X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=countgroupscommand.cpp;h=ccf8988e39308fd2816f6eb0a6ff0454ab944d19;hb=078d7227da8dda9ae8620822fa32d51ec2706fc3;hp=af9993c8ef6f8ee794be8bf7b3825aa34d1a44e7;hpb=d3aed959ca3b68890eeb7b815e24210bcfeb256c;p=mothur.git

diff --git a/countgroupscommand.cpp b/countgroupscommand.cpp
index af9993c..ccf8988 100644
--- a/countgroupscommand.cpp
+++ b/countgroupscommand.cpp
@@ -34,7 +34,7 @@ vector<string> CountGroupsCommand::setParameters(){
 string CountGroupsCommand::getHelpString(){	
 	try {
 		string helpString = "";
-		helpString += "The count.groups command counts sequences from a specfic group or set of groups from the following file types: group or shared file.\n";
+		helpString += "The count.groups command counts sequences from a specific group or set of groups from the following file types: group or shared file.\n";
 		helpString += "The count.groups command parameters are accnos, group, shared and groups. You must provide a group or shared file.\n";
 		helpString += "The accnos parameter allows you to provide a file containing the list of groups.\n";
 		helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like.  You can separate group names with dashes.\n";
@@ -127,7 +127,7 @@ CountGroupsCommand::CountGroupsCommand(string option)  {
 			if (groups == "not found") { groups = ""; }
 			else {
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 			}
 			
 			sharedfile = validParameter.validFile(parameters, "shared", true);
@@ -153,7 +153,7 @@ CountGroupsCommand::CountGroupsCommand(string option)  {
 				}
 			}
 			
-			if ((accnosfile == "") && (Groups.size() == 0)) { Groups.push_back("all"); m->Groups = Groups; }
+			if ((accnosfile == "") && (Groups.size() == 0)) { Groups.push_back("all"); m->setGroups(Groups); }
 		}
 		
 	}
@@ -170,7 +170,7 @@ int CountGroupsCommand::execute(){
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//get groups you want to remove
-		if (accnosfile != "") { readAccnos(); }
+		if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); }
 		
 		if (groupfile != "") {
 			GroupMap groupMap(groupfile);
@@ -179,7 +179,8 @@ int CountGroupsCommand::execute(){
 			//make sure groups are valid
 			//takes care of user setting groupNames that are invalid or setting groups=all
 			SharedUtil util;
-			util.setGroups(Groups, groupMap.namesOfGroups);
+			vector<string> nameGroups = groupMap.getNamesOfGroups();
+			util.setGroups(Groups, nameGroups);
 			
 			for (int i = 0; i < Groups.size(); i++) {
 				m->mothurOut(Groups[i] + " contains " + toString(groupMap.getNumSeqs(Groups[i])) + "."); m->mothurOutEndLine();
@@ -207,31 +208,5 @@ int CountGroupsCommand::execute(){
 	}
 }
 //**********************************************************************************************************************
-void CountGroupsCommand::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();		
-		
-		m->Groups = Groups;
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "CountGroupsCommand", "readAccnos");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************