core/segment.{cpp,h}: remembers the evalue when it is computed, and output in .json

algo/core/segment.cpp

@@ -194,6 +194,7 @@ KmerSegmenter::KmerSegmenter(Sequence seq, Germline *germline)
   Dend=0;
   because = 0 ; // Cause of unsegmentation
   score = 0 ;
+  evalue = NO_LIMIT_VALUE;
 
   int s = (size_t)germline->index->getS() ;
   int length = sequence.length() ;
@@ -348,9 +349,15 @@ KmerMultiSegmenter::KmerMultiSegmenter(Sequence seq, MultiGermline *multigermlin
       }
     } // end for (Germlines)
 
+  // E-value threshold
   if (threshold_nb_expected > NO_LIMIT_VALUE)
-    if (the_kseg->isSegmented() && getNbExpected() > threshold_nb_expected)
-      the_kseg->setSegmentationStatus(UNSEG_NOISY);
+    if (the_kseg->isSegmented()) {
+        // the_kseg->evalue also depends on the number of germlines from the *Multi*KmerSegmenter
+        the_kseg->evalue = getNbExpected();
+        if (the_kseg->evalue > threshold_nb_expected) {
+          the_kseg->setSegmentationStatus(UNSEG_NOISY);
+        }
+      }
 }
 
 double KmerSegmenter::getProbabilityAtLeastOrAbove(int at_least) const {
@@ -936,6 +943,9 @@ void KmerSegmenter::toJsonList(JsonList *seg)
 {
     int sequenceSize = sequence.size();
 
+    if (evalue > NO_LIMIT_VALUE)
+      seg->add("evalue", evalue);
+
     JsonList *json_affectValues;
     json_affectValues=new JsonList();
     json_affectValues->add("start", 0);

algo/core/segment.h

@@ -76,6 +76,7 @@ protected:
   string seg_V, seg_N, seg_J, system;
 
   int best_D;
+  int evalue;
   string seg_N1, seg_D, seg_N2;
   Cost segment_cost;
 

algo/vidjil.cpp

@@ -1233,8 +1233,8 @@ int main (int argc, char **argv)
 
         seg.toJsonList(&json_seg);
 
-        // Re-launch also a KmerMultiSegmenter, for debug purposes
-        KmerMultiSegmenter kmseg(seg.getSequence(), multigermline, 0);
+        // Re-launch also a KmerMultiSegmenter, for control purposes (affectations, evalue)
+        KmerMultiSegmenter kmseg(seg.getSequence(), multigermline, 0, expected_value);
         KmerSegmenter *kseg = kmseg.the_kseg ;
         kseg->toJsonList(&json_seg);