added Jensen-Shannon calc. working on get.communitytype command. fixed bug in get...

[mothur.git] / pam.h

diff --git a/pam.h b/pam.h
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+//
+//  pam.h
+//  Mothur
+//
+//  Created by SarahsWork on 12/10/13.
+//  Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#ifndef Mothur_pam_h
+#define Mothur_pam_h
+
+#include "communitytype.h"
+
+/**************************************************************************************************/
+
+class Pam : public CommunityTypeFinder {
+    
+public:
+    Pam(vector<vector<int> >, vector<vector<double> >, int);
+    vector<double> calcSilhouettes(vector< vector< double> >);
+    double calcCHIndex(vector< vector< double> >);
+    
+private:
+    set<int> medoids;
+    map<int, int> medoid2Partition;
+    double largestDist;
+    vector<vector<double> > dists;
+    vector<vector< double> > Dp; // [numSamples][2] - It contains Dp and Ep. Dp is in [numSamples][0] and Ep is in [numSamples][1]. Dp is the distance between p and the closest sample in S and Ep is the distance between p and the second closest object in S. Both are used in the build and swap phases.
+    
+    int buildPhase();
+    int swapPhase();
+    int updateDp();
+    
+    
+    
+/**************************************************************************************************/
+};
+
+
+#endif