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Commits on Aug 18, 2009
  1. merge in trunk changes

    svn path=/bioperl-dev/branches/nexml-arbgeno/; revision=15985
    maj committed Aug 18, 2009
Commits on Aug 16, 2009
  1. fix details of Population -> Bio::Phylo

    conversion
    
    svn path=/bioperl-dev/branches/nexml-arbgeno/; revision=15950
    maj committed Aug 16, 2009
  2. fix annotation calls

    svn path=/bioperl-dev/branches/nexml-arbgeno/; revision=15949
    maj committed Aug 16, 2009
Commits on Aug 15, 2009
  1. unixize (maybe someday I'll get a real OS)

    svn path=/bioperl-dev/branches/nexml-arbgeno/; revision=15941
    maj committed Aug 15, 2009
  2. a Bio::PopGen::IO module for read/write of

    NeXML files containing arbitrary data types
    
    
    svn path=/bioperl-dev/branches/nexml-arbgeno/; revision=15940
    maj committed Aug 15, 2009
  3. run-time checking for Bio::Phylo availability;

    added create_bphylo_popn();
    
    polymorphize create_bphylo_taxa() to handle
    Bio::PopGen::Population objs;
    
    
    
    svn path=/bioperl-dev/branches/nexml-arbgeno/; revision=15939
    maj committed Aug 15, 2009
  4. make methods consistent with respect to

    use of $self parameter;
    
    "polymorphize" the biophylo conversion 
    arguments (allow for both seq-based and
    popn-based objects);
    
    kludge for importing SeqFeatures not
    contained by the object, but allowing
    a standard default interface.
    
    
    svn path=/bioperl-dev/branches/nexml-arbgeno/; revision=15936
    maj committed Aug 15, 2009
  5. some refactoring; works now for existing

    t/nexml.t
    
    svn path=/bioperl-dev/branches/nexml-arbgeno/; revision=15935
    maj committed Aug 15, 2009
Commits on Aug 14, 2009
  1. bioperl-dev/nexml-arbgeno branch of Bio::PopGen::IO

    svn path=/bioperl-dev/branches/nexml-arbgeno/; revision=15934
    maj committed Aug 14, 2009
  2. adding support for Bio::PopGen objects

    in Factory
    
    svn path=/bioperl-dev/branches/nexml-arbgeno/; revision=15930
    maj committed Aug 14, 2009
  3. Rearranged the arguments for create_bphylo_seq,

    making the "$feat" argument optional (only 
    provided if the seq object can't contain its
    own features)
    
    Made the creation of the unique {_NexmlID} more
    robust
    
    Set keyword substitutions
    
    svn path=/bioperl-dev/trunk/; revision=15928
    maj committed Aug 14, 2009
Commits on Aug 13, 2009
  1. Fixed some of the nexml t scripts

    svn path=/bioperl-dev/trunk/; revision=15926
    chmille4 committed Aug 13, 2009
  2. Added checks for ID having spaces

    svn path=/bioperl-dev/trunk/; revision=15925
    chmille4 committed Aug 13, 2009
  3. added a Bio::Root::IO->flush to the

    respective write_*() routines before
    return
    
    svn path=/bioperl-dev/trunk/; revision=15924
    maj committed Aug 13, 2009
  4. Adding existence checks for tree, taxon attributes,

    some rationalizing of create_bperl_tree, which 
    fixes some test data parsing errors.
    
    svn path=/bioperl-dev/trunk/; revision=15923
    maj committed Aug 13, 2009
  5. Added extraction methods and tests

    svn path=/bioperl-dev/trunk/; revision=15921
    chmille4 committed Aug 13, 2009
  6. make output "compact"; i.e., write

    sequences as sequence strings, rather
    than each residue as an individual 
    <cell> element
    
    svn path=/bioperl-dev/trunk/; revision=15920
    maj committed Aug 13, 2009
  7. typo

    svn path=/bioperl-dev/trunk/; revision=15919
    maj committed Aug 13, 2009
  8. adding a final flush to the write() method

