minor mods to seq.error

[mothur.git] / parselistscommand.cpp

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index 6e4082e0c139b76435aa073cd1f0c7013b85dca3..e2c3e011c028a71bf79585519a7bbd9e25439c74 100644 (file)
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -37,7 +37,7 @@ string ParseListCommand::getHelpString(){
                helpString += "The label parameter is used to read specific labels in your input you want to use.\n";
                helpString += "The parse.list command should be used in the following format: parse.list(list=yourListFile, group=yourGroupFile, label=yourLabels).\n";
                helpString += "Example: parse.list(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03).\n";
-               helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -66,6 +66,7 @@ ParseListCommand::ParseListCommand(string option)  {
                        
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -122,7 +123,7 @@ ParseListCommand::ParseListCommand(string option)  {
                                        abort = true;
                                                
                                }
-                       }       
+                       }else { m->setListFile(listfile); }     
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
@@ -136,6 +137,7 @@ ParseListCommand::ParseListCommand(string option)  {
                                        if (error == 1) { abort = true; }
                                }else { m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine();  abort = true; } 
                        }else {  
+                               m->setGroupFile(groupfile);
                                groupMap = new GroupMap(groupfile);
                                
                                int error = groupMap->readMap();