changes while testing

[mothur.git] / sharedjackknife.cpp

diff --git a/sharedjackknife.cpp b/sharedjackknife.cpp
index c267a0789ae294edc3086d42bc88d8bc028cbb0c..0998db8fe3106bbb40c26dc8621d37030fb275c3 100644 (file)
--- a/sharedjackknife.cpp
+++ b/sharedjackknife.cpp
@@ -3,7 +3,7 @@
  *  Mothur
  *
  *  Created by Thomas Ryabin on 3/30/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
@@ -12,7 +12,7 @@
 /***************************************************************************************
 
 ***************************************************************************************/
-double SharedJackknife::simpson(int abunds[], double numInd, int numBins){
+double SharedJackknife::simpson(vector<int> abunds, double numInd, int numBins){
        double denom = numInd*(numInd-1);
        double sum = 0;
        for(int i = 0; i < numBins; i++)
@@ -25,7 +25,7 @@ double SharedJackknife::simpson(int abunds[], double numInd, int numBins){
 
 double* SharedJackknife::jackknife(){          
        int numBins = groups.at(0)->getNumBins()-1;
-       int cArray[numBins];
+       vector<int> cArray(numBins);
        for(int i = 0; i < numBins; i++)
                cArray[i] = 0;
 
@@ -39,7 +39,7 @@ double* SharedJackknife::jackknife(){
 
        double baseD = 1/simpson(cArray, numInd, numBins);
        
-       double pseudoVals[numBins];
+       vector<double> pseudoVals(numBins);
        double jackknifeEstimate = 0;
        for(int i = 0; i < numGroups; i++) {
                for(int j = 0; j < numBins-1; j++) {
@@ -88,8 +88,7 @@ EstOutput SharedJackknife::getValues(vector<SharedRAbundVector*> vectorShared){
                SharedRAbundVector* shared1 = vectorShared[0];
                SharedRAbundVector* shared2 = vectorShared[1];
                if(numGroups == -1) {
-                       globaldata = GlobalData::getInstance();
-                       numGroups = globaldata->Groups.size();
+                       numGroups = m->getNumGroups();
                }
 
                if(callCount == numGroups*(numGroups-1)/2) {
@@ -116,17 +115,11 @@ EstOutput SharedJackknife::getValues(vector<SharedRAbundVector*> vectorShared){
                        data[0] = rdata[0];
                        data[1] = rdata[1];
                        data[2] = rdata[2];
-                       
-                       //cout << "sT = " << data[0] << "    lower confLimit = " << data[1] << "     upper confLimit = " << data[2] << "\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[0])) { data[2] = 0; }
                        
-                       /*for(int i = 0; i < groups.size(); i++)
-                               cout << groups.at(i)->getGroup() << " ";
-                       cout << "\n";
-                       cout << groups.size() << "     " << data[0] << "    " << data[1] << "     " << data[2] << "\n\n";*/
-                       
                        return data;
                }
                
@@ -142,13 +135,9 @@ EstOutput SharedJackknife::getValues(vector<SharedRAbundVector*> vectorShared){
        }
                
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedJackknife class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedJackknife", "getValues");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedJackknife class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/