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Bio-Grep-v0.10.0
River stage zero No dependents

Changes for version 0.10.0 - 2007-08-21

  • POD improvements:
    • methods now grouped in CONSTRUCTOR, ACCESSORS/MUTATORS, PACKAGE METHODS, INTERNAL METHODS, ABSTRACT METHODS
    • notes now under IMPORTANT NOTES, not DESCRIPTION
  • code cleanup:
    • standard testfile "header" now in BioGrepTest, requires ToolSet
  • more tests:
    • features.alignments
  • New Features:
    • Bio::Seq objects as query
  • Bugfixes:
    • bgrep not installed witch Build.PL
    • Added Bioperl dependency (ticket #28881, thanks siddhartha)
    • $res->query, $res->alignments not equal in back-ends now, '(reverse complement)' is added to $query->desc

Documentation

Bio::Grep::Benchmarks
Bio::Grep Benchmarks
Bio::Grep::Cookbook
Bio::Grep Cookbook
bgrep
Wrapper for several suffix array tools

Modules

Bio::Grep
Perl extension for searching in DNA and protein sequences
Bio::Grep::Backend::Agrep
Agrep back-end
Bio::Grep::Backend::BackendI
Superclass for all back-ends
Bio::Grep::Backend::GUUGle
GUUGle back-end
Bio::Grep::Backend::RE
Perl Regular Expression back-end
Bio::Grep::Backend::Vmatch
Vmatch back-end
Bio::Grep::Filter::FilterI
Superclass for all filter modules
Bio::Grep::Filter::FilterRemoveDuplicates
Example Filter
Bio::Grep::Root
Superclass for all Bio::Grep* packages
Bio::Grep::SearchResult
Data structure for a back-end search hit
Bio::Grep::SearchSettings
Data structure for all search settings

Other files