X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readblast.h;h=97ce6c74cbf768aeec8d2f879fb7c8ad887a1042;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hp=0b47b5942d7126cec59ce0923a66c1bc4c6ff4e1;hpb=c82900be3ceed3d9bc491bdc98b1819ef85c1af7;p=mothur.git

diff --git a/readblast.h b/readblast.h
index 0b47b59..97ce6c7 100644
--- a/readblast.h
+++ b/readblast.h
@@ -10,18 +10,9 @@
  */
 
 #include "mothur.h"
-#include "sparsematrix.hpp"
+#include "sparsedistancematrix.h"
 #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.
@@ -34,11 +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<DistNode> 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;
@@ -47,10 +38,11 @@ private:
 	bool minWanted;  //if true choose min bsr, if false choose max bsr
 	bool hclusterWanted;
 	
-	SparseMatrix* matrix;
-	vector<DistNode> overlap;
+	SparseDistanceMatrix* matrix;
+	vector<seqDist> overlap;
+	MothurOut* m;
 	
-	void readNames(NameAssignment*);
+	int readNames(NameAssignment*);
 };
 
 /*******************************************************************************************/