Core 0.6.1 0.6.2 delta

These are detailed notes on changes made between bioperl-06-1 and release-06-2.

Bio::AlignIO

Initial install of AlignIO files

Bio::AlignIO::clustalw

Initial install of AlignIO files

Bio::AlignIO::fasta

Initial install of AlignIO files

Bio::AlignIO::mase

Initial install of AlignIO files

Bio::AlignIO::msf

Initial install of AlignIO files

Bio::AlignIO::pfam

Initial install of AlignIO files

Bio::AlignIO::prodom

Initial install of AlignIO files

Bio::AlignIO::selex

Initial install of AlignIO files

Bio::AlignIO::stockholm

Initial install of AlignIO files

Bio::Annotation

added CVS ID tag to top of module. cdagdigian

Added object type test to ->add_DBLink and fixed examples in synopsis

Added functions for removing

Some doc bugs (updating mailing address for bioperl)

Bio/Annotation.pm - update for 0.6.2 o corrected whitespace in SYNOPSIS (C) o corrected SYNOPSIS to talk about $link->database rather than $link->db (D) o corrected ->add_Reference documentation line (D) o added check to see if argument isa() Bio::Annotation::DBLink in add_DBLink (B)

Bio::Annotation::DBLink

Added examples and ->_initialize code

Bio::Annotation::Reference

Removed implementation of comment() -- is inherited. Added pubmed(). Changed database() to allow for changing the hard-coded default MEDLINE.

Corrected a left-over from copy-and-paste.

Fixed doc of rp(). Given the code, the value supplied is never parsed, regardless of its contents.

Fixed bug in _initialize(): args were not passed on.

Comitted apparently forgotten minor fixes.

Fixed propagation of arguments to delegation methods.

Bio::DB::GenBank

Added the option to set and change the retrieval format. So far, GenBank and Fasta are supported. See method request_format().

Forgot get_Seq_by_id().

Bio::DB::GenPept

Bug#242

Bug #243 and more error checking

Added capability to retrieve sequences in both Genbank and Fasta format. See request_format().

Bio::DB::RandomAccessI

Needed a space before =head

Bio::DB::UpdateableSeqI

Added updateable seq interface

Bio::DBLinkContainerI

added CVS ID tag and updated email-list address info. cdagdigian

Bio::Index::Abstract

added CVS Id tags and updated bioperl mailing list info where necessary. cdagdigian.

Add throw on make index on write only

Merged stable branch fixes in

Fix to Bio::Root::RootI::_rearrange method which assigned empty strings to variables when called without arguments. Added allow_relative_paths() to Bio::Index::Abstract Added throwing an exception to Bio::Index::AbstractSeq::fetch if ID given is not in index.

Bio::Index::AbstractSeq

Changed abstractseq

Did kris fix to abstractseq.pm

V. minor tidy up

V. minor tidy up

Fixed AbstractSeq.pm so it doesn't throw an exception if the seq requested isn't in the index

added CVS Id tags and updated bioperl mailing list info where necessary. cdagdigian.

Fixed get_all_primary_ids bug

Merged in changes from stable

Fix to Bio::Root::RootI::_rearrange method which assigned empty strings to variables when called without arguments. Added allow_relative_paths() to Bio::Index::Abstract Added throwing an exception to Bio::Index::AbstractSeq::fetch if ID given is not in index.

Excessive compulsive checking on object before adding primary_id

Documentation fix and insure $seq exists before calling $seq->primary_id()

Bio::Index::EMBL

added CVS Id tags and updated bioperl mailing list info where necessary. cdagdigian.

Fixed abstract to throw on readonly write; fixed documentation bugs

Merged stable branch fixes in

Bio::Index::Fasta

added CVS Id tags and updated bioperl mailing list info where necessary. cdagdigian.

Fixed abstract to throw on readonly write; fixed documentation bugs

Merged stable branch fixes in

Bio::Index::GenBank

added CVS Id tags and updated bioperl mailing list info where necessary. cdagdigian.

Bio::Index::SwissPfam

added CVS Id tags and updated bioperl mailing list info where necessary. cdagdigian.

Bio::Index::Swissprot

Added Swissprot index file

added CVS Id tags and updated bioperl mailing list info where necessary. cdagdigian.

Bio::LocatableSeq

Some doc bugs (updating mailing address for bioperl)

Fixed sort_alphabetically bug

Merged simpled align bug fixes across

Bio::PrimarySeq

Made some changes to improve efficiency when working with large sequences: - Deleted the line in seq() that needlessly made an extra copy of the sequence just before the method returned. - subseq() uses data members directly instead of the accessor method call (i.e., $self->{'seq'} instead of $self->seq()). This may upset the OO purists, but for simple accessors within the class that manages the data, I think it is fine.

Made some changes to improve efficiency when working with large sequences: - Deleted the line in seq() that needlessly made an extra copy of the sequence just before the method returned. - Added definition of length() (moved from PrimarySeqI.pm. This prevents another sequence from being created when PrimarySeqI::length() called seq(). - subseq(), length() use data members directly instead of the get accessor method call (i.e., $self->{'seq'} instead of $self->seq()). This may upset the OO purists, but for simple accessors within the class that manages the data, I think it is fine.

Fixed bug in SeqIO/(embl|genbank) which caused accession to become "unknown". Was due to Bio::PrimarySeq being made directly, which is not necessary.

Some doc bugs (updating mailing address for bioperl)

Move bug fixes of simplealign and rev_and_trans to main trunk

Bio::PrimarySeqI

Made some changes to improve efficiency when working with large sequences: - Made length() virtual so that it must be defined in concrete subclasses (PrimarySeq::length()) where it can call CORE::length() directly on its seq data member. This prevents another sequence from being created when PrimarySeqI::length() called seq().

Added code into the translate method to replace the first amino acid into M if it is not M and the codon is valid the initiator codon.

Fixed method translate to put M as the first amino acid when the first codon is a valid initiator codon

Added seq ID when warning for non initiator start codon (warns only when verbose is true)

Fixed molecular weight bug in SeqStats.pm where Mwts were calculated without taking into account H20

2nd attempt on fixing initator codons in translate

Some doc bugs (updating mailing address for bioperl)

Fixed subtle bug wrt to Ensembl. We need translate to give the completely computationally "unedited" translation. New option to translate function in PrimarySeqI to not edit. Probably should move this out into a Util area and make interfaces pure sometime....

Fixed seqpattern case bug

Small changes in revcom() and trunc() to retain the description in the returned sequence object.

Handle null $char vals

Fixed GCG_checksum to handle null $char values

Final fixes?

Bio::Range

ToString() now includes strand information.

ToString() now includes strand information.

Doc fix

Some doc bugs (updating mailing address for bioperl)

Bio::RangeI

- Modified intersection() and union() to preserve strand information if the strands of all ranges being compared are the same. Otherwise, strand in the result is 0. Previously, it was always returning 0 for strand. - Fixed calls to _testStrand() to include the range object being compared. Previously, some salls to _testStrand() only included the strand option scalar. - Fixed bug in _strong(): using = instead of ==

- Modified intersection() and union() to preserve strand information if the strands of all ranges being compared are the same. Otherwise, strand in the result is 0. Previously, it was always returning 0 for strand. - Fixed calls to _testStrand() to include the range object being compared. Previously, some salls to _testStrand() only included the strand option scalar. - Fixed bug in _strong(): using = instead of ==

Some doc bugs (updating mailing address for bioperl)

Bio::Root::Err

updated mailing list address info where necessary. cdagdigian.

Silly doc bug

Doc fix

Bio::Root::Global

updated mailing list address info where necessary. cdagdigian.

Bio::Root::IOManager

updated mailing list address info where necessary. cdagdigian.

Bio::Root::Object

updated mailing list address info where necessary. cdagdigian.

Moved _set_warning from Bio::Root::Object to Bio::Root::RootI, because RootI needs it

Moved _set_err_state from Bio::Root::Object to Bio::Root::RootI, because RootI needs it

Moved subs _set_warning and _set_err_state from Bio::Root::Object to Bio::Root::RootI

Bio::Root::RootI

updated mailing list address info where necessary. cdagdigian.

Moved _set_warning from Bio::Root::Object to Bio::Root::RootI, because RootI needs it

Moved _set_err_state from Bio::Root::Object to Bio::Root::RootI, because RootI needs it

Moved subs _set_warning and _set_err_state from Bio::Root::Object to Bio::Root::RootI

Verbosity undef caused some silly errors

Fix to Bio::Root::RootI::_rearrange method which assigned empty strings to variables when called without arguments. Added allow_relative_paths() to Bio::Index::Abstract Added throwing an exception to Bio::Index::AbstractSeq::fetch if ID given is not in index.

Bio::Root::Utilities

Fixed bug in create_filehandle(). Now checks that client is a ref.

updated mailing list address info where necessary. cdagdigian.

