X-Git-Url: https://ruin.nu/git/?a=blobdiff_plain;f=src%2Fgenealgorithms.cpp;h=ed68b67ab4b798483da9003dbb37478165ef760c;hb=cc3e3bd109d72d82826629b96f8e6721d5243cf7;hp=a32968eaea3454f1081649335a34c7e8c201077f;hpb=052ccbc26078638efee3614cd7cc2ea485313cad;p=germs.git

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index a32968e..ed68b67 100644
--- 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){