countCycles implemented and passess test

[germs.git] / src / genealgorithms.cpp

diff --git a/src/genealgorithms.cpp b/src/genealgorithms.cpp
index 7dc832f252c208900b92c234879c8f09b5a93c24..d9d86a3dd8fcb651ce497180b062fa3ddc562612 100644 (file)
--- 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 +56,70 @@ 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);
+       }
+};
+
+
+std::vector<Interval> findIntervalsAtPoints(const vector<Interval>& intervals){
+       vector<Interval> points;
+       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;
-       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-1].first];
+               while (marked.find(p) == marked.end()){
+                       marked.insert(p);
+                       if (i == intervals[points[p-1].first])
+                               i = intervals[points[p-1].second];
+                       else
+                               i = intervals[points[p-1].first];
+
+                       if (p == i.first)
+                               p = i.second;
+                       else
+                               p = i.first;
+               }
+               ++cycles;
        }
        return cycles;
 }
@@ -69,6 +128,37 @@ 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;
 }
+