X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedkstest.cpp;h=d91478801678c53ddb87dce7b1474272a2b30275;hp=1da7c90c1e3b4bcda6ae0a0aee70e60995c9c8e8;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=51cf89e90eef8b300c2786eb1560dd89e6e83445

diff --git a/sharedkstest.cpp b/sharedkstest.cpp
index 1da7c90..d914788 100644
--- a/sharedkstest.cpp
+++ b/sharedkstest.cpp
@@ -11,28 +11,28 @@
 
 /***********************************************************************/
 
-EstOutput KSTest::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;
@@ -43,35 +43,22 @@ EstOutput KSTest::getValues(SharedRAbundVector* shared1, SharedRAbundVector* sha
 		//double pVal = exp(-2*pow(maxDiff/a,2));
 		double critVal = 1.36*a*numNZ1*numNZ2;
 		
-		/*cout << "Kolmogorov-Smirnov 2-sample test:\n";
-		if(numNZ1 > 25 && numNZ2 > 25) //If the sample sizes are both bigger than 25.
-			cout << "P-Value = " << pVal << "\nP-Value is the probability that the data sets are significantly different.\n";
-		else
-		{	
-			//cout << "90% Confidence Critical Value = " << 1.22*a*numNZ1*numNZ2 << "\n";
-			cout << "D-Statistic = " << DStatistic << "\n";
-			cout << "95% Confidence Critical Value = " << critVal << "\n";
-			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 KSTest class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "KSTest", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the KSTest class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/