core/kmerstore.h: labels in IKmerStore are now a reference to a Fasta object

Labels were introduced in df19d79c, for -c germlines, and were later used for -2.
Even if they were previously strings, they always designated some file.

algo/core/kmerstore.h

@@ -54,7 +54,7 @@ public:
   int id; // id of this index
   int refs; // number of germlines using this index
 
-  list< pair <T, string> > labels;
+  list< pair <T, Fasta> > labels;
 
   /**
    * @param input: A single FASTA file
@@ -125,7 +125,7 @@ public:
    * @param kmer: a kmer
    * @return one label associated with the kmer
    */
-  string getLabel(T kmer) const;
+  Fasta getLabel(T kmer) const;
 
   /**
    * @param seq: a sequence
@@ -225,10 +225,10 @@ void IKmerStore<T>::insert(Fasta& input,
     insert(input.sequence(r), label, true, keep_only);
   }
 
-  labels.push_back(make_pair(T(label, 1), label)) ;
+  labels.push_back(make_pair(T(label, 1), input)) ;
 
   if (revcomp_indexed  && ! T::hasRevcompSymetry()) {
-    labels.push_back(make_pair(T(label, -1), label)) ;
+    labels.push_back(make_pair(T(label, -1), input)) ;
   }
 }
 
@@ -334,11 +334,11 @@ string IKmerStore<T>::getSeed() const {
 }
 
 template<class T>
-string IKmerStore<T>::getLabel(T kmer) const {
-  for (typename list< pair<T, string> >::const_iterator it = labels.begin(); it != labels.end(); ++it)
+Fasta IKmerStore<T>::getLabel(T kmer) const {
+  for (typename list< pair<T, Fasta> >::const_iterator it = labels.begin(); it != labels.end(); ++it)
     if (it->first == kmer)
       return it->second ;
-  return "?" ;
+  return FASTA_AMBIGUOUS ;
 }
 
 // .getResults()

algo/core/segment.cpp

@@ -706,9 +706,9 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c,
 
           code_short = "Unexpected ";
 
-          code_short += left.toStringSigns() + germline->index->getLabel(left);
+          code_short += left.toStringSigns() + germline->index->getLabel(left).name;
           code_short += "/";
-          code_short += right.toStringSigns() + germline->index->getLabel(right);
+          code_short += right.toStringSigns() + germline->index->getLabel(right).name;
           info_extra += " " + left.toString() + "/" + right.toString() + " (" + code_short + ")";
         }
       return ;

algo/vidjil.cpp

@@ -917,10 +917,10 @@ int main (int argc, char **argv)
       IKmerStore<KmerAffect> *index = multigermline->index ;
 
       // Initialize statistics, with two additional categories
-      index->labels.push_back(make_pair(KmerAffect::getAmbiguous(), AFFECT_AMBIGUOUS_SYMBOL));
-      index->labels.push_back(make_pair(KmerAffect::getUnknown(), AFFECT_UNKNOWN_SYMBOL));
+      index->labels.push_back(make_pair(KmerAffect::getAmbiguous(), FASTA_AMBIGUOUS));
+      index->labels.push_back(make_pair(KmerAffect::getUnknown(), FASTA_UNKNOWN));
       
-      for (list< pair <KmerAffect, string> >::const_iterator it = index->labels.begin(); it != index->labels.end(); ++it)
+      for (list< pair <KmerAffect, Fasta> >::const_iterator it = index->labels.begin(); it != index->labels.end(); ++it)
 	{
 	  char key = affect_char(it->first.affect) ;
 	  stats_kmer[key] = 0 ;
@@ -972,7 +972,7 @@ int main (int argc, char **argv)
 	   << endl ;
       cout << "\t" << " max" << "\t\t" << "        kmers" << "\n" ;
 
-      for (list< pair <KmerAffect, string> >::const_iterator it = index->labels.begin(); it != index->labels.end(); ++it)
+      for (list< pair <KmerAffect, Fasta> >::const_iterator it = index->labels.begin(); it != index->labels.end(); ++it)
 	{
           if (it->first.getStrand() == -1)
             continue ;
@@ -987,7 +987,7 @@ int main (int argc, char **argv)
 	  cout << setw(12) << stats_kmer[key] << " " ;
 	  cout << setw(6) << fixed << setprecision(2) <<  (float) stats_kmer[key] / total_length * 100 << "%" ;
 
-	  cout << "     " << key << " " << it->second << endl ;
+	  cout << "     " << key << " " << it->second.name << endl ;
 	}
       
       delete index;