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

[mothur.git] / bstick.cpp

diff --git a/bstick.cpp b/bstick.cpp
deleted file mode 100644 (file)
index 67507a9..0000000
--- a/bstick.cpp
+++ /dev/null
@@ -1,88 +0,0 @@
-/*
- *  bstick.cpp
- *  Mothur
- *
- *  Created by Thomas Ryabin on 3/6/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "bstick.h"
-
-
-/***********************************************************************/
-double BStick::invSum(int index, double numSpec)
-{
-       double sum = 0;
-       for(int i = index; i <= numSpec; i++)
-               sum += 1/(double)i;
-       return sum;
-}
-/***********************************************************************/
-RAbundVector BStick::getRAbundVector(SAbundVector* rank){
-               vector <int> rData;
-               int mr = 1;
-               int nb = 0;
-               int ns = 0;
-               
-               for(int i = rank->size()-1; i > 0; i--) {
-                       double 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 BStick::getValues(SAbundVector* rank){
-       try {
-               data.resize(3,0);
-               rdata = getRAbundVector(rank);
-               double numInd = (double)rdata.getNumSeqs();
-               double numSpec = (double)rdata.getNumBins();
-               
-               double sumExp = 0;
-               double sumObs = 0;
-               double maxDiff = 0;
-
-               for(int i = 0; i < rdata.size(); i++) {
-                       sumObs += rdata.get(i);
-                       sumExp += numInd/numSpec*invSum(i+1,numSpec);
-                       double diff = fabs(sumObs-sumExp);
-                       if(diff > maxDiff)
-                               maxDiff = diff;
-               }
-               
-
-               data[0] = maxDiff/numInd;
-               data[1] = 0.886/sqrt(rdata.size());
-               data[2] = 1.031/sqrt(rdata.size());
-
-               /*m->mothurOut(critVal); m->mothurOutEndLine();
-               m->mothurOut("If D-Statistic is less than the critical value then the data fits the Broken Stick model w/ 95% confidence.\n");*/
-               
-
-               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, "BStick", "getValues");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-