X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=libshuffcommand.cpp;h=96abbbe995918d779e4cd9086e650b7aa63a8a7b;hb=19fcbbdba99658f5eca244803280f9ee7f9f6607;hp=c827b524649fefe49545aa8769401d781ff016c1;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index c827b52..96abbbe 100644
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -86,6 +86,7 @@ LibShuffCommand::LibShuffCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -137,7 +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);
@@ -149,7 +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"){	
@@ -221,7 +222,7 @@ int LibShuffCommand::execute(){
 			m->openOutputFile(newGroupFile, outGroups);
 			
 			for (int i = 0; i < matrix->getNumSeqs(); i++) {
-				if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); remove(newGroupFile.c_str()); return 0; }
+				if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); m->mothurRemove(newGroupFile); return 0; }
 				
 				Names temp = matrix->getRowInfo(i);
 				outGroups << temp.seqName << '\t' << temp.groupName << endl;
@@ -237,12 +238,16 @@ int LibShuffCommand::execute(){
 			groupMap = new GroupMap(groupfile);
 			groupMap->readMap();
 			
-			if (m->control_pressed) { delete groupMap; delete matrix; remove(newGroupFile.c_str()); return 0; }
+			if (m->control_pressed) { delete groupMap; delete matrix; m->mothurRemove(newGroupFile); return 0; }
 		}
 		
 			
 		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
@@ -315,7 +320,7 @@ int LibShuffCommand::execute(){
 		
 		delete matrix; delete groupMap;
 		
-		if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+		if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
 
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();