sorting without hurdles seems to work

[germs.git] / src / genealgorithms.h

diff --git a/src/genealgorithms.h b/src/genealgorithms.h
index b0e75b9f65790e184eabe46b6bf9ec9dba8d1002..6bc133fa96174478746cd828659a476e02ea52ec 100644 (file)
--- 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.