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

new(*arg)

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

[Source]

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

new2(*arg)

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

[Source]

          # 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.

[Source]

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

[Validate]