Class: MS::Lipid::Search::Bin

Inherits:
Bin
  • Object
show all
Defined in:
lib/ms/lipid/search/bin.rb

Overview

A Search::Bin is a range that contains the entire query spectrum (not just the portion covered by the range). the query spectrum, and a ProbabilityDistribution – the probability that a peak’s delta to nearest peak is that small by chance.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(range_obj, db_spectrum) ⇒ Bin

Returns a new instance of Bin.



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# File 'lib/ms/lipid/search/bin.rb', line 16

def initialize(range_obj, db_spectrum)
  super(range_obj.begin, range_obj.end, range_obj.exclude_end?)
  @db_spectrum = db_spectrum
end

Instance Attribute Details

#db_spectrum ⇒ Object

the intensity value of the query spectrum should be a query



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# File 'lib/ms/lipid/search/bin.rb', line 13

def db_spectrum
  @db_spectrum
end

#probability_distribution ⇒ Object

Returns the value of attribute probability_distribution.



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# File 'lib/ms/lipid/search/bin.rb', line 14

def probability_distribution
  @probability_distribution
end

Instance Method Details

#<<(query) ⇒ Object 



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# File 'lib/ms/lipid/search/bin.rb', line 21

def <<(query)
  @data << query
end

#best_hits(query, num_hits) ⇒ Object

returns a HitGroup object



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# File 'lib/ms/lipid/search/bin.rb', line 48

def best_hits(query, num_hits)
  query_mz = query.mz
  #puts "MZ: #{query_mz}"
  db_mzs = @db_spectrum.mzs
  index = @db_spectrum.find_nearest_index(query_mz)
  _min = index - (num_hits-1)
  (_min >= 0) || (_min = 0)
  _max = index + (num_hits-1)
  (_max < db_mzs.size) || (_max = @db_spectrum - 1)
  delta_index_pairs = (_min.._max).map {|i| [query_mz.-(db_mzs[i]).abs, i] }
  closest_delta_index_pairs = delta_index_pairs.sort
  top_num_hits_delta_index_pairs = closest_delta_index_pairs[0, num_hits]
  top_num_hit_indices = top_num_hits_delta_index_pairs.map(&:last)
  hit_group = top_num_hit_indices.map do |index|
    Hit.new( :db_isobar_group => @db_isobar_groups_by_index[index], :observed_mz => query_mz)
  end
  HitGroup.new(hit_group)
end

#inspect ⇒ Object 



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# File 'lib/ms/lipid/search/bin.rb', line 67

def inspect
  "<(#{super}) @db_spectrum(points size)=#{db_spectrum.mzs.size} @probability_distribution=#{probability_distribution}>"
end

#queries_to_hit_groups!(num_hits = 1) ⇒ Object

returns the nearest num_hits MS::Lipid::Search::Hits sorted by delta

with tie going to the lower m/z

searches all queries and removes them from the data queue



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# File 'lib/ms/lipid/search/bin.rb', line 28

def queries_to_hit_groups!(num_hits=1)
  queries = @data.dup
  @data.clear

  @db_isobar_groups_by_index = @db_spectrum.intensities

  hit_groups = queries.map do |query|
    best_hits(query, num_hits)
  end

  all_top_hits = hit_groups.map(&:first)

  # updates the pvalues for all the hits
  pvalues = probability_distribution.pvalues( all_top_hits )
  all_top_hits.zip(pvalues) {|hit, pvalue| hit.pvalue = pvalue }

  hit_groups
end

#to_range ⇒ Object 



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# File 'lib/ms/lipid/search/bin.rb', line 71

def to_range
  Range.new( self.begin, self.end, self.exclude_end? )
end