X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=bstick.cpp;h=67507a9967ef82effe923662298960ecf00618b8;hp=3a0e0e91a873f6692b585463ec324e33d3b2cd82;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=eb1c88346fb246e95a6b38935b103f95e38b82ca

diff --git a/bstick.cpp b/bstick.cpp
index 3a0e0e9..67507a9 100644
--- a/bstick.cpp
+++ b/bstick.cpp
@@ -3,12 +3,12 @@
  *  Mothur
  *
  *  Created by Thomas Ryabin on 3/6/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
 #include "bstick.h"
-#include "calculator.h"
+
 
 /***********************************************************************/
 double BStick::invSum(int index, double numSpec)
@@ -18,16 +18,15 @@ double BStick::invSum(int index, double numSpec)
 		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--)
-		{
-			int cur = rank->get(i);
+		for(int i = rank->size()-1; i > 0; i--) {
+			double cur = rank->get(i);
 			if(mr == 1 && cur > 0)
 				mr = i;
 			nb += cur;
@@ -46,7 +45,7 @@ RAbundVector BStick::getRAbundVector(SAbundVector* rank){
 /***************************************************************************/
 EstOutput BStick::getValues(SAbundVector* rank){
 	try {
-		data.resize(2,0);
+		data.resize(3,0);
 		rdata = getRAbundVector(rank);
 		double numInd = (double)rdata.getNumSeqs();
 		double numSpec = (double)rdata.getNumBins();
@@ -55,8 +54,7 @@ EstOutput BStick::getValues(SAbundVector* rank){
 		double sumObs = 0;
 		double maxDiff = 0;
 
-		for(int i = 0; i < rdata.size(); i++)
-		{
+		for(int i = 0; i < rdata.size(); i++) {
 			sumObs += rdata.get(i);
 			sumExp += numInd/numSpec*invSum(i+1,numSpec);
 			double diff = fabs(sumObs-sumExp);
@@ -64,38 +62,25 @@ EstOutput BStick::getValues(SAbundVector* rank){
 				maxDiff = diff;
 		}
 		
-		double DStatistic = maxDiff/numInd;
-		double critVal = 0;
-		/*cout << "BStick:\n";
-		cout << "D-Statistic = " << DStatistic << "\n";
-		cout << "Critical value for 95% confidence interval = ";*/
-		if(rdata.size() > 20)
-		{
-			critVal = .886/sqrt(rdata.size());
-		}
-		else
-		{
-			KOSTable table;
-			critVal = table.getConfLimit(numSpec);
-		}
-		/*cout << critVal << "\n";
-		cout << "If D-Statistic is less than the critical value then the data fits the Broken Stick model w/ 95% confidence.\n\n";*/
+
+		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");*/
 		
-		data[0] = DStatistic;
-		data[1] = critVal;
+
 		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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the NPShannon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "BStick", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the NPShannon class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/