X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=countgroupscommand.cpp;h=ccf8988e39308fd2816f6eb0a6ff0454ab944d19;hb=ccae9eef0b44f2d63fdf4a707d0d40243aa1b990;hp=24b4214dd5600ef0f0625ba7acf0da2a8f328108;hpb=55386dddad84cc1140d736cabaf4dd0ae16f2e01;p=mothur.git

diff --git a/countgroupscommand.cpp b/countgroupscommand.cpp
index 24b4214..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";
@@ -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);
@@ -208,31 +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->setGroups(Groups);
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "CountGroupsCommand", "readAccnos");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************