plugin.rb in seqtrimnext-2.0.52

- old
+ new

@@ -13,27 +13,52 @@
 class Plugin
 
   attr_accessor :stats
 
   #Loads the plugin's execution whit the sequence "seq"
-  def initialize(seq,params)
-    # $LOG.debug self.class.to_s + " processing sequence: " + seq.seq_name
-    # if (!(self.class.to_s=='PluginLowQuality') )
+  def initialize(seq, params)
     @params = params
     @stats ={}
-    execute(seq)
-    # puts self.class.to_s + ' PPPPPPPPPP'
-    # else
-    # $LOG.error " Quality File haven't been provided. It's impossible to execute " +self.class.to_s + seq.seq_qual.nil?.to_s
-    # end
+    
+    if can_execute?
+      execute(seq)
+    end
+    
   end
 
+  def can_execute?
+    return true
+  end
+
   #Begins the plugin's execution whit the sequence "seq"
   def execute(seqs)
+    blasts=do_blasts(seqs)
 
+    if !blasts.empty?
+      
+      if blasts.is_a?(Array)
+        queries=blasts
+      else
+        queries = blasts.querys
+      end
+      
+      seqs.each_with_index do |s,i|
+        exec_seq(s,queries[i])
+      end
+
+    else # there is no blast
+
+      seqs.each do |s|
+        exec_seq(s,nil)
+      end
+
+    end
   end
 
+  def do_blasts(seqs)
+    return []
+  end
 
   #Initializes the structure stats  to the given key and value , only when it is neccesary, and increases its counter
   def add_stats(key,value)
 
     @stats[key]={} if @stats[key].nil?
@@ -67,18 +92,23 @@
     #     puts "-------"
     #puts "overlap? (#{r1_start}<=#{r2_end}) and (#{r1_end}>=#{r2_start})"
     return ((r1_start<=r2_end+1) and (r1_end>=r2_start-1) )
   end
 
-  def merge_hits(hits,merged_hits,merged_ids=nil)
+  def merge_hits(hits,merged_hits,merged_ids=nil, merge_different_ids=true)
     # puts " merging ============"
     # hits.each do |hit|
     hits.sort{|h1,h2| (h1.q_end-h1.q_beg+1)<=>(h2.q_end-h2.q_beg+1)}.reverse_each do |hit|
 
       merged_ids.push hit.definition if !merged_ids.nil? && (! merged_ids.include?(hit.definition))
       # if new hit's position is already contained in hits, then ignore the new hit
-      c=merged_hits.find{|c| overlapX?(hit.q_beg, hit.q_end,c.q_beg,c.q_end)}
+      if merge_different_ids
+        c=merged_hits.find{|c| overlapX?(hit.q_beg, hit.q_end,c.q_beg,c.q_end)}
+      else
+        # overlap with existent hit and same subject id
+        c=merged_hits.find{|c| (overlapX?(hit.q_beg, hit.q_end,c.q_beg,c.q_end) && (hit.subject_id==c.subject_id))}
+      end
       # puts " c #{c.inspect}"
 
       if (c.nil?)
         # add new contaminant
         #puts "NEW HIT #{hit.inspect}"
@@ -87,13 +117,13 @@
         #
       else
 
         # one is inside each other, just ignore
         if ((hit.q_beg>=c.q_beg && hit.q_end <=c.q_end) || (c.q_beg>=hit.q_beg && c.q_end <= hit.q_end))
-            # puts "* #{hit.subject_id} inside #{c.subject_id}"
+          # puts "* #{hit.subject_id} inside #{c.subject_id}"
         else
           # merge with old contaminant
-                      # puts "#{hit.subject_id} NOT inside #{c.subject_id}"
+          # puts "#{hit.subject_id} NOT inside #{c.subject_id}"
           min=[c.q_beg,hit.q_beg].min
           max=[c.q_end,hit.q_end].max
 
           c.q_beg=min
           c.q_end=max