X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=libshuffcommand.cpp;h=a51b3270f855062a0e2ee92fab63779b38b50877;hb=81ff02ef4064fe4dec986ea3110c1cb8e1285fe6;hp=9ab9108f23ca4d63c3479bb8c6a27d27e08704ea;hpb=9e07ea7484097a73e0e9ce3e379c12bfa0a4e55d;p=mothur.git

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index 9ab9108..a51b327 100644
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -7,6 +7,12 @@
  *
  */
 
+/* This class is designed to implement an integral form of the Cramer-von Mises statistic.
+	you may refer to the "Integration of Microbial Ecology and Statistics: A Test To Compare Gene Libraries" 
+	paper in Applied and Environmental Microbiology, Sept. 2004, p. 5485-5492 0099-2240/04/$8.00+0  
+	DOI: 10.1128/AEM.70.9.5485-5492.2004 Copyright 2004 American Society for Microbiology for more information. */
+
+
 #include "libshuffcommand.h"
 
 //**********************************************************************************************************************
@@ -108,7 +114,7 @@ int LibShuffCommand::execute(){
 					//don't save AA to AA
 					if (i != j) {
 						//(Caa - Cab)^2
-						deltaValues[p].push_back( (abs(cValues[p][i][i]-cValues[p][i][j]) * abs(cValues[p][i][i]-cValues[p][i][j])) ); 
+						deltaValues[p].push_back((cValues[p][i][i]-cValues[p][i][j]) * (cValues[p][i][i]-cValues[p][i][j]));
 						sumDelta[count] += deltaValues[p][count];
 						count++;
 					}
@@ -146,24 +152,18 @@ int LibShuffCommand::execute(){
 						//don't save AA to AA
 						if (i != j) {
 							//(Caa - Cab)^2
-							rsumDelta[count][m] += ((abs(cValues[p][i][i]-cValues[p][i][j]) * abs(cValues[p][i][i]-cValues[p][i][j])));
+							rsumDelta[count][m] += ((cValues[p][i][i]-cValues[p][i][j]) * (cValues[p][i][i]-cValues[p][i][j]));
 							count++;
 						}
 					}
 				}
 				
 			}
-//cout << "iter " << m << endl;
+
 			//clear out old Values
 			reading->update(m);
 			cValues.clear();
 			
-//cout << "random sum delta for iter " << m << endl;
-//for (int i = 0; i < rsumDelta.size(); i++) {
-//	cout << setprecision(6) << rsumDelta[i][m] << '\t';
-//}
-//cout << endl;
-
 		}
 		
 		reading->finish();