Bio::Pfam::Annotation -> Bio::Annotation

Added add/remove/each_gene_name(). Made gene_name() deprecated.

Bio::Annotation::Comment

Got annotation objects up to 0.7 spec. Made tests more robust to non present modules

Changed to new RootI chained new structure

Bio::Annotation::DBLink

Got annotation objects up to 0.7 spec. Made tests more robust to non present modules

Changed to new RootI chained new structure

Bio::Annotation::Reference

Got annotation objects up to 0.7 spec. Made tests more robust to non present modules

Changed to new RootI chained new structure

Bio::DB::Ace

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Bio::DB::GDB

Changed to new RootI chained new structure

Length set properly and include HTML::Parser explictly

Length is really in kilobases

Removed reference to bioperl-guts-l list.

Documentation cruft fix

Fail gracefully on no network connection

Bio::DB::GenBank

Migrated to use LWP

Some bulletproofing

Added a swissprot lookup via web expasy can be customized to be used on a local expasy

Changed IO::String creation to OO style. Would not work otherwise.

Even though we are going to revamp this module, missing a 'use IO::String' causes it to fail

Centralized common code in Bio::DB::WebDBSeqI and Bio::DB::NCBIHandler This reorganized Bio::DB::GenPept and Bio::DB::GenBank to use a centralized module and LWP

Fixed the documentation of several methods.

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Bio::DB::GenPept

Added a swissprot lookup via web expasy can be customized to be used on a local expasy

Centralized common code in Bio::DB::WebDBSeqI and Bio::DB::NCBIHandler This reorganized Bio::DB::GenPept and Bio::DB::GenBank to use a centralized module and LWP

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Bio::DB::NCBIHelper

Added Bio::DB::NCBIHelper to centralize code for communicating with NCBI web sequence databases

Fixed request_method() not to ignore a value it doesn't find in the table of predefined formats. Fixed documentation of this method.

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Bio::DB::SRS

Added experimental SRS module for sequence retrieving

Hilmar told me to delete this

Bio::DB::SwissProt

Added a swissprot lookup via web expasy can be customized to be used on a local expasy

Did not need Batch request for swissprot

Corrected include stmt

Changed IO::String creation to OO style. Would not work otherwise.

Updated to use Bio::DB::WebDBSeqI interface

Quoted unquoted string literals used as hash keys.

Suppressed one-at-a-time warning for array refs if array has only one element.

Changed to new RootI chained new structure

Bio::DB::WebDBSeqI

Removed TEMPDIR in DESTROY

Quoted unquoted string literals used as hash keys.

Fixed get_Seq_XXX() methods to delegate to get_Stream_XXX() methods. Fixed a bug in a get_Stream_XXX() method (-mode not specified). Fixed documentation of request_method().

Changed to new RootI chained new structure

Removed File::Spec dependancy, tempfile creation is handled in Bio::Root::RootI now

Changed to adopt Bio::Root::IO.

Bio::DBLinkContainerI

RootI compliance and some documentation reformatting

Removed reference to bioperl-guts-l list.

Bio::Factory::DriverFactory

Initial revision.

Added driver_table() and more documentation.

Fixed _load_module() to construct the module's pathname platform independently (hopefully).

Use Root::IO to do catfile in file loading methods rather than File::Spec of DriverFactory

Bio::Factory::SeqAnalysisParserFactory

Initial revision.

Added hmmer and blast (bplite as a synonym) to supported methods.

Added GFF and Sim4.

Bio::Factory::SeqAnalysisParserFactoryI

Initial revision.

Added documentation. Corrected documentation bugs.

Bio::Index::Abstract

RootI compliance and some documentation reformatting

Changed to new RootI chained new structure

Accidentially removed use DB_File, caused a bug also removed routine verbose as this is handled by upstream Bio::Root::RootI behaviour is to print msgs to STDERR when verbose > 0

Bug #860 fixed Index now supports dynamic including of dbm_package

Removed reference to bioperl-guts-l list.

Update to RootI

Updated to work with File::Spec from perl 5.00503 which does not have cwd or rel2abs

Fixed new location of FILESPECLOADED.

Bio::Index::AbstractSeq

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Update to RootI

Bio::Index::EMBL

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Bio::Index::Fasta

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Bio::Index::GenBank

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Bio::Index::SwissPfam

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

†corrected documentation error (SYNOPSIS)

Bio::Index::Swissprot

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Fixed bug #874. (Needed also code to reset @acc and $id.)

Bio::LiveSeq::AARange

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.

Fixed LiveSeq for 5.0004 compatbility

Quoted unquoted string literals used as hash keys.

Bio::LiveSeq::Analyser

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.

Bio::LiveSeq::Chain

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.

Slight modifications done when creating the tests.

Fixed LiveSeq for 5.0004 compatbility

Quoted unquoted string literals used as hash keys.

->label_exists gave a warning as a side effect when label did not exist

Bio::LiveSeq::ChainI

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

Bio::LiveSeq::DNA

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.

Quoted unquoted string literals used as hash keys.

Bio::LiveSeq::Exon

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.

Quoted unquoted string literals used as hash keys.

Bio::LiveSeq::Gene

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.

Fixed LiveSeq for 5.0004 compatbility

Quoted unquoted string literals used as hash keys.

Method delete_Obj added to all LiveSeq objects. Since they contain circular references, memory was not freed properly after losing the $gene (top level) reference. Thanks to Arne for help on this.

Fixed small Issue #1215 /Bio/LiveSeq/Gene.pm: lines 380, 385, 393

All tests pass on 5.0004 except GDB.t! Hurray!

Bio::LiveSeq::IO::BioPerl

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.

Fixed LiveSeq for 5.0004 compatbility

Quoted unquoted string literals used as hash keys.

Changed EMBL-feature loading code to use the new SplitLocation

Fixed call of deprecated each_secondary_accessions().

$featlocation->isa('Bio::Location::FuzzyLocationI') code added. Tests pass again.

LocationI and Coordinate Polisy now in place, I could remove the code added to take FuzzyLocations into account. In effect reverted to version 1.7.

Bio::LiveSeq::IO::Loader

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

Restructured Mutator.pm. Added Mutation.pm to hold mutation information. Tests for both. Example script.

- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.

Slight modifications done when creating the tests.

No more warnings. $exoncount and $introncount array index variables were not initialized to 0 before using.

Quoted unquoted string literals used as hash keys.

Default to 0 if element is undef in 'rangeofarray'

Added 'use Bio::Tools::CodonTable'. This wasn't expected to and indeed doesn't fix the errors triggered in t/LiveSeq.t.

