Class: Bio::Tcoffee

Inherits:

Alignment::FactoryTemplate::FileInFileOutWithTree

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

Defined in:

lib/bio/appl/tcoffee.rb

Overview

Bio::Tcoffee is a wrapper class to execute t-coffee.

Please refer documents in bio/apple/tcoffee.rb for references.

Constant Summary

DEFAULT_PROGRAM =

default program name

't_coffee'.freeze

DEFAULT_PARSER =

default report parser

Bio::ClustalW::Report

Instance Attribute Summary

Attributes inherited from Alignment::FactoryTemplate::FileInFileOutWithTree

#output_dnd

Attributes inherited from Alignment::FactoryTemplate::Simple

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

Method Summary

Methods inherited from Alignment::FactoryTemplate::FileInFileOutWithTree

#reset

Methods inherited from Alignment::FactoryTemplate::Simple

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

Constructor Details

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