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Commits on Jul 23, 2009
  1. more comments

    svn path=/bioperl-dev/branches/maj-nexml/; revision=15885
    maj committed Jul 23, 2009
  2. code review--

    design comments for Chase
    
    
    svn path=/bioperl-dev/branches/maj-nexml/; revision=15883
    maj committed Jul 23, 2009
Commits on Jul 22, 2009
  1. A style review

    svn path=/bioperl-dev/branches/maj-nexml/; revision=15882
    maj committed Jul 22, 2009
Commits on Jul 21, 2009
  1. refactor to use Bio::Root::Test

    some detabification
    
    svn path=/bioperl-dev/branches/maj-nexml/; revision=15879
    maj 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=15876
    chmille4 committed Jul 21, 2009
  3. 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
Commits on Jun 17, 2009
  1. Test scripts for Bio::AlignIO::nexml, Bio::SeqIO::nexml, and Bio::Tre…

    …eIO::nexml modules
    
    svn path=/bioperl-dev/trunk/; revision=15798
    chmille4 committed Jun 17, 2009
Commits on Jun 16, 2009
  1. Created Bio::Nexml.pm module with very minimal functionality

    svn path=/bioperl-dev/trunk/; revision=15794
    chmille4 committed Jun 16, 2009
  2. Updated code to address several comments by Mark Jensen.

    svn path=/bioperl-dev/trunk/; revision=15793
    chmille4 committed Jun 16, 2009
  3. updated code to make use of factory for sequence creation. Addressed …

    …several comments by Mark Jensen.
    
    svn path=/bioperl-dev/trunk/; revision=15792
    chmille4 committed Jun 16, 2009
  4. bug fixes

    svn path=/bioperl-dev/trunk/; revision=15784
    chmille4 committed Jun 16, 2009
Commits on Jun 15, 2009
  1. Implemented write_tree function.

    svn path=/bioperl-dev/trunk/; revision=15775
    chmille4 committed Jun 15, 2009
  2. Implemented write_seq function.

    svn path=/bioperl-dev/trunk/; revision=15774
    chmille4 committed Jun 15, 2009
  3. Implemented write_aln function. However it currently throws an error …

    …because of the error checking of Bio::Phylo. This will go away as soon as the taxa data can be linked to the Bio::Phylo:Matrices::Matrix object.
    
    svn path=/bioperl-dev/trunk/; revision=15773
    chmille4 committed Jun 15, 2009
Commits on Jun 9, 2009
  1. some helpful(?) comments to Chase

    svn path=/bioperl-dev/trunk/; revision=15750
    maj committed Jun 9, 2009
  2. some helpful(?) comments to Chase

    svn path=/bioperl-dev/trunk/; revision=15749
    maj committed Jun 9, 2009
  3. some helpful(?) comments to Chase

    svn path=/bioperl-dev/trunk/; revision=15748
    maj committed Jun 9, 2009
Commits on Jun 8, 2009
  1. Preliminary version of TreeIO::nexml->next_tree() method.

    svn path=/bioperl-dev/trunk/; revision=15747
    chmille4 committed Jun 8, 2009
  2. Changed the way Bio::Phylo objects' data were being accessed

    svn path=/bioperl-dev/trunk/; revision=15746
    chmille4 committed Jun 8, 2009
Commits on Jun 1, 2009
  1. Adding preliminary version of of Bio::SeqIO::nexml->next_seq() and Bi…

    …o::AlignIO::next_aln() methods. More mapping of attributes could probably be done and the error handling needs to be more robust.
    
    svn path=/bioperl-dev/trunk/; revision=15735
    chmille4 committed Jun 1, 2009
  2. has_strand info for tblastn

    svn path=/bioperl-dev/trunk/; revision=15728
    maj committed Jun 1, 2009
  3. tests ready for prime time

    svn path=/bioperl-dev/trunk/; revision=15727
    maj committed Jun 1, 2009
  4. doh.

    svn path=/bioperl-dev/trunk/; revision=15726
    maj committed Jun 1, 2009
  5. handling for strand-only contexts;

    predicates _has_strand, _has_frame and 
    concommitant additions to the alg lookup table
    
    
    svn path=/bioperl-dev/trunk/; revision=15725
    maj committed Jun 1, 2009
Commits on May 31, 2009
  1. context for tiling iterator

    svn path=/bioperl-dev/trunk/; revision=15724
    maj committed May 31, 2009
  2. Refactor of strand/frame context handling; correct length conversions…

    … now in _calc_coverage_map
    
    svn path=/bioperl-dev/trunk/; revision=15723
    maj committed May 31, 2009