X-Git-Url: https://ruin.nu/git/index.pl?a=blobdiff_plain;f=src%2Fgenealgorithms.cpp;h=e96c9be63e9d378187a0d58b9413905bf6517e20;hb=bd6d14a70222d80caf00cee73b3014d392dbc69f;hp=04875daca3031c0803ed527b9a36742d8965289a;hpb=172455c7649ea714eb13f9ac1fd96652f0617ca0;p=germs.git

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index 04875da..e96c9be 100644
--- a/src/genealgorithms.cpp
+++ b/src/genealgorithms.cpp
@@ -65,40 +65,6 @@ struct FindP{
 };
 
 
-std::vector<Interval> findIntervalsAtPoints(const vector<Interval>& intervals){
-	vector<Interval> points;
-	points.push_back(Interval(intervals.size(),intervals.size())); //Dummy interval to match point and index
-	for (size_t p = 1; p <= intervals.size(); ++p){
-		size_t f = 0;
-		size_t s = 0;
-		bool found = false;
-		size_t n = 0;
-		for (vector<Interval>::const_iterator i = intervals.begin(); i != intervals.end(); ++i, ++n){
-			if (i->first == p){
-				if (!found){
-					f = n;
-					found = true;
-				}else{
-					s = n;
-					break;
-				}
-			}
-			if (i->second == p){
-				if (!found){
-					f = n;
-					found = true;
-				}else{
-					s = n;
-					break;
-				}
-			}
-		}
-		points.push_back(Interval(f,s));
-	}
-	return points;
-
-}
-
 int countCycles(const GeneOrder& go){
 	int cycles = 0;
 	set<size_t> marked;
@@ -130,36 +96,39 @@ 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;
 }
 
+/**
+ * 
+ */
+std::vector<Interval> findIntervalsAtPoints(const vector<Interval>& intervals){
+	size_t max = intervals.size()+1;
+	vector<Interval> points(max,Interval(max,max));
+	size_t n = 0;
+	for (vector<Interval>::const_iterator i = intervals.begin(); i != intervals.end(); ++i, ++n){
+		if (points[i->first].first == max){
+			points[i->first].first = n;
+		}else
+			points[i->first].second = n;
+			
+		if (points[i->second].first == max){
+			points[i->second].first = n;
+		}else
+			points[i->second].second = n;
+	}
+	return points;
+
+}