X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlistcountcommand.cpp;h=980c886cc0cb79f51f892ee13fe4dc2c3061b812;hb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6;hp=404d35379730d3e3859a87654e795739f3f9b5cf;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp
index 404d353..980c886 100644
--- a/getlistcountcommand.cpp
+++ b/getlistcountcommand.cpp
@@ -40,7 +40,7 @@ string GetListCountCommand::getHelpString(){
 		helpString += "Example get.otulist(list=amazon.fn.list, label=0.10).\n";
 		helpString += "The default value for label is all lines in your inputfile.\n";
 		helpString += "The get.otulist command outputs a .otu file for each distance you specify listing the bin number and the names of the sequences in that bin.\n";
-		helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -69,6 +69,7 @@ GetListCountCommand::GetListCountCommand(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();
@@ -113,6 +114,7 @@ GetListCountCommand::GetListCountCommand(string option)  {
 				else { 	m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
 			}
 			else if (listfile == "not open") { abort = true; }	
+			else { m->setListFile(listfile); }
 			
 		
 			//check for optional parameter and set defaults
@@ -147,7 +149,7 @@ int GetListCountCommand::execute(){
 		set<string> processedLabels;
 		set<string> userLabels = labels;
 		
-		if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());	} return 0;  }
+		if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);	} return 0;  }
 		
 		while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 			
@@ -155,7 +157,7 @@ int GetListCountCommand::execute(){
 			
 				process(list);
 				
-				if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());	} return 0;  }
+				if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);	} return 0;  }
 							
 				processedLabels.insert(list->getLabel());
 				userLabels.erase(list->getLabel());
@@ -169,7 +171,7 @@ int GetListCountCommand::execute(){
 				
 				process(list);
 				
-				if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());	} return 0;  }
+				if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);	} return 0;  }
 
 													
 				processedLabels.insert(list->getLabel());
@@ -206,7 +208,7 @@ int GetListCountCommand::execute(){
 				
 			process(list);	
 			
-			if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());	} return 0;  }
+			if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);	} return 0;  }
 			
 			delete list;  
 		}