Class: Ms::Mascot::Mgf::Entry

Inherits:
Object
  • Object
show all
Defined in:
lib/ms/mascot/mgf/entry.rb

Overview

Represents a mascot generic file (mgf) formatted entry. 

BEGIN IONS
TITLE=7100401blank.190.190.2.dta
CHARGE=2+
PEPMASS=321.571138
100.266 2.0
111.323 2.5
...
496.110 3.3
601.206 1.3
END IONS

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(headers = {}, data = []) ⇒ Entry

Initialized a new Entry using the headers and data. Set charge and pepmass using the CHARGE and PEPMASS headers.



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# File 'lib/ms/mascot/mgf/entry.rb', line 73

def initialize(headers={}, data=[])
  @headers = {}
  @pepmass = nil
  @charge = nil
  @data = data

  headers.each_pair do |key, value|
    self[key] = value
  end
end

Instance Attribute Details

#charge ⇒ Object

The charge of the entry



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# File 'lib/ms/mascot/mgf/entry.rb', line 53

def charge
  @charge
end

#data ⇒ Object

The data (mz/intensity) for the entry



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# File 'lib/ms/mascot/mgf/entry.rb', line 69

def data
  @data
end

#headers ⇒ Object (readonly)

A hash of mgf headers, not including CHARGE and PEPMASS



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# File 'lib/ms/mascot/mgf/entry.rb', line 50

def headers
  @headers
end

#pepmass ⇒ Object

The peptide mass of the entry



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# File 'lib/ms/mascot/mgf/entry.rb', line 56

def pepmass
  @pepmass
end

Class Method Details

.parse(str) ⇒ Object

Parses the entry string into an Mgf::Entry. The entry must be complete and properly formatted, ie it must begin with a ‘BEGIN IONS’ line and end with an ‘END IONS’ line.



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# File 'lib/ms/mascot/mgf/entry.rb', line 24

def parse(str)
  entry = Entry.new

  lines = str.strip.split(/\s*\r?\n\s*/)

  unless lines.shift == "BEGIN IONS"
    raise ArgumentError, "input should begin with 'BEGIN IONS'"
  end

  unless lines.pop == "END IONS"
    raise ArgumentError, "input should end with 'END IONS'"
  end

  lines.each do |line|
    if line =~ /^(.*?)=(.*)$/
      entry[$1] = $2
    else
      entry.data << line.split(/\s+/, 2).collect {|i| i.to_f }
    end
  end

  entry
end

Instance Method Details

#[](key) ⇒ Object

Retrieve a header using an mgf header string. CHARGE and PEPMASS headers can be retrieved using [], and will reflect the current values of charge and pepmass. Keys are stringified and upcased.



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# File 'lib/ms/mascot/mgf/entry.rb', line 87

def [](key)
  key = key.to_s.upcase
  case key
  when "PEPMASS" then pepmass.to_s
  when "CHARGE" then charge_to_s
  else headers[key]
  end
end

#[]=(key, value) ⇒ Object

Set a header using an mgf header string. CHARGE and PEPMASS headers may be set using using []=, and will modify the current values of charge and pepmass. Keys are stringified and upcased.



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# File 'lib/ms/mascot/mgf/entry.rb', line 99

def []=(key, value)
  key = key.to_s.upcase
  case key
  when "PEPMASS" 
    self.pepmass = value.to_f
  when "CHARGE" 
    value = case value
    when Fixnum then value
    when /^(\d+)([+-])$/ then $1.to_i * ($2 == "+" ? 1 : -1) 
    else raise "charge should be an number, or a string formatted like '1+' or '1-'"
    end
    
    self.charge = value
  else
    headers[key] = value
  end
end

#dump(target = "", options = {}) ⇒ Object

Formats and puts self to the target. Use the options to modify the output:

headers

an array of headers to include (by default all headers will be included; pepmass and charge will always be included)

pepmass_precision

integer value specifying precision of pepmass

mz_precision

integer value specifying precision of mz values

intensity_precision

integer value specifying precision of intensity values



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# File 'lib/ms/mascot/mgf/entry.rb', line 127

def dump(target="", options={})
  options = {
    :mz_precision => nil,
    :intensity_precision => nil,
    :pepmass_precision => nil,
    :headers => nil
  }.merge(options)

  target << "BEGIN IONS\n"
  (options[:headers] || headers.keys).each do |key|
    target << "#{key.upcase}=#{headers[key]}\n"
  end
  
  if charge
    target << "CHARGE=#{charge_to_s}\n"
  end
  
  if pepmass
    target << "PEPMASS=#{format options[:pepmass_precision]}\n" % pepmass
  end
  
  entry = data[0]
  data_format = case
  when entry == nil then nil
  when entry.kind_of?(Array) && entry.length == 2
    "#{format options[:mz_precision]} #{format options[:intensity_precision]}\n"
  else
    "#{format options[:mz_precision]}\n"
  end
  
  data.each do |data_point|
    target << (data_format % data_point)
  end
  
  target << "END IONS\n"
  target
end

#title ⇒ Object

returns the title of the entry (or nil if none)



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# File 'lib/ms/mascot/mgf/entry.rb', line 59

def title
  @headers['TITLE']
end

#title=(string) ⇒ Object

sets the title



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# File 'lib/ms/mascot/mgf/entry.rb', line 64

def title=(string)
  @headers['TITLE'] = string
end

#to_s ⇒ Object

Returns self formatted as a string



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# File 'lib/ms/mascot/mgf/entry.rb', line 166

def to_s
  dump
end