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

Inherits:
FileInFileOut show all
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 collapse

Attributes inherited from Simple

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

Instance Method Summary collapse

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_dndObject (readonly)

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


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

def output_dnd
  @output_dnd
end

Instance Method Details

#resetObject


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

def reset
  @output_dnd = nil
  super
end