calculate the proper distance, with hurdles

[germs.git] / src / genealgorithms.cpp

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index 7f54109dc6c0103251cafff77bef93d92fa9f1e4..3fb2aaac0c7f180bd73edde5918731c7bcc8c8e0 100644 (file)
--- a/src/genealgorithms.cpp
+++ b/src/genealgorithms.cpp
@@ -20,6 +20,7 @@
 
 #include "genealgorithms.h"
 #include "geneorder.h"
+#include "componenttree.h"
 
 #include <algorithm>
 #include <set>
@@ -92,6 +93,23 @@ size_t countCycles(const GeneOrder& go){
        return cycles;
 }
 
+size_t inversionDistance(const GeneOrder& go){
+       size_t distance = go.size() - 1;
+       distance -= countCycles(go);
+
+       ComponentTree t(findComponents(go));
+       t.makeUnoriented();
+       size_t leaves = t.countLeaves();
+       distance += leaves;
+       if (leaves % 2 != 0){
+               size_t sb = t.shortBranches();
+               if (sb == 0)
+                       distance += 1;
+       }
+
+       return distance;
+}
+
 int sign(Gene g){
        if (g > 0)
                return 1;
@@ -140,7 +158,7 @@ std::vector<Component> findComponents(const GeneOrder& go){
                        s = Sdir.top();
                }
                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])));
+                       components.push_back(Component(p[s],p[i],(s+1 == i ? 0 : os[s]),s,i));
 
                //Reverse
                if (p[i-1] < p[i])
@@ -156,7 +174,7 @@ std::vector<Component> findComponents(const GeneOrder& go){
                        s = Srev.top();
                }
                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])));
+                       components.push_back(Component(-p[s],-p[i],(s+1 == i ? 0 : os[s]),s,i));
 
                //Update stacks
                if (go[i] > 0)
@@ -167,18 +185,40 @@ 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()));
+       const 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){
+       const GeneOrder::iterator end = go.end();
+       for (GeneOrder::iterator g = go.begin(); g != 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);
+                       if (i < max - 1){
+                               Interval& curr = intervals[i];
+                               curr.first = n + (*g >= 0 ? 1 : 0);
+
+                               if (curr.second == max)
+                                       curr.oriented = *g < 0;
+                               else
+                                       curr.oriented ^=  *g < 0;
+                       }
+                       if (i > 0){
+                               Interval& prev = intervals[i-1];
+                               prev.second = n + (*g < 0 ? 1 : 0);
+
+                               if (prev.first == max)
+                                       prev.oriented = *g < 0;
+                               else
+                                       prev.oriented ^=  *g < 0;
+                       }
+
        }
        return intervals;
 }
@@ -188,7 +228,7 @@ 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){