Added some move validation on client before running get_newline

Ref() instead of !

Bio::Root::Vector

updated mailing list address info where necessary. cdagdigian.

Bio::Root::Xref

updated mailing list address info where necessary. cdagdigian.

Bio::SearchDist

Some doc bugs (updating mailing address for bioperl)

Bio::Seq

Fixed add_SeqFeature in Bio::SeqFeature::Generic, and added tests to t/SeqFeature.t

Made some changes to improve efficiency when working with large sequences: - Add length() method to Seq.pm that delegates to its PrimarySeq. This is necessary now that PrimarySeqI::length() is virtual. - subseq() uses data members directly instead of the accessor method call (i.e., $self->{'primary_seq'} instead of $self->primary_seq()). This may upset the OO purists, but for simple accessors within the class that manages the data, I think it is fine.

Bio/Seq.pm: added a new method, feature_count(), which returns the number of SeqFeature objects contained in a sequence. Bio/SeqIO/embl.pm: changed next_seq() to handle EMBL files without feature table (FH/FT) or incomplete FT (FH without FT). changed write_seq() to only write FH lines if there are SeqFeatures to write out (uses feature_count() method)

Method accession now references method accession_number and data is no longer stored in $obj->{'accession'}.

Changed reference from $seq->accession to $seq->accession_number and made accession routine point to accession_number in Bio::Seq

Fixed add_SeqFeature -- now correctly adds a primary_seq

Fixed version bug

Fixed bug in SeqIO/(embl|genbank) which caused accession to become "unknown". Was due to Bio::PrimarySeq being made directly, which is not necessary.

Doc fix (update mailing list addres)

Removed sub_species(). Use $seq->species()->sub_species() for that.

Final fixes?

Bio::Seq::LargePrimarySeq

Added LargePrimarySeq in Bio::Seq; added test; removed annoying EMBL test case; tests pass

Added a check for existence of fh before trying to close

Bio::SeqAnalysisParserI

Interfaces for abstracting automated feature additions from analysis program output

Fixed a bug in parse() doc.

Bio::SeqFeature::FeaturePair

Added has_tag() and each_tag_value() as dummies (they are required by SeqFeatureI).

Removed methods implementing Bio::SeqFeatureI required methods without functionality. Changed to inherit off Bio::SeqFeature::Generic.

Removed methods implementing Bio::SeqFeatureI required methods without functionality. Changed to inherit off Bio::SeqFeature::Generic.

Fixed unquoted hash keys.

Corrected a bug in _initialize(): @args were not passed on.

Removed length() (inherited).

Bio::SeqFeature::GeneStructure

Initial revision.

Bug corrections. Added correct_phase() and the option to call it in cds().

Added the option to provide the id of the codon table to be used to cds().

Fixed bug #842.

Fixed documentation (NAME section).

Removed _tag_value (moved to SeqFeature::Generic).

Corrected a bug in cds().

Bio::SeqFeature::Generic

Fixed add_SeqFeature in Bio::SeqFeature::Generic, and added tests to t/SeqFeature.t

Corrected a bug in _initialize() preventing tag/value pairs passed to the constructor to be set properly.

Fixed frame() (allowed for 1,2,3 instead of 0,1,2). Added annotation().

Splitted out _expand_region() from add_sub_SeqFeature(). This may be usefule for derived classes as well.

BPlite now uses Bio::SeqFeature::SimilarityPair instead of FeaturePair

Made some fixes on the branch for checking start/end feature sets and other things

Fixed bug #848 (had already been fixed on the main trunk).

Fix to Bio::Root::RootI::_rearrange method which assigned empty strings to variables when called without arguments. Added allow_relative_paths() to Bio::Index::Abstract Added throwing an exception to Bio::Index::AbstractSeq::fetch if ID given is not in index.

Added _tag_value(). This seems to be useful for many derived modules.

Small modification to add_sub_SeqFeature() in order to suppress 'uninitialized value' warnings. (do we really need equality to EXPAND instead of just something evaluating to TRUE?)

Fixed strand() and frame() to catch attempts to set to undefined.

Bio::SeqFeature::Similarity

Initial revision.

Fixed bug #842.

Fixed documentation (NAME section). Added documentation.

Removed _tag_value (moved to SeqFeature::Generic).

Bio::SeqFeature::SimilarityPair

Initial revision.

Fixed documentation (NAME section).

Corrected a doc bug and a code bug.

Fixed the propagation of arguments to delegation methods.

