worked on trim.seqs - added in the groupfiles for allfiles=t, cleaned up the outputNa...

[mothur.git] / listseqscommand.cpp

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index c8c82971a1cf53d0eb2ba4834c281cc310d8984b..406085728838262b79100a70133600639e6c47a2 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -26,7 +26,7 @@ vector<string> ListSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 ListSeqsCommand::ListSeqsCommand(){    
        try {
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["accnos"] = tempOutNames;
        }
@@ -62,10 +62,10 @@ vector<string> ListSeqsCommand::getRequiredFiles(){
 
 ListSeqsCommand::ListSeqsCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -205,7 +205,7 @@ void ListSeqsCommand::help(){
 int ListSeqsCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //read functions fill names vector
                if (fastafile != "")            {       inputFileName = fastafile;      readFasta();    }
@@ -259,7 +259,7 @@ int ListSeqsCommand::readFasta(){
                ifstream in;
                m->openInputFile(fastafile, in);
                string name;
-       
+               
                while(!in.eof()){
                        
                        if (m->control_pressed) { in.close(); return 0; }
@@ -366,7 +366,7 @@ int ListSeqsCommand::readGroup(){
                        
                        if (m->control_pressed) { in.close(); return 0; }
                        
-                       in >> name;                             //read from first column
+                       in >> name;     m->gobble(in);                  //read from first column
                        in >> group;                    //read from second column
                        
                        names.push_back(name);
@@ -444,6 +444,7 @@ int ListSeqsCommand::readTax(){
                        names.push_back(firstCol);
                        
                        m->gobble(in);
+                       
                }
                in.close();