X-Git-Url: https://ruin.nu/git/?a=blobdiff_plain;f=src%2Fgenealgorithms.h;h=59e8f9caee921c452553829d3b1e66bedf32250b;hb=HEAD;hp=4c519a7e3167a40384893a86dea243f20d1ac6d9;hpb=74e3465418ae60633025efb581e399308ffdf4b1;p=germs.git

diff --git a/src/genealgorithms.h b/src/genealgorithms.h
index 4c519a7..59e8f9c 100644
--- a/src/genealgorithms.h
+++ b/src/genealgorithms.h
@@ -24,6 +24,23 @@
 #include <vector>
 
 class GeneOrder;
+struct Component;
+
+/**
+ * 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;
+};
 
 /**
  * Returns the length of the longest increasing sequence and the longest
@@ -32,8 +49,37 @@ class GeneOrder;
 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.
+ */
+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<Component> findComponents(const GeneOrder& go);
+
+/**
+ * Find intervals.
+ */
+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