Bio::LiveSeq::IO::SRS

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.

Quoted unquoted string literals used as hash keys.

Bio::LiveSeq::Intron

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.

Bio::LiveSeq::Mutation

Restructured Mutator.pm. Added Mutation.pm to hold mutation information. Tests for both. Example script.

Corrected a minor bug that denied mutation inputs with length==0

Bio::LiveSeq::Mutator

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

Restructured Mutator.pm. Added Mutation.pm to hold mutation information. Tests for both. Example script.

Moved the pre CVS history away from the module: # Version history: # Thu Apr 13 18:09:55 BST 2000 v 1.0 begun # Thu Apr 13 19:15:28 BST 2000 v 1.1 first tentative version, to be tested # Fri Apr 14 03:13:18 BST 2000 v 1.2 deIssue #2000 v.2.75 complete rewrite into a class

Fixed some errors that were causing messages in make test

- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.

Quoted unquoted string literals used as hash keys.

Coded the workaround to understand if rna is affected in the case where some new labels have been inserted (requiring the use of the method follow() instead than the faster but errorprone use of < and >). Introduced an "RNApostlabel" to fix the problems of "end of exon" mutations when retrieveing the RNAdownstreamsequences.

Bio::LiveSeq::Prim_Transcript

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.

Bio::LiveSeq::Range

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.

Bio::LiveSeq::Repeat_Region

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.

Bio::LiveSeq::Repeat_Unit

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.

Bio::LiveSeq::SeqI

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

Fixed some errors that were causing messages in make test

- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.

Fixed LiveSeq for 5.0004 compatbility

Quoted unquoted string literals used as hash keys.

Method delete_Obj added to all LiveSeq objects. Since they contain circular references, memory was not freed properly after losing the $gene (top level) reference. Thanks to Arne for help on this.

Fixed small Issue #1215 /Bio/LiveSeq/Gene.pm: lines 380, 385, 393

Removed DOS LFs

Bio::LiveSeq::Transcript

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

Fixed some errors that were causing messages in make test

- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.

Slight modifications done when creating the tests.

Fixed some more warnings.

Fixed LiveSeq for 5.0004 compatbility

Quoted unquoted string literals used as hash keys.

Fixed doc format bug.

Bio::LiveSeq::Translation

1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana

- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.

Quoted unquoted string literals used as hash keys.

Bio::LocatableSeq

RootI compliance and some documentation reformatting

Moved PrimarySeq and Seq to RootI style news. Fixed the knock on effects. LargeSeq/LargeFasta fail - cant fix them

Bio::Location::AvWithinCoordPolicy

Initial revision.

Bio::Location::CoordinatePolicyI

Initial revision.

Documentation update (more precide about return type).

Bio::Location::Fuzzy

Split, Fuzzy Location

Separate method for range fuzziness (not just start/end fuzziness)

Current solution to Fuzziness, still needs to be worked on to handle more cases

Complete fuzzy feature cycle of in fuzzy feature -> out fuzzy feature via SeqIO::genbank works

Handle SNP variations more properly and better SplitLocation handling -- handle 'order' and 'join'

More robustness for Location handling -- especially better handling of Fuzziness

Correct location behavior to return min_start == max_start when start is defined SplitLocation->start will return the value of the 1st (sorted) contained location Location.t was updated to test for this as well

Start/end default to '0' when start/end are fuzzy -- this is instead of undef

Corrected to handle Location start/end as '0' when point is fuzzy

Changed _fuzzyencode to _fuzzydecode. Made sure this returns proper type/min/max, setting the right end possibly to undef. Adapted hash of patterns accordingly. Changed way of storing/setting coordinates, is now fully overridable. Works with coord policy.

Fixed missing check for reverse strand feature location string should include complement and fixed Fuzzy::to_FTstring to properly return fuzzified location string

More fixes to Fuzzy location string generation and extra tests to help

Location output strings corrected for fuzzy

Corrected documentation

Bio::Location::FuzzyLocationI

Moved to Location object

Added some documentation to the interfaces

Split, Fuzzy Location

Separate method for range fuzziness (not just start/end fuzziness)

Current solution to Fuzziness, still needs to be worked on to handle more cases

Complete fuzzy feature cycle of in fuzzy feature -> out fuzzy feature via SeqIO::genbank works

Handle SNP variations more properly and better SplitLocation handling -- handle 'order' and 'join'

Corrected documentation for _fuzzypointencode() and _fuzzyrangeencode().

More robustness for Location handling -- especially better handling of Fuzziness

Corrected a doc bug.

Corrected documentation

Bio::Location::NarrowestCoordPolicy

Initial revision.

Corrected doc bug.

Removed 'use Bio::LocationI': not needed and may cause a loop (due to the BEGIN block in Bio::LocationI).

Bio::Location::Simple

Moved to Location object

Added some documentation to the interfaces

Current solution to Fuzziness, still needs to be worked on to handle more cases

More robustness for Location handling -- especially better handling of Fuzziness

Revised way of storing the coordinates. min/max now don't call start/end. Improved documentation.

Fixed missing check for reverse strand feature location string should include complement and fixed Fuzzy::to_FTstring to properly return fuzzified location string

Bio::Location::Split

Split, Fuzzy Location

Max_end/min_start added

Handle SNP variations more properly and better SplitLocation handling -- handle 'order' and 'join'

More robustness for Location handling -- especially better handling of Fuzziness

Correct location behavior to return min_start == max_start when start is defined SplitLocation->start will return the value of the 1st (sorted) contained location Location.t was updated to test for this as well

DB.t now skips tests correctly

Corrected to handle Location start/end as '0' when point is fuzzy

Added implementation of is_single_sequence(). Revised several methods to work with coord policy. Revised sorting in sub_Location() (now also deals with sublocs on more than one seq). Added documentation.

Fixed missing check for reverse strand feature location string should include complement and fixed Fuzzy::to_FTstring to properly return fuzzified location string

Corrected documentation

Bio::Location::SplitLocationI

Moved to Location object

Added some documentation to the interfaces

Split, Fuzzy Location

Max_end/min_start added

Handle SNP variations more properly and better SplitLocation handling -- handle 'order' and 'join'

More robustness for Location handling -- especially better handling of Fuzziness

Removed method that forced SplitLocationI implementations to be mutable

Added is_single_sequence().

Corrected documentation

Bio::Location::WidestCoordPolicy

Initial revision.

Removed 'use Bio::LocationI': not needed and causes a loop (due to the BEGIN block in Bio::LocationI).

Bio::LocationI

Moved to Location object

Added some documentation to the interfaces

Seq_id method added

More robustness for Location handling -- especially better handling of Fuzziness

Added coordinate_policy().

