good to have a inversion distance function

[germs.git] / src / genealgorithms.h

diff --git a/src/genealgorithms.h b/src/genealgorithms.h
index b0e75b9f65790e184eabe46b6bf9ec9dba8d1002..7f07d17f47476f617018e62494b7cb0ed9e738c6 100644 (file)
--- a/src/genealgorithms.h
+++ b/src/genealgorithms.h
@@ -27,6 +27,9 @@ 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;
@@ -46,7 +49,12 @@ 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.