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

[mothur.git] / geom.cpp

diff --git a/geom.cpp b/geom.cpp
deleted file mode 100644 (file)
index 5bd150e..0000000
--- a/geom.cpp
+++ /dev/null
@@ -1,101 +0,0 @@
-/*
- *  geom.cpp
- *  Mothur
- *
- *  Created by Thomas Ryabin on 2/23/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "geom.h"
-
-/***********************************************************************/
-
-double Geom::kEq(double k, double spec){
-       return k/(1-k)*pow(1-k, spec)/(1-pow(1-k, spec));
-}
-
-RAbundVector Geom::getRAbundVector(SAbundVector* rank){
-               vector <int> rData;
-               int mr = 1;
-               int nb = 0;
-               int ns = 0;
-               
-               for(int i = rank->size()-1; i > 0; i--) {
-                       int cur = rank->get(i);
-                       if(mr == 1 && cur > 0)
-                               mr = i;
-                       nb += cur;
-                       ns += i*cur;
-                       for(int j = 0; j < cur; j++)
-                               rData.push_back(i);
-               }
-               
-               RAbundVector rav = RAbundVector(rData, mr, nb, ns);
-               rav.setLabel(rank->getLabel());
-               return rav;
-}
-
-/***********************************************************************************/
-
-/***********************************************************************************/
-EstOutput Geom::getValues(SAbundVector* rank){
-       try {
-               data.resize(3,0);
-               
-               rdata = getRAbundVector(rank);
-               double numInd = rdata.getNumSeqs();
-               double numSpec = rdata.getNumBins();
-               double min = rdata.get(rdata.size()-1);
-               double k = .5;
-               double step = .49999;
-               
-               while(fabs(min - numInd*kEq(k, (double)numSpec)) > .0001) { //This uses a binary search to find the value of k.
-                       if(numInd*kEq(k, numSpec) > min)
-                               k += step;
-                       else
-                               k -= step;
-                       step /= 2;
-               }
-               
-               double cK = 1/(1-pow(1-k, numSpec));
-               double sumExp = 0;
-               double sumObs = 0;
-               double maxDiff = 0;
-               
-               for(int i = 0; i < numSpec; i++)
-               {
-                       sumObs += rdata.get(i);
-                       sumExp += numInd*cK*k*pow(1-k, i);
-                       
-                       double diff = fabs(sumObs-sumExp);
-                       if(diff > maxDiff)      {       maxDiff = diff;         }
-                       
-               }
-
-
-               data[0] = maxDiff/numInd;
-               data[1] = 0.886/sqrt(numSpec);
-               data[2] = 1.031/sqrt(numSpec);
-
-               
-               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
-               if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
-               if (isnan(data[2]) || isinf(data[2])) { data[2] = 0; }
-               
-               return data;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "Geom", "getValues");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-
-
-
-
-
-