working on anosim command

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 3711a1d52c796006a354e3a341e4ba250fd8cf20..3d667227ae2219347f2523ee1ff8286988299423 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -30,8 +30,7 @@ vector<string> DistanceCommand::getValidParameters(){
 //**********************************************************************************************************************
 DistanceCommand::DistanceCommand(){    
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["phylip"] = tempOutNames;
                outputTypes["column"] = tempOutNames;
@@ -67,11 +66,11 @@ vector<string> DistanceCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 DistanceCommand::DistanceCommand(string option) {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                Estimators.clear();
                                
                //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
@@ -242,7 +241,7 @@ void DistanceCommand::help(){
 int DistanceCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                int startTime = time(NULL);
                
@@ -1151,6 +1150,8 @@ bool DistanceCommand::sanityCheck() {
                        remove(outputFile.c_str()); //temp file is bad because file mismatch above
                }
                
+               return good;
+               
        }
        catch(exception& e) {
                m->errorOut(e, "DistanceCommand", "sanityCheck");