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[germs.git] / src / genealgorithms.cpp

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index b2d7fa6132b0463ee9a1b1cdf8f240bddf1204f9..e96c9be63e9d378187a0d58b9413905bf6517e20 100644 (file)
--- 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 +55,80 @@ 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;
+}
+
+/**
+ * 
+ */
+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;
+
+}