Corrected documentation

Bio::PrimarySeq

Added id() method (copy from Seq.pm)

Removed debugging cruft

Safer length call

Fixed regex bug in _guess_type

Moved PrimarySeq and Seq to RootI style news. Fixed the knock on effects. LargeSeq/LargeFasta fail - cant fix them

Doc bug

Changed to new RootI chained new structure

Added capability of initializing to an empty sequence.

Changed hash access to method seq() call in substr(), length(), and _guess_type().

Moved initialization stuff to the top for better maintenance.

Bio::PrimarySeqI

Interface should define desc - even as abstract

Added PrimarySeqI->translate fixes from Alex Bateman that speed up translating 2x. Unambiguous two character codons at the end of the sequence [like 'AC' (ACN > T) and 'GT' (GTN > V)] did not translate to an amino acid when PrimarySeqI->translated! Fixed that. Added tests.

The last option to translate (throw or warn when errors in fullCDS translating) was implemented wrong way round. Added testing for terminator codons inside CDS.

Removed documentation for deprecated methods. Reorganized ordering of methods to move private and deprecated ones to the end. Changed way of object creation in trunc(), translate(), and revcom().

Reverted to choosing class of sequence to be instantiated in trunc/revcom/translate, based on can_call_new().

Removed GCG_checksum() (now in SeqIO::gcg).

Bio::Range

Corrected documentation (-end instead of -stop) and fixed _new() to allow also 0 as coordinate.

RootI compliance and some documentation reformatting

Quoted unquoted string literals used as hash keys.

Changed to new RootI chained new structure

Clean up of Bio::Range and Bio::RangeI. Attributes can now be set one by one in Bio::Range. Doc fixes. Methods now check that attributes are set before doing operations. Important: Interface for methods 'union' and 'intersection' redifined. Both now return an object.

Bio::RangeI

Corrected documentation (-end instead of -stop).

RootI compliance and some documentation reformatting

Corrected copy-paste errors in documentation. Added documentation for strand option.

Slightly safer check to be sure it is a range object in contains()

Clean up of Bio::Range and Bio::RangeI. Attributes can now be set one by one in Bio::Range. Doc fixes. Methods now check that attributes are set before doing operations. Important: Interface for methods 'union' and 'intersection' redifined. Both now return an object.

Bio::Root::Err

Bugs 855 857 863

This test will only work from bioperl-live/

Removed reference to bioperl-guts-l list.

Fixing :std bug again

Bio::Root::IO

Initial revision.

A couple of fixes. Added $FILESPECLOADED (redundant to !$PATHSEP, though). Added recognition of -input.

Changed to be literal string rather than doubled quote to prevent interpretation of \T in C:\TEMP

Tests to verify tempfiles are being removed

Removed some debugging cruft and theoretically added protection for case when File::Spec is installed but tempdir is not included (perl 5.004)

Too many ')'

Test to see that 'can' call 'tempfile' even when File::Temp is loaded

Correct 'can' syntax to make 5.005 happy. Sigh

Added automatic registration of _io_cleanup(). Added _io_cleanup(), which simply delegates to DESTROY.

For unkown reasons the loop to DESTROY ended up in recursion, even though I thought I prevented this. Moved functionality to _io_cleanup(), removed DESTROY.

Bio::Root::IOManager

Removed reference to bioperl-guts-l list.

Bio::Root::Object

Removed reference to bioperl-guts-l list.

Added note about deprecation to documentation. Added warning to _initialize().

Bio::Root::RootI

Fix in Bio::Root::RootI::_rearrange

Beginning the migration to RootI only

Got annotation objects up to 0.7 spec. Made tests more robust to non present modules

RootI new changed to check if caller is a reference or a class

Added correction for storing verbose value A more correct solution to all the (verbose,strict) needs to be implemented in the new RootI code

Tempfile and tempdir capability added

Removed debugging code

Always remove tmp files even if created by File::Temp

Better tempfile/tempdir handling

Quoted unquoted string literals used as hash keys.

Refactored RootI to handle chained new instead of chained _initialize left an empty _initialize for backwards compatibility verbose, strict, should work now

Fixed doc format bug.

Refactored (heavily) RootI. Alot of code removal. I think it is short and sweet now

Test LargeSeq, added better inheritance model

Lost comma, uncessary use

Cleanup to support 5.00404

Changed verbose() to resort to default $VERBOSITY if called as a class method. The consequence is that warn() and throw() are now callable as class methods (which is convenient, isn't it).

Moved tempfile() etc to Bio::Root::IO. Also moved loading attempts of File::Spec and friends.

Added a toplevel (empty) DESTROY so that all objects have a DESTROY method (was causing IUPAC tUPAC, which uses AUTOLOAD, to complain)

Properly removing tempfiles

Added DESTROY and _register_for_cleanup().

Bio::Root::Utilities

Removed reference to bioperl-guts-l list.

Copied code from IOManager to ignore alarm() if it's not provided in the runtime system.

Changed inheritance to RootI. Changed date_format() to accept also a epoch time to be formatted. Changed file_date() to use stat instead of 'ls -gla'; the date will be taken from the mtime field.

Bio::Root::Vector

Removed reference to bioperl-guts-l list.

Corrected ambiguity due to Vector.pm's shift() sub

Bio::Root::Xref

Removed reference to bioperl-guts-l list.

Bio::Search::Hit::Fasta

Likely meaningless changes as we will probably chuck these modules

Removed premature and currently unmaintained modules.

Bio::Search::Hit::HitI

Removed premature and currently unmaintained modules.

Bio::Search::Processor

Likely meaningless changes as we will probably chuck these modules

Removed premature and currently unmaintained modules.

Bio::Search::Result::Fasta

Likely meaningless changes as we will probably chuck these modules

Removed premature and currently unmaintained modules.

Bio::Search::Result::ResultI

Likely meaningless changes as we will probably chuck these modules

Removed premature and currently unmaintained modules.

Bio::SearchDist

RootI compliance and some documentation reformatting

Migrate to chained new with new Bio::Root::RootI

Fixed RootI-transition related bugs. Fixed other bugs consisting of calling non-existent functions etc. Did this module ever work? The call to fit_EVD() still needs to be fixed, because the C-function expects one additional parameter.

Fix compile time error; now have a run-time error for SearchDist

Fixed searchdist stuff. Not a numerically sensible test, but ensures you can actually call the routines

Bio::Seq

Changed documentation for display_id() (get/set) Made id() a real synonym for display_id (get/set) Removed unused variable declarations in primary_id()

Commented out fetch_SeqFeature. Is not required by any interface, and is not implemented.

