#include "geneorder.h"
#include <algorithm>
+#include <set>
+#include <stack>
#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);
+ }
+};
+
+
+size_t countCycles(const GeneOrder& go){
+ size_t 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;
+}
+
+size_t inversionDistance(const GeneOrder& go){
+ size_t cycles = countCycles(go);
+
+ return go.size() - 1 - cycles;
+}
+
+int sign(Gene g){
+ if (g > 0)
+ return 1;
+ if (g < 0)
+ return -1;
+ return 0;
+}
+
+struct Abs{
+ Gene operator()(Gene x) const{
+ return abs(x);
+ }
+};
+std::vector<Component> findComponents(const GeneOrder& go){
+ vector<Component> components;
+ vector<int> os(go.size()-1);
+ for (size_t i = 0; i < os.size(); ++i)
+ os[i] = (go[i]*go[i+1] > 0 ? sign(go[i]) : 0);
+ stack<Gene> Mdir;
+ Mdir.push(go.size()-1);
+ stack<Gene> Mrev;
+ Mrev.push(0);
+ stack<size_t> Sdir;
+ Sdir.push(0);
+ stack<size_t> Srev;
+ Srev.push(0);
+ vector<Gene> dir;
+ dir.push_back(go.size()-1);
+ vector<Gene> rev;
+ rev.push_back(0);
+ size_t s;
+ vector<Gene> p(go.list());
+ transform(p.begin(),p.end(),p.begin(),Abs());
+ for (size_t i = 1; i < go.size(); ++i){
+ //Directed
+ if (p[i-1] > p[i])
+ Mdir.push(p[i-1]);
+ else while (Mdir.top() < p[i])
+ Mdir.pop();
+ dir.push_back(Mdir.top());
+
+ s = Sdir.top();
+ while(p[Sdir.top()] > p[i] || dir[Sdir.top()] < p[i]){
+ Sdir.pop();
+ os[Sdir.top()] = (os[Sdir.top()] == os[s] ? os[s] : 0);
+ s = Sdir.top();
+ }
+ if (go[i] > 0 && dir[i] == dir[s] && static_cast<Gene>(i - s) == p[i] - p[s])
+ components.push_back(Component(p[s],p[i],(s+1 == i ? 0 : os[s])));
+
+ //Reverse
+ if (p[i-1] < p[i])
+ Mrev.push(p[i-1]);
+ else while (Mrev.top() > p[i])
+ Mrev.pop();
+ rev.push_back(Mrev.top());
+
+ s = Srev.top();
+ while((p[s] < p[i] || rev[s] > p[i]) && s > 0){
+ Srev.pop();
+ os[Srev.top()] *= (os[Srev.top()] == os[s] ? 1 : 0);
+ s = Srev.top();
+ }
+ if (go[i] < 0 && rev[i] == rev[s] && static_cast<Gene>(i - s) == p[s] - p[i])
+ components.push_back(Component(-p[s],-p[i],(s+1 == i ? 0 : os[s])));
+
+ //Update stacks
+ if (go[i] > 0)
+ Sdir.push(i);
+ else
+ Srev.push(i);
+ }
+ return components;
+}
+
+int sign2(Gene g){
+ if (g < 0)
+ return -1;
+ return 1;
+}
+/**
+ *
+ */
+std::vector<Interval> findIntervals(const GeneOrder& go){
+ const size_t max = go.size();
+ vector<Interval> intervals(go.size()-1,Interval(max,max,false));
+ size_t n = 0;
+ const GeneOrder::iterator end = go.end();
+ for (GeneOrder::iterator g = go.begin(); g != end; ++g, ++n){
+ size_t i = abs(*g);
+ if (i < max - 1){
+ Interval& curr = intervals[i];
+ curr.first = n + (*g >= 0 ? 1 : 0);
+
+ if (curr.second == max)
+ curr.oriented = *g < 0;
+ else
+ curr.oriented ^= *g < 0;
+ }
+ if (i > 0){
+ Interval& prev = intervals[i-1];
+ prev.second = n + (*g < 0 ? 1 : 0);
+
+ if (prev.first == max)
+ prev.oriented = *g < 0;
+ else
+ prev.oriented ^= *g < 0;
+ }
+
+ }
+ return intervals;
+}
+
+/**
+ *
+ */
+std::vector<Interval> findIntervalsAtPoints(const vector<Interval>& intervals){
+ size_t max = intervals.size()+1;
+ vector<Interval> points(max,Interval(max,max,false));
+ 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;
+
+}