moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / sharedlennon.cpp

diff --git a/sharedlennon.cpp b/sharedlennon.cpp
deleted file mode 100644 (file)
index 5219275..0000000
--- a/sharedlennon.cpp
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- *  sharedlennon.cpp
- *  Mothur
- *
- *  Created by Sarah Westcott on 3/24/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "sharedlennon.h"
-
-/***********************************************************************/
-
-EstOutput Lennon::getValues(vector<SharedRAbundVector*> shared) {
-       try {
-               double S1, S2, S12, tempA, tempB, min;
-               S1 = 0; S2 = 0; S12 = 0; tempA = 0; tempB = 0; min = 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);
-                       
-                       if (tempA != 0) { S1++; }
-                       if (tempB != 0) { S2++; } 
-
-                       //they are shared
-                       if ((tempA != 0) && (tempB != 0)) {     S12++; }
-               }
-               
-               
-               tempA = S1 - S12;  tempB = S2 - S12;
-               
-               if (tempA < tempB) { min = tempA; }
-               else { min = tempB; }
-               
-               data[0] = 1.0 - S12 / (float)(S12 + min);
-               
-               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
-               
-               return data;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "Lennon", "getValues");
-               exit(1);
-       }
-}
-
-/***********************************************************************/