X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readblast.h;h=ef5ff9afa182f5fb7f7226c506481a0252964962;hb=ea4f373c28543cd1002b0dd7dc6e55c526647d59;hp=128c144fc3d29109453331c059b478c18f7a6bfe;hpb=b5a791c81d432082bf38755a08b33863f255341d;p=mothur.git

diff --git a/readblast.h b/readblast.h
index 128c144..ef5ff9a 100644
--- 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;	}
@@ -38,10 +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*);
 };
 
 /*******************************************************************************************/