Class: Mascot::DAT::Query

Inherits:
Object
  • Object
show all
Defined in:
lib/mascot/dat/query.rb

Overview

A class to represent mass spectrum query objects in Mascot DAT files. Here is an example:

--gc0p4Jq0M2Yt08jU534c0p
Content-Type: application/x-Mascot; name="query3"

title=253%2e131203405971_503
rtinseconds=503
index=5
charge=2+
mass_min=88.063115
mass_max=392.171066
int_min=6.064e+05
int_max=6.064e+05
num_vals=10
num_used1=-1
Ions1=88.063115:6.064e+05,196.589171:6.064e+05,331.143454:6.064e+05,392.171066:6.064e+05,114.570773:6.064e+05,228.134269:6.064e+05,139.567707:6.064e+05,278.128138:6.064e+05,166.075365:6.064e+05,175.118953:6.064e+05

Things to note are:

* the spectrum title is encoded to produce nice output in HTML
* the m/z and intensity values are given as pairs of values
* the m/z and intensity values are not in increasing values of m/z

This parser accounts for these in the attributes like so:

* spectrum title is de-encoded
* the pairs of m/z and intensity are accessible via the {#peaks} method
* the {#peaks} are ordered in accordance to increasing m/z
* there are {#mz} and {#intensity} methods to get the individual array of values for each

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(query_str) ⇒ Query

Returns a new instance of Query.



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# File 'lib/mascot/dat/query.rb', line 68

def initialize(query_str)
  query_str.split(/\n/).each do |l|
    next unless l =~ /(\w+)\=(.+)$/
    k,v = $1,$2
    case k
    when "name"
      @name = v.gsub('"','')
    when "title"
      @title = URI.decode(v)
    when "index"
      @index = v.to_i
    when "rtinseconds"
      @rtinseconds = v.to_i
    when "charge"
      @charge = v
    when "mass_min"
      @mass_min = v.to_f
    when "mass_max"
      @mass_max = v.to_f
    when "int_min"
      @int_min = v.to_f
    when "int_max"
      @int_max = v.to_f
    when "num_vals"
      @num_vals = v.to_i
    when "num_used1"
      @num_used1 = v.to_i
    when "Ions1"
      parse_ions1(v)
    else
      @attributes[k.to_sym] = v
    end
  end
end

Instance Attribute Details

#attributes ⇒ Object (readonly)

All other attributes from DAT query sections not covered above



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# File 'lib/mascot/dat/query.rb', line 66

def attributes
  @attributes
end

#charge ⇒ Object (readonly)

Charge state of the parent MS1 ion



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# File 'lib/mascot/dat/query.rb', line 45

def charge
  @charge
end

#index ⇒ Object (readonly)

No clue what this is



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# File 'lib/mascot/dat/query.rb', line 41

def index
  @index
end

#int_max ⇒ Object (readonly)

The maximum intensity of the values



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# File 'lib/mascot/dat/query.rb', line 53

def int_max
  @int_max
end

#int_min ⇒ Object (readonly)

The minimum intensity of the values



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# File 'lib/mascot/dat/query.rb', line 51

def int_min
  @int_min
end

#intensity ⇒ Object (readonly)

An Array of intensity values, ordered by the corresponding m/z value in the #mz Array



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# File 'lib/mascot/dat/query.rb', line 63

def intensity
  @intensity
end

#mass_max ⇒ Object (readonly)

The maximum m/z of the values



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# File 'lib/mascot/dat/query.rb', line 49

def mass_max
  @mass_max
end

#mass_min ⇒ Object (readonly)

The minimum m/z of the values



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# File 'lib/mascot/dat/query.rb', line 47

def mass_min
  @mass_min
end

#mz ⇒ Object (readonly)

An Array of m/z values, ordered by increasing m/z



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# File 'lib/mascot/dat/query.rb', line 61

def mz
  @mz
end

#name ⇒ Object (readonly)

The name of the query in Mascot DAT file, e.g. the MIME section header



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# File 'lib/mascot/dat/query.rb', line 37

def name
  @name
end

#num_used1 ⇒ Object (readonly)

No clue what this is



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# File 'lib/mascot/dat/query.rb', line 57

def num_used1
  @num_used1
end

#num_vals ⇒ Object (readonly)

The number of peaks



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# File 'lib/mascot/dat/query.rb', line 55

def num_vals
  @num_vals
end

#peaks ⇒ Object (readonly)

An Array of [m/z, intensity] tuples, ordered by increasing m/z values



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# File 'lib/mascot/dat/query.rb', line 59

def peaks
  @peaks
end

#rtinseconds ⇒ Object (readonly)

Retention time in seconds



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# File 'lib/mascot/dat/query.rb', line 43

def rtinseconds
  @rtinseconds
end

#title ⇒ Object (readonly)

The spectrum title from the source mass spectrum file



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# File 'lib/mascot/dat/query.rb', line 39

def title
  @title
end