X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=libshuffcommand.cpp;h=c993a06282d4abec617318d87ec9ec18bb64c5e2;hb=1a1ed6dda1d655ff006459f15c712f057c93ddaf;hp=02104142c753b626f245f256e910c4ed3351e6bb;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index 0210414..c993a06 100644
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -138,7 +138,7 @@ LibShuffCommand::LibShuffCommand(string option)  {
 					m->mothurOut("You must provide a phylip file."); m->mothurOutEndLine(); 
 					abort = true;
 				} 
-			}	
+			}else { m->setPhylipFile(phylipfile); }	
 			
 			//check for required parameters
 			groupfile = validParameter.validFile(parameters, "group", true);
@@ -150,7 +150,7 @@ LibShuffCommand::LibShuffCommand(string option)  {
 					m->mothurOut("You must provide a group file."); m->mothurOutEndLine(); 
 					abort = true;
 				} 
-			}	
+			}else { m->setGroupFile(groupfile); }	
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
@@ -243,7 +243,11 @@ int LibShuffCommand::execute(){
 		
 			
 		setGroups();								//set the groups to be analyzed and sorts them
-			
+		
+		if (numGroups < 2) { m->mothurOut("[ERROR]: libshuff requires at least 2 groups, you only have " + toString(numGroups) + ", aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
+		
+		if (m->control_pressed) { delete groupMap; delete matrix; return 0; }
+		
 		/********************************************************************************************/
 		//this is needed because when we read the matrix we sort it into groups in alphabetical order
 		//the rest of the command and the classes used in this command assume specific order