added sharedbraycurtis, sharedmorisirahorn, sharedkulczynski, sharedkulczynskicody...

[mothur.git] / sharedmorisitahorn.cpp

diff --git a/sharedmorisitahorn.cpp b/sharedmorisitahorn.cpp
new file mode 100644 (file)
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+++ b/sharedmorisitahorn.cpp
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+/*
+ *  sharedmorisitahorn.cpp
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 3/24/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "sharedmorisitahorn.h"
+
+/***********************************************************************/
+EstOutput SharedMorHorn::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+       try {   
+               data.resize(1,0);
+               
+               int Atotal, Btotal, tempA, tempB;
+               Atotal = 0; Btotal = 0; 
+               float  morhorn, sumSharedA, sumSharedB, a, b, d;
+               morhorn = 0.0; sumSharedA = 0.0; sumSharedB = 0.0; a = 0.0; b = 0.0; d = 0.0;
+               
+               //get the total values we need to calculate the theta denominator sums
+               for (int i = 0; i < shared1->size(); i++) {
+                       //store in temps to avoid multiple repetitive function calls
+                       Atotal += shared1->getAbundance(i);
+                       Btotal += shared2->getAbundance(i);
+               }
+               
+               //calculate the theta denominator sums
+               for (int j = 0; j < shared1->size(); j++) {
+                       //store in temps to avoid multiple repetitive function calls
+                       tempA = shared1->getAbundance(j);
+                       tempB = shared2->getAbundance(j);
+                       
+                       //they are shared
+                       if ((tempA != 0) && (tempB != 0)) {
+                               if (Atotal != 0)        { sumSharedA = (tempA / (float)Atotal); }
+                               if (Btotal != 0)        { sumSharedB = (tempB / (float)Btotal); }
+                       
+                               a += sumSharedA * sumSharedA;
+                               b += sumSharedB * sumSharedB;
+                               d += sumSharedA * sumSharedB;
+                       }
+               }
+
+               morhorn = (2 * d) / (float) (a + b);
+               
+               if (isnan(morhorn) || isinf(morhorn)) { morhorn = 0; }
+               
+               data[0] = morhorn;
+               
+               return data;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the SharedMorHorn class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the SharedMorHorn class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
+
+/***********************************************************************/
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