X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=logsd.cpp;h=6a795415d832f265325138422f48d77afe3315be;hp=782af2a5dc0514c838a0be217d44fab1ceffdecd;hb=615301e57c25e241356a9c2380648d117709458d;hpb=c196b6b4768ccb84955d773ff0f22e4994d1ba7b

diff --git a/logsd.cpp b/logsd.cpp
index 782af2a..6a79541 100644
--- a/logsd.cpp
+++ b/logsd.cpp
@@ -14,6 +14,7 @@
 double LogSD::logS(double x){
 	return -(1-x)*log(1-x)/x;
 }
+/***********************************************************************/
 EstOutput LogSD::getValues(SAbundVector* rank){
 	try {
 		
@@ -29,8 +30,8 @@ EstOutput LogSD::getValues(SAbundVector* rank){
 		SAbundVector *rank = &rankw;*/
 		
 		data.resize(3,0);
-		int numInd = rank->getNumSeqs();
-		int numSpec = rank->getNumBins();
+		double numInd = rank->getNumSeqs();
+		double numSpec = rank->getNumBins();
 		double snRatio = (double)numSpec/numInd;
 		double x = .5;
 		double step = .4999999999;
@@ -44,7 +45,7 @@ EstOutput LogSD::getValues(SAbundVector* rank){
 		}
 		double alpha = numInd*(1-x)/x;
 
-		int oct = 1;
+		double oct = 1;
 		double octSumObs = 0;
 		double sumObs = 0;
 		double octSumExp = 0;
@@ -74,13 +75,6 @@ EstOutput LogSD::getValues(SAbundVector* rank){
 				maxDiff = diff;
 		}
 
-
-		/*cout << "LogSD:\n";
-		cout << "D Test Statistic = " << DStatistic << "\n";
-		cout << ".05 confidence value = " << .89196/sqrt(numSpec) << "\n";
-		cout << "If D Test Statistic is greater than the critical value then the data fits the Log Series Distribution model w/ 95% confidence.\n\n";*/
-		
-
 		data[0] = (maxDiff + .5)/numSpec;
 		data[1] = 0.886/sqrt(numSpec);
 		data[2] = 1.031/sqrt(numSpec);
@@ -92,13 +86,9 @@ EstOutput LogSD::getValues(SAbundVector* rank){
 		return data;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the LogSD class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "LogSD", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the LogSD class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/