X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bstick.cpp;fp=bstick.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=67507a9967ef82effe923662298960ecf00618b8;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

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