RootI compliance and some documentation reformatting

Moved PrimarySeq and Seq to RootI style news. Fixed the knock on effects. LargeSeq/LargeFasta fail - cant fix them

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Added documentation to {top,all}_SeqFeature() methods. Removed unnecessary code and documentation.

Added RichSeq implementation - converted genbank/embl/swiss to use this - all tests pass. LiveSeq calls some deprecated methods

Made SeqI interface broader to include some methods from Seq

Added an empty DESTROY method to keep the autoloader from IUPAC.pm happy -- I know this is stupid, but I caused tempfile cleanup problems adding a blank DESTROY to RootI.pm

Bio::Seq::LargePrimarySeq

SeqIO support for largge sequence files in fasta format

Corrected where I used same variable name twice

Added better fallbacks for temp dir and next_seq returns a SeqI compliant object

Updated to use File::Temp

Moved PrimarySeq and Seq to RootI style news. Fixed the knock on effects. LargeSeq/LargeFasta fail - cant fix them

Changed over to IO::File for wrapping tempfile handle

Use Bio::Root::RootI for tempfile creation

Unlink file on object destruction don't wait on program to exit (File::Temp's behavior)

Test LargeSeq, added better inheritance model

Changed to adopt Bio::Root::IO.

Switched filehandle from IO::File to GLOB.

Bio::Seq::LargeSeq

Added better fallbacks for temp dir and next_seq returns a SeqI compliant object

Moved PrimarySeq and Seq to RootI style news. Fixed the knock on effects. LargeSeq/LargeFasta fail - cant fix them

Test LargeSeq, added better inheritance model

Lost comma, uncessary use

Fixed mailing lists.

Bio::Seq::RichSeq

Added RichSeq implementation - converted genbank/embl/swiss to use this - all tests pass. LiveSeq calls some deprecated methods

Corrected mailing lists and removed documentation for deprecated methods.

Added documentation (return types) (still insufficient).

Added some documentation and implementation of pid().

Somebody forgot a semicolon in Bio::Seq::RichSeq, which was screwing up GenBank imports

Bio::Seq::RichSeqI

Rich seq interface - 1st attempt

Initial revision.

Completed RichSeqI interface

Added pid() and improved some documentation.

Added returning TRUE at the end of the module.

Bio::SeqAnalysisParserI

RootI compliance and some documentation reformatting

Removed method parse(). Added documentation. Added documentation about expected new() parameters.

Made sure user does not explictly call new on Bio::SeqAnalysisParserI

Bio::SeqFeature::Computation

Generic object for a computation

Changed to take advantage of OO inheritance

Make 1 error message go away

Fixed doc format bug.

Removed due to design changes pending (will be incompatible with the current).

Bio::SeqFeature::FeaturePair

Migrated to RootI compliance

Migrated to new RootI

Moved to Location object

Delegate location to feature1

Bio::SeqFeature::Gene::Exon

Initial revision.

Added is_coding().

Fixed bug in cds().

Improved documentation.

Bio::SeqFeature::Gene::ExonI

Initial revision.

Added is_coding().

Improved documentation.

Bio::SeqFeature::Gene::GeneStructure

Initial revision.

Fixed and improved documentation.

Added warning about experimental status to promoter methods.

Bio::SeqFeature::Gene::GeneStructureI

Initial revision.

Added method introns().

Added warning about experimental status to promoter methods.

Bio::SeqFeature::Gene::Transcript

Initial revision.

Fixed forgotten $self at several places. Added sorting of exon types to exons() if strand is unambiguous. Now passes t/Genpred.t.

Fixed and improved documentation. UTR objects must now also implement Bio::SeqFeature::Gene::ExonI. Changed _make_cds() to omit phase/frame correction at exon boundaries if the next exon doesn't have a valid frame.

Added warning about experimental status to promoter methods.

Bio::SeqFeature::Gene::TranscriptI

Initial revision.

Added warning about experimental status to promoter methods.

Bio::SeqFeature::GeneStructure

Fixed wrong spelling of promoter.

Migrated to RootI compliance

Migrated to new RootI

Obsoleted by Bio::SeqFeature::Gene::* interfaces and stuff.

Bio::SeqFeature::Generic

Corrected passing on arguments to base class in _initialize().

Added mailing lists and author.

Standardization of doc, code layout, and adding explict call to CORE::length over local length routine

Migrated to RootI compliance

Migrated to new RootI

Moved to Location object

The two _from_gff_string routines now handle frame of '.', and also fixed a bug in the import of the attributes field in _from_gff2_string where I originally mis-read the GFF2 docs and was requiring an '=' sign between the tag and the value, which is not correct for GFF2.

Changed location() to check its parameter for implementing Bio::LocationI.

Added documentation for seq method

Added method gff_format() for get/set of the GFF interpreter. Removed _from_gff2_string(). Rewrote _from_gff_string() to delegate to the GFF interpreter. Removed -gff2_string initialization parameter, this is now the default. Added -gff1_string, which automatically installs a GFF1-format interpreter.

Frame of undef means no frame information, using undef rather than '.', however method to reset the frame to 'undef' for an instantiated object

Allow frame to be '.'

Reset frame to undef when user specifies a '.'

Switched BPpl test to == from eq (I guess) for expectation value to deal with formatting changes in expectation 5.0004 <=> 5.6.0

Moved seq formatter to run-time static function rather than compile time loading (which was looped as well)

Fixed a doc bug.

Bio::SeqFeature::Similarity

Migrated to RootI compliance

Migrated to new RootI

Bio::SeqFeature::SimilarityPair

Corrected _initialize().

Migrated to RootI compliance

Migrated to new RootI

Moved to Location object

Bio::SeqFeatureI

Added new method gff2_string, which outputs the feature in GFF2 format as described on the Sanger website. Attribute fields are now semicolon delimited, tags may have more than one space delimited value, free text is quoted and newline and tab characters are translated into their textual equivalents. Please contact me if you find errors in this routine. Mark

RootI compliance and some documentation reformatting

Fix doc so code snippet works (missing comma)

SeqFeature supports location

The gff2_string dumping routine for Features now dumps the attributes in ACeDB tag value format, without an '=' sign between them. This corrects my mis-reading of the GFF2 specs a couple of months ago. sorry.

Added variable $GFF_FORMATTER, initialized to a Bio::Tools::GFF instance with -gff_version set to 2. Removed gff2_string(). Rewrote gff_string(), it now simply delegates to $GFF_FORMATTER.

