#include "geneorder.h"
#include <algorithm>
+#include <set>
#include <cstdlib>
+#include <iostream>
using namespace std;
std::pair<int,int> longestSequences(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){
+ 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;
+
+}