fixed catchall "clunky" names

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index e6ccc9b70455089d5dffc1c6f512f3e17ca1d76e..0fb9370d191440562b9e6f6e7727ed00366b160b 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -26,7 +26,7 @@ vector<string> PreClusterCommand::getValidParameters(){
 //**********************************************************************************************************************
 PreClusterCommand::PreClusterCommand(){        
        try {
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
                outputTypes["name"] = tempOutNames;
@@ -63,10 +63,10 @@ vector<string> PreClusterCommand::getRequiredFiles(){
 
 PreClusterCommand::PreClusterCommand(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
@@ -166,7 +166,7 @@ void PreClusterCommand::help(){
 int PreClusterCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                int start = time(NULL);
                
@@ -245,7 +245,19 @@ int PreClusterCommand::execute(){
                m->mothurOut(newFastaFile); m->mothurOutEndLine();      outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile);
                m->mothurOut(newNamesFile); m->mothurOutEndLine();      outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile);
                m->mothurOutEndLine();
-
+               
+               //set fasta file as new current fastafile
+               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); }
+               }
+               
                return 0;
                
        }