#include <vector>
class GeneOrder;
+struct Component;
-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;
+
+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;
}
- int begin;
- int end;
- int sign;
+ size_t first;
+ size_t second;
+ bool oriented;
};
-typedef std::pair<size_t,size_t> Interval;
/**
* Returns the length of the longest increasing sequence and the longest
*/
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.
*/