X-Git-Url: https://ruin.nu/git/?a=blobdiff_plain;f=src%2Fgenealgorithms.cpp;h=3fb2aaac0c7f180bd73edde5918731c7bcc8c8e0;hb=6ce65cd9df9c007b0c7ad0e37fb82ac04a802a90;hp=ed68b67ab4b798483da9003dbb37478165ef760c;hpb=7e811915a713eeef44f03385a1fc1f74a5301c30;p=germs.git

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index ed68b67..3fb2aaa 100644
--- 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>
@@ -93,9 +94,20 @@ size_t countCycles(const GeneOrder& go){
 }
 
 size_t inversionDistance(const GeneOrder& go){
-	size_t cycles = countCycles(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 go.size() - 1 - cycles;
+	return distance;
 }
 
 int sign(Gene g){
@@ -146,7 +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])
@@ -162,7 +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)
@@ -182,26 +194,29 @@ int sign2(Gene g){
  * 
  */
 std::vector<Interval> findIntervals(const GeneOrder& go){
-	size_t max = 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 < max - 1){
+				Interval& curr = intervals[i];
+				curr.first = n + (*g >= 0 ? 1 : 0);
 
-				if (intervals[i].second == max)
-					intervals[i].oriented = *g < 0;
+				if (curr.second == max)
+					curr.oriented = *g < 0;
 				else
-					intervals[i].oriented ^=  *g < 0;
+					curr.oriented ^=  *g < 0;
 			}
 			if (i > 0){
-				intervals[i-1].second = n + (*g < 0 ? 1 : 0);
+				Interval& prev = intervals[i-1];
+				prev.second = n + (*g < 0 ? 1 : 0);
 
-				if (intervals[i-1].first == max)
-					intervals[i-1].oriented = *g < 0;
+				if (prev.first == max)
+					prev.oriented = *g < 0;
 				else
-					intervals[i-1].oriented ^=  *g < 0;
+					prev.oriented ^=  *g < 0;
 			}
 
 	}