Revision history for Perl extension Bio::Homology::InterologWalk.

0.57	Tue Nov 1 14:41:07 2011
	-improved documentation
        -setup_ensembl_adaptor(): added support for set_reconnect_when_lost() - introduced in API v64


0.55	Thu Sep 8 15:06:45 2011
	interface changes:
        - get_direct_interactions(): introduced flag to allow for retrieval of chimeric (taxonA != taxonB)
          PPIs if desired
        - do_attributes(): removed label_type flag. Now only "external name" can be used to populate
          name attribute file
        - do_attributes(): introduced 'label_chimeric' to comply with changes in get_direct_interactions().
          Introduced dynamic retrieval of gene_adaptor to find chimeric species and label gene names by
          species name
        bugfixes:
        - _get_interactor_name(): fixed (gene name) problem due to intact change
        - _get_ens_id_from_props(): included 'flybase' case due to intact change in properties field
        - _get_ens_id_from_props(): introduced ensembl ID count: if only 1, accepted, if more, ambiguous case.

0.52    Wed Aug 17 12:09:02 2011
        - removed hard-coded species hash
        - updated interface and documentation
        - added warnings for unsupported usage of non-metazoan Ensemblgenomes species
        - get_backward_orthologies(): introduced basic support for NCBI taxonomy climb for cases of unrecognised taxon
          scientific name/taxon id

0.511   Sat Aug 6 10:56:09 2011
        - updated species hash in main module

0.510   Thu Jul 21 18:06:34 2011
	- removed no_output flags throughout
        - documentation update
        - changed get_forward_orthologies() interface to explicity allow appending data to partial file after
          remote connection failure

0.505   Fri Jul 1 16:10:52 2011
	- naming corrections
        - documentation update

0.501   Sat May 7 14:02:02 2011
	- compute_confidence_score(): boolean variables restored
        - corrected version bug

0.5   Fri May 6 12:46:25 2011
	- First Beta Release
        - _get_ens_id(): added cygid option to deal with embedded yeast ids
        - merged get_ensembl_id_from_ensembl() and get_ensembl_id_from_uniprot()
        - merged all duplicates between the pacakges: Bio::Homology::InterologWalk and
          Bio::Homology::InterologWalk::Direct
        - get_direct_interactions(): rewritten and moved to Bio::Homology::InterologWalk
        - removed Bio:Homology::InterologWalk::Direct package. All unmerged subroutines moved to
          Bio::Homology::InterologWalk
        - get_interactions(): rewritted to gather 'properties' field from MITAB data
        - get_backward_orthologies(): rewritten to use 'properties' field from MITAB data 
        - _clean_ids(): removed

0.12  Wed Jan 12 12:07:01 2011
        - Modified Makefile.PL  to avoid failing tests when prerequisite
          software on testers' machines is missing

0.11  Thu Dec 16 11:45:26 2010
        - InterologWalk.pm: introduced look-up table for Genomes Taxa
        - changed db names throughout for better readability
        - setup_ensembl_adaptor(): fixed pan_homology bug
        - setup_ensembl_adaptor(): removed 'default' db
        - get_forward_orthologies(): updated docs
        - get_forward_orthologies(): introduced genome name check when taxon id fails
        - get_backward_orthologies(): updated docs
        - get_backward_orthologies(): introduced genome name check when taxon id fails
        - process_homologies(): introduced protein adaptor check

0.09  Tue Oct 19 18:45:26 2010
        - fixed undefined canonical peptide member bug in _process_homologies()
        - fixed registry timeout bug in compute_multiple_taxa_mean()

0.08  Thu Oct 07 12:12:26 2010
        - removed commented lines in doScores.pl
        - fixed empty candidate bug in get_backward_orthologies()

0.07  Tue Oct 05 14:50:26 2010
        - rewrote _process_homologies() to get rid of "possible_ortholog"
          paralogy class
        - fixed extension bug in getDirectInteractions.pl

0.06  Sat Sep 18 19:50:26 2010
        - introduced new method for computing conservation score for the
          putative PPI: compute_conservation_score(). Status is experimental.
        - rewritten doScores.pl to show usage of compute_conservation_score().
        - rewritten Makefile.PL with new prerequisite checking scheme.
        - rewritten interface to _build_query_options().
        
0.05  Thu Sep 09 18:50:26 2010
        - do_attributes() now writes two attribute files: name attribute
          and novel id attribute.
        - Interface redesigned for do_networks() and do_attributes()
          to simplify introduction of new node attribute file
        - sample usage file doNets.pl rewritten to show usage of new interface
          for the two methods

0.04  Fri Sep 03 01:09:26 2010
        - removed version bug
        - removed local library requirement in test script

0.03  Thu Sep 02 15:42:09 2010
        - Relaxed Perl Version Requirement to 5.8.6
        - fixed input namefile bug in getDirectInteractions.pl
        - Removed DBI requirement (implicitly required by DBD::CSV)
        - included MAC note in README
        - changed arguments in compute_multiple_taxa_mean() in doScores.pl
        - included "usage" conditions in doScores.pl and doNets.pl. No "default" filename anymore:
          ensembl version in filename is dynamic, it would have broken soon.

0.02  Tue Aug 31 09:51:26 2010
        - POD reformatted

0.01  Sun Aug 29 19:09:26 2010
	- original version; created by h2xs 1.23 with options
		-XA -n Bio::Homology::InterologWalk

