Merge branch 'feature-a/clean-dbscan' into 'dev'

Cleaning some clustering aspects

See merge request !152

algo/core/cluster-junctions.cpp

@@ -65,7 +65,7 @@ void comp_matrix::compare(ostream &out, Cost cluster_cost)
             j2=it1->first;
             DynProg dp = DynProg(j1, j2, DynProg::Local, compareCost);
             int score=dp.compute();
-            int distance = max(j1.size(), j2.size())-score;
+            int distance = max(j1.size(), j2.size()) * compareCost.match - score;
             m[c2][c1]=distance;
             m[c1][c2]=distance;
             c1++;

algo/vidjil.cpp

@@ -1189,9 +1189,6 @@ int main (int argc, char **argv)
     list <list <junction> > clones_windows;
     comp_matrix comp=comp_matrix(sort_clones);
       
-    //$$ Further analyze some clones (-z)
-    if (command == CMD_CLONES) {
-
     if (epsilon || forced_edges.size())
       {
 	cout << "Cluster similar windows" << endl ;
@@ -1221,6 +1218,9 @@ int main (int argc, char **argv)
       }
 
 
+    //$$ Further analyze some clones (-z)
+    if (command == CMD_CLONES) {
+
     // TODO: output clones_windows (.data, other places ?)
 
     // TODO: Are these constraints checked somewhere ? keepInterestingWindows ?