X-Git-Url: https://ruin.nu/git/?a=blobdiff_plain;f=src%2Fgenealgorithms.cpp;h=a32968eaea3454f1081649335a34c7e8c201077f;hb=052ccbc26078638efee3614cd7cc2ea485313cad;hp=4315cb391e46bfad6c7d10073ee485f2962a4158;hpb=778905d507474784ec6be37fe8f2e5d9c179ae59;p=germs.git

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index 4315cb3..a32968e 100644
--- a/src/genealgorithms.cpp
+++ b/src/genealgorithms.cpp
@@ -23,6 +23,7 @@
 
 #include <algorithm>
 #include <set>
+#include <stack>
 #include <cstdlib>
 #include <iostream>
 using namespace std;
@@ -91,8 +92,80 @@ int countCycles(const GeneOrder& go){
 	return cycles;
 }
 
+int sign(Gene g){
+	if (g > 0)
+		return 1;
+	if (g < 0)
+		return -1;
+	return 0;
+}
+
+struct Abs{
+	Gene operator()(Gene x) const{
+		return abs(x);
+	}
+};
 std::vector<Component> findComponents(const GeneOrder& go){
-	return vector<Component>();
+	vector<Component> components;
+	vector<int> os(go.size()-1);
+	for (size_t i = 0; i < os.size(); ++i)
+		os[i] = (go[i]*go[i+1] > 0 ? sign(go[i]) : 0);
+	stack<Gene> Mdir;
+	Mdir.push(go.size()-1);
+	stack<Gene> Mrev;
+	Mrev.push(0);
+	stack<size_t> Sdir;
+	Sdir.push(0);
+	stack<size_t> Srev;
+	Srev.push(0);
+	vector<Gene> dir;
+	dir.push_back(go.size()-1);
+	vector<Gene> rev;
+	rev.push_back(0);
+	size_t s;
+	vector<Gene> p(go.list());
+	transform(p.begin(),p.end(),p.begin(),Abs());
+	for (size_t i = 1; i < go.size(); ++i){
+		//Directed
+		if (p[i-1] > p[i])
+			Mdir.push(p[i-1]);
+		else while (Mdir.top() < p[i])
+			Mdir.pop();
+		dir.push_back(Mdir.top());
+
+		s = Sdir.top();
+		while(p[Sdir.top()] > p[i] || dir[Sdir.top()] < p[i]){
+			Sdir.pop();
+			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])
+			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]);
+		else while (Mrev.top() > p[i])
+			Mrev.pop();
+		rev.push_back(Mrev.top());
+
+		s = Srev.top();
+		while((p[s] < p[i] || rev[s] > p[i]) && s > 0){
+			Srev.pop();
+			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]));
+
+		//Update stacks
+		if (go[i] > 0)
+			Sdir.push(i);
+		else
+			Srev.push(i);
+	}
+	return components;
 }
 
 /**
@@ -112,38 +185,22 @@ std::vector<Interval> findIntervals(const GeneOrder& go){
 }
 
 /**
- * TODO: Think of a better than O(n^2) implementation.
- * Possibly move to cache result
+ * 
  */
 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));
+	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;