added full matrix files

[mothur.git] / fullmatrix.h

diff --git a/fullmatrix.h b/fullmatrix.h
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+++ b/fullmatrix.h
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+#ifndef FULLMATRIX_H
+#define FULLMATRIX_H
+/*
+ *  fullmatrix.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 3/6/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "mothur.h"
+#include "groupmap.h"
+
+class FullMatrix {
+       
+public:
+       FullMatrix(){};
+       FullMatrix(ifstream&);
+       ~FullMatrix();
+       
+       int getNumSeqs();
+       
+private:
+       void sortGroups();  //this function sorts the sequences within the matrix.  
+       vector< vector<float> > matrix;  //a 2D distance matrix of all the sequences and their distances to eachother.
+       GroupMap* groupmap;  //maps sequences to groups they belong to.
+       int numSeqs;
+
+};
+
+#endif
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