X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getotuscommand.cpp;h=8d20e63b65b9a99b6476608fe4a108ce233718f0;hb=e8e13c129ba8184ec5932a090773f353f3ae3406;hp=b94b42a8a37038d188bf19a430a7ee8951f2f86c;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/getotuscommand.cpp b/getotuscommand.cpp
index b94b42a..8d20e63 100644
--- a/getotuscommand.cpp
+++ b/getotuscommand.cpp
@@ -53,7 +53,27 @@ string GetOtusCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string GetOtusCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "group")            {   outputFileName = "pick" + m->getExtension(inputName);  }
+            else if (type == "list")        {   outputFileName = "pick" + m->getExtension(inputName);  }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetOtusCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 GetOtusCommand::GetOtusCommand(){	
 	try {
@@ -182,12 +202,14 @@ int GetOtusCommand::execute(){
 		groupMap->readMap();
 		
 		//get groups you want to get
-		if (accnosfile != "") { readAccnos(); }
+		if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); }
 		
 		//make sure groups are valid
 		//takes care of user setting groupNames that are invalid or setting groups=all
 		SharedUtil* util = new SharedUtil();
-		util->setGroups(Groups, groupMap->namesOfGroups);
+		vector<string> gNamesOfGroups = groupMap->getNamesOfGroups();
+		util->setGroups(Groups, gNamesOfGroups);
+		groupMap->setNamesOfGroups(gNamesOfGroups);
 		delete util;
 		
 		if (m->control_pressed) { delete groupMap; return 0; }
@@ -229,14 +251,14 @@ int GetOtusCommand::readListGroup(){
 	try {
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick." + label +  m->getExtension(listfile);
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + label + "." + getOutputFileNameTag("list", listfile);
 		
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		
 		string GroupOutputDir = outputDir;
 		if (outputDir == "") {  GroupOutputDir += m->hasPath(groupfile);  }
-		string outputGroupFileName = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick." + label  + m->getExtension(groupfile);
+		string outputGroupFileName = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + label + "." + getOutputFileNameTag("group", groupfile);
 		
 		ofstream outGroup;
 		m->openOutputFile(outputGroupFileName, outGroup);
@@ -398,29 +420,5 @@ int GetOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream
 	}
 }
 //**********************************************************************************************************************
-void GetOtusCommand::readAccnos(){
-	try {
-		Groups.clear();
-		
-		ifstream in;
-		m->openInputFile(accnosfile, in);
-		string name;
-		
-		while(!in.eof()){
-			in >> name;
-			
-			Groups.push_back(name);
-			
-			m->gobble(in);
-		}
-		in.close();		
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "GetOtusCommand", "readAccnos");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************