Module

Bio::Alignment

In:

lib/bio/appl/mafft/report.rb
lib/bio/alignment.rb

About Bio::Alignment

Bio::Alignment is a namespace of classes/modules for multiple sequence alignment.

Multiple alignment container classes

Bio::Alignment::OriginalAlignment

Bio::Alignment::SequenceArray

Bio::Alignment::SequenceHash

Bio::Alignment::Site

Modules

Bio::Alignment::EnumerableExtension

Mix-in for classes included Enumerable.

Bio::Alignment::ArrayExtension

Mix-in for Array or Array-like classes.

Bio::Alignment::HashExtension

Mix-in for Hash or Hash-like classes.

Bio::Alignment::SiteMethods

Bio::Alignment::PropertyMethods

Bio::Alignment::GAP

Compatibility from older BioRuby

Methods

new new2 readfiles

Classes and Modules

Module Bio::Alignment::ArrayExtension
Module Bio::Alignment::EnumerableExtension
Module Bio::Alignment::FactoryTemplate
Module Bio::Alignment::GAP
Module Bio::Alignment::HashExtension
Module Bio::Alignment::OriginalPrivate
Module Bio::Alignment::Output
Module Bio::Alignment::PropertyMethods
Module Bio::Alignment::SiteMethods
Class Bio::Alignment::MultiFastaFormat
Class Bio::Alignment::OriginalAlignment
Class Bio::Alignment::SequenceArray
Class Bio::Alignment::SequenceHash
Class Bio::Alignment::Site

Public Class methods

creates a new Bio::Alignment::OriginalAlignment object. Please refer document of OriginalAlignment.new.

      # File lib/bio/alignment.rb, line 2188
2188:     def self.new(*arg)
2189:       OriginalAlignment.new(*arg)
2190:     end

creates a new Bio::Alignment::OriginalAlignment object. Please refer document of OriginalAlignment.new2.

      # File lib/bio/alignment.rb, line 2194
2194:     def self.new2(*arg)
2195:       OriginalAlignment.new2(*arg)
2196:     end

readfiles(*files)

creates a new Bio::Alignment::OriginalAlignment object. Please refer document of OriginalAlignment.readfiles.

      # File lib/bio/alignment.rb, line 2200
2200:     def self.readfiles(*files)
2201:       OriginalAlignment.readfiles(*files)
2202:     end