added sharedbraycurtis, sharedmorisirahorn, sharedkulczynski, sharedkulczynskicody...

[mothur.git] / sharedkulczynskicody.cpp

diff --git a/sharedkulczynskicody.cpp b/sharedkulczynskicody.cpp
new file mode 100644 (file)
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--- /dev/null
+++ b/sharedkulczynskicody.cpp
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+/*
+ *  sharedkulczynskicody.cpp
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 3/24/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "sharedkulczynskicody.h"
+
+/***********************************************************************/
+
+EstOutput SharedKulczynskiCody::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+       try {
+               int S1, S2, S12, tempA, tempB;
+               S1 = 0; S2 = 0; S12 = 0; tempA = 0; tempB = 0; 
+               
+               /*S1, S2 = number of OTUs observed or estimated in A and B 
+               S12=number of OTUs shared between A and B */
+
+               data.resize(1,0);
+               
+               for (int i = 0; i < shared1->size(); i++) {
+                       //store in temps to avoid multiple repetitive function calls
+                       tempA = shared1->getAbundance(i);
+                       tempB = shared2->getAbundance(i);
+                       
+                       if (tempA != 0) { S1++; }
+                       if (tempB != 0) { S2++; } 
+
+                       //they are shared
+                       if ((tempA != 0) && (tempB != 0)) {     S12++; }
+               }
+               
+               data[0] = 0.5 * ((S12 / (float)S1) + (S12 / (float)S2));
+               
+               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+               
+               return data;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the SharedKulczynskiCody class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the SharedKulczynskiCody class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
+
+/***********************************************************************/