CVS log for bioperl-live/Bio/PrimarySeq.pm
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removed pointless print of 0-length string

improved diagnostic error message when reporting on Incorrect parameters

indentification...

merge from HEAD

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

seq() does not take named parameters

use base, return true

merge from HEAD

merge from HEAD, server problems should skip and pass in test suite

merge from HEAD, bugfixes and new PullParserI and hmmer parser

Updating emails

Updated bug reporting

Fixed spaces

Fixed spaces and URL's

Added extra validated symbols to POD

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

cleaning unnecessary "return undef"s

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

Filled in empty stubs in POD, eg. _guess_alphabet()

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

Merged from HEAD to 1.5.1 branch, changes which remove old bug email address and point to bugzilla.bioperl.org website for bug submission

Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.

Edits

parameterize the valid character pattern so it can be augmented when numbers are allowed to be encoded in a sequence string

Add X to class of ambiguous characters, _guess_alphabet

fix bug #1670 on the branch

Nathan says correct regexp

Allow unsetting of the primary ID.

fixing docs to indicate that these objects have get/set on the alphabet call

support desc as an alias for description

Fixed a bug in seq() that would not invalidate length if it had been set
without a sequence, and then a sequence was set.

relocated is_circular to the object away from the interface as this is not getting set with a value upon initialization from SeqIO

support is_circular properly

Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature

Minor editing

Bugfixes on the freaky dev branch.  Some of the tests were failing.  A few still do.  This is a work in progres..

Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future.  No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein.  Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.

changed IdentifiableI to GloballyIdentifiableI

Fixed typo in error message of subseq(). Also split out error conditions in other throw call.

Let's not talk about moltype's at all. And in throw() let's call the values returned by alphabet() 'alphabet'. Also, I think the doc in validate_seq is incorrect, there is no ref() call, all it's doing is looking for non-alphabetic characters.

final documentation fixes for 1.2

fixed docs (little) wrt primary_id; fasta parser; swissprot output on fuzzies

fixed primary seq seq setting call

fixed seq documentation

Allowed description to be set to undef.

Added recognition of all IdentifiableI parameters to PrimarySeq. Added
object_factory() as an alias for <type>_factory methods in several places.

Tidied up Cluster interfaces. Changed Cluster::UniGene to implement
ClusterI, IdentifiableI, and DescribableI. Added display_id to ClusterI.
Removed members() from ClusterI. Added namespace and authority defaults
to Cluster::UniGene.

Replaced bio.perl.org/bioperl-bugs/ with bugzilla.bioperl.org.

Added check to PrimarySeq::length that throws an exception if someone
lies about the length. Fixed bug #1317.

Added documentation to SeqBuilder. Unified and fixed all delegation
calls in Seq not to prescribe the number of arguments and to allow
passing undef. Changed PrimarySeq::length to possibly be a real attribute.

flush moved up into Root/IO to allow perl 5.5 work around

Small fixes. Added -namespace as parameter to Bio::PrimarySeq constructor.

speed ups for fasta file parsing

Root/RootI changes - sliming the create path and new ref_to_seq constructor pattern

pod fixes

removed unnecessary BEGIN block to initialize global, static %valid_type

SequenceFactoryI wasn't inheriting from ObjectFactoryI. Fixed. DBLink is
now IdentifiableI. Otherwise minor things.

Fixed messed up decision whether or not to guess the alphabet.
Restructured the code and added comments, so intentions maybe are clearer
now.

Added alias accession for accession_number, with deprecation warning.

initial commit of Bio::Seq::EncodedSeq and corresponding required patches to make LocatableSeq work (and to get PrimarySeq to quit calling guess_alphabet so willy nilly)

Separated IdentifiableI and DescribableI from PrimarySeqI. Made both
PrimarySeq and Seq fully comply with both interfaces. Added tests to
test for IdentifiableI and DescribableI compliance.

made seq() take an (optional) alphabet argument, so as to override any (incorrect) automatic guessing

Simplified and cleaned up subseq().

added translate and translate_as_string helper functions to Bio::Perl

first commits of describable and identifiable interfaces - primaryseqI modified

report the offending characters in the throw string

bug #1211

POD fixes

optimize PrimarySeq _guess_alphabet to be more efficient using tr// to count rather than editing the sequence string

update doc to describe circular feature

protect against calling length on empty string

line wrapping, typos

line wrapping, typos

remove deprecated methods (getseq, ary, out_fasta, setseq, type, seq_len,str)

handle with error msg when start/end are undefined in subseq

Minor POD corrections.

POD fixes

renamed _guess_type() into _guess_alphabet() and fixed the error message

Sweeping change:

Bio::Root::RootI is now a pure abstract interface and cannot be
inherited from unless you implement several of its abstract methods.
Most people will want to inherit from Bio::Root::Root.

This change was necessary in order to support Bioperl objects that
were not based on hashrefs.

Some improved error messages

subseq retrieval using a Bio::LocationI

insure lowercase moltypes

changed moltype() into alphabe()

new method is_circular(); code and synopsis update

Added '?' into characters ignored by _guess_type()

update synopsis documentation

POD and doc fixes

documentation about 'new' to be added to 0.7.2

adding much needed documentation to PrimarySeq

validate_seq() accepts '?' characters into sequence

merge of branch-07 to head. Mostly POD changes.

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

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

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

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

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

POD fixes

Moved initialization stuff to the top for better maintenance.

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

Added capability of initializing to an empty sequence.

changed to new RootI chained new structure

doc bug

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

fixed regex bug in _guess_type

safer length call

removed debugging cruft

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

move bug fixes of simplealign and rev_and_trans to main trunk

Fixes to bioperl mailing lists in POD

some doc bugs (updating mailing address for bioperl)

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

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.

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.

*** empty log message ***

Fixed typo PrimaySeq to PrimarySeq and require 'Bio::PrimarySeq' changed to require Bio::PrimarySeq

Added r to Bio::PrimaySeq->new() in SYNOPSIS

fixed bad reference to seq not self object

made more jitterbug fixes

Improvements to Index system, and eliminated warnings from CodonTable

Alowing stop codons in PrimarySeq.

added new files

got the tests to pass

started the big renaming

removed some cruft

did primaryseq making etc