X-Git-Url: https://ruin.nu/git/?a=blobdiff_plain;f=src%2Fgenealgorithms.h;h=59e8f9caee921c452553829d3b1e66bedf32250b;hb=HEAD;hp=4c938e394bd42fa1ea3eb710239811dd32277e99;hpb=e7953f0050007cd1999d64d985d0a063b9ddc99b;p=germs.git

diff --git a/src/genealgorithms.h b/src/genealgorithms.h
index 4c938e3..59e8f9c 100644
--- a/src/genealgorithms.h
+++ b/src/genealgorithms.h
@@ -24,14 +24,23 @@
 #include <vector>
 
 class GeneOrder;
+struct Component;
 
-struct Component{
-	Component(int b,int e,int s):begin(b),end(e),sign(s){}
-	int begin;
-	int end;
-	int 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;
+	}
+	//!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
@@ -40,13 +49,20 @@ typedef std::pair<size_t,size_t> Interval;
 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);
 
 /**
  * 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 +74,12 @@ std::vector<Component> findComponents(const GeneOrder& go);
  */
 std::vector<Interval> findIntervals(const GeneOrder& go);
 
+/**
+ * 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);
+
 #endif