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

[mothur.git] / secondarystructurecommand.cpp

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index 36e0f609ca67bd3cd37e7c0d33a98e88cee65e6f..c9002cab4a458c1ef9fbb3a2acb85706e01513dc 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -25,7 +25,7 @@ vector<string> AlignCheckCommand::getValidParameters(){
 //**********************************************************************************************************************
 AlignCheckCommand::AlignCheckCommand(){        
        try {
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["aligncheck"] = tempOutNames;
        }
@@ -61,11 +61,11 @@ vector<string> AlignCheckCommand::getRequiredFiles(){
 
 AlignCheckCommand::AlignCheckCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                haderror = 0;
                        
                //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
@@ -154,7 +154,7 @@ void AlignCheckCommand::help(){
 int AlignCheckCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //get secondary structure info.
                readMap();