X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getotuscommand.cpp;h=335ebc4506ca99ac3a0e3dc9a2d068b0f1c41cd7;hp=b94b42a8a37038d188bf19a430a7ee8951f2f86c;hb=615301e57c25e241356a9c2380648d117709458d;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607

diff --git a/getotuscommand.cpp b/getotuscommand.cpp
index b94b42a..335ebc4 100644
--- a/getotuscommand.cpp
+++ b/getotuscommand.cpp
@@ -15,13 +15,13 @@
 //**********************************************************************************************************************
 vector<string> GetOtusCommand::setParameters(){	
 	try {
-		CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
-		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
-		CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
-		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-		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 pgroup("group", "InputTypes", "", "", "none", "none", "none","group",false,true, true); parameters.push_back(pgroup);
+		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","list",false,true, true); parameters.push_back(plist);
+		CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+		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);		}
@@ -53,7 +53,22 @@ string GetOtusCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string GetOtusCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "group")       {   pattern = "[filename],[tag],pick,[extension]";    }
+        else if (type == "list")        {   pattern = "[filename],[tag],pick,[extension]";    }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "GetOtusCommand", "getOutputPattern");
+        exit(1);
+    }
+}
 //**********************************************************************************************************************
 GetOtusCommand::GetOtusCommand(){	
 	try {
@@ -182,12 +197,14 @@ 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 +246,20 @@ 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);
+        map<string, string> variables; 
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+        variables["[tag]"] = label;
+        variables["[extension]"] = m->getExtension(listfile);
+		string outputFileName = getOutputFileName("list", variables);
 		
 		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);
+        variables["[filename]"] = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile));
+        variables["[extension]"] = m->getExtension(groupfile);
+		string outputGroupFileName = getOutputFileName("group", variables);
 		
 		ofstream outGroup;
 		m->openOutputFile(outputGroupFileName, outGroup);
@@ -398,29 +421,5 @@ 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);
-	}
-}
-//**********************************************************************************************************************