X-Git-Url: https://ruin.nu/git/?a=blobdiff_plain;f=src%2Fgenealgorithms.cpp;h=d85cd8d16caba9f60a2cefb104be7c6962729ea1;hb=0ab5dc19d2a874aeda2b277f8f322db0cccc1d03;hp=b2d7fa6132b0463ee9a1b1cdf8f240bddf1204f9;hpb=3db2f8d8f21614408dfd072cc45e618c7905461f;p=germs.git

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index b2d7fa6..d85cd8d 100644
--- a/src/genealgorithms.cpp
+++ b/src/genealgorithms.cpp
@@ -22,7 +22,9 @@
 #include "geneorder.h"
 
 #include <algorithm>
+#include <set>
 #include <cstdlib>
+#include <iostream>
 using namespace std;
 
 std::pair<int,int> longestSequences(const GeneOrder& go){
@@ -53,3 +55,81 @@ 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;
+	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;
+}
+
+std::vector<Component> findComponents(const GeneOrder& go){
+	return vector<Component>();
+}
+
+/**
+ * 
+ */
+std::vector<Interval> findIntervals(const GeneOrder& go){
+	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;
+}
+
+/**
+ * TODO: Think of a better than O(n^2) implementation.
+ * Possibly move to cache result
+ */
+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;
+
+}