added sparseDistanceMatrix class. Modified cluster commands to use the new sparse...

[mothur.git] / sparsedistancematrix.h

diff --git a/sparsedistancematrix.h b/sparsedistancematrix.h
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+++ b/sparsedistancematrix.h
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+#ifndef Mothur_sparsedistancematrix_h
+#define Mothur_sparsedistancematrix_h
+
+//
+//  sparsedistancematrix.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 7/16/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "mothur.h"
+#include "mothurout.h"
+
+
+class ListVector;
+
+
+/* For each distance in a sparse matrix we have a row, column and distance.  
+ The PDistCell consists of the column and distance.
+ We know the row by the distances row in the seqVec matrix.  
+ SeqVec is square and each row is sorted so the column values are ascending to save time in the search for the smallest distance. */
+
+/***********************************************************************/
+struct PDistCellMin{
+       ull row;
+    ull col;
+       //PDistCell* cell;
+       PDistCellMin(ull r, ull c) :  col(c), row(r) {}
+};
+/***********************************************************************/
+
+
+
+class SparseDistanceMatrix {
+       
+public:
+       SparseDistanceMatrix();
+       ~SparseDistanceMatrix(){ clear(); }
+       int getNNodes();
+       ull getSmallestCell(ull& index);                //Return the cell with the smallest distance
+       float getSmallDist();
+       
+       int rmCell(ull, ull);
+    int updateCellCompliment(ull, ull);
+    void resize(ull n) { seqVec.resize(n);  }
+    void clear();
+       void addCell(ull, PDistCell);
+    vector<vector<PDistCell> > seqVec;
+    
+private:
+       PDistCell smallCell;                            //The cell with the smallest distance
+       int numNodes;
+    
+    bool sorted;
+    int sortSeqVec();
+       float smallDist, aboveCutoff;
+    
+       MothurOut* m;
+};
+
+/***********************************************************************/
+
+
+
+#endif