X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedbraycurtis.cpp;fp=sharedbraycurtis.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=3711ce77cbb312e5dc2ee2aba14e1856bb942d12;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/sharedbraycurtis.cpp b/sharedbraycurtis.cpp
deleted file mode 100644
index 3711ce7..0000000
--- a/sharedbraycurtis.cpp
+++ /dev/null
@@ -1,52 +0,0 @@
-/*
- *  sharedbraycurtis.cpp
- *  Mothur
- *
- *  Created by Sarah Westcott on 3/24/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "sharedbraycurtis.h"
-
-/***********************************************************************/
-//This is used by SharedJAbund and SharedSorAbund
-EstOutput BrayCurtis::getValues(vector<SharedRAbundVector*> shared) {
-	try {	
-		data.resize(1,0);
-		
-		double sumSharedA, sumSharedB, sumSharedAB, tempA, tempB;
-		sumSharedA = 0; sumSharedB = 0; sumSharedAB = 0; 
-		
-		/*Xi, Yi = abundance of the ith shared OTU in A and B 
-		sumSharedA = the number of otus in A
-		sumSharedB = the sum of all shared otus in B
-		sumSharedAB = the sum of the minimum otus int all shared otus in AB.
-		*/
-		
-		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);
-			
-			sumSharedA += tempA;
-			sumSharedB += tempB;
-				
-			//sum the min of tempA and tempB
-			if (tempA < tempB) { sumSharedAB += tempA; }
-			else  { sumSharedAB += tempB; }				
-		}
-		
-		data[0] = 1.0 - (2 * sumSharedAB) / (float)( sumSharedA + sumSharedB);
-		
-		if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
-				
-		return data;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "BrayCurtis", "getValues");
-		exit(1);
-	}
-}
-
-/***********************************************************************/