    (fixes a bork on my system; don't think it 
    can hurt)
    
    svn path=/bioperl-dev/trunk/; revision=15918
    maj committed Aug 13, 2009
Commits on Aug 12, 2009
  1. a little pod housekeeping

    svn path=/bioperl-dev/trunk/; revision=15917
    maj committed Aug 12, 2009
  2. Added Pod documentation for each method

    svn path=/bioperl-dev/trunk/; revision=15916
    chmille4 committed Aug 12, 2009
Commits on Aug 6, 2009
  1. minor fix

    svn path=/bioperl-dev/trunk/; revision=15891
    chmille4 committed Aug 6, 2009
Commits on Aug 5, 2009
  1. Refactored the linking of taxa, Added tests associated with taxa link…

    …ing.
    
    svn path=/bioperl-dev/trunk/; revision=15890
    chmille4 committed Aug 5, 2009
Commits on Jul 29, 2009
  1. Turned Bio::Nexml::Util module into Bio::Nexml::Factory module. Adres…

    …sed some comments about coding style from Mark Jenson
    
    svn path=/bioperl-dev/trunk/; revision=15889
    chmille4 committed Jul 29, 2009
Commits on Jul 21, 2009
  1. Fixed some bugs for the handling of linking taxa data to matrices and…

    … trees
    
    svn path=/bioperl-dev/trunk/; revision=15876
    chmille4 committed Jul 21, 2009
  2. Fixed some bugs for the handling of linking taxa data to matrices and…

    … trees
    
    svn path=/bioperl-dev/trunk/; revision=15875
    chmille4 committed Jul 21, 2009
Commits on Jul 15, 2009
  1. keyword subst

    svn path=/bioperl-dev/trunk/; revision=15856
    maj committed Jul 15, 2009
Commits on Jul 14, 2009
  1. Added more robust handling of writing nexml, specifically complete ne…

    …xml documents. Added better handling of linking taxa data to matrices and trees
    
    svn path=/bioperl-dev/trunk/; revision=15852
    chmille4 committed Jul 14, 2009
  2. Added More test for nexml, focusing on tests for writing a complete n…

    …exml document
    
    svn path=/bioperl-dev/trunk/; revision=15851
    chmille4 committed Jul 14, 2009
Commits on Jun 30, 2009
  1. Added More test for nexml, focusing on tests for writing to a nexml d…

    …ocument
    
    svn path=/bioperl-dev/trunk/; revision=15808
    chmille4 committed Jun 30, 2009
  2. Refactored unparsing code from Bio::*IO::nexml modules into Bio::Nexm…

    …l::Util module
    
    svn path=/bioperl-dev/trunk/; revision=15807
    chmille4 committed Jun 30, 2009
Commits on Jun 24, 2009
  1. Now supports reading of an entire Nexml document while parsing it onl…

    …y once.
    
    svn path=/bioperl-dev/trunk/; revision=15802
    chmille4 committed Jun 24, 2009
  2. Created Bio::Nexml::Util to handle parsing of nexml document. Refacto…

    …red code from Bio::AlignIO::nexml, Bio::SeqIO::nexml, and Bio::TreeIO::nexml into Bio::Nexml::Util.
    
    svn path=/bioperl-dev/trunk/; revision=15801
    chmille4 committed Jun 24, 2009
Commits on Jun 22, 2009
  1. This script uses Rutger's www.nexml.org site to

    check whether an input file is valid NeXML
    see pod for details...
    
    svn path=/bioperl-dev/trunk/; revision=15800
    maj committed Jun 22, 2009
  2. these are are a bunch of NeXML test data set up by Arlin

    at the DB Interop Hackathon
    
    svn path=/bioperl-dev/trunk/; revision=15799
    maj committed Jun 22, 2009