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

[mothur.git] / rarecalc.cpp

diff --git a/rarecalc.cpp b/rarecalc.cpp
deleted file mode 100644 (file)
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);
-       }
-}
-
-/***********************************************************************/