Moved seq formatter to run-time static function rather than compile time loading (which was looped as well)

Removed left-over GFF_FORMATTER variable.

Bio::SeqFeatureProducer

Added simplified helper class for adding analysis results as features to sequence objects through the SeqAnalysisParserI interface Only MZEF and Genscan were added through the initialize method but GFF and GAME should be considered

Quoted unquoted string literals used as hash keys.

Migrate to chained new with new Bio::Root::RootI

Modules phased out. Functionality moved to Bio::Factory::*.

Bio::SeqFeatureProducerI

Modules phased out. Functionality moved to Bio::Factory::*.

Bio::SeqI

Made SeqI interface broader to include some methods from Seq

Bio::SeqIO

Removed RootI dependence

Quoted unquoted string literals used as hash keys.

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Added warn/exception documentation to next_seq(). Changed validation in moltype() (deferred to Bio::PrimarySeq).

Changed to adopt Bio::Root::IO. Kept _filehandle() as a synonym to _fh().

Bio::SeqIO::FTHelper

Removed RootI dependence

Changed to new RootI chained new structure

FTHelper migrated to use Location::Split & Location::Fuzzy

Separate method for range fuzziness (not just start/end fuzziness)

Current solution to Fuzziness, still needs to be worked on to handle more cases

Complete fuzzy feature cycle of in fuzzy feature -> out fuzzy feature via SeqIO::genbank works

Handle SNP variations more properly and better SplitLocation handling -- handle 'order' and 'join'

Removed reference to bioperl-guts-l list.

Write items in sorted order

Updated to handle new LocationI syntax location of the type (5.12)..20 are still not parsed properly by FTHelper and are ignored

More robust regexp for getting more complicated features into location parsing

Regexp corrections

Bug #246 couldn't parse lines of complement(join(....)) since pattern expected only one 'word' directive before location info, remove complement string after assigning strandedness in _parse_loc

Bio::SeqIO::GAMEHandler

Corrected indication of module name in doc.

Removed RootI dependence

Updates to game.pm including feature recursion. game.pm's handler's moved to Bio/SeqIO/game. GAMEHandler.pm removed.

Bio::SeqIO::MultiFile

Removed RootI dependence

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Bio::SeqIO::ace

Removed RootI dependence

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Added use statements.

Bio::SeqIO::bioxml

Small correction in the comment header.

Removed RootI dependence

Quoted unquoted string literals used as hash keys.

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Added use statement.

Emoved bioxml.pm. bioxml users should switch to game.pm.

Bio::SeqIO::embl

Removed RootI dependence

Changed to new RootI chained new structure

Verbosity is shared now so can set verbosity at the top (Bio::SeqIO) level and will have messages silenced when verbosity= -1

Id generation func now takes a paramter for supporting different embl and genbank lines

Removed reference to bioperl-guts-l list.

Added RichSeq implementation - converted genbank/embl/swiss to use this - all tests pass. LiveSeq calls some deprecated methods

Bio::SeqIO::fasta

Commented out buggy lines

Removed multiple fasta parsing bug

Elia bug redux This should allow handling of both files with multiple fasta seqs and single fasta files and lines with >description >> 0.1

Removed RootI dependence

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Added capability of reading and writing empty sequences.

Added use statement.

Bio::SeqIO::featureHandler

Checking in game.pm into SeqIO. Helper classes are idHandler.pm, seqHandler.pm, and featureHandler.pm. Test script is t/game.t. Test data is t/test.game. Enjoy. Brad

Updates to game.pm including feature recursion. game.pm's handler's moved to Bio/SeqIO/game. GAMEHandler.pm removed.

Bio::SeqIO::game

Checking in game.pm into SeqIO. Helper classes are idHandler.pm, seqHandler.pm, and featureHandler.pm. Test script is t/game.t. Test data is t/test.game. Enjoy. Brad

Modifications to handle new RootI setup

Updates to game.pm including feature recursion. game.pm's handler's moved to Bio/SeqIO/game. GAMEHandler.pm removed.

Doc formatting fix

Made arguments SeqIO like

More revisions to not complain when certain things are null

This test will only work from bioperl-live/

Updated Bio::SeqIO::game. It now deals with filehandles and supports the 'chunkable' notation discussed on the mailing list. Brad

Fixed initializiation errors that were making noise in make test

Quoted unquoted string literals used as hash keys.

Changed to new RootI chained new structure

Bio::SeqIO::game::featureHandler

Updates to game.pm including feature recursion. game.pm's handler's moved to Bio/SeqIO/game. GAMEHandler.pm removed.

More revisions to not complain when certain things are null

Quoted unquoted string literals used as hash keys.

Changed to new RootI chained new structure

Added use statement.

Bio::SeqIO::game::idHandler

Updates to game.pm including feature recursion. game.pm's handler's moved to Bio/SeqIO/game. GAMEHandler.pm removed.

Quoted unquoted string literals used as hash keys.

Changed to new RootI chained new structure

Bio::SeqIO::game::seqHandler

Updates to game.pm including feature recursion. game.pm's handler's moved to Bio/SeqIO/game. GAMEHandler.pm removed.

Not using global variables

More revisions to not complain when certain things are null

Removing debugging code

Made it possible to import multiple sequences in one game file

Fixed initializiation errors that were making noise in make test

Quoted unquoted string literals used as hash keys.

Changed to new RootI chained new structure

Added use statement.

Bio::SeqIO::gcg

Removed RootI dependence

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Added use statement.

Moved GCG_checksum here from PrimarySeqI.

Bio::SeqIO::genbank

Removed RootI dependence

Changed to new RootI chained new structure

Verbosity is shared now so can set verbosity at the top (Bio::SeqIO) level and will have messages silenced when verbosity= -1

Id generation func now takes a paramter for supporting different embl and genbank lines

Bug that caused Title to smoosh words from second line

Removed reference to bioperl-guts-l list.

Added RichSeq implementation - converted genbank/embl/swiss to use this - all tests pass. LiveSeq calls some deprecated methods

Fixes for ensembl dumps. approved by Ewan :)

Removed semicolons from LOCUS line (for ensembl dumping)

Fix to deal with writing non richseqs out to genbank, still need to create and store the default date

Made LOCUS line parsing more robust (if it's genbank, get at the ID as a minimum. Some entries lack the molecule although they are nucleotide.

Fixed bug introduced by previous change (wrong syntax).

Fixes for ensembl dumps

Fixed parsing and writing of PID. Fixed parsing and writing of secondary accessions and seq version. Fixed print of too many spaces after REFERENCE. Now prints "residues" if it's protein.

