X-Git-Url: https://ruin.nu/git/?a=blobdiff_plain;f=src%2Fgenealgorithms.cpp;h=24e7b43575ac30a04c46723283a3ee81390a8592;hb=500fc81f4ccf04414ebbd495d167eb2d6b2ac82d;hp=7dc832f252c208900b92c234879c8f09b5a93c24;hpb=e7953f0050007cd1999d64d985d0a063b9ddc99b;p=germs.git

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index 7dc832f..24e7b43 100644
--- a/src/genealgorithms.cpp
+++ b/src/genealgorithms.cpp
@@ -24,6 +24,7 @@
 #include <algorithm>
 #include <set>
 #include <cstdlib>
+#include <iostream>
 using namespace std;
 
 std::pair<int,int> longestSequences(const GeneOrder& go){
@@ -55,12 +56,37 @@ std::vector<std::vector<int> > robinsonSchensted(const GeneOrder& go){
 	return v;
 }
 
+struct FindP{
+	size_t p;
+	FindP(size_t p) : p(p) {}
+	bool operator()(Interval i){
+		return (i.first == p || i.second == p);
+	}
+};
+
+
 int countCycles(const GeneOrder& go){
 	int cycles = 0;
 	set<size_t> marked;
-	for (size_t p = 1; p < go.size() - 1; ++p){
+	vector<Interval> intervals = findIntervals(go);
+	vector<Interval> points = findIntervalsAtPoints(intervals);
+	for (size_t p = 1; p < go.size(); ++p){
 		if (marked.find(p) != marked.end())
 			continue;
+		Interval i = intervals[points[p].first];
+		while (marked.find(p) == marked.end()){
+			marked.insert(p);
+			if (i == intervals[points[p].first])
+				i = intervals[points[p].second];
+			else
+				i = intervals[points[p].first];
+
+			if (p == i.first)
+				p = i.second;
+			else
+				p = i.first;
+		}
+		++cycles;
 	}
 	return cycles;
 }
@@ -69,6 +95,74 @@ std::vector<Component> findComponents(const GeneOrder& go){
 	return vector<Component>();
 }
 
+/**
+ * TODO: Think of a better than O(n^2) implementation
+ * Possibly move it to GeneOrder too
+ */
 std::vector<Interval> findIntervals(const GeneOrder& go){
-	return vector<Interval>();
+	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));
+	}
+	return intervals;
+}
+
+/**
+ * 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));
+	}
+	return points;
+
 }