fixed bug with displaying info for collect.shared() and summary.shared().

[mothur.git] / sharedsobscollectsummary.cpp

diff --git a/sharedsobscollectsummary.cpp b/sharedsobscollectsummary.cpp
new file mode 100644 (file)
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