X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedkstest.cpp;h=f65f271abbf39224b6eb052a3d83d2142968d141;hb=786d5631d9cd5baa6ed6ef16f8b4b384cbc7470f;hp=897432d57a20973cae256a14839b56a209c5ab0d;hpb=29351fe29c017d2225366418973ed0e000ce5293;p=mothur.git

diff --git a/sharedkstest.cpp b/sharedkstest.cpp
index 897432d..f65f271 100644
--- a/sharedkstest.cpp
+++ b/sharedkstest.cpp
@@ -3,38 +3,36 @@
  *  Mothur
  *
  *  Created by Thomas Ryabin on 3/6/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
 #include "sharedkstest.h"
-#include "calculator.h"
-#include <algorithm>
 
 /***********************************************************************/
 
-EstOutput SharedKSTest::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
+EstOutput KSTest::getValues(vector<SharedRAbundVector*> shared){
 	try {
-		data.resize(2,0);
-		
+		data.resize(3,0);
+
 		//Must return shared1 and shared2 to original order at conclusion of kstest
-		vector <individual> initData1 = shared1->getData();
-		vector <individual> initData2 = shared2->getData();
-		shared1->sortD();
-		shared2->sortD();
+		vector <individual> initData1 = shared[0]->getData();
+		vector <individual> initData2 = shared[1]->getData();
+		shared[0]->sortD();
+		shared[1]->sortD();
 
-		int numNZ1 = shared1->numNZ();
-		int numNZ2 = shared2->numNZ();
-		double numInd1 = (double)shared1->getNumSeqs();
-		double numInd2 = (double)shared2->getNumSeqs();
+		int numNZ1 = shared[0]->numNZ();
+		int numNZ2 = shared[1]->numNZ();
+		double numInd1 = (double)shared[0]->getNumSeqs();
+		double numInd2 = (double)shared[1]->getNumSeqs();
 		
 		double maxDiff = -1;
 		double sum1 = 0;
 		double sum2 = 0;
-		for(int i = 1; i < shared1->getNumBins(); i++)
+		for(int i = 1; i < shared[0]->getNumBins(); i++)
 		{
-			sum1 += shared1->get(i).abundance;
-			sum2 += shared2->get(i).abundance;
+			sum1 += shared[0]->get(i).abundance;
+			sum2 += shared[1]->get(i).abundance;
 			double diff = fabs((double)sum1/numInd1 - (double)sum2/numInd2);
 			if(diff > maxDiff)
 				maxDiff = diff;
@@ -56,22 +54,24 @@ EstOutput SharedKSTest::getValues(SharedRAbundVector* shared1, SharedRAbundVecto
 			cout << "If D-Statistic is greater than the critical value then the data sets are significantly different at the 95% confidence level.\n\n";
 		}*/
 		
-		shared1->setData(initData1);
-		shared2->setData(initData2);
+		shared[0]->setData(initData1);
+		shared[1]->setData(initData2);
 		
 		data[0] = DStatistic;
 		data[1] = critVal;
+		data[2] = 0;
+		
 		if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
 		if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
 
 		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";
+		cout << "Standard Error: " << e.what() << " has occurred in the KSTest class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 		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";
+		cout << "An unknown error has occurred in the KSTest class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 		exit(1);
 	}	
 }