findIntervals is now O(n)

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index 24e7b43575ac30a04c46723283a3ee81390a8592..4315cb391e46bfad6c7d10073ee485f2962a4158 100644 (file)
--- a/src/genealgorithms.cpp
+++ b/src/genealgorithms.cpp
@@ -96,35 +96,17 @@ std::vector<Component> findComponents(const GeneOrder& go){
 }
 
 /**
- * TODO: Think of a better than O(n^2) implementation
- * Possibly move it to GeneOrder too
+ * 
  */
 std::vector<Interval> findIntervals(const GeneOrder& go){
-       vector<Interval> intervals;
-       for (size_t i = 0; i < go.size() - 1; ++i){
-               size_t f = 0;
-               size_t s = 0;
-               bool found = false;
-               size_t n = 0;
-               for (GeneOrder::iterator g = go.begin(); g != go.end(); ++g, ++n){
-                       if (static_cast<size_t>(abs(*g)) == i){
-                               f = n;
-                               if (*g >= 0)
-                                       ++f;
-                               if (found)
-                                       break;
-                               found = true;
-                       }
-                       if(static_cast<size_t>(abs(*g)) == i+1){
-                               s = n;
-                               if (*g < 0)
-                                       ++s;
-                               if (found)
-                                       break;
-                               found = true;
-                       }
-               }
-               intervals.push_back(Interval(f,s));
+       vector<Interval> intervals(go.size()-1,Interval(go.size(),go.size()));
+       size_t n = 0;
+       for (GeneOrder::iterator g = go.begin(); g != go.end(); ++g, ++n){
+                       size_t i = abs(*g);
+                       if (i < go.size() - 1)
+                               intervals[i].first = n + (*g >= 0 ? 1 : 0);
+                       if (i > 0)
+                               intervals[i-1].second = n + (*g < 0 ? 1 : 0);
        }
        return intervals;
 }

diff --git a/src/test/genealgorithmstest.cpp b/src/test/genealgorithmstest.cpp
index b06f416922797087cb7cca7bc4ab9589421d3395..1d7f2d04e2a2d3597d4fb78e8de3815302257466 100644 (file)
--- a/src/test/genealgorithmstest.cpp
+++ b/src/test/genealgorithmstest.cpp
@@ -94,8 +94,10 @@ protected:
                CPPUNIT_ASSERT_EQUAL(16ul,v.size());
                Interval go20(1,2);
                Interval go22(4,2);
+               Interval go215(8,16);
                CPPUNIT_ASSERT(go20 == v[0]);
                CPPUNIT_ASSERT(go22 == v[2]);
+               CPPUNIT_ASSERT(go215 == v[15]);
        }
        void testFindIntervalsAtPoints (){
                GeneOrder go(_validPerm.begin(),_validPerm.end());