X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getgroupcommand.cpp;h=2847db149ac5e40defdbfdedfd9d99ae3df5d583;hb=3fd6dd6e4f19a458ac2966ee5458787e998a1bde;hp=b645517f938928c44eb5faa5871e4171c40fb800;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index b645517..2847db1 100644
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -9,6 +9,54 @@
 
 #include "getgroupcommand.h"
 
+//**********************************************************************************************************************
+vector<string> GetgroupCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetgroupCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+GetgroupCommand::GetgroupCommand(){	
+	try {
+		abort = true;
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["bootgroup"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> GetgroupCommand::getRequiredParameters(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetgroupCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> GetgroupCommand::getRequiredFiles(){	
+	try {
+		string Array[] =  {"shared"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetgroupCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 GetgroupCommand::GetgroupCommand(string option)  {
 	try {
@@ -32,6 +80,10 @@ 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 output directory command factory will send this info to us in the output parameter 
 			string outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = "";		}
 			
@@ -40,12 +92,12 @@ GetgroupCommand::GetgroupCommand(string option)  {
 			if (abort == false) {
 				//open shared file
 				sharedfile = globaldata->getSharedFile();
-				openInputFile(sharedfile, in);
+				m->openInputFile(sharedfile, in);
 		
 				//open output file
-				if (outputDir == "") { outputDir += hasPath(sharedfile); }
-				outputFile = outputDir + getRootName(getSimpleName(sharedfile)) + "bootGroups";
-				openOutputFile(outputFile, out);
+				if (outputDir == "") { outputDir += m->hasPath(sharedfile); }
+				outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "bootGroups";
+				m->openOutputFile(outputFile, out);
 
 			}
 		}
@@ -102,10 +154,14 @@ int GetgroupCommand::execute(){
 			in >> inputData;
 		}
 		
+		if (m->control_pressed) { outputTypes.clear(); in.close();  out.close(); remove(outputFile.c_str());   return 0; }
+
 		if (in.eof() != true) { in >> nextLabel; }
 		
 		//read the rest of the groups info in
 		while ((nextLabel == holdLabel) && (in.eof() != true)) {
+			if (m->control_pressed) {  outputTypes.clear(); in.close();  out.close(); remove(outputFile.c_str());   return 0; }
+			
 			in >> groupN >> num;
 			count++;
 			
@@ -124,9 +180,11 @@ int GetgroupCommand::execute(){
 		in.close();
 		out.close();
 		
+		if (m->control_pressed) {  remove(outputFile.c_str());   return 0; }
+		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-		m->mothurOut(outputFile); m->mothurOutEndLine();	
+		m->mothurOut(outputFile); m->mothurOutEndLine();	outputNames.push_back(outputFile); outputTypes["bootgroup"].push_back(outputFile);
 		m->mothurOutEndLine();
 		
 		return 0;