lib/macroape/counting.rb in macroape-3.3.6 vs lib/macroape/counting.rb in macroape-3.3.7

@@ -1,24 +1,18 @@
+require 'bioinform'
+
 module Bioinform
   class PWM
     # sets or gets limit size of calculation hash. It's a defence against overuse CPU resources by non-appropriate data
-    def max_hash_size!(new_max_hash_size)
-      @max_hash_size = new_max_hash_size
-      self
-    end
+    make_parameters :max_hash_size
     
-    def max_hash_size(*args)
-      case args.size
-      when 0 then @max_hash_size
-      when 1 then max_hash_size!(args.first)
-      else raise ArgumentError, '#max_hash_size method can get 0 or 1 argument'
-      end
-    end
-    
     def threshold(pvalue)
       thresholds(pvalue){|_, thresh, _| return thresh }
     end
+    def threshold_and_real_pvalue(pvalue)
+      thresholds(pvalue){|_, thresh, real_pv| return thresh, real_pv }
+    end
 
     def thresholds(*pvalues)
       thresholds_by_pvalues(*pvalues).each do |pvalue,(thresholds, counts)|
         threshold = thresholds.begin + 0.1 * (thresholds.end - thresholds.begin)
         real_pvalue = counts.end.to_f / vocabulary_volume
@@ -78,10 +72,10 @@
       new_scores = Hash.new(0)
       scores.each do |score, count|
         4.times do |letter|
           new_score = score + column[letter]
           if new_score >= least_sufficient
-            new_scores[new_score] += count * @background[letter]
+            new_scores[new_score] += count * background[letter]
           end
         end
       end
       new_scores
     end
\ No newline at end of file