X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedjackknife.cpp;h=0998db8fe3106bbb40c26dc8621d37030fb275c3;hp=c267a0789ae294edc3086d42bc88d8bc028cbb0c;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=c196b6b4768ccb84955d773ff0f22e4994d1ba7b

diff --git a/sharedjackknife.cpp b/sharedjackknife.cpp
index c267a07..0998db8 100644
--- 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);
-	}	
 }
 
 /***********************************************************************/