Added more doxygen documentation

[germs.git] / src / genealgorithms.h

diff --git a/src/genealgorithms.h b/src/genealgorithms.h
index 4c938e394bd42fa1ea3eb710239811dd32277e99..a91f67ddcae2345497c24841ff93dc6d6d5ebf82 100644 (file)
--- a/src/genealgorithms.h
+++ b/src/genealgorithms.h
@@ -24,14 +24,21 @@
 #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;
+       }
+       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
@@ -40,13 +47,20 @@ 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 +72,10 @@ 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