struct Component{
Component(int b,int e,int s):begin(b),end(e),sign(s){}
+ bool operator==(const Component& c){
+ return begin == c.begin && end == c.end && sign == c.sign;
+ }
int begin;
int end;
int sign;
};
-typedef std::pair<size_t,size_t> Interval;
+
+struct Interval{
+ Interval(size_t f,size_t s,bool o = false):first(f),second(s),oriented(o){}
+ bool operator==(const Interval& i){
+ return first == i.first && second == i.second && oriented == i.oriented;
+ }
+ size_t first;
+ size_t second;
+ bool oriented;
+};
/**
* Returns the length of the longest increasing sequence and the longest
/**
* Counts the number of cycles in the gene order.
*/
-int countCycles(const GeneOrder& go);
+size_t countCycles(const GeneOrder& go);
+
+/**
+ * Calculates the inversion distance for this gene order
+ */
+size_t inversionDistance(const GeneOrder& go);
/**
* Finds the components in the gene order.
*/
std::vector<Interval> findIntervals(const GeneOrder& go);
+/**
+ * Creates a list with the intervals at each point.
+ */
+std::vector<Interval> findIntervalsAtPoints(const std::vector<Interval>& intervals);
+
#endif