Bio::SeqFeatureI

Corrected the documentation of has_tag() to correctly reflect naming and implementation as, e.g., implemented in SeqFeature::Generic.

Made example code 'actually' work (missing some commas)

Further corrected documentation. Added each_tag_value() as a consequence of the has_tag() fix.

Some doc bugs (updating mailing address for bioperl)

Fixed documentation. Added missing each_tag_value(). (Fixes propagated from the main trunk.)

Small change in gff_string to get rid of 'uninitialized value' warnings.

Bio::SeqFeatureProducerI

SeqFeatureProducerI and GFF implementor added for producing sequence features

MZEF SeqFeatureProducer added

Corrected doc bugs (and spelling of my name :-)

Interfaces for abstracting automated feature additions from analysis program output

Added SeqFeatureProducer interface

Fixed documentation (NAME section).

Bio::SeqI

Some doc bugs (updating mailing address for bioperl)

Bio::SeqIO

Added _concatenate_lines() needed to fix a bug in embl.pm. May be useful for other SeqIO modules, too.

Added _concatenate_lines() needed to fix a bug in embl.pm. May be useful for other SeqIO modules, too.

Bio::SeqIO::FTHelper

Updated mailing list address on maintrunk

Bio::SeqIO::GAMEHandler

Updated mailing list address on maintrunk

Bio::SeqIO::MultiFile

Updated mailing list address on maintrunk

Bio::SeqIO::ace

Updated mailing list address on maintrunk

Bio::SeqIO::bioxml

Updated mailing list address on maintrunk

Bio::SeqIO::embl

Bio/Seq.pm: added a new method, feature_count(), which returns the number of SeqFeature objects contained in a sequence. Bio/SeqIO/embl.pm: changed next_seq() to handle EMBL files without feature table (FH/FT) or incomplete FT (FH without FT). changed write_seq() to only write FH lines if there are SeqFeatures to write out (uses feature_count() method)

Changed reference from $seq->accession to $seq->accession_number to provide a cleaner inteface (and eliminate confusion as to where accession is actually stored)

Changed reference from $seq->accession to $seq->accession_number and made accession routine point to accession_number in Bio::Seq

Fixed molecular weight bug in SeqStats.pm where Mwts were calculated without taking into account H20

Fixed bug in SeqIO/(embl|genbank) which caused accession to become "unknown". Was due to Bio::PrimarySeq being made directly, which is not necessary.

Fixed DE lines not being added to "desc" field

Genbank and embl SeqIO description fixes

Some error checking

Fixed accession number reference

Propagated some fixes concerning accnr and prim.seq. setting in order to test for bug fix.

Fixed all issues reported in #239 (partly in a different way, some were already fixed).

Fixed all issues reported in #239 (partly in a different way, some were already fixed).

Propagated fixes from the main trunk in order to be able to test.

Removed superfluous label.

Updated mailing list address on maintrunk

Bio::SeqIO::fasta

Changed Bio::SeqIO::fasta::write_seq to check that the "desc" method can be called before calling it

Changed SeqIO::fasta to see if a seq can "desc" before it calls desc

Fixed bug #254.

Corrected next_seq() to be able to deal with even more consecutive greater chars in the description.

Fixed mailing list address

Updated mailing list address on maintrunk

Handle > in the description line of fasta files hilmar's fix propigated to branch from main trunk

Bio::SeqIO::gcg

Updated mailing list address on maintrunk

Bio::SeqIO::genbank

Changed reference from $seq->accession to $seq->accession_number to provide a cleaner inteface (and eliminate confusion as to where accession is actually stored)

Changed reference from $seq->accession to $seq->accession_number and made accession routine point to accession_number in Bio::Seq

Added handling for featureless files

Adj LOCUS pattern in case Date is not in GenBank file

Fixed bug #833. Partially revised and fixed read_GenBank_References, there were other bugs, too, which haven't been exposed yet.

Fixed the code to be able to deal with GenPept. Tried to tidy up some of the branching etc in next_seq().

Fixed bug in SeqIO/(embl|genbank) which caused accession to become "unknown". Was due to Bio::PrimarySeq being made directly, which is not necessary.

Fixed DE lines not being added to "desc" field

Genbank and embl SeqIO description fixes

Fixed bug #838: qualifiers not satisfying the /tag=value syntax are reported through warn(), not throw().

Bug 838 and accession_number to accession routine migration

Fix to Bio::Root::RootI::_rearrange method which assigned empty strings to variables when called without arguments. Added allow_relative_paths() to Bio::Index::Abstract Added throwing an exception to Bio::Index::AbstractSeq::fetch if ID given is not in index.

