X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getcommandinfocommand.cpp;h=b61236dbac71421d0e63a2dbd5c89071182652e2;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=7ca245369136a19da6ec607d0055a1b0351d2cc7;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/getcommandinfocommand.cpp b/getcommandinfocommand.cpp
index 7ca2453..b61236d 100644
--- a/getcommandinfocommand.cpp
+++ b/getcommandinfocommand.cpp
@@ -12,9 +12,9 @@
 //**********************************************************************************************************************
 vector<string> GetCommandInfoCommand::setParameters(){	
 	try {
-		CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter poutput("output", "String", "", "", "", "", "","",false,false); parameters.push_back(poutput);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -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
@@ -111,17 +113,31 @@ 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;
 				
-				if (thisOutputTypes.size() == 0) { out << "outputTypes=none" << endl; }
+				if (thisOutputTypes.size() == 0) { out << "outputTypesNames=0" << endl; }
 				else {
-					string types = "";
-					for (itTypes = thisOutputTypes.begin(); itTypes != thisOutputTypes.end(); itTypes++) {	types += itTypes->first + "-";	}
+					//string types = "";
+					//for (itTypes = thisOutputTypes.begin(); itTypes != thisOutputTypes.end(); itTypes++) {	types += itTypes->first + "-";	}
 					//rip off last -
-					types = types.substr(0, types.length()-1);
-					out << "outputTypes=" << types << endl;
+					//types = types.substr(0, types.length()-1);
+					out << "outputTypesNames=" << thisOutputTypes.size() << endl;
+                    
+                    for (itTypes = thisOutputTypes.begin(); itTypes != thisOutputTypes.end(); itTypes++) {
+                        out << itTypes->first << "=" << thisCommand->getOutputPattern(itTypes->first) << endl;
+                    }
 				}
 				
 				vector<string> booleans; vector<string> numbers; vector<string> multiples; vector<string> Strings;
@@ -174,7 +190,7 @@ 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();
@@ -200,34 +216,54 @@ int GetCommandInfoCommand::getInfo(vector<CommandParameter> para, vector<string>
 		for (int i = 0; i < para.size(); i++) {
 			if ((para[i].name == "inputdir") || (para[i].name == "outputdir")) {} //ignore
 			else {
+                string important = "|F";
+                if (para[i].important || para[i].required) { important = "|T"; }
+                
+                string outputType = "|none";
+                if (para[i].outputTypes != "") { outputType = "|" + para[i].outputTypes; }
+                
 				if (para[i].type == "Boolean") {
-					string temp = para[i].name + "=" + para[i].optionsDefault;
+					string temp = para[i].name + "=" + para[i].optionsDefault + important + outputType;
 					booleans.push_back(temp);
 				}else if (para[i].type == "Multiple") {
 					string multAllowed = "F";
 					if (para[i].multipleSelectionAllowed) { multAllowed = "T"; }
-					string temp = para[i].name + "=" + para[i].options + "|" + para[i].optionsDefault + "|" + multAllowed;
+					string temp = para[i].name + "=" + para[i].options + "|" + para[i].optionsDefault + "|" + multAllowed + important + outputType;
 					multiples.push_back(temp);
 				}else if (para[i].type == "Number") {
-					string temp = para[i].name + "=" + para[i].optionsDefault;
+					string temp = para[i].name + "=" + para[i].optionsDefault + important + outputType;
 					numbers.push_back(temp);
 				}else if (para[i].type == "String") {
-					string temp = para[i].name + "=" + para[i].optionsDefault;
+					string temp = para[i].name + "=" + para[i].optionsDefault + important + outputType;
 					strings.push_back(temp);
 				}else if (para[i].type == "InputTypes") {
 					string required = "F";
 					if (para[i].required) { required = "T"; }
-					string temp = required + "|" + para[i].chooseOnlyOneGroup + "|" + para[i].chooseAtLeastOneGroup + "|" + para[i].linkedGroup;
+					string temp = required + important + "|" + para[i].chooseOnlyOneGroup + "|" + para[i].chooseAtLeastOneGroup + "|" + para[i].linkedGroup + outputType;
 					inputTypes[para[i].name] = temp;
 					
 					//add choose only one groups
-					groups[para[i].chooseOnlyOneGroup].insert(para[i].name);
-					
+                    vector<string> tempGroups;
+                    m->splitAtDash(para[i].chooseOnlyOneGroup, tempGroups);
+                    for (int l = 0; l < tempGroups.size(); l++) {
+                        groups[tempGroups[l]].insert(para[i].name);
+                    }
+					tempGroups.clear();
+                    
 					//add at least one group names
-					groups[para[i].chooseAtLeastOneGroup].insert(para[i].name);
+                    m->splitAtDash(para[i].chooseAtLeastOneGroup, tempGroups);
+                    for (int l = 0; l < tempGroups.size(); l++) {
+                        groups[tempGroups[l]].insert(para[i].name);
+                    }
+					tempGroups.clear();
+					
 					
 					//add at linked group names
-					groups[para[i].linkedGroup].insert(para[i].name);
+                    m->splitAtDash(para[i].linkedGroup, tempGroups);
+                    for (int l = 0; l < tempGroups.size(); l++) {
+                        groups[tempGroups[l]].insert(para[i].name);
+                    }
+					tempGroups.clear();
 						  
 				}else { m->mothurOut("[ERROR]: " + para[i].type + " is an unknown parameter type, please correct."); m->mothurOutEndLine(); }
 			}