X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=getgroupcommand.cpp;h=ab3ccfa36f3f2d4e6a7e1f5af6a38434640f3105;hb=03acfa01ede71b107817966fcf27cd728038b3c9;hp=4d439592127e53ff8b61fc465ef5e27db238e49e;hpb=825512fb96e5bb00e08665396d9fa6a8c4da5a68;p=mothur.git

diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index 4d43959..ab3ccfa 100644
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -9,28 +9,119 @@
 
 #include "getgroupcommand.h"
 
-
-GetgroupCommand::GetgroupCommand(){
+//**********************************************************************************************************************
+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; calledHelp = true; 
+		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 {
 		globaldata = GlobalData::getInstance();
+		abort = false; calledHelp = false;   
 		
-		//open shared file
-		sharedfile = globaldata->getSharedFile();
-		openInputFile(sharedfile, in);
+		//allow user to run help
+		if(option == "help") { help(); abort = true; calledHelp = true; }
+		
+		else {
+			//valid paramters for this command
+			string Array[] =  {"outputdir","inputdir"};
+			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			
+			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;  }
+			}
+			
+			//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 = "";		}
+			
+			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();
+				m->openInputFile(sharedfile, in);
 		
-		//open output file
-		outputFile = getRootName(globaldata->inputFileName) + "bootGroups";
-		openOutputFile(outputFile, out);
+				//open output file
+				if (outputDir == "") { outputDir += m->hasPath(sharedfile); }
+				outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "bootGroups";
+				m->openOutputFile(outputFile, out);
+
+			}
+		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the GetgroupCommand class Function GetgroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the GetgroupCommand class function GetgroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+
+void GetgroupCommand::help(){
+	try {
+		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) {
+		m->errorOut(e, "GetgroupCommand", "help");
 		exit(1);
-	}	
-			
+	}
 }
 
 //**********************************************************************************************************************
@@ -42,6 +133,9 @@ GetgroupCommand::~GetgroupCommand(){
 
 int GetgroupCommand::execute(){
 	try {
+	
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
+	
 		int num, inputData, count;
 		count = 0;  
 		string holdLabel, nextLabel, groupN, label;
@@ -51,7 +145,7 @@ int GetgroupCommand::execute(){
 		holdLabel = label;
 		
 		//output first group
-		cout << groupN << endl;
+		m->mothurOut(groupN); m->mothurOutEndLine();
 		out << groupN << '\t' << groupN << endl;	
 			
 		//get rest of line
@@ -59,15 +153,19 @@ 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++;
 			
 			//output next group
-			cout << groupN << endl;
+			m->mothurOut(groupN); m->mothurOutEndLine();
 			out << groupN << '\t' << groupN << endl;				
 			
 			//fill vector.  
@@ -78,18 +176,23 @@ int GetgroupCommand::execute(){
 			if (in.eof() != true) { in >> nextLabel; }
 		}
 		
+		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();	outputNames.push_back(outputFile); outputTypes["bootgroup"].push_back(outputFile);
+		m->mothurOutEndLine();
+		
 		return 0;	
 	}
 
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the GetgroupCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "GetgroupCommand", "execute");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the GetgroupCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }