core/segment.{cpp,h}, vidjil.cpp: refactor ::toJsonList(), extract KmerSegmenter::toJsonList()

Each segmenter has now its own toJsonList() method.
This is more flexible and allows to output the KmerSegmenter even when the FineSegmenter failed.

algo/core/segment.cpp

@@ -868,34 +868,21 @@ void FineSegmenter::findCDR3(){
     
 }
 
-JsonList FineSegmenter::toJsonList(Germline *germline){
-  JsonList result;
-
-  //string str = getSequence().sequence;
-
-  // KmerMultiSegmenter kmseg(getSequence(), multigermline, 0);
-  // KmerSegmenter *kseg = kmseg.the_kseg ;
-  
-  KmerSegmenter *kseg = new KmerSegmenter(getSequence(), germline);
-  result.add("sequence", revcomp(sequence, reversed) );
-
+void FineSegmenter::toJsonList(JsonList *seg){
 
   if (isSegmented()) {
-    result.add("name", code_short);
-    
-    JsonList seg;
-    seg.add("5", germline->rep_5.label(best_V));
-    seg.add("5start", 0);
-    seg.add("5end", Vend);
+    seg->add("5", segmented_germline->rep_5.label(best_V));
+    seg->add("5start", 0);
+    seg->add("5end", Vend);
     
     if (score_D.size()>0){
-      seg.add("4", germline->rep_4.label(best_D));
-      seg.add("4start", Dstart);
-      seg.add("4end", Dend);      
+      seg->add("4", segmented_germline->rep_4.label(best_D));
+      seg->add("4start", Dstart);
+      seg->add("4end", Dend);
     }
     
-    seg.add("3", germline->rep_3.label(best_J));
-    seg.add("3start", Jstart);
+    seg->add("3", segmented_germline->rep_3.label(best_J));
+    seg->add("3start", Jstart);
 
     if (CDR3start >= 0)
       {
@@ -903,32 +890,30 @@ JsonList FineSegmenter::toJsonList(Germline *germline){
     json_cdr=new JsonList();
     json_cdr->add("start", CDR3start);
     json_cdr->add("stop", CDR3end);
-    seg.add("cdr3", *json_cdr);
+    seg->add("cdr3", *json_cdr);
       }
 
+  }
+}
 
+void KmerSegmenter::toJsonList(JsonList *seg)
+{
     int sequenceSize = sequence.size();
 
     JsonList *json_affectValues;
     json_affectValues=new JsonList();
     json_affectValues->add("start", 0);
     json_affectValues->add("stop", sequenceSize); 
-    json_affectValues->add("seq", kseg->getKmerAffectAnalyser()->toStringValues());
-    seg.add("affectValues", *json_affectValues);
+    json_affectValues->add("seq", getKmerAffectAnalyser()->toStringValues());
+    seg->add("affectValues", *json_affectValues);
       
 
-     JsonList *json_affectSigns;
+    JsonList *json_affectSigns;
     json_affectSigns=new JsonList();
     json_affectSigns->add("start", 0);
     json_affectSigns->add("stop", sequenceSize); 
-    json_affectSigns->add("seq", kseg->getKmerAffectAnalyser()->toStringSigns());
-    seg.add("affectSigns", *json_affectSigns);
-
-    result.add("seg", seg);
-
-    delete kseg ;
-  }
-  return result;
+    json_affectSigns->add("seq", getKmerAffectAnalyser()->toStringSigns());
+    seg->add("affectSigns", *json_affectSigns);
 }
 
 

algo/core/segment.h

@@ -174,6 +174,8 @@ class KmerSegmenter : public Segmenter
    */
   KmerAffectAnalyser *getKmerAffectAnalyser() const;
 
+  void toJsonList(JsonList *seg);
+
  private:
   void computeSegmentation(int strand, KmerAffect left, KmerAffect right);
 };
@@ -214,7 +216,7 @@ class FineSegmenter : public Segmenter
   void FineSegmentD(Germline *germline);
   void findCDR3();
 
-  JsonList toJsonList(Germline *germline);
+  void toJsonList(JsonList *seg);
   
 };
 

algo/vidjil.cpp

@@ -1178,9 +1178,29 @@ int main (int argc, char **argv)
 	out_clone << seg << endl ;
 	out_clones << seg << endl ;
 
-        // Output segmentation to .json
-        json_data_segment[it->first]=seg.toJsonList(segmented_germline);
+
+        // Prepare .json data segment
+        JsonList json_clone;
+        JsonList json_seg;
+
+        // From FineSegmenter
+        json_clone.add("sequence", seg.getSequence().sequence);
         
+        if (seg.isSegmented())
+          json_clone.add("name", seg.code_short);
+
+        seg.toJsonList(&json_seg);
+
+        // Re-launch also a KmerMultiSegmenter, for debug purposes
+        KmerMultiSegmenter kmseg(seg.getSequence(), multigermline, 0);
+        KmerSegmenter *kseg = kmseg.the_kseg ;
+        kseg->toJsonList(&json_seg);
+
+        // Save .json data segment
+        json_clone.add("seg", json_seg);
+        json_data_segment[it->first] = json_clone;
+
+
         if (seg.isSegmented())
 	  {
 	      // Check for identical code, outputs to out_edge