X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getgroupcommand.cpp;h=529ed934d5b194d1a1d82869c44053ca4f7bbaf2;hp=4d439592127e53ff8b61fc465ef5e27db238e49e;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=825512fb96e5bb00e08665396d9fa6a8c4da5a68

diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index 4d43959..529ed93 100644
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -8,88 +8,135 @@
  */
 
 #include "getgroupcommand.h"
+#include "inputdata.h"
 
-
-GetgroupCommand::GetgroupCommand(){
+//**********************************************************************************************************************
+vector<string> GetgroupCommand::setParameters(){	
 	try {
-		globaldata = GlobalData::getInstance();
-		
-		//open shared file
-		sharedfile = globaldata->getSharedFile();
-		openInputFile(sharedfile, in);
+		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);
 		
-		//open output file
-		outputFile = getRootName(globaldata->inputFileName) + "bootGroups";
-		openOutputFile(outputFile, out);
+		vector<string> myArray;
+		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
+		return myArray;
 	}
 	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", "setParameters");
 		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";
+}
+//**********************************************************************************************************************
+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";
+		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";
+		helpString += "Example get.group().\n";
+		return helpString;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetgroupCommand", "getHelpString");
 		exit(1);
-	}	
-			
+	}
 }
 
 //**********************************************************************************************************************
-
-GetgroupCommand::~GetgroupCommand(){
+GetgroupCommand::GetgroupCommand(){	
+	try {
+		abort = true; calledHelp = true; 
+		setParameters();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
+		exit(1);
+	}
 }
-
 //**********************************************************************************************************************
-
-int GetgroupCommand::execute(){
+GetgroupCommand::GetgroupCommand(string option)  {
 	try {
-		int num, inputData, count;
-		count = 0;  
-		string holdLabel, nextLabel, groupN, label;
+		abort = false; calledHelp = false;   
 		
-		//read in first row since you know there is at least 1 group.
-		in >> label >> groupN >> num;
-		holdLabel = label;
+		//allow user to run help
+		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
-		//output first group
-		cout << groupN << endl;
-		out << groupN << '\t' << groupN << endl;	
+		else {
+			vector<string> myArray = setParameters();
 			
-		//get rest of line
-		for(int i=0;i<num;i++){
-			in >> inputData;
-		}
-		
-		if (in.eof() != true) { in >> nextLabel; }
-		
-		//read the rest of the groups info in
-		while ((nextLabel == holdLabel) && (in.eof() != true)) {
-			in >> groupN >> num;
-			count++;
+			OptionParser parser(option);
+			map<string,string> parameters = parser.getParameters();
+			map<string,string>::iterator it;
 			
-			//output next group
-			cout << groupN << endl;
-			out << groupN << '\t' << groupN << endl;				
+			ValidParameters validParameter;
+			//check to make sure all parameters are valid for command
+			for (it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+			}
 			
-			//fill vector.  
-			for(int i=0;i<num;i++){
-				in >> inputData;
+			//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 = "";		}
+			else {
+				string path;
+				it = parameters.find("shared");
+				//user has given a template file
+				if(it != parameters.end()){ 
+					path = m->hasPath(it->second);
+					//if the user has not given a path then, add inputdir. else leave path alone.
+					if (path == "") {	parameters["shared"] = inputDir + it->second;		}
+				}
 			}
 			
-			if (in.eof() != true) { in >> nextLabel; }
+			//get shared file
+			sharedfile = validParameter.validFile(parameters, "shared", true);
+			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
+			else if (sharedfile == "not found") { 
+				//if there is a current shared file, use it
+				sharedfile = m->getSharedFile(); 
+				if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+				else { 	m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
+			}else { m->setSharedFile(sharedfile); }
+			
+			
+			//if the user changes the output directory command factory will send this info to us in the output parameter 
+			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = m->hasPath(sharedfile);		}
 		}
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+
+int GetgroupCommand::execute(){
+	try {
+	
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
+					
+		InputData input(sharedfile, "sharedfile");
+		vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
+		
+		for (int i = 0; i < lookup.size(); i++) {
+			m->mothurOut(lookup[i]->getGroup()); m->mothurOutEndLine();
+			delete lookup[i];
+		}
+			
+		m->mothurOutEndLine();
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+		m->mothurOutEndLine();
 		
-		out.close();
 		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);
-	}	
 }
+//**********************************************************************************************************************