added count file to get.groups and remove.groups. added shortcut parameter to classif...

[mothur.git] / readblast.h

diff --git a/readblast.h b/readblast.h
index 536d1af05db87dce20deaf344bd6410b952a61cb..ef5ff9afa182f5fb7f7226c506481a0252964962 100644 (file)
--- a/readblast.h
+++ b/readblast.h
@@ -10,7 +10,7 @@
  */
 
 #include "mothur.h"
-#include "sparsematrix.hpp"
+#include "sparsedistancematrix.h"
 #include "nameassignment.hpp"
 
 /****************************************************************************************/
@@ -25,8 +25,8 @@ public:
        ReadBlast(string, float, float, int, bool, bool); //blastfile, cutoff, penalty, length of overlap, min or max bsr, hclusterWanted
        ~ReadBlast() {}
        
-       void read(NameAssignment*);
-       SparseMatrix* getDistMatrix()           {       return matrix;          }
+       int read(NameAssignment*);
+       SparseDistanceMatrix* getDistMatrix()           {       return matrix;          }
        vector<seqDist> getOverlapMatrix()      {       return overlap;         }
        string getOverlapFile()                         {       return overlapFile;     }
        string getDistFile()                            {       return distFile;        }
@@ -38,11 +38,11 @@ private:
        bool minWanted;  //if true choose min bsr, if false choose max bsr
        bool hclusterWanted;
        
-       SparseMatrix* matrix;
+       SparseDistanceMatrix* matrix;
        vector<seqDist> overlap;
        MothurOut* m;
        
-       void readNames(NameAssignment*);
+       int readNames(NameAssignment*);
 };
 
 /*******************************************************************************************/