working on pam

[mothur.git] / sharedkstest.cpp

diff --git a/sharedkstest.cpp b/sharedkstest.cpp
index 897432d57a20973cae256a14839b56a209c5ab0d..d91478801678c53ddb87dce7b1474272a2b30275 100644 (file)
--- 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;
@@ -45,35 +43,22 @@ EstOutput SharedKSTest::getValues(SharedRAbundVector* shared1, SharedRAbundVecto
                //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 NPShannon 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 NPShannon class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/