X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedsobscollectsummary.cpp;fp=sharedsobscollectsummary.cpp;h=d39e66e58a7bb79b9d4cc5f326b53d169778d181;hb=44c1323a88b2a697c7047df1b3bb8c59eadd15b1;hp=0000000000000000000000000000000000000000;hpb=b2dca66a02f8f82aa5528e531eace60fbbd2967b;p=mothur.git

diff --git a/sharedsobscollectsummary.cpp b/sharedsobscollectsummary.cpp
new file mode 100644
index 0000000..d39e66e
--- /dev/null
+++ b/sharedsobscollectsummary.cpp
@@ -0,0 +1,46 @@
+/*
+ *  sharedsobscollectsummary.cpp
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 2/12/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "sharedsobscollectsummary.h"
+
+/***********************************************************************/
+//This returns the number of shared species observed in several groups.  
+//The shared vector is each groups sharedrabundvector.
+
+EstOutput SharedSobsCS::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
+	try {
+		data.resize(1,0);
+		int observed = 0;
+		int tempA, tempB;
+
+		//loop through the species in each group
+		for (int k = 0; k < shared1->size(); k++) {
+			tempA = shared1->getAbundance(k); //store in temps to avoid calling getAbundance multiple times
+			tempB = shared2->getAbundance(k);
+
+			//if you have found a new species
+			if ((tempA != 0) && (tempB != 0)) {//they are shared
+				observed++;
+			}
+		}
+
+		data[0] = observed;
+		return data;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the SharedSobsCS class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the SharedSobsCS class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
+
+/***********************************************************************/
\ No newline at end of file