#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.
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; }
bool hclusterWanted;
SparseMatrix* matrix;
- vector<DistNode> overlap;
+ vector<seqDist> overlap;
+ MothurOut* m;
- void readNames(NameAssignment*);
+ int readNames(NameAssignment*);
};
/*******************************************************************************************/