X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getcurrentcommand.cpp;h=d74786ce1eaaa8767164a0fbd670d06843388b44;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=bd7539a25a30a2c972dfa9157a1b25ceb3349c33;hpb=348de0f8b17d84ede77081dcf67bd6ef43496677;p=mothur.git

diff --git a/getcurrentcommand.cpp b/getcurrentcommand.cpp
index bd7539a..d74786c 100644
--- a/getcurrentcommand.cpp
+++ b/getcurrentcommand.cpp
@@ -9,48 +9,46 @@
 
 #include "getcurrentcommand.h"
 
-
 //**********************************************************************************************************************
-vector<string> GetCurrentCommand::getValidParameters(){	
+vector<string> GetCurrentCommand::setParameters(){	
 	try {
-		string Array[] =  {"outputdir","inputdir","clear"};
-		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		CommandParameter pclear("clear", "String", "", "", "", "", "","",false,false); parameters.push_back(pclear);
+		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);		}
 		return myArray;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "GetCurrentCommand", "getValidParameters");
+		m->errorOut(e, "GetCurrentCommand", "setParameters");
 		exit(1);
 	}
 }
 //**********************************************************************************************************************
-GetCurrentCommand::GetCurrentCommand(){	
+string GetCurrentCommand::getHelpString(){	
 	try {
-		abort = true; calledHelp = true; 
+		string helpString = "";
+		helpString += "The get.current command outputs the current files saved by mothur.\n";
+		helpString += "The get.current command has one parameter: clear.\n";
+		helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
+		helpString += "The get.current command should be in the following format: \n";
+		helpString += "get.current() or get.current(clear=fasta-name-accnos)\n";
+		return helpString;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "GetCurrentCommand", "GetCurrentCommand");
+		m->errorOut(e, "GetCurrentCommand", "getHelpString");
 		exit(1);
 	}
 }
 //**********************************************************************************************************************
-vector<string> GetCurrentCommand::getRequiredParameters(){	
-	try {
-		vector<string> myArray;
-		return myArray;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "GetCurrentCommand", "getRequiredParameters");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-vector<string> GetCurrentCommand::getRequiredFiles(){	
+GetCurrentCommand::GetCurrentCommand(){	
 	try {
-		vector<string> myArray;
-		return myArray;
+		abort = true; calledHelp = true;
+		setParameters();
 	}
 	catch(exception& e) {
-		m->errorOut(e, "GetCurrentCommand", "getRequiredFiles");
+		m->errorOut(e, "GetCurrentCommand", "GetCurrentCommand");
 		exit(1);
 	}
 }
@@ -61,11 +59,10 @@ GetCurrentCommand::GetCurrentCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
-			//valid paramters for this command
-			string Array[] =  {"outputdir","inputdir","clear"};
-			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			vector<string> myArray = setParameters();
 			
 			OptionParser parser(option);
 			map<string,string> parameters = parser.getParameters();
@@ -89,25 +86,6 @@ GetCurrentCommand::GetCurrentCommand(string option)  {
 }
 //**********************************************************************************************************************
 
-void GetCurrentCommand::help(){
-	try {
-		m->mothurOut("The get.current command outputs the current files saved by mothur.\n");
-		m->mothurOut("The get.current command has one parameter: clear.\n");
-		m->mothurOut("The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n");
-		m->mothurOut("The get.current command should be in the following format: \n");
-		m->mothurOut("get.current() or get.current(clear=fasta-name-accnos)\n");
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "GetCurrentCommand", "help");
-		exit(1);
-	}
-}
-
-//**********************************************************************************************************************
-GetCurrentCommand::~GetCurrentCommand(){}
-//**********************************************************************************************************************
-
 int GetCurrentCommand::execute(){
 	try {
 		
@@ -157,7 +135,17 @@ int GetCurrentCommand::execute(){
 				}else if (types[i] == "accnos") {
 					m->setAccnosFile("");
 				}else if (types[i] == "taxonomy") {
-						m->setTaxonomyFile("");
+					m->setTaxonomyFile("");
+				}else if (types[i] == "flow") {
+					m->setFlowFile("");
+                }else if (types[i] == "biom") {
+					m->setBiomFile("");
+                }else if (types[i] == "count") {
+					m->setCountTableFile("");
+                }else if (types[i] == "summary") {
+					m->setSummaryFile("");
+				}else if (types[i] == "processors") {
+					m->setProcessors("1");
 				}else if (types[i] == "all") {
 					m->clearCurrentFiles();
 				}else {
@@ -166,8 +154,10 @@ int GetCurrentCommand::execute(){
 			}
 		}
 		
-		m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
-		m->printCurrentFiles();
+		if (m->hasCurrentFiles()) {
+			m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
+			m->printCurrentFiles();
+		}
 		
 		return 0;	
 	}