X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedkulczynski.cpp;fp=sharedkulczynski.cpp;h=30c8c7a34a9b1d79f99637fa6c1874df2dd0f3d9;hb=25cde7ff05bbe741da1712f2c740e0bc8706e523;hp=0000000000000000000000000000000000000000;hpb=39a9b207d1046f3409781c45e38b7a871133d224;p=mothur.git

diff --git a/sharedkulczynski.cpp b/sharedkulczynski.cpp
new file mode 100644
index 0000000..30c8c7a
--- /dev/null
+++ b/sharedkulczynski.cpp
@@ -0,0 +1,52 @@
+/*
+ *  sharedkulczynski.cpp
+ *  Mothur
+ *
+ *  Created by John Westcott on 3/24/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "sharedkulczynski.h"
+
+/***********************************************************************/
+
+EstOutput SharedKulczynski::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] = S12 / (float)(S1 + S2 - (2 * S12));
+		
+		if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+		
+		return data;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the SharedKulczynski class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the SharedKulczynski class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
+
+/***********************************************************************/