Fixed problem with possible HTML tags in SOURCE/ORGANISM lines. Fixed unawareness of organelle in input and output.

Fixed missing handling of EOF in the middle of parsing.

Bio::SeqIO::idHandler

Checking in game.pm into SeqIO. Helper classes are idHandler.pm, seqHandler.pm, and featureHandler.pm. Test script is t/game.t. Test data is t/test.game. Enjoy. Brad

Updates to game.pm including feature recursion. game.pm's handler's moved to Bio/SeqIO/game. GAMEHandler.pm removed.

Bio::SeqIO::largefasta

SeqIO support for largge sequence files in fasta format

Added write support for large fasta and some more doc

Added better fallbacks for temp dir and next_seq returns a SeqI compliant object

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Bio::SeqIO::pir

Removed RootI dependence

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Added use statement.

Bio::SeqIO::raw

Removed RootI dependence

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Added use statement.

Bio::SeqIO::scf

Removed RootI dependence

Changed to new RootI chained new structure

Removed reference to bioperl-guts-l list.

Added use statement.

Bio::SeqIO::seqHandler

Checking in game.pm into SeqIO. Helper classes are idHandler.pm, seqHandler.pm, and featureHandler.pm. Test script is t/game.t. Test data is t/test.game. Enjoy. Brad

Modifications to handle new RootI setup

Updates to game.pm including feature recursion. game.pm's handler's moved to Bio/SeqIO/game. GAMEHandler.pm removed.

Bio::SeqIO::swiss

Removed RootI dependence

Changed to new RootI chained new structure

Verbosity is shared now so can set verbosity at the top (Bio::SeqIO) level and will have messages silenced when verbosity= -1

Added use statement.

Added RichSeq implementation - converted genbank/embl/swiss to use this - all tests pass. LiveSeq calls some deprecated methods

Simplified DBLink parsing code.

Fixed using RichSeq::seq_version() instead of sv().

Fixed bug #900: multiple gene names, separated by " OR ". Please someone check on a real example.

Bio::SeqUtils

Holder class for miscellaneous sequence methods. Created with seq3 and seq3in methods for handling three letter IUPAC amino acid code output and input.

Added a noncoded amino acid selenocystein which has one and three letter symbols.

Bio::SimpleAlign

Added parsing of phiBLAST reports to BPlite and BPpsilite. Modified consensus methods in SimpleAlign to enable thresholds. Added threshold varying example to standaloneblast.pl

RootI compliance and some documentation reformatting

Quoted unquoted string literals used as hash keys.

Migrate to chained new with new Bio::Root::RootI

Fixed clustalw alignIO module to honor input file order

Removed reference to bioperl-guts-l list.

Bio::Species

Named parameter for classification and migrate to new Bio::Root:RootI chained new

Bio::Tools::AlignFactory

Migrated to new Bio::Root::RootI chained new

Fixed to be RootI dependant

Fixed pSW bugs

Bio::Tools::Alignment::Clustalw

Added clustal.pl; also minor bug fixes

Minor code cleanup - Clustalw, AlignIO

Fixed passing of arguments to base class in _initialize(). Fixed exists_clustal() to return false upon missing program even though $@ is empty. Moved returning true to the end of the module (looks weird if in the middle). Fixed mailing lists in docs.

Fixed bug in Clustalw.pm sub exists_clustal

Did some doc and code formatting

Corrections and standardizations

Simplier way to unlink

Seqfiles are now created as tempfile rather than hardcoded names

Migrated to Bio::Tools::Run::Alignment

Bio::Tools::Alignment::TCoffee

Added TCoffee alignment

Simplier way to unlink

Seqfiles are now created as tempfile rather than hardcoded names

Migrated to Bio::Tools::Run::Alignment

Bio::Tools::AnalysisResult

Fixed wrong spelling of promoter.

Doc changes for standardization

Root I compliance

Migrated to new Bio::Root::RootI chained new

Commented out documentation for parse() (was required by Bio::SeqAnalysisParserI, but is now discouraged).

Changed to adopt Bio::Root::IO.

Bio::Tools::BPbl2seq

Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)

Removed RootI dependence and added some standardization

Quoted unquoted string literals used as hash keys.

Migrated to new Bio::Root::RootI chained new

Some cleanup to support 5.00404

BPlite changes to make BPlite a SeqAnalysisParserI object BPbl2seq now requires named input parameter (no longer can just pass in filehandle reference, must pass in -fh => $filehandle) Assundry changes made to related files to handle these changes

Corrected documentation.

Fixed queryname field to not override -query line for Similarity, tagname is now -queryname

Changed to adopt Bio::Root::IO.

Bio::Tools::BPlite

Added documentation of functions

Added parsing of phiBLAST reports to BPlite and BPpsilite. Modified consensus methods in SimpleAlign to enable thresholds. Added threshold varying example to standaloneblast.pl

Aesthetics and removal of uneeded variables, some bulletproofing

Removed RootI dependence and added some standardization

Cleaned up BPpsi stuff, in particular for 5.00004

Quoted unquoted string literals used as hash keys.

Migrated to new Bio::Root::RootI chained new

BPlite changes to make BPlite a SeqAnalysisParserI object BPbl2seq now requires named input parameter (no longer can just pass in filehandle reference, must pass in -fh => $filehandle) Assundry changes made to related files to handle these changes

Changed to adopt Bio::Root::IO.

Bio::Tools::BPlite::HSP

Added documentation of functions

Added parsing of phiBLAST reports to BPlite and BPpsilite. Modified consensus methods in SimpleAlign to enable thresholds. Added threshold varying example to standaloneblast.pl

Removed RootI dependance and some standardization

Quoted unquoted string literals used as hash keys.

Migrated to new Bio::Root::RootI chained new

Bug #885; tblastn parsing supported now, added a method 'frame' to BPlite::HSP to store this value

Corrected to use frame method from Bio::SeqFeature::Generic

Frame map from blast frame to gff frames

Handle frame mapping from BLAST to GFF

Frame of undef means no frame information, using undef rather than '.', however method to reset the frame to 'undef' for an instantiated object

Bio::Tools::BPlite::Iteration

Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)

Added parsing of phiBLAST reports to BPlite and BPpsilite. Modified consensus methods in SimpleAlign to enable thresholds. Added threshold varying example to standaloneblast.pl

Removed RootI dependance and some standardization

Cleaned up BPpsi stuff, in particular for 5.00004

Quoted unquoted string literals used as hash keys.

Migrated to new Bio::Root::RootI chained new

Small fixes in -fh handling. Fixed nextSbjct to return undef instead of 0 on failure.

