Class: Bio::Alignment::FactoryTemplate::FileInFileOutWithTree

Inherits:

FileInFileOut

• Object
• Simple
• FileInFileOut
• Bio::Alignment::FactoryTemplate::FileInFileOutWithTree

Defined in:

lib/bio/alignment.rb

Overview

Template class for alignment application factory. The program needs: input: file (cannot accept stdin), format = fasta format output: file (parser should be specified by DEFAULT_PARSER) Tree (*.dnd) output is also supported.

Direct Known Subclasses

Tcoffee

Instance Attribute Summary

• #output_dnd ⇒ Object readonly

  alignment guide tree generated by the program (*.dnd file).

Attributes inherited from Simple

#command, #data_stdout, #exit_status, #options, #output, #program, #report

Instance Method Summary

• #reset ⇒ Object

Methods inherited from Simple

#initialize, #query, #query_align, #query_alignment, #query_by_filename, #query_string

Constructor Details

This class inherits a constructor from Bio::Alignment::FactoryTemplate::Simple

Instance Attribute Details

#output_dnd ⇒ Object (readonly)

alignment guide tree generated by the program (*.dnd file)

# File 'lib/bio/alignment.rb', line 2483

def output_dnd
  @output_dnd
end

Instance Method Details

#reset ⇒ Object

# File 'lib/bio/alignment.rb', line 2485

def reset
  @output_dnd = nil
  super
end