X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removeotuscommand.cpp;h=16fd8dce8bab96b030a57effd81d218e122628a5;hp=25ed99eacbbd3c6dcbcad18daf5fef44ec13b746;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=55386dddad84cc1140d736cabaf4dd0ae16f2e01

diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp
index 25ed99e..16fd8dc 100644
--- a/removeotuscommand.cpp
+++ b/removeotuscommand.cpp
@@ -14,13 +14,13 @@
 //**********************************************************************************************************************
 vector<string> RemoveOtusCommand::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);		}
@@ -52,7 +52,22 @@ string RemoveOtusCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string RemoveOtusCommand::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, "RemoveOtusCommand", "getOutputPattern");
+        exit(1);
+    }
+}
 ///**********************************************************************************************************************
 RemoveOtusCommand::RemoveOtusCommand(){	
 	try {
@@ -182,7 +197,7 @@ int RemoveOtusCommand::execute(){
 		groupMap->readMap();
 		
 		//get groups you want to remove
-		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
@@ -230,14 +245,20 @@ int RemoveOtusCommand::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);
@@ -407,30 +428,6 @@ int RemoveOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstr
 	}
 }
 //**********************************************************************************************************************
-void RemoveOtusCommand::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, "RemoveOtusCommand", "readAccnos");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************