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Contents
require 'ms/precursor'
module Ms ; end
# 0 1 2 3 4 5 6 7 8
MsScanAtts = [:num, :ms_level, :time, :start_mz, :end_mz, :num_peaks, :tic, :precursor, :spectrum]
Ms::Scan = Struct.new(*MsScanAtts) do
# time in seconds
# everything else in float/int
def to_s
"<Scan num=#{num} ms_level=#{ms_level} time=#{time}>"
end
undef_method :inspect
def inspect
atts = %w(num ms_level time start_mz end_mz)
display = atts.map do |att|
if val = send(att.to_sym)
"#{att}=#{val}"
else
nil
end
end
display.compact!
spec_display =
if spectrum
spectrum.mzs.size
else
'nil'
end
"<Ms::Scan:#{__id__} " + display.join(", ") + " precursor=#{precursor.inspect}" + " spectrum(size)=#{spec_display}" + " >"
end
# if > cutoff is below the precusure, then it is considered a +1 charge,
# otherwise > 1
# Algorithm from the MzXML2Search code by Jimmy Eng
def plus1?(cutoff=0.95)
prec_mz = precursor.mz
mzs, intens = spectrum.mzs_and_intensities
tic = 0.0
below = 0.0
mzs.zip(intens) do |mz, int|
if mz < prec_mz
below += int
end
tic += int
end
tic == 0.0 || below/tic > cutoff
end
# returns the string (space delimited): "ms_level num time [prec_mz prec_inten]"
def to_index_file_string
arr = [ms_level, num, time]
if precursor then arr << precursor.mz end
if x = precursor.intensity then arr << x end
arr.join(" ")
end
end
Version data entries
11 entries across 11 versions & 1 rubygems