[Bioperl-l] 0.6.2: really, now

[Peter van Heusden]

Ok, here's the list of what I imported from the HEAD for branch-06. If a
file is not listed, it is either because it didn't change, or because I
didn't import the diffs because they added incompatible functionality.

Please look particularly at the comments marked NOTE: - these are
outstanding issues that need dealing with.

A short guide:

(C) means cosmetic change
(B) means bugfix
(F) means functionality
(BF) means bugfix which changes functionality

I've got a local copy of the code with these changes merged, which I will
make available as a tar.gz to testers. Is there somewhere with more
bandwidth than our FTP site where I can make this available? bio.perl.org
perhaps?

PLATFORMS
 o new PLATFORMS file (C)
README
 o new email / WWW addresses (C)
 o removed reference to external modules, now refers to WWW page (C)
biodesign.pod
 o new information on how to wrap external objects in bioperl - replaces
   previous section on bioperl IDL (C)
bioperl.pod
 o update mail / WWW addresses (C)
Bio/Annotation.pm
 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 methods: remove_Reference, remove_Comment, remove_DBLink (F)
 o added check to see if argument isa() Bio::Annotation::DBLink (FB)
Bio/DBLinkContainerI.pm
 o doesn't exist in branch-06 - not added
Bio/LocatableSeq.pm
 o NOTE: branch-06 seems to be more 'modern' than HEAD!
Bio/PrimarySeq.pm
 o ->subseq: merge seperate sanity checks for sane start and end into one (B)
 o change indent of ->accession_number (C)
Bio/PrimarySeqI.pm
 o documentation update in accession_number (C)
 o documentation update in translate (C)
 o initiator codon / stop codon handling only if sequence is a full CSD (F)
Bio/Seq.pm
 o changed reference from ->primary_seq to ->{'primary_seq'} (F) - not merged
 o removed length() method (F) - not merged
 o add documentation for return value of add_SeqFeature (C)
 o use can("entire_seq") instead of can("seq") in add_SeqFeature (F) - not
   merged
 o added feature_count() method, used in SeqIO::embl (F)
 o added sub_species() method (F) - not merged
 o added blank line to accession() (C)
Bio/SeqFeatureI.pm
 o added example of ->source_tag() use to SYNOPSIS (C)
 o added example of ->each_tag_value() and ->sub_SeqFeature() to SYNOPSIS (CF) - each_tag_value example not merged
 o reformat of documentation at start of file (C)
 o update of documentation for has_tag (C)
 o add each_tag_value() (F) - not merged
 o remove blank lines (C)
Bio/SimpleAlign.pm
 o read_MSF changed to make initial whitespace on an alignment line optional. (F)
 o write_MSF changed to write out 2 blank lines to MSF file, not stdout. (B)
Bio/UnivAln.pm
 o fixed test for empty list of parameters in _initialize (B)
 o get sequence as array use $seq->ary rather than split() in _seqs (C)
Bio/Annotation/Comment.pm:
 o NOTE: branch-06 version is more 'modern' than HEAD!
Bio/Annotation/DBLink.pm
 o update annotation in SYNOPSIS (C)
 o update documentation in Description (C)
 o add Ewan as contact (C)
 o add code to _initialize, so that it is possible to creat DBLink
   objects directly, rather than only receiving them as SeqFeatures (F)
Bio/Annotation/Reference.pm
 o NOTE: branch-06 version is more 'modern' than HEAD!
Bio/DB/Ace.pm
 o change addresses of mailing lists and WWW pages (C)
Bio/DB/GenBank.pm
 o NOTE: not updated on advice from Hilmar Lapp
Bio/DB/GenPept.pm
 o NOTE: not updated on advice from Hilmar Lapp
Bio/DB/RandomAccessI.pm
 o added CVS $Id$ line (C)
Bio/DB/SeqI.pm
 o added CVS $Id$ line (C)
Bio/Index/Abstract.pm
 o added CVS $Id$ line, mailing list address changes (C)
Bio/Index/AbstractSeq.pm
 o added CVS $Id$ line, mailing list address changes (C)
 o in fetch(), only set display_id if $seq is defined. (B)
 o documentation bugfix in _get_SeqIO_object (C)
Bio/Index/EMBL.pm
 o mailing list info update (C)
Bio/Index/Fasta.pm
 o mailing list info update (C)
 o change handling of main indexing loop (B)
 o add last record to index (B)
Bio/Index/SwissPfam.pm
 o mailing list info update (C)
Bio/Root/Global.pm
 o Blank lines removed (C)
Bio/Root/IOManager.pm
 o Mailing list addresses and WWW page info. (C)
Bio/Root/Utilities.pm
 o mailing list and WWW info update (C)
 o in create_filehandle(), check for (not ref $client), instead of (not $client) (B)
Bio/Root/Vector.pm
 o mailing list and WWW info update (C)
Bio/Root/Xref.pm
 o mailing list and WWW info update (C)
Bio/SeqFeature/FeaturePair.pm
 o two attributes in object hash renamed: feature1 -> _feature1 and feature2 -> _feature2 (C)
 o has_tag and each_tag_value implementation added. (F)
Bio/SeqIO/embl.pm
 o seq->accession($acc) changed to $seq->accession_number (F)
 o handle absence of Feature Table when reading/writing sequences - in
   next_seq() and write_seq() (F)
 o use $seq->seq() to set sequence, instead of making a new
   PrimarySeq and setting set->primary_seq() (BF)
 o can('accession_number') rather than can('accession') in write_seq (F)
 o check that $line is defined in _write_line_EMBL_regex (B)
 o return '' if @lines is empty in _write_line_EMBL_regex (B)
 o set $s to '' if !defined in _write_line_EMBL_regex (B)
Bio/SeqIO/fasta.pm
 o deal with FASTA entries with > in description (B)
Bio/SeqIO/gcg.pm
 o use vars '@ISA' instead of use vars qw(@ISA) (C)
Bio/SeqIO/genbank.pm
 o NOTE: substantial rewrite by Hilmar Lapp
Bio/SeqIO/pir.pm
 o NOTE: need guidance on this
 o throw away everything to first empty line (F)
 o print extra >P1;, followdd by seq->id() (F)
Bio/SeqIO/swiss.pm
 o NOTE: substatial updates - need guidance
Bio/Tools/Blast.pm
 o only version differences (C)
Bio/Tools/CodonTable.pm
 o documentation update (C)
 o update of mailing list and WWW info (C)
Bio/Tools/RestrictionEnzyme.pm
 o NOTE: branch-06 version appears to be more modern than HEAD!
Bio/Tools/SeqPatterm.pm
 o NOTE: branch-06 versions appears to be more modern than HEAD!
Bio/Tools/SeqStats.pm
 o NOTE: require guidance on this one
 o more precise amino acid residue weights (F)
 o reformatting (C)
 o get_mol_wt: removal of H2O during peptide bond formation (F)
Bio/Tools/SeqWords.pm
 o NOTE: branch-06 version appears to be more modern than HEAD!
Bio/Tools/pSW.pm
 o updated to use new-style BioPerl ->seq() method (F)
 o use Bio::LocatableSeq instead of Bio::Seq (F)
Bio/Tools/Blast/HSP.pm
 o only version number differs
Bio/Tools/Blast/HTML.pm
 o only version number differs
Bio/Tools/Blast/Sbjct.pm
 o only version number differs
Bio/Tools/Blast/Run/LocalBlast.pm
 o only version number differs
Bio/Tools/Blast/Run/Webblast.pm
 o only version number differs
examples/blast/blast_config.pl
 o only version number differs
examples/blast/blast_seq.pl
 o only version number differs
examples/blast/parse_positions.pl
 o cosmetic change in variable declaration (C)
examples/blast/print_blasts.pl
 o only version number differs
examples/blast/run_blast_remote.pl
 o only version number differs
scripts/bpfetch.pl
 o allow output in Swissprot format (from indexed Swissprot files) (F)
scripts/bpindex
 o allow the indexing of Swissprot files (F)
t/Annotation.t
 o exercise Annotation::DBLink module with extra tests (F)
t/Index.t
 o only version numbers differ
t/PrimarySeq.t
 o really test translation (F)
t/Range.t
 o change how strand is specified ("+1" to 1) (F)
t/Seq.t
 o only version numbers differ
t/SeqFeature.t
 o add 4 extra tests related to attaching a SeqFeature to a Seq (F)
t/SeqIO.t
 o NOTE: many changes - not yet done
t/SimpleAlign.t
 o NOTE: branch-06 is more modern than HEAD!
t/Species.t
 o only version number differs
t/Tools.t
 o NOTE: branch-06 is more modern than HEAD!

