lib/spec_id/sequest.rb in mspire-0.3.1 vs lib/spec_id/sequest.rb in mspire-0.3.9

@@ -1,5 +1,33 @@
 require 'spec_id/sequest/params'
+require 'hash_by'
+require 'sort_by_attributes.rb'
 
 module Sequest
+
+  # returns one array of peptide hits:  indexes hits based on index_by, takes
+  # the uniq ones and then sorts the group by sort_by (compatible with
+  # sort_by_attributes) then slices from first_index to last_index
+  # (inclusive).
+  def self.other_hits(peps, first_index=1, last_index=9, index_by=[:base_name, :first_scan, :charge], sort_by=[:xcorr, {:down => :xcorr}])
+    all_hits = []
+    peps.hash_by(*index_by).each do |scan_key, peps_per_scan|
+      if peps_per_scan.size >= (first_index + 1)
+        all_hits.push( *(peps_per_scan.uniq.sort_by_attributes(*sort_by)[first_index..last_index]) )
+      end
+    end
+    all_hits.compact
+  end
+
+  def self.other_hits_sorted_by_xcorr(peps, first_index, last_index, index_by=[:base_name, :first_scan, :charge])
+    all_hits = []
+    peps.hash_by(*index_by).each do |scan_key, peps_per_scan|
+      if peps_per_scan.size >= (first_index + 1)
+        all_hits.push( *(peps_per_scan.uniq.sort_by {|x| x.xcorr }.reverse[first_index..last_index]) )
+      end
+    end
+    all_hits.compact
+
+  end
+
 end