Module: Bio::Command::Wrapper::ClassMethods

Defined in:
lib/wrapper.rb

Constant Summary collapse

OUTPUT =

TODO: do I need to set a default program name using class name or not ?

or do we need to specify somewhere a defaitl path and looking for a real binary ?

[:file, :stdout, :stdin]

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#aliases ⇒ Object

output = :stdout=>



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# File 'lib/wrapper.rb', line 242

def aliases
  @aliases
end

#options ⇒ Object

output = :stdout=>



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# File 'lib/wrapper.rb', line 242

def options
  @options
end

#output ⇒ Object

output = :stdout=>



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# File 'lib/wrapper.rb', line 242

def output
  @output
end

#program ⇒ Object

output = :stdout=>



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# File 'lib/wrapper.rb', line 242

def program
  @program
end

#sub_program ⇒ Object

output = :stdout=>



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# File 'lib/wrapper.rb', line 242

def sub_program
  @sub_program
end

Instance Method Details

#add_option(name, opt = {}) ⇒ Object

external_parameter can be an array a string or an hash def validate_parameters(external_parameters)



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# File 'lib/wrapper.rb', line 259

def add_option(name, opt={})
  @options = (@options || {}).merge(name.to_s=>opt)
end

#delete_option(name) ⇒ Object

Remove an option from the class



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# File 'lib/wrapper.rb', line 264

def delete_option(name)
  @options.delete(name)
end

#inherited(subclass) ⇒ Object

Propagate class variable in the superclass to the inherited class, so options defined in a previous wrap can be recicled.



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# File 'lib/wrapper.rb', line 230

def inherited(subclass)
  self.instance_variables.each do |var|
    subclass.instance_variable_set(var, self.instance_variable_get(var))
  end
end

#set_output(output_type = :file) ⇒ Object

TODO I don’t like this way, Is it possible to configure the variable as global and default ?



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# File 'lib/wrapper.rb', line 245

def set_output(output_type=:file)
  if OUTPUT.include? output_type
    @output = output_type
  else
    raise "Output type #{output_type} is not suported. Valid types are #{OUTPUT}"
  end
end

#use_aliases ⇒ Object 



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# File 'lib/wrapper.rb', line 253

def use_aliases
  @aliases = true
end