X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readblast.h;h=97ce6c74cbf768aeec8d2f879fb7c8ad887a1042;hp=536d1af05db87dce20deaf344bd6410b952a61cb;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0

diff --git a/readblast.h b/readblast.h
index 536d1af..97ce6c7 100644
--- a/readblast.h
+++ b/readblast.h
@@ -10,7 +10,7 @@
  */
 
 #include "mothur.h"
-#include "sparsematrix.hpp"
+#include "sparsedistancematrix.h"
 #include "nameassignment.hpp"
 
 /****************************************************************************************/
@@ -25,11 +25,11 @@ 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;		}
-	vector<seqDist> getOverlapMatrix()	{	return overlap;		}
-	string getOverlapFile()				{	return overlapFile;	}
-	string getDistFile()				{	return distFile;	}
+	int read(NameAssignment*);
+	SparseDistanceMatrix* getDistMatrix()		{	return matrix;		}
+	vector<seqDist> getOverlapMatrix()          {	return overlap;		}
+	string getOverlapFile()                     {	return overlapFile;	}
+	string getDistFile()                        {	return distFile;	}
 	
 private:
 	string blastfile, overlapFile, 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*);
 };
 
 /*******************************************************************************************/