X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getgroupcommand.cpp;h=cf47661bb6a8084740262d8a6b4b157181a2b0ab;hb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;hp=9014031d5a58556493b712282fbf4bfc5535d5e2;hpb=92dde9a6d6c638fcbbd5dbaa5c79167564f90e49;p=mothur.git

diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index 9014031..cf47661 100644
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -10,7 +10,7 @@
 #include "getgroupcommand.h"
 
 //**********************************************************************************************************************
-GetgroupCommand::GetgroupCommand(string option){
+GetgroupCommand::GetgroupCommand(string option)  {
 	try {
 		globaldata = GlobalData::getInstance();
 		abort = false;
@@ -19,24 +19,39 @@ GetgroupCommand::GetgroupCommand(string option){
 		if(option == "help") { help(); abort = true; }
 		
 		else {
-			if (option != "") { mothurOut("There are no valid parameters for the get.group command."); mothurOutEndLine(); abort = true; }
+			//valid paramters for this command
+			string Array[] =  {"outputdir","inputdir"};
+			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
-			if ((globaldata->getSharedFile() == "")) { mothurOut("You must use the read.otu command to read a groupfile or a sharedfile before you can use the get.group command."); mothurOutEndLine(); abort = true; }
+			OptionParser parser(option);
+			map<string,string> parameters = parser.getParameters();
+			
+			ValidParameters validParameter;
+			//check to make sure all parameters are valid for command
+			for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+			}
+			
+			//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 = "";		}
+			
+			if ((globaldata->getSharedFile() == "")) { m->mothurOut("You must use the read.otu command to read a groupfile or a sharedfile before you can use the get.group command."); m->mothurOutEndLine(); abort = true; }
 				
 			if (abort == false) {
 				//open shared file
 				sharedfile = globaldata->getSharedFile();
-				openInputFile(sharedfile, in);
+				m->openInputFile(sharedfile, in);
 		
 				//open output file
-				outputFile = getRootName(sharedfile) + "bootGroups";
-				openOutputFile(outputFile, out);
+				if (outputDir == "") { outputDir += m->hasPath(sharedfile); }
+				outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "bootGroups";
+				m->openOutputFile(outputFile, out);
 
 			}
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "GetgroupCommand", "GetgroupCommand");
+		m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
 		exit(1);
 	}
 }
@@ -44,16 +59,16 @@ GetgroupCommand::GetgroupCommand(string option){
 
 void GetgroupCommand::help(){
 	try {
-		mothurOut("The get.group command can only be executed after a successful read.otu command.\n");
-		//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");
-		mothurOut("You may not use any parameters with the get.group command.\n");
-		mothurOut("The get.group command should be in the following format: \n");
-		mothurOut("get.group()\n");
-		mothurOut("Example get.group().\n");
+		m->mothurOut("The get.group command can only be executed after a successful read.otu command.\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");
+		m->mothurOut("You may not use any parameters with the get.group command.\n");
+		m->mothurOut("The get.group command should be in the following format: \n");
+		m->mothurOut("get.group()\n");
+		m->mothurOut("Example get.group().\n");
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "GetgroupCommand", "help");
+		m->errorOut(e, "GetgroupCommand", "help");
 		exit(1);
 	}
 }
@@ -79,7 +94,7 @@ int GetgroupCommand::execute(){
 		holdLabel = label;
 		
 		//output first group
-		mothurOut(groupN); mothurOutEndLine();
+		m->mothurOut(groupN); m->mothurOutEndLine();
 		out << groupN << '\t' << groupN << endl;	
 			
 		//get rest of line
@@ -87,15 +102,19 @@ int GetgroupCommand::execute(){
 			in >> inputData;
 		}
 		
+		if (m->control_pressed) { 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) { in.close();  out.close(); remove(outputFile.c_str());   return 0; }
+			
 			in >> groupN >> num;
 			count++;
 			
 			//output next group
-			mothurOut(groupN); mothurOutEndLine();
+			m->mothurOut(groupN); m->mothurOutEndLine();
 			out << groupN << '\t' << groupN << endl;				
 			
 			//fill vector.  
@@ -108,11 +127,19 @@ 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->mothurOutEndLine();
+		
 		return 0;	
 	}
 
 	catch(exception& e) {
-		errorOut(e, "GetgroupCommand", "execute");
+		m->errorOut(e, "GetgroupCommand", "execute");
 		exit(1);
 	}
 }