Bio::Tools::BPlite::Sbjct

Added documentation of functions

Added parsing of phiBLAST reports to BPlite and BPpsilite. Modified consensus methods in SimpleAlign to enable thresholds. Added threshold varying example to standaloneblast.pl

Removed RootI dependance and some standardization

Cleaned up BPpsi stuff, in particular for 5.00004

Quoted unquoted string literals used as hash keys.

Migrated to new Bio::Root::RootI chained new

BPlite changes to make BPlite a SeqAnalysisParserI object BPbl2seq now requires named input parameter (no longer can just pass in filehandle reference, must pass in -fh => $filehandle) Assundry changes made to related files to handle these changes

Bug #885; tblastn parsing supported now, added a method 'frame' to BPlite::HSP to store this value

Bio::Tools::BPpsilite

Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)

Added example script standaloneblast.pl. Also some mods to StandAloneBlast.pm and BPpsilite.pm

Added parsing of phiBLAST reports to BPlite and BPpsilite. Modified consensus methods in SimpleAlign to enable thresholds. Added threshold varying example to standaloneblast.pl

Doc formatting

Removed RootI dependence and added some standardization

Cleaned up BPpsi stuff, in particular for 5.00004

Quoted unquoted string literals used as hash keys.

Migrated to new Bio::Root::RootI chained new

Some cleanup to support 5.00404

BPlite changes to make BPlite a SeqAnalysisParserI object BPbl2seq now requires named input parameter (no longer can just pass in filehandle reference, must pass in -fh => $filehandle) Assundry changes made to related files to handle these changes

Tiny and purely cosmetic change.

Changed to adopt Bio::Root::IO. Tempfiles for iterations are not multi cpu-safe yet and need to be fixed.

Properly removing tempfiles

Bio::Tools::Blast

Documentation formatting

Bio::Tools::CodonTable

Migrated to new Bio::Root::RootI chained new

Added code #23: Thraustochytrium Mitochondrial

Bio::Tools::ESTScan

Fixed bugs in annotation of insertions/deletions, and others, too.

Migrated to new Bio::Root::RootI chained new

Added documentation to synopsis section.

Fixed to use _fh() instead of fh().

Bio::Tools::GFF

Added the GFF module that both reads and writes GFF formatted features. It is minimaly documented, and the GFF2 version doesn't seem to parse its own output.

Made a small change to the _gff2_string subroutine to fix the problem of fusing together multiple values of a single tag

Added close method, and proper testing of fields

Added a bunch of documentation. Made next_feature() safe. Some other very small changes.

Added gff_string() and from_gff_string() (version independent).

Changed to adopt Bio::Root::IO.

Added a 'chomp' to the from_gff2_string routine because frame information was being recorded with the newline character trailing. This is not required in the _from_gff_string method as this routine insists (wrongly) that a valid frame of 0,1, or 2 should be present, and defaults it to 0 if it doesn't see one of these options.

Added use Bio::SeqFeature::Generic, which is called by the next_feature method...

Bio::Tools::Genscan

Fixed wrong spelling of promoter.

Doc changes for standardization

Migrated to new Bio::Root::RootI chained new

Added frame recognition for each individual exon.

Added documentation to synopsis section.

Changed to use the new parent classes of Prediction::{Gene,Exon}.

Bio::Tools::HMMER::Domain

Migrated to new Bio::Root::RootI chained new

Added revision-Id line. Commented out documentation for deprecated methods. Changed initialization of feature1 and feature2 in new() to allow for parameter parsing.

Bio::Tools::HMMER::Results

Migrated to new Bio::Root::RootI chained new

Move from start_hmm to hstart & from end_hmm to hend

Made HMMER::Results SeqAnalysisParserI compliant

Changed to adopt Bio::Root::IO.

Bio::Tools::HMMER::Set

Migrated to new Bio::Root::RootI chained new

Added revision-Id line.

Bio::Tools::IUPAC

Migrated to new Bio::Root::RootI chained new

Fixed to be RootI dependant

Fixed to use named parameter -seq (is backward compatible though).

Bio::Tools::MZEF

Doc changes for standardization

Migrated to new Bio::Root::RootI chained new

Added documentation to synopsis section.

Changed to use the new parent classes of Prediction::{Gene,Exon}.

Bio::Tools::OddCodes

Migrated to new Bio::Root::RootI chained new

Added $Id$ line

Fixed to use named parameter -seq (is backward compatible though).

Bio::Tools::Prediction::Exon

Doc changes for standardization

Migrated to new Bio::Root::RootI chained new

Changed inheritance to SeqFeature::Gene::Exon. Fixed new(), no special primary_tag by default.

Bio::Tools::Prediction::Gene

Doc changes for standardization

Migrated to new Bio::Root::RootI chained new

Changed inheritance to SeqFeature::Gene::Transcript.

Bio::Tools::RestrictionEnzyme

Corrected mailing lists in doc.

Migrated to new Bio::Root::RootI chained new

Fixed bug introduced by chained new migration, added routined called cut_locations which reports the locations enzyme would cut rather than returning an htmlified seq str

Refactored (heavily) RootI. Alot of code removal. I think it is short and sweet now

Removed reference to bioperl-guts-l list.

Bio::Tools::Run::StandAloneBlast

Migrated code that runs tools to Bio::Tools::Run

Renaming packages for new dir structure

Fixed to PROPER usage of tempfile

Migrated to new Bio::Root::RootI chained new

Fixed several doc format bugs. (Why is an unprotected -p in the DESCRIPTION section disallowed and somewhere else it is not? Anyway, perldoc is quiet now.)

Fixed inclusion of 'use Bio::Root::RootI' instead of Bio::Root::Object. Fixed exists_blast() (didn't work due to missing braces).

Updated bptutorial and other documentation

BPlite changes to make BPlite a SeqAnalysisParserI object BPbl2seq now requires named input parameter (no longer can just pass in filehandle reference, must pass in -fh => $filehandle) Assundry changes made to related files to handle these changes

Changed to adopt Bio::Root::IO.

Bio::Tools::SeqAnal

Corrected mailing lists.

Bio::Tools::SeqPattern

Aesthetics and removal of uneeded variables, some bulletproofing

SeqPattern.pm fixes and revisions

Fixed to be RootI dependant

Bio::Tools::SeqStats

Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)

Migrated to new Bio::Root::RootI chained new

Doc cleanup - variable initialization moved to BEGIN block

Fixed bugs and cleaned up code in SeqStats.pm and SeqStats.t

SeqStats clean up

Code cleanup, BEGIN block established, -seq supported as arg to new

Fixed documentation to use named parameter notation.

Bio::Tools::SeqWords

Fixed mailing lists. Fixed documentation to require arguments to new() in named parameter style for consistency. Changed inheritance to RootI, added a proper new(), which still allows for the argument being passed unnamed. Fixed count_words() to allow call as class method as the documentation promised.

Bio::Tools::Sigcleave

per request of Sanger Center webteam I've removed a dead URL that used to point to the EGCG docs. cdagdigian

Moved PrimarySeq and Seq to RootI style news. Fixed the knock on effects. LargeSeq/LargeFasta fail - cant fix them

Quoted unquoted string literals used as hash keys.

Bio::Tools::Sim4::Exon

Added 'use Bio::SeqFeature::SimilarityPair'.

Migrated to new Bio::Root::RootI chained new

Bio::Tools::Sim4::Results

Corrected a bug (wrong method name in call) in parse_next_alignment().

Migrated to new Bio::Root::RootI chained new

Explict call of fileparse needed to support 5.00404

Removed a left-over variable.

Bio::Tools::StandAloneBlast

Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)

Added example script standaloneblast.pl. Also some mods to StandAloneBlast.pm and BPpsilite.pm

Documentation reformat

Doc changes for standardization

Changed to use temporary files

Use tempfile creation from RootI

Migrated to Bio::Tools::Run

Bio::Tools::WWW

Fixed to be RootI dependant

Bio::Tools::pSW

Moved BEGIN block before use statements Now uses die when require fails so that the exception can be catched

Fixed pSW bugs

Bio::UnivAln

Quoted unquoted string literals used as hash keys.

Migrate to chained new with new Bio::Root::RootI

Bio::Variation::AAChange

Added $id$ lines, checked that modules end in 1;

Outdated methods in the constructor, '$self->' missing

Bio::Variation::AAReverseMutate

Added $id$ lines, checked that modules end in 1;

Bio::Variation::Allele

Added $id$ lines, checked that modules end in 1;

Inheritance from RootI

Bio::Variation::DNAMutation

Added $id$ lines, checked that modules end in 1;

Outdated methods in the constructor, '$self->' missing

Bio::Variation::IO

Removed RootI dependance

Added $id$ lines, checked that modules end in 1;

Moved PRINT method from Bio::SeqIO to supress a warning

Removed old, non-functional code from the constructor. Joys of copy and paste (in this case from Bio::SeqIO)!

Bio::Variation::IO::flat

Removed RootI dependance

Reverted to 1.2 code that was unintentionally overwritten

Added $id$ lines, checked that modules end in 1;

Negative genomic locations were off by 1.

Deleted (unused) code for adding HTML hypertext links into the output. It did not really belong here.

Bio::Variation::IO::xml

Removed RootI dependance

Changed IO::String creation to OO style. Appears to be required.

Added $id$ lines, checked that modules end in 1;

Bio::Variation::RNAChange

Added $id$ lines, checked that modules end in 1;

Fixed outdated method calls

Bio::Variation::SeqDiff

Added $id$ lines, checked that modules end in 1;

Added quotes around hash keyword to prevent a warning

Added two new methods: 1. rna_offset to hold the offset from the start of the mRNA to the coding start 2. $rna_id to hold the UID for the transcript used

Added ->seqobj which returns the original or mutated dna, rna or protein sequence as a PrimarySeq object. Bio::Variation objects now link better with the rest of the bioperl. Migrated tests to Test and added a few for the seqobj method.

Fixed incompatibility with earlier perl5 versions: $self->$value which works with latest perl has to be written: $self->{$value}

Fixed the example in synopsis section of docs.

Bio::Variation::VariantI

Added $id$ lines, checked that modules end in 1;

Removed DOS LF

Makefile.PL

Added XML::* and IO::* dependencies.

Added missing commas

Silly capitalization mistake

Added File::Temp dependancy

Added dependcy check for XML::Node which is needed by Bio::Variation::IO::xml.pm

Added HTML::Parser dependancy

Updated MANIFEST file to reflect all the new files in the 07 distribution. Tweaked the warning message in Makefile.PL and updated VERSION to 0.07. Added OpenBSd entry to PLATFORMS. cdagdigian.

When doing 'make dist' noticed that version was incorecctly set to "0.07.0". I changed this to "0.7" - cdagdigian

bioperl.lisp

Replaced bioperl-guts-l@bioperl.org by bioperl-l@bioperl.org

bioperl.pod

Replaced: bioperl-guts-l@bioperl.org and vsns-bcd-perl-guts@lists.uni-bielefeld.de by bioperl-l@bioperl.org (File seems to be out of date anyway: sending mail to bioperl-bugs)

Took trivial doc changes I made in branch-07 and committed them to head. cdagdigian

bptutorial.pl

Initial commit of bptutorial.pl introductory tutorial & tutorial script.

Removed /013 characaters (^M) and wraped text in paragraphs

The examples can be run now. 'require Bio::Tools::pSW' failing is handled gracefully. ... really minor formatting changes were done in the text part.

Translate & liveseq revisions to bptutorial

SeqPattern.pm fixes and revisions

Updated bptutorial and other documentation

Added appendix listing available methods to bptutorial.pl

Fixed bug #886.

Adopted changes to BPbl2seq calling

examples/change_gene.pl

Restructured Mutator.pm. Added Mutation.pm to hold mutation information. Tests for both. Example script.

Changed EMBL-feature loading code to use the new SplitLocation

examples/clustalw.pl

Added clustal.pl; also minor bug fixes

Fixed bug in Clustalw.pm sub exists_clustal

Added parsing of phiBLAST reports to BPlite and BPpsilite. Modified consensus methods in SimpleAlign to enable thresholds. Added threshold varying example to standaloneblast.pl

Migrated alignment code to new dir structure in Bio::Tools

examples/getGenBank.pl

How to retrieve GenBank entries over the Web

examples/hitdisplay.pl

Hitdisplay.pl is a demo of the HitDisplay.pm module in Bio::Tk

Fix: Changed @data into correct variable @hits. Script works now.

examples/standaloneblast.pl

Added example script standaloneblast.pl. Also some mods to StandAloneBlast.pm and BPpsilite.pm

Added parsing of phiBLAST reports to BPlite and BPpsilite. Modified consensus methods in SimpleAlign to enable thresholds. Added threshold varying example to standaloneblast.pl

Migrated alignment code to new dir structure in Bio::Tools

scripts/bpindex.pl

Correct location behavior to return min_start == max_start when start is defined SplitLocation->start will return the value of the 1st (sorted) contained location Location.t was updated to test for this as well

scripts/subsequence.cgi

Extract a short subsequence of DNA from a large GenBank entry