};
-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(); ++p){
if (marked.find(p) != marked.end())
continue;
- Interval i = intervals[points[p-1].first];
+ Interval i = intervals[points[p].first];
while (marked.find(p) == marked.end()){
marked.insert(p);
- if (i == intervals[points[p-1].first])
- i = intervals[points[p-1].second];
+ if (i == intervals[points[p].first])
+ i = intervals[points[p].second];
else
- i = intervals[points[p-1].first];
+ i = intervals[points[p].first];
if (p == i.first)
p = i.second;
}
/**
- * TODO: Think of a better than O(n^2) implementation
- * Possibly move it to GeneOrder too
+ *
*/
std::vector<Interval> findIntervals(const GeneOrder& go){
- vector<Interval> intervals;
- for (size_t i = 0; i < go.size() - 1; ++i){
+ 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 (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)
+ 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;
- found = true;
+ }
}
- if(static_cast<size_t>(abs(*g)) == i+1){
- s = n;
- if (*g < 0)
- ++s;
- if (found)
+ if (i->second == p){
+ if (!found){
+ f = n;
+ found = true;
+ }else{
+ s = n;
break;
- found = true;
+ }
}
}
- intervals.push_back(Interval(f,s));
+ points.push_back(Interval(f,s));
}
- return intervals;
-}
+ return points;
+}