Class: Sequest::PepXML::TerminalModification

Inherits:
Object
  • Object
show all
Includes:
SpecIDXML
Defined in:
lib/ms/sequest/pepxml.rb

Overview

Modified aminoacid, static or variable

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(hash = nil) ⇒ TerminalModification

Returns a new instance of TerminalModification.



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# File 'lib/ms/sequest/pepxml.rb', line 1167

def initialize(hash=nil)
  instance_var_set_from_hash(hash) if hash # can use unless there are weird methods
end

Instance Attribute Details

#description ⇒ Object

Returns the value of attribute description.



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# File 'lib/ms/sequest/pepxml.rb', line 1165

def description
  @description
end

#mass ⇒ Object

Mass of modified terminus



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# File 'lib/ms/sequest/pepxml.rb', line 1156

def mass
  @mass
end

#massdiff ⇒ Object

Mass difference with respect to unmodified terminus



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# File 'lib/ms/sequest/pepxml.rb', line 1154

def massdiff
  @massdiff
end

#protein_terminus ⇒ Object

whether modification can reside only at protein terminus (specified n or c)



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# File 'lib/ms/sequest/pepxml.rb', line 1164

def protein_terminus
  @protein_terminus
end

#symbol ⇒ Object

MSial symbol used by search engine to designate this modification



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# File 'lib/ms/sequest/pepxml.rb', line 1161

def symbol
  @symbol
end

#terminus ⇒ Object

n for N-terminus, c for C-terminus



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# File 'lib/ms/sequest/pepxml.rb', line 1152

def terminus
  @terminus
end

#variable ⇒ Object

Y if both modified and unmodified terminus could be present in the dataset, N if only modified terminus can be present



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# File 'lib/ms/sequest/pepxml.rb', line 1159

def variable
  @variable
end

Instance Method Details

#to_pepxml ⇒ Object 



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# File 'lib/ms/sequest/pepxml.rb', line 1171

def to_pepxml
  #short_element_xml_from_instance_vars("terminal_modification")
  short_element_xml_and_att_string("terminal_modification", "terminus=\"#{terminus}\" massdiff=\"#{massdiff.to_plus_minus_string}\" mass=\"#{mass}\" variable=\"#{variable}\" symbol=\"#{symbol}\" protein_terminus=\"#{protein_terminus}\" description=\"#{description}\"")
end