X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parselistscommand.cpp;h=61cb2454b52ee9e05cf1027995906371b5463762;hb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e;hp=bb096d8646873f74c42bd8970b9eef9693a3252e;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index bb096d8..61cb245 100644
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -12,11 +12,11 @@
 //**********************************************************************************************************************
 vector<string> ParseListCommand::setParameters(){	
 	try {
-		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
-		CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
-		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","list",false,true,true); parameters.push_back(plist);
+		CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pgroup);
+		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+		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);		}
@@ -46,6 +46,21 @@ string ParseListCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string ParseListCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "list") {  pattern = "[filename],[group],list"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ParseListCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 ParseListCommand::ParseListCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -170,7 +185,8 @@ int ParseListCommand::execute(){
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//set fileroot
-		string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
+		map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
 		
 		//fill filehandles with neccessary ofstreams
 		int i;
@@ -180,7 +196,8 @@ int ParseListCommand::execute(){
 			temp = new ofstream;
 			filehandles[gGroups[i]] = temp;
 			
-			string filename = fileroot +  gGroups[i] + ".list";
+            variables["[group]"] = gGroups[i];
+			string filename = getOutputFileName("list",variables);
 			outputNames.push_back(filename); outputTypes["list"].push_back(filename);
 			m->openOutputFile(filename, *temp);
 		}