added modify names parameter to set.dir

[mothur.git] / qstat.cpp

diff --git a/qstat.cpp b/qstat.cpp
index cac06be7289d3a96913bd65abbc2b94e0c798f41..e07cdb3fb860b96a17ba2972474f0abb8bf05d7e 100644 (file)
--- a/qstat.cpp
+++ b/qstat.cpp
@@ -3,7 +3,7 @@
  *  Mothur
  *
  *  Created by Thomas Ryabin on 3/4/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
@@ -31,22 +31,19 @@ EstOutput QStat::getValues(SAbundVector* rank){
                int r3 = -1;
                int r1Ind = 0;
                int r3Ind = 0;
-               int sumSpec = 0;
-               int iqSum = 0;
-               for(int i = 1; i < rank->size(); i++)
-               {
+               double sumSpec = 0;
+               double iqSum = 0;
+               for(int i = 1; i < rank->size(); i++) {
                        if(r1 != -1 && r3 != -1)
                                i = rank->size();
                                
                        sumSpec += rank->get(i);
                        
-                       if(r1 == -1 && sumSpec >= numSpec*.25)
-                       {
+                       if(r1 == -1 && sumSpec >= numSpec*.25) {
                                r1 = rank->get(i);
                                r1Ind = i;
                        }
-                       else if(r3 == -1 && sumSpec >= numSpec*.75)
-                       {
+                       else if(r3 == -1 && sumSpec >= numSpec*.75) {
                                r3 = rank->get(i);
                                r3Ind = i;
                        }
@@ -55,7 +52,6 @@ EstOutput QStat::getValues(SAbundVector* rank){
                }
                
                double qstat = (.5*r1 + iqSum + .5*r3)/log((double)r3Ind/r1Ind);
-               //cout << "QStat:\nQStatistic = " << qstat << "\n\n";
                
                data[0] = qstat;
                if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
@@ -63,13 +59,9 @@ EstOutput QStat::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, "QStat", "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);
-       }       
 }
 
 /***********************************************************************/