#include "genealgorithms.h"
#include "geneorder.h"
+#include "componenttree.h"
#include <algorithm>
#include <set>
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])));
+ components.push_back(Component(p[s],p[i],(s+1 == i ? 0 : os[s]),s,i));
//Reverse
if (p[i-1] < p[i])
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])));
+ components.push_back(Component(-p[s],-p[i],(s+1 == i ? 0 : os[s]),s,i));
//Update stacks
if (go[i] > 0)
*
*/
std::vector<Interval> findIntervals(const GeneOrder& go){
- size_t max = go.size();
+ const size_t max = go.size();
vector<Interval> intervals(go.size()-1,Interval(max,max,false));
size_t n = 0;
- for (GeneOrder::iterator g = go.begin(); g != go.end(); ++g, ++n){
+ const GeneOrder::iterator end = go.end();
+ for (GeneOrder::iterator g = go.begin(); g != end; ++g, ++n){
size_t i = abs(*g);
- if (i < go.size() - 1){
- intervals[i].first = n + (*g >= 0 ? 1 : 0);
+ if (i < max - 1){
+ Interval& curr = intervals[i];
+ curr.first = n + (*g >= 0 ? 1 : 0);
- if (intervals[i].second == max)
- intervals[i].oriented = *g < 0;
+ if (curr.second == max)
+ curr.oriented = *g < 0;
else
- intervals[i].oriented ^= *g < 0;
+ curr.oriented ^= *g < 0;
}
if (i > 0){
- intervals[i-1].second = n + (*g < 0 ? 1 : 0);
+ Interval& prev = intervals[i-1];
+ prev.second = n + (*g < 0 ? 1 : 0);
- if (intervals[i-1].first == max)
- intervals[i-1].oriented = *g < 0;
+ if (prev.first == max)
+ prev.oriented = *g < 0;
else
- intervals[i-1].oriented ^= *g < 0;
+ prev.oriented ^= *g < 0;
}
}