Removed _filehandle() -- is inherited.

Updated mailing list address on maintrunk

Bio::SeqIO::pir

Made some fixes on the branch for checking start/end feature sets and other things

Updated mailing list address on maintrunk

Bio::SeqIO::raw

Updated mailing list address on maintrunk

Bio::SeqIO::scf

Updated mailing list address on maintrunk

Bio::SeqIO::swiss

Changed reference from $seq->accession to $seq->accession_number to provide a cleaner inteface (and eliminate confusion as to where accession is actually stored)

Changed reference from $seq->accession to $seq->accession_number and made accession routine point to accession_number in Bio::Seq

Small bugfix

Another small fix

Improved writing functionality

Reference to $acc was not correct

Even more improved writing, thx to james gilbert and andrew su

Added swiss format to scripts

Fixed bug #839: display_id() used for default construction of the id-line.

Fixed mailing list doc.

Merged swiss-prot fix for bug 839

Added _$div back to swiss output

Removed again _$div from output ID line generation. Guys, you cannot have there $seq->display_id()."_".$div, it is simply wrong. display_id() is set to the *full* ID (primary_id()."_".$div) in next_seq(), and adding $div a second time cannot be correct. This also means that any sequence _read_ by swiss.pm should have the correct ID on output. If this is not the case for you please indicate an example record (hlapp@gmx.net). In addition, it makes seqs retrieved from GenPept being written with at least the correct ID, which is essential IMHO.

Revoked my bad edit on the branch (adding _div) - see Hilmar's message for good explaination

Some bugfixes and enhancements for writing (viruses!)

Corrected a comment.

RX line now using optional PubMed method from Annotation::Reference

Fixed bug consisting of explicit creation of PrimarySeq.

Applied primary_seq fix in next_seq().

Added warning to write_seq(). DO NOT propagate this to the main trunk.

Bio::SimpleAlign

Fixed bug #826 by applying the provided fix. Added file descriptor to another print statement (not sure whether this is correct).

Fixed bug #827 with the solution given there.

Fixed bugs #840 (fasta in simplealign) #845 (rev_and_trans.pl in examples)

Move bug fixes of simplealign and rev_and_trans to main trunk

Fixed sort_alphabetically bug

Merged simpled align bug fixes across

Final fixes?

Bio::Tools::Alignment::Clustalw

Initial commit of clustalw wrapper files

Bio::Tools::AnalysisResult

Initial revision.

Bio::Tools::BPlite

Added BPlite module and began porting...

First running version of BPlite port

Small enhancemants to BPlite module, added test script

Small fix in ->seqname

BPlite now uses Bio::SeqFeature::SimilarityPair instead of FeaturePair

Bio::Tools::BPlite::HSP

First running version of BPlite port

Small enhancemants to BPlite module, added test script

BPlite now uses Bio::SeqFeature::SimilarityPair instead of FeaturePair

Bio::Tools::BPlite::Sbjct

First running version of BPlite port

Small enhancemants to BPlite module, added test script

BPlite now uses Bio::SeqFeature::SimilarityPair instead of FeaturePair

Bio::Tools::Blast

Fixed false (in the sense that Perl complains) range in [\w-.] to [\w-\.].

Fixed failure on empty (single) reports. Fixed ambiguous [] range in regexp.

Fixed regexps in hit() to unambiguously identify the options.

Silly doc bug

Doc fix

Fixed bugs #834 and #835.

Synchronized with the head version (there were solely bug fixes).

Bio::Tools::CodonTable

Fixed speed problem in translate method as suggested by Kim Rutherford <kmr@sanger.ac.uk>

Method translate now is faster when there are no ambuigities in the codon. Fix suggested by Kim Rutherford <kmr@sanger.ac.uk>

Corrected a bug affecting terminator codons in ->revtranslate

Fixed bug in ->revtranslaed affecting stop codons

Documentation changes

Added a note in the documentaion that translation from codon table 11, "Bacterial" is identical to the standard tranlation.

Bio::Tools::ESTScan

Initial revision.

Fixed the remaining bug in next_prediction() for reverse strand strand predictions.

Bio::Tools::Genscan

Initial revision.

Corrected a small documentation legacy left over.

Changed storage of predicted sequences to storing Bio::PrimarySeq objects. Recorded Ns prepended to predicted CDS as frame.

Fixed a potential incompatibility with Perl 5.6.0.

