lib/genomer-plugin-summary/metrics.rb in genomer-plugin-summary-0.0.3 vs lib/genomer-plugin-summary/metrics.rb in genomer-plugin-summary-0.0.4

@@ -1,15 +1,17 @@
 require 'genomer'
+require 'genomer-plugin-summary/enumerators'
 require 'lazing'
 
 module GenomerPluginSummary::Metrics
+  include GenomerPluginSummary::Enumerators
 
   ALL = :all
 
   def gc_content(type,scfd)
-    gc   = enumerator_for(type,scfd).mapping{|i|   gc(i)}.inject(:+) || 0.0
-    atgc = enumerator_for(type,scfd).mapping{|i| atgc(i)}.inject(:+) || 0.0
+    gc   = enumerator_for(type,scfd).mapping{|i|   gc(i[:sequence])}.inject(:+) || 0.0
+    atgc = enumerator_for(type,scfd).mapping{|i| atgc(i[:sequence])}.inject(:+) || 0.0
     gc / atgc * 100
   end
 
   def count(type,scfd)
     enumerator_for(type,scfd).count
@@ -19,23 +21,35 @@
     length(type,scfd) / length(ALL,scfd).to_f * 100
   end
 
   def length(type,scfd)
     enumerator_for(type,scfd).
-      mapping(&:sequence).
+      mapping{|i| i[:sequence]}.
       mapping(&:length).
       inject(:+) || 0
   end
 
-  def gc(entry)
-    entry.sequence.gsub(/[^GCgc]/,'').length.to_f
+  def gc(sequence)
+    sequence.gsub(/[^GCgc]/,'').length.to_f
   end
 
-  def atgc(entry)
-    entry.sequence.gsub(/[^ATGCatgc]/,'').length.to_f
+  def atgc(sequence)
+    sequence.gsub(/[^ATGCatgc]/,'').length.to_f
   end
 
-  def enumerator_for(type,scaffold)
-    scaffold.selecting{|i| [ALL,i.entry_type].include? type }
+  def sequence_total(seqs)
+    return Hash[[:start, :stop, :size, :percent, :gc].map{|i| [i, 0]}] if seqs.empty?
+
+    totals = seqs.inject({:size => 0, :percent => 0, :gc => 0}) do |hash,entry|
+      hash[:start]  ||= entry[:start]
+      hash[:stop]     = entry[:stop]
+      hash[:size]    += entry[:size]
+      hash[:percent] += entry[:percent]
+      hash[:gc]      += entry[:gc] * entry[:size]
+
+      hash
+    end
+    totals[:gc] /= totals[:size]
+    totals
   end
 
 end