X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readdistcommand.cpp;h=8bf6996333b246814a28009d309ab8f3b6bf8718;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=d3cbbb1ff22335b346cb5c01ac90b8dd7c560149;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index d3cbbb1..8bf6996 100644
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -19,6 +19,7 @@ ReadDistCommand::ReadDistCommand(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 {
 			/*//valid paramters for this command
@@ -120,7 +121,7 @@ ReadDistCommand::ReadDistCommand(string option) {
 			//get user cutoff and precision or use defaults
 			string temp;
 			temp = validParameter.validFile(parameters, "precision", false);		if (temp == "not found") { temp = "100"; }
-			convert(temp, precision); 
+			m->mothurConvert(temp, precision); 
 			
 			temp = validParameter.validFile(parameters, "sim", false);				if (temp == "not found") { temp = "F"; }
 			sim = m->isTrue(temp); 
@@ -196,7 +197,7 @@ int ReadDistCommand::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;
@@ -213,7 +214,7 @@ int ReadDistCommand::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; }
 	
 				globaldata->gGroupmap = groupMap;
 			}