Reorganized some of the initialization code. Adapted in order to implement the SeqAnalysisParserI interface.

Fixed a doc bug.

Fixed a potential bug in re-initialization (wasn't an issue before).

Adapted to inheriting and utilizing Bio::Tools::AnalysisResult.

Corrected storing of method and version as parsed from the result file.

Corrected a bug assigning the wrong predicted protein/CDS if there were predictions not giving rise to a sequence (e.g. promotor only).

Bio::Tools::HMMER::Domain

Changed to inherit off Bio::SeqFeature::FeaturePair directly.

Changed to inherit off Bio::SeqFeature::FeaturePair directly.

Bio::Tools::MZEF

Initial revision.

Adapted to inherit off Bio::Tools::AnalysisResult.

Bio::Tools::OddCodes

Added OddCodes

Bio::Tools::Prediction::Exon

Initial revision.

Fixed bug #842.

Fixed documentation (NAME section).

Removed _tag_value (moved to SeqFeature::Generic). Added predicted_cds() and predicted_protein().

Bio::Tools::Prediction::Gene

Initial revision.

Changed documentation of predicted_protein() and predicted_cds() to return/accept Bio::PrimarySeqI objects instead of strings -- however, it is not ensured currently.

Fixed doc bug.

Bio::Tools::SeqPattern

Fixed seqpattern case bug

Bio::Tools::SeqStats

Fixed molecular weight bug in SeqStats.pm where Mwts were calculated without taking into account H20

SeqStats.pm: minor documentation corrections

Bio::Tools::Sim4::Exon

Fixed sim4 code to compile

Revised code and documentation. Fixed _initialize(). Added est_hit() for clarity.

Remove Sim4 parser because it was never functional.

Added and corrected documentation. Changed to inherit off Bio::SeqFeature::SimilarityPair. Changed percentage_id() to alias to frac_identical() if supported.

Bio::Tools::Sim4::ExonSet

Added ExonSet object

Removed because no longer needed.

Bio::Tools::Sim4::Results

Major code revision. New functions for parsing (parse_next_alignment, and next_exonset). Adapted documentation. No longer depends on ExonSet. Tests ok so far.

Small codefix to remove a legacy left-over.

Remove Sim4 parser because it was never functional.

Modified to inherit off Bio::Tools::AnalysisResult and implement Bio::SeqAnalysisParserI. Improved code in parse_next_alignment by adding fall-backs.

Bio::Tools::pSW

Bug #823

Fixed bug #824 (Bio::Seq instead of Bio::LocatableSeq).

Final fixes?

Bio::UnivAln

Fixed bug #832.

Defined (@array) is deprecated

Fixed doc bug and defined(@array)

Not using ary function on seqs

Bio::Variation::AAChange

The first version of Bio::Variation classes and 185 tests.

Bio::Variation::AAReverseMutate

The first version of Bio::Variation classes and 185 tests.

Bio::Variation::Allele

The first version of Bio::Variation classes and 185 tests.

Bio::Variation::DNAMutation

The first version of Bio::Variation classes and 185 tests.

Bio::Variation::IO

The first version of Bio::Variation classes and 185 tests.

Bio::Variation::IO::flat

The first version of Bio::Variation classes and 185 tests.

Bio::Variation::IO::xml

The first version of Bio::Variation classes and 185 tests.

Bio::Variation::MutationI

The first version of Bio::Variation classes and 185 tests.

Added my mistake.

Bio::Variation::README

A general introductin to Bio::Variation classes.

Bio::Variation::RNAChange

The first version of Bio::Variation classes and 185 tests.

Bio::Variation::SeqDiff

The first version of Bio::Variation classes and 185 tests.

Bio::Variation::VariantI

The first version of Bio::Variation classes and 185 tests.

Makefile.PL

Final fixes?

examples/gsequence

Just renamed

examples/gsequence.pl

Added script to cvs

Just renamed

examples/rev_and_trans.pl

Fixed bugs #840 (fasta in simplealign) #845 (rev_and_trans.pl in examples)

Move bug fixes of simplealign and rev_and_trans to main trunk

examples/test-genscan.pl

Initial revision.

Adapted to API change in Bio::Tools::Prediction::Gene.

scripts/blast_fetch.pl

Added simple script to parse a blast file and download all the sequences automagically from genbank

More versitile blast parse + download seqs example script

scripts/bpfetch.pl

Added swiss format to scripts

scripts/bpindex.pl

Added swiss format to scripts