X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=setdircommand.cpp;h=043c0acc8ec524c1b510da28c36c149d300f215a;hb=11c115c802602be50e106aae56969e15d2c49a62;hp=a23b61dbcaf4c6f78705a96df5d80f3d4843cfa8;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/setdircommand.cpp b/setdircommand.cpp
index a23b61d..043c0ac 100644
--- a/setdircommand.cpp
+++ b/setdircommand.cpp
@@ -11,7 +11,7 @@
 
 //**********************************************************************************************************************
 
-SetDirectoryCommand::SetDirectoryCommand(string option){
+SetDirectoryCommand::SetDirectoryCommand(string option)  {
 	try {
 		abort = false;
 		
@@ -20,7 +20,7 @@ SetDirectoryCommand::SetDirectoryCommand(string option){
 		
 		else {
 			//valid paramters for this command
-			string Array[] =  {"output","input","outputdir","inputdir"};
+			string Array[] =  {"output","input","tempdefault","outputdir","inputdir"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
 			OptionParser parser(option);
@@ -37,14 +37,17 @@ SetDirectoryCommand::SetDirectoryCommand(string option){
 			
 			input = validParameter.validFile(parameters, "input", false);			
 			if (input == "not found") {  input = "";  }
+			
+			tempdefault = validParameter.validFile(parameters, "tempdefault", false);			
+			if (tempdefault == "not found") {  tempdefault = "";  }
 				
-			if ((input == "") && (output == "")) {	
-				mothurOut("You must provide either an input or output for the set.outdir command."); mothurOutEndLine(); abort = true;
+			if ((input == "") && (output == "") && (tempdefault == "")) {	
+				m->mothurOut("You must provide either an input, output or tempdefault for the set.outdir command."); m->mothurOutEndLine(); abort = true;
 			}
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
+		m->errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
 		exit(1);
 	}
 }
@@ -52,17 +55,22 @@ SetDirectoryCommand::SetDirectoryCommand(string option){
 
 void SetDirectoryCommand::help(){
 	try {
-		mothurOut("The set.dir command can be used to direct the output files generated by mothur to a specific place, the directory must exist.\n");
-		mothurOut("The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n");
-		mothurOut("The set.dir command parameter is output and is required.\n");
-		mothurOut("To return the output to the same directory as the input files you may enter: output=clear.\n");
-		mothurOut("To return the input to the same directory as the mothur.exe you may enter: input=clear.\n");
-		mothurOut("The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory).\n");
-		mothurOut("Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n");
-		mothurOut("Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n\n");
+		m->mothurOut("The set.dir command can be used to direct the output files generated by mothur to a specific place, the directory must exist.\n");
+		m->mothurOut("The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n");
+		m->mothurOut("The set.dir command can also be used to override or set the default location mothur will look for files if it is unable to find them, the directory must exist.\n");
+		m->mothurOut("The set.dir command parameters are input, output and tempdefault and one is required.\n");
+		m->mothurOut("To return the output to the same directory as the input files you may enter: output=clear.\n");
+		m->mothurOut("To return the input to the current working directory you may enter: input=clear.\n");
+		m->mothurOut("To set the output to the directory where mothur.exe is located you may enter: output=default.\n");
+		m->mothurOut("To set the input to the directory where mothur.exe is located you may enter: input=default.\n");
+		m->mothurOut("To return the tempdefault to the default you provided at compile time you may enter: tempdefault=clear.\n");
+		m->mothurOut("To set the tempdefault to the directory where mothur.exe is located you may enter: tempdefault=default.\n");
+		m->mothurOut("The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory, tempdefault=yourTempDefault).\n");
+		m->mothurOut("Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n");
+		m->mothurOut("Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n\n");
 	}
 	catch(exception& e) {
-		errorOut(e, "SetDirectoryCommand", "help");
+		m->errorOut(e, "SetDirectoryCommand", "help");
 		exit(1);
 	}
 }
@@ -79,10 +87,16 @@ int SetDirectoryCommand::execute(){
 		
 		commandFactory = CommandFactory::getInstance();
 		
