changing command name classify.shared to classifyrf.shared

[mothur.git] / geom.cpp

diff --git a/geom.cpp b/geom.cpp
index 755c1ec81cd282224ad44f574ec13627a9fd1408..5bd150ef7f8201254a392a52a7583b07b83e0b00 100644 (file)
--- a/geom.cpp
+++ b/geom.cpp
@@ -21,8 +21,7 @@ RAbundVector Geom::getRAbundVector(SAbundVector* rank){
                int nb = 0;
                int ns = 0;
                
-               for(int i = rank->size()-1; i > 0; i--)
-               {
+               for(int i = rank->size()-1; i > 0; i--) {
                        int cur = rank->get(i);
                        if(mr == 1 && cur > 0)
                                mr = i;
@@ -45,14 +44,13 @@ EstOutput Geom::getValues(SAbundVector* rank){
                data.resize(3,0);
                
                rdata = getRAbundVector(rank);
-               int numInd = rdata.getNumSeqs();
-               int numSpec = rdata.getNumBins();
-               int min = rdata.get(rdata.size()-1);
+               double numInd = rdata.getNumSeqs();
+               double numSpec = rdata.getNumBins();
+               double min = rdata.get(rdata.size()-1);
                double k = .5;
                double step = .49999;
                
-               while(fabs(min - numInd*kEq(k, (double)numSpec)) > .0001) //This uses a binary search to find the value of k.
-               {
+               while(fabs(min - numInd*kEq(k, (double)numSpec)) > .0001) { //This uses a binary search to find the value of k.
                        if(numInd*kEq(k, numSpec) > min)
                                k += step;
                        else
@@ -76,17 +74,11 @@ EstOutput Geom::getValues(SAbundVector* rank){
                }
 
 
-               /*cout << "Geom:\n";
-               cout << "D-Statistic = " << DStatistic << "\n";
-               cout << "Critical value for 95% confidence interval = ";*/
-
                data[0] = maxDiff/numInd;
                data[1] = 0.886/sqrt(numSpec);
                data[2] = 1.031/sqrt(numSpec);
 
-               /*cout << critVal << "\n";
-               cout << "If D-Statistic is less than the critical value then the data fits the Geometric Series model w/ 95% confidence.\n\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; }
@@ -94,13 +86,9 @@ EstOutput Geom::getValues(SAbundVector* rank){
                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, "Geom", "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);
-       }       
 }
 
 /***********************************************************************/