X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarecalc.cpp;fp=rarecalc.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=9145061255d415eb7a48749bdbaaa405b78425fd;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/rarecalc.cpp b/rarecalc.cpp
deleted file mode 100644
index 9145061..0000000
--- a/rarecalc.cpp
+++ /dev/null
@@ -1,53 +0,0 @@
-/*
- *  rarecalc.cpp
- *  Dotur
- *
- *  Created by Sarah Westcott on 1/7/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "rarecalc.h"
-
-/***********************************************************************/
-
-EstOutput RareCalc::getValues(int n){
-	try {
-		EstOutput output(3,0);
-
-		double richness = (double)numBins;
-		double varS = 0.0000;
-	
-		double varTerm1 = 0.0000;
-		double varTerm2 = 0.0000;
-	
-		double rSummation = 0;
-		for(int i=0;i<numBins;i++){
-			int N_ni = numSeqs - bins->get(i);
-			rSummation += (bMatrix[N_ni][n]);
-		
-			varTerm1 += (bMatrix[N_ni][n] * (1.0 - bMatrix[N_ni][n] / bMatrix[numSeqs][n]));
-
-			for(int j=i+1;j<numBins;j++){
-				varTerm2 += ( bMatrix[N_ni-bins->get(j)][n] - bMatrix[N_ni][n] * bMatrix[numSeqs-bins->get(j)][n] / bMatrix[numSeqs][n]);
-			}
-		
-		}
-		richness -= (rSummation / bMatrix[numSeqs][n]);
-		varS = (varTerm1 + 2 * varTerm2) / bMatrix[numSeqs][n];
-		float sd = pow(varS, 0.5);
-	
-
-		output[0] = richness;
-		output[1] = richness - 1.96 * sd;	
-		output[2] = richness + 1.96 * sd;
-	
-		return output;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "RareCalc", "getValues");
-		exit(1);
-	}
-}
-
-/***********************************************************************/