Files that don't exist in branch-06:

SeqFeatureProducerI.pm
DB/UpdateableSeqI.pm
Index/Genbank.pm
Index/Swissprot.pm
SeqFeature/GeneStructure.pm
SeqFeature/Similarity.pm
SeqFeature/SimilarityPair.pm
SeqFeatureProducer/GFF.pm
SeqFeatureProducer/MZEF.pm
SeqIO/GAMEHandler.pm
SeqIO/ace.pm
SeqIO/bioxml.pm
Tools/BPLite.pm
Tools/Genscan.pm
Tools/MZEF.pm
Tools/OddCodes.pm
Tools/BPLite/HSP.pm
Tools/BPLite/Sbjct.pm
Tools/PPSEARCH/Parse.pm
Tools/PRFSCAN/Parse.pm
Tools/PRINTS/Parse.pm
Tools/Prediction/Exon.pm
Tools/Prediction/Gene.pm
Tools/Sim4/ExonSet.pm
Variation/AAChange.pm
Variation/AAReverseMutate.pm
Variation/Allele.pm
Variation/DNAMutation.pm
Variation/IO.pm
Variation/README
Variation/RNAChange.pm
Variation/SeqDiff.pm
Variation/VariantI.pm
Variation/IO/flat.pm
Variation/IO/xml.pm

_______________/\/eGenetics.com\/\_______________
Peter van Heusden				pvh@egenetics.com
Electric Genetics