changing command name classify.shared to classifyrf.shared

[mothur.git] / logsd.cpp

diff --git a/logsd.cpp b/logsd.cpp
index 782af2a5dc0514c838a0be217d44fab1ceffdecd..6a795415d832f265325138422f48d77afe3315be 100644 (file)
--- 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);
-       }       
 }
 
 /***********************************************************************/