#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;
+/**
+ * Simple interval struct, holds the indexes + information if the interval is
+ * oriented or not.
+ */
+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;
+ //!The start index for this elementary interval
+ size_t first;
+ //!The end interval for this elementary interval
+ size_t second;
+ bool oriented;
};
-typedef std::pair<size_t,size_t> Interval;
/**
* Returns the length of the longest increasing sequence and the longest
std::pair<int,int> longestSequences(const GeneOrder& go);
/**
+ * Uses the Robinson-Schensted algorithm on the gene order. Gives the longest
+ * increasing and decreasing subsequences.
*/
std::vector<std::vector<int> > robinsonSchensted(const GeneOrder& go);
std::vector<Interval> findIntervals(const GeneOrder& go);
/**
- * Creates a list with the intervals at each point.
+ * Creates a list with the intervals at each point. The first and second members
+ * of the returned Intervals are elementary intervals that start, or end, at the
+ * specific point.
*/
std::vector<Interval> findIntervalsAtPoints(const std::vector<Interval>& intervals);