X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedanderbergs.cpp;fp=sharedanderbergs.cpp;h=77888b50b456abf5bb16222ec165a55c4b4e37b4;hb=2657127a3e1f3b5463f2b3a3b49bc19843f5c9d2;hp=0000000000000000000000000000000000000000;hpb=d345542d7f1ed7cb3a23704f7f6685699d78421a;p=mothur.git

diff --git a/sharedanderbergs.cpp b/sharedanderbergs.cpp
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--- /dev/null
+++ b/sharedanderbergs.cpp
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+/*
+ *  sharedanderberg.cpp
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 3/23/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "sharedanderbergs.h"
+
+/***********************************************************************/
+
+EstOutput SharedAnderberg::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)((2 * S1) + (2 * S2) - (3 * 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 SharedAnderberg class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the SharedAnderberg class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
+
+/***********************************************************************/