removing chime source files from mother project.

[mothur.git] / readblast.h

diff --git a/readblast.h b/readblast.h
index 0b47b5942d7126cec59ce0923a66c1bc4c6ff4e1..fd32380c20c1a7145a8c65d07700b54d2d5bc63b 100644 (file)
--- a/readblast.h
+++ b/readblast.h
@@ -13,15 +13,6 @@
 #include "sparsematrix.hpp"
 #include "nameassignment.hpp"
 
-/****************************************************************************************/
-struct DistNode {
-       int seq1;
-       int seq2;
-       float dist;
-       DistNode(int s1, int s2, float d) : seq1(s1), seq2(s2), dist(d) {}
-       DistNode() {}
-       ~DistNode() {}
-};
 /****************************************************************************************/
 
 //Note: this class creates a sparsematrix and list if the read is executed, but does not delete them on deconstruction.
@@ -34,9 +25,9 @@ public:
        ReadBlast(string, float, float, int, bool, bool); //blastfile, cutoff, penalty, length of overlap, min or max bsr, hclusterWanted
        ~ReadBlast() {}
        
-       void read(NameAssignment*);
+       int read(NameAssignment*);
        SparseMatrix* getDistMatrix()           {       return matrix;          }
-       vector<DistNode> getOverlapMatrix()     {       return overlap;         }
+       vector<seqDist> getOverlapMatrix()      {       return overlap;         }
        string getOverlapFile()                         {       return overlapFile;     }
        string getDistFile()                            {       return distFile;        }
        
@@ -48,9 +39,10 @@ private:
        bool hclusterWanted;
        
        SparseMatrix* matrix;
-       vector<DistNode> overlap;
+       vector<seqDist> overlap;
+       MothurOut* m;
        
-       void readNames(NameAssignment*);
+       int readNames(NameAssignment*);
 };
 
 /*******************************************************************************************/