X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getcommandinfocommand.cpp;h=03c6b17a8a9be441c52070f2af24705eb8f3a168;hb=0cefb55a2616975bd4a144fc345693695ffc9bb6;hp=7ca245369136a19da6ec607d0055a1b0351d2cc7;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/getcommandinfocommand.cpp b/getcommandinfocommand.cpp
index 7ca2453..03c6b17 100644
--- a/getcommandinfocommand.cpp
+++ b/getcommandinfocommand.cpp
@@ -45,6 +45,7 @@ GetCommandInfoCommand::GetCommandInfoCommand(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();
@@ -91,7 +92,7 @@ int GetCommandInfoCommand::execute(){
 		//loop through each command outputting info
 		for (it = commands.begin(); it != commands.end(); it++) {
 			
-			if (m->control_pressed) { m->mothurOut("[ERROR]: did not complete making the file."); m->mothurOutEndLine(); out.close(); remove((output+".temp").c_str()); }
+			if (m->control_pressed) { m->mothurOut("[ERROR]: did not complete making the file."); m->mothurOutEndLine(); out.close(); m->mothurRemove((output+".temp")); }
 			
 			Command* thisCommand = commandFactory->getCommand(it->first);
 			
@@ -101,6 +102,7 @@ int GetCommandInfoCommand::execute(){
 				
 				//general info
 				out << "commandName=" << thisCommand->getCommandName() << endl;
+				//cout << thisCommand->getCommandName() << " current citation = " << thisCommand->getCitation() << endl;
 				out << "commandCategory=" << thisCommand->getCommandCategory() << endl;
 				
 				//remove /n from help string since gui reads line by line
@@ -111,6 +113,16 @@ int GetCommandInfoCommand::execute(){
 				}
 				out << "help=" << newHelpString << endl;
 				
+				//remove /n from citation string since gui reads line by line
+				string mycitationString = thisCommand->getCitation();
+				string newCitationString = "";
+				for (int i = 0; i < mycitationString.length(); i++) { 
+					if (mycitationString[i] != '\n') { newCitationString += mycitationString[i]; }
+				}
+				out << "citation=" << newCitationString << endl;
+				
+				out << "description=" << thisCommand->getDescription() << endl;
+				
 				//outputTypes - makes something like outputTypes=fasta-name-qfile
 				map<string, vector<string> > thisOutputTypes = thisCommand->getOutputFiles();
 				map<string, vector<string> >::iterator itTypes;
@@ -174,7 +186,7 @@ int GetCommandInfoCommand::execute(){
 		out2.close();
 		
 		m->appendFiles(output+".temp", output);
-		remove((output+".temp").c_str());
+		m->mothurRemove((output+".temp"));
 	
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();