X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getgroupcommand.cpp;h=529ed934d5b194d1a1d82869c44053ca4f7bbaf2;hp=8dae3f30092d0ae94e8b709119e933252f946f4a;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc

diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index 8dae3f3..529ed93 100644
--- 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);
 	}
 }
+//**********************************************************************************************************************