Revert to previous commit

[mothur.git] / libshuff.h

diff --git a/libshuff.h b/libshuff.h
new file mode 100644 (file)
index 0000000..ef0e1b0
--- /dev/null
+++ b/libshuff.h
@@ -0,0 +1,48 @@
+#ifndef LIBSHUFF
+#define LIBSHUFF
+
+/*
+ *  libshuff.h
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 4/8/09.
+ *  Copyright 2009 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+#include "fullmatrix.h"
+
+class Libshuff {
+       
+public:
+       Libshuff(FullMatrix*, int, float, float);
+       virtual vector<vector<double> > evaluateAll() = 0;
+       virtual float evaluatePair(int,int) = 0;
+       void randomizeGroups(int, int);
+       void resetGroup(int);
+       vector<vector<vector<double> > > getSavedMins();
+
+protected:
+       void initializeGroups(FullMatrix*);
+       vector<double> getMinX(int);
+       vector<double> getMinXY(int, int);
+       
+       vector<vector<vector<double> > > savedMins;
+       
+       
+       FullMatrix* matrix;
+       vector<int> groupSizes;
+       vector<string> groupNames;
+       vector<vector<int> > groups;
+       vector<vector<int> > savedGroups;
+       vector<double> minX;
+       vector<double> minXY;
+       float cutOff;
+       int iters;
+       float stepSize;
+       
+       int numGroups;
+       MothurOut* m;
+};
+
+#endif