working on pam

[mothur.git] / getgroupcommand.cpp

diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index 8dae3f30092d0ae94e8b709119e933252f946f4a..529ed934d5b194d1a1d82869c44053ca4f7bbaf2 100644 (file)
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -13,9 +13,9 @@
 //**********************************************************************************************************************
 vector<string> GetgroupCommand::setParameters(){       
        try {
-               CommandParameter pshared("shared", "InputTypes", "", "current", "none", "none", "none",false,true); parameters.push_back(pshared);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pshared("shared", "InputTypes", "", "current", "none", "none", "none","",false,true, true); parameters.push_back(pshared);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -31,7 +31,6 @@ string GetgroupCommand::getHelpString(){
        try {
                string helpString = "";
                helpString += "The get.group command parameter is shared and it's required if you have no valid current file.\n";
-               //m->mothurOut("The get.group command outputs a .bootGroups file to you can use in addition to the tree file generated by the bootstrap.shared command to run the consensus command.\n");
                helpString += "You may not use any parameters with the get.group command.\n";
                helpString += "The get.group command should be in the following format: \n";
                helpString += "get.group()\n";
@@ -43,13 +42,12 @@ string GetgroupCommand::getHelpString(){
                exit(1);
        }
 }
+
 //**********************************************************************************************************************
 GetgroupCommand::GetgroupCommand(){    
        try {
                abort = true; calledHelp = true; 
                setParameters();
-               vector<string> tempOutNames;
-               outputTypes["bootgroup"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
@@ -78,10 +76,6 @@ GetgroupCommand::GetgroupCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
-                       //initialize outputTypes
-                       vector<string> tempOutNames;
-                       outputTypes["bootgroup"] = tempOutNames;
-                       
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
                        if (inputDir == "not found"){   inputDir = "";          }
@@ -122,27 +116,17 @@ int GetgroupCommand::execute(){
        try {
        
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
-                       
-               //open output file
-               outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "bootGroups";
-               m->openOutputFile(outputFile, out);
-               
+                                       
                InputData input(sharedfile, "sharedfile");
                vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
                
                for (int i = 0; i < lookup.size(); i++) {
-                       out << lookup[i]->getGroup() << '\t' << lookup[i]->getGroup() << endl;
                        m->mothurOut(lookup[i]->getGroup()); m->mothurOutEndLine();
                        delete lookup[i];
                }
-               
-               out.close();
-               
-               if (m->control_pressed) {  m->mothurRemove(outputFile);   return 0; }
-               
+                       
                m->mothurOutEndLine();
-               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-               m->mothurOut(outputFile); m->mothurOutEndLine();        outputNames.push_back(outputFile); outputTypes["bootgroup"].push_back(outputFile);
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                m->mothurOutEndLine();
                
                return 0;       
@@ -153,5 +137,6 @@ int GetgroupCommand::execute(){
                exit(1);
        }
 }
+//**********************************************************************************************************************