Module: Bio::Alignment

Defined in:
lib/bio/alignment.rb,
lib/bio/appl/mafft/report.rb

Overview

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

Defined Under Namespace

Modules: ArrayExtension, EnumerableExtension, FactoryTemplate, GAP, HashExtension, OriginalPrivate, Output, PropertyMethods, SiteMethods Classes: MultiFastaFormat, OriginalAlignment, SequenceArray, SequenceHash, Site

Class Method Summary (collapse)

Class Method Details

+ (Object) new(*arg)

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



2188
2189
2190
# File 'lib/bio/alignment.rb', line 2188

def self.new(*arg)
  OriginalAlignment.new(*arg)
end

+ (Object) new2(*arg)

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



2194
2195
2196
# File 'lib/bio/alignment.rb', line 2194

def self.new2(*arg)
  OriginalAlignment.new2(*arg)
end

+ (Object) readfiles(*files)

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



2200
2201
2202
# File 'lib/bio/alignment.rb', line 2200

def self.readfiles(*files)
  OriginalAlignment.readfiles(*files)
end