sorting without hurdles seems to work

[germs.git] / src / genealgorithms.cpp

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index a32968eaea3454f1081649335a34c7e8c201077f..ed68b67ab4b798483da9003dbb37478165ef760c 100644 (file)
--- a/src/genealgorithms.cpp
+++ b/src/genealgorithms.cpp
@@ -66,8 +66,8 @@ struct FindP{
 };
 
 
-int countCycles(const GeneOrder& go){
-       int cycles = 0;
+size_t countCycles(const GeneOrder& go){
+       size_t cycles = 0;
        set<size_t> marked;
        vector<Interval> intervals = findIntervals(go);
        vector<Interval> points = findIntervalsAtPoints(intervals);
@@ -92,6 +92,12 @@ int countCycles(const GeneOrder& go){
        return cycles;
 }
 
+size_t inversionDistance(const GeneOrder& go){
+       size_t cycles = countCycles(go);
+
+       return go.size() - 1 - cycles;
+}
+
 int sign(Gene g){
        if (g > 0)
                return 1;
@@ -139,10 +145,9 @@ std::vector<Component> findComponents(const GeneOrder& go){
                        os[Sdir.top()] = (os[Sdir.top()] == os[s] ? os[s] : 0);
                        s = Sdir.top();
                }
-               if (go[i] > 0 && dir[i] == dir[s] && i - s == p[i] - p[s])
+               if (go[i] > 0 && dir[i] == dir[s] && static_cast<Gene>(i - s) == p[i] - p[s])
                        components.push_back(Component(p[s],p[i],(s+1 == i ? 0 : os[s])));
 
-
                //Reverse
                if (p[i-1] < p[i])
                        Mrev.push(p[i-1]);
@@ -156,8 +161,8 @@ std::vector<Component> findComponents(const GeneOrder& go){
                        os[Srev.top()] *= (os[Srev.top()] == os[s] ? 1 : 0);
                        s = Srev.top();
                }
-               if (go[i] < 0 && rev[i] == rev[s] && i - s == p[s] - p[i])
-                       components.push_back(Component(-p[s],-p[i],os[s]));
+               if (go[i] < 0 && rev[i] == rev[s] && static_cast<Gene>(i - s) == p[s] - p[i])
+                       components.push_back(Component(-p[s],-p[i],(s+1 == i ? 0 : os[s])));
 
                //Update stacks
                if (go[i] > 0)
@@ -168,18 +173,37 @@ std::vector<Component> findComponents(const GeneOrder& go){
        return components;
 }
 
+int sign2(Gene g){
+       if (g < 0)
+               return -1;
+       return 1;
+}
 /**
  * 
  */
 std::vector<Interval> findIntervals(const GeneOrder& go){
-       vector<Interval> intervals(go.size()-1,Interval(go.size(),go.size()));
+       size_t max = go.size();
+       vector<Interval> intervals(go.size()-1,Interval(max,max,false));
        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)
+                       if (i < go.size() - 1){
                                intervals[i].first = n + (*g >= 0 ? 1 : 0);
-                       if (i > 0)
+
+                               if (intervals[i].second == max)
+                                       intervals[i].oriented = *g < 0;
+                               else
+                                       intervals[i].oriented ^=  *g < 0;
+                       }
+                       if (i > 0){
                                intervals[i-1].second = n + (*g < 0 ? 1 : 0);
+
+                               if (intervals[i-1].first == max)
+                                       intervals[i-1].oriented = *g < 0;
+                               else
+                                       intervals[i-1].oriented ^=  *g < 0;
+                       }
+
        }
        return intervals;
 }
@@ -189,7 +213,7 @@ std::vector<Interval> findIntervals(const GeneOrder& go){
  */
 std::vector<Interval> findIntervalsAtPoints(const vector<Interval>& intervals){
        size_t max = intervals.size()+1;
-       vector<Interval> points(max,Interval(max,max));
+       vector<Interval> points(max,Interval(max,max,false));
        size_t n = 0;
        for (vector<Interval>::const_iterator i = intervals.begin(); i != intervals.end(); ++i, ++n){
                if (points[i->first].first == max){