fixed catchall "clunky" names

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 9cc99732e715d40f0ef06743bb85870a147f7036..78c39f7c1c16e5bce1c4d0475ad06839ebe0758b 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -38,8 +38,7 @@ inline bool compareGroup(repStruct left, repStruct right){
 //**********************************************************************************************************************
 GetOTURepCommand::GetOTURepCommand(){  
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
                outputTypes["name"] = tempOutNames;
@@ -88,13 +87,13 @@ vector<string> GetOTURepCommand::getRequiredFiles(){
 GetOTURepCommand::GetOTURepCommand(string option)  {
        try{
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                allLines = 1;
                labels.clear();
                                
                //allow user to run help
                if (option == "help") { 
-                       help(); abort = true;
+                       help(); abort = true; calledHelp = true;
                } else {
                        //valid paramters for this command
                        string Array[] =  {"fasta","list","label","name","weighted", "group", "sorted", "phylip","column","large","cutoff","precision","groups","outputdir","inputdir"};
@@ -299,7 +298,7 @@ GetOTURepCommand::~GetOTURepCommand(){}
 int GetOTURepCommand::execute(){
        try {
        
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                int error;
                
                if (!large) {
@@ -544,6 +543,18 @@ int GetOTURepCommand::execute(){
                
                if (m->control_pressed) {  return 0; }
                
+               //set fasta file as new current fastafile - use first one??
+               string current = "";
+               itTypes = outputTypes.find("fasta");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+               }
+               
+               itTypes = outputTypes.find("name");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+               }
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }