Class: RawFormatter

Inherits:
Object show all
Defined in:
lib/bioinform/formatters/raw_formatter.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(motif, options = {}) ⇒ RawFormatter

Returns a new instance of RawFormatter.



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# File 'lib/bioinform/formatters/raw_formatter.rb', line 4

def initialize(motif, options = {})
  @motif = motif
  
  default_options = {with_name: true, letters_as_rows: false}
  @options = default_options.merge(options)
end

Instance Attribute Details

#motif ⇒ Object

Returns the value of attribute motif.



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# File 'lib/bioinform/formatters/raw_formatter.rb', line 2

def motif
  @motif
end

#options ⇒ Object

Returns the value of attribute options.



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# File 'lib/bioinform/formatters/raw_formatter.rb', line 2

def options
  @options
end

Instance Method Details



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# File 'lib/bioinform/formatters/raw_formatter.rb', line 32

def footer
  # "\n"
  ''
end

#header ⇒ Object 



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# File 'lib/bioinform/formatters/raw_formatter.rb', line 15

def header
  if options[:with_name] && name
    name + "\n"
  else
    ''
  end
end

#matrix_string ⇒ Object 



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# File 'lib/bioinform/formatters/raw_formatter.rb', line 23

def matrix_string
  if options[:letters_as_rows]
    hsh = motif.to_hash
    [:A,:C,:G,:T].collect{|letter| "#{letter}|" + hsh[letter].join("\t")}.join("\n")
  else
    motif.each_position.map{|pos| pos.join("\t")}.join("\n")
  end
end

#name ⇒ Object 



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# File 'lib/bioinform/formatters/raw_formatter.rb', line 11

def name
  motif.name
end

#to_s ⇒ Object 



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# File 'lib/bioinform/formatters/raw_formatter.rb', line 38

def to_s
  header + matrix_string + footer
end