X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedsorclass.cpp;fp=sharedsorclass.cpp;h=85609dad69311e08474a2115755d74761052ab13;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/sharedsorclass.cpp b/sharedsorclass.cpp
new file mode 100644
index 0000000..85609da
--- /dev/null
+++ b/sharedsorclass.cpp
@@ -0,0 +1,49 @@
+/*
+ *  sharedsorclass.cpp
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 1/8/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "sharedsorclass.h"
+
+/***********************************************************************/
+
+EstOutput SorClass::getValues(vector<SharedRAbundVector*> shared) {
+	try {
+		double 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 < shared[0]->getNumBins(); i++) {
+			//store in temps to avoid multiple repetitive function calls
+			tempA = shared[0]->getAbundance(i);
+			tempB = shared[1]->getAbundance(i);
+
+			//find number of bins in shared1 and shared2
+			if (tempA != 0) { S1++; }
+			if (tempB != 0) { S2++; } 
+			
+			//they are shared
+			if ((tempA != 0) && (tempB != 0)) {	S12++; }
+		}
+		
+		data[0] = 1.0-(2 * S12) / (float)(S1 + S2);
+		
+		if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+		
+		return data;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SorClass", "getValues");
+		exit(1);
+	}
+}
+
+/***********************************************************************/