X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=setdircommand.cpp;h=043c0acc8ec524c1b510da28c36c149d300f215a;hb=11c115c802602be50e106aae56969e15d2c49a62;hp=001ae235dd11ff0f015ebeba76de10ee3bcb2dbf;hpb=515c3398ea27e2105f616fc5662b2a7ceb486aa0;p=mothur.git

diff --git a/setdircommand.cpp b/setdircommand.cpp
index 001ae23..043c0ac 100644
--- a/setdircommand.cpp
+++ b/setdircommand.cpp
@@ -60,8 +60,11 @@ void SetDirectoryCommand::help(){
 		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 same directory as the mothur.exe you may enter: input=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");
@@ -86,7 +89,14 @@ int SetDirectoryCommand::execute(){
 		
 		//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)
@@ -112,7 +122,14 @@ int SetDirectoryCommand::execute(){
 		
 		//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)
@@ -148,6 +165,13 @@ int SetDirectoryCommand::execute(){
 				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);