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Bio-Grep-v0.10.2
River stage zero No dependents

Changes for version 0.10.2 - 2007-09-23

  • code cleanup:
    • renamed test data files
    • perlcritic
    • renamed FilterI->reset to FilterI->reset_filter because reset is a buildin function
    • renamed SearchSettings->set to SearchSettings->set_attributes cause set is an ambigious name
  • more tests:
    • features.updownstream (more or less moved from guugle/RE specific tests)
  • New Features:
    • upstream / downstream in SearchResult
    • reverse_complement in SearchResult
  • Bugfixes:
    • Vmatch: $res->sequence undef when available downstream region to small

Documentation

Bio::Grep::Benchmarks
Bio::Grep Benchmarks
Bio::Grep::Cookbook
Bio::Grep Cookbook

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

Examples

Other files