X-Git-Url: https://ruin.nu/git/?a=blobdiff_plain;f=src%2Fgenealgorithms.h;h=6bc133fa96174478746cd828659a476e02ea52ec;hb=efe42ca948704593c847996d0ae8da71d15bb75b;hp=4c938e394bd42fa1ea3eb710239811dd32277e99;hpb=e7953f0050007cd1999d64d985d0a063b9ddc99b;p=germs.git

diff --git a/src/genealgorithms.h b/src/genealgorithms.h
index 4c938e3..6bc133f 100644
--- a/src/genealgorithms.h
+++ b/src/genealgorithms.h
@@ -27,11 +27,23 @@ class GeneOrder;
 
 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
@@ -46,7 +58,12 @@ std::vector<std::vector<int> > robinsonSchensted(const GeneOrder& go);
 /**
  * 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.
@@ -58,5 +75,10 @@ std::vector<Component> findComponents(const GeneOrder& go);
  */
 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