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Improvements in the Bio::Assembly::ContigSpectrum module and update o…

…f its dependencies

svn path=/bioperl-live/trunk/; revision=16457
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1 parent 9b9d327 commit 576f7bf838194e4ad484e0339df0e9fe9f1f20a3 @fangly fangly committed Dec 11, 2009
Showing with 203 additions and 139 deletions.
  1. +200 −137 Bio/Assembly/Tools/ContigSpectrum.pm
  2. +1 −2 Build.PL
  3. +2 −0 DEPENDENCIES
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@@ -50,8 +50,7 @@ my $build = Bio::Root::Build->new(
# we actually need 1.01 of Class::AutoClass, but unfortunately it is versioned as 1.0
'Clone' => '0/cloning objects/Bio::Tools::Primer3',
'Convert::Binary::C' => '0/strider functionality/Bio::SeqIO::strider',
- # we specifically want Graph::Directed, but that has no VERSION
- 'Graph' => '0/ontology engine implementation for the GO parser/Bio::PhyloNetwork',
+ 'Graph' => '0/Phylogenetic Networks, ontology engine implementation, contig analysis/Bio::PhyloNetwork,Bio::Ontology::SimpleGOEngine::GraphAdaptor,Bio::Assembly::Tools::ContigSpectrum',
'GraphViz' => '0/Phylogenetic Network Visulization/Bio::PhyloNetwork::GraphViz',
'HTML::Entities' => '0/remote analysis POST submissions/Bio::SearchIO::blastxml',
'HTML::HeadParser' => '3/parsing <HEAD> section of HTML docs/Bio::Tools::Analysis::DNA::ESEfinder',
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@@ -118,11 +118,13 @@ NB: This list of packages is not authoritative. See the 'requires',
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
| Graph | * Graph::Directed - NA | None |
+| | * Graph::Undirected - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
| * Bio::PhyloNetwork - Graph::Directed |
| * Bio::Ontology::SimpleGOEngine::GraphAdaptor - Graph::Directed |
+| * Bio::Assembly::Tools::ContigSpectrum - Graph::Undirected |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |

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