-		
 		//redirect output
 		if ((output == "clear") || (output == "")) {  output = "";  commandFactory->setOutputDirectory(output);  }
-		else {
+		else if (output == "default") { 
+			GlobalData* globaldata = GlobalData::getInstance();
+			string exepath = globaldata->argv;
+			output = exepath.substr(0, (exepath.find_last_of('m')));
+			
+			m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();  
+			commandFactory->setOutputDirectory(output);
+		}else {
 			//add / to name if needed
 			string lastChar = output.substr(output.length()-1);
 			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
@@ -97,17 +111,25 @@ int SetDirectoryCommand::execute(){
 			ofstream out;
 			out.open(outTemp.c_str(), ios::trunc);
 			if(!out) {
-				mothurOut(output + " directory does not exist or is not writable."); mothurOutEndLine(); 
+				m->mothurOut(output + " directory does not exist or is not writable."); m->mothurOutEndLine(); 
 			}else{
+				out.close();
 				remove(outTemp.c_str());
-				mothurOut("Changing output directory to " + output); mothurOutEndLine();  
+				m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();  
 				commandFactory->setOutputDirectory(output);
 			}
 		}
 		
 		//redirect input
 		if ((input == "clear") || (input == "")) {  input = "";  commandFactory->setInputDirectory(input);  }
-		else {
+		else if (input == "default") { 
+			GlobalData* globaldata = GlobalData::getInstance();
+			string exepath = globaldata->argv;
+			input = exepath.substr(0, (exepath.find_last_of('m')));
+			
+			m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();  
+			commandFactory->setInputDirectory(input);
+		}else {
 			//add / to name if needed
 			string lastChar = input.substr(input.length()-1);
 			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
@@ -122,18 +144,51 @@ int SetDirectoryCommand::execute(){
 			ofstream in;
 			in.open(inTemp.c_str(), ios::trunc);
 			if(!in) {
-				mothurOut(input + " directory does not exist or is not writable."); mothurOutEndLine(); 
+				m->mothurOut(input + " directory does not exist or is not writable."); m->mothurOutEndLine(); 
 			}else{
+				in.close();
 				remove(inTemp.c_str());
-				mothurOut("Changing input directory to " + input); mothurOutEndLine();  
+				m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();  
 				commandFactory->setInputDirectory(input); 
 			}
 		}
+		
+		//set default
+		if (tempdefault == "clear") {  
+			#ifdef MOTHUR_FILES
+				string temp = MOTHUR_FILES; 
+				m->mothurOut("Resetting default directory to " + temp); m->mothurOutEndLine();  
+				m->setDefaultPath(temp);
+			#else
+				string temp = ""; 
+				m->mothurOut("No default directory defined at compile time."); m->mothurOutEndLine();  
+				m->setDefaultPath(temp);
+			#endif
+		}else if (tempdefault == "") {  //do nothing
+		}else if (tempdefault == "default") { 
+			GlobalData* globaldata = GlobalData::getInstance();
+			string exepath = globaldata->argv;
+			tempdefault = exepath.substr(0, (exepath.find_last_of('m')));
+			
+			m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();  
+			m->setDefaultPath(tempdefault);
+		}else {
+			//add / to name if needed
+			string lastChar = tempdefault.substr(tempdefault.length()-1);
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				if (lastChar != "/") { tempdefault += "/"; }
+			#else
+				if (lastChar != "\\") { tempdefault += "\\"; }	
+			#endif
+			
+			m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();  
+			m->setDefaultPath(tempdefault);
+		}
 
 		return 0;
 	}
 	catch(exception& e) {
-		errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
+		m->errorOut(e, "SetDirectoryCommand", "execute");
 		exit(1);
 	}
 }