X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=setdircommand.cpp;h=67a1f59f8388dbfec55ae7b552f02640b5d6b93f;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=16e93b5e4f5e8feeb864693a3d4a96ac75b9ed61;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/setdircommand.cpp b/setdircommand.cpp
index 16e93b5..67a1f59 100644
--- a/setdircommand.cpp
+++ b/setdircommand.cpp
@@ -43,7 +43,7 @@ string SetDirectoryCommand::getHelpString(){
 		helpString += "To set the tempdefault to the directory where mothur.exe is located you may enter: tempdefault=default.\n";
 		helpString += "The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory, tempdefault=yourTempDefault).\n";
 		helpString += "Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n";
-		helpString += "Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -59,11 +59,10 @@ SetDirectoryCommand::SetDirectoryCommand(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[] =  {"output","input","tempdefault","outputdir","inputdir"};
-			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			vector<string> myArray = setParameters();
 			
 			OptionParser parser(option);
 			map<string, string> parameters = parser.getParameters();
@@ -102,13 +101,23 @@ int SetDirectoryCommand::execute(){
 		
 		commandFactory = CommandFactory::getInstance();
 		
+		string tag = "";
+#ifdef USE_MPI
+		int pid; 
+		MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+		
+		tag = toString(pid);
+#endif
+		
+		m->mothurOut("Mothur's directories:"); m->mothurOutEndLine();
+		
 		//redirect output
 		if ((output == "clear") || (output == "")) {  output = "";  commandFactory->setOutputDirectory(output);  }
 		else if (output == "default") { 
 			string exepath = m->argv;
 			output = exepath.substr(0, (exepath.find_last_of('m')));
 			
-			m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();  
+			m->mothurOut("outputDir=" + output); m->mothurOutEndLine();  
 			commandFactory->setOutputDirectory(output);
 		}else {
 			//add / to name if needed
@@ -121,15 +130,15 @@ int SetDirectoryCommand::execute(){
 			
 			//test to make sure directory exists
 			output = m->getFullPathName(output);
-			string outTemp = output + "temp";
+			string outTemp = output + tag + "temp";
 			ofstream out;
 			out.open(outTemp.c_str(), ios::trunc);
 			if(!out) {
 				m->mothurOut(output + " directory does not exist or is not writable."); m->mothurOutEndLine(); 
 			}else{
 				out.close();
-				remove(outTemp.c_str());
-				m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();  
+				m->mothurRemove(outTemp);
+				m->mothurOut("outputDir=" + output); m->mothurOutEndLine();  
 				commandFactory->setOutputDirectory(output);
 			}
 		}
@@ -140,7 +149,7 @@ int SetDirectoryCommand::execute(){
 			string exepath = m->argv;
 			input = exepath.substr(0, (exepath.find_last_of('m')));
 			
-			m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();  
+			m->mothurOut("inputDir=" + input); m->mothurOutEndLine();  
 			commandFactory->setInputDirectory(input);
 		}else {
 			//add / to name if needed
@@ -153,15 +162,15 @@ int SetDirectoryCommand::execute(){
 			
 			//test to make sure directory exists
 			input = m->getFullPathName(input);
-			string inTemp = input + "temp";
+			string inTemp = input + tag + "temp";
 			ofstream in;
 			in.open(inTemp.c_str(), ios::trunc);
 			if(!in) {
 				m->mothurOut(input + " directory does not exist or is not writable."); m->mothurOutEndLine(); 
 			}else{
 				in.close();
-				remove(inTemp.c_str());
-				m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();  
+				m->mothurRemove(inTemp);
+				m->mothurOut("inputDir=" + input); m->mothurOutEndLine();  
 				commandFactory->setInputDirectory(input); 
 			}
 		}
@@ -170,7 +179,7 @@ int SetDirectoryCommand::execute(){
 		if (tempdefault == "clear") {  
 			#ifdef MOTHUR_FILES
 				string temp = MOTHUR_FILES; 
-				m->mothurOut("Resetting default directory to " + temp); m->mothurOutEndLine();  
+				m->mothurOut("tempDefault=" + temp); m->mothurOutEndLine();  
 				m->setDefaultPath(temp);
 			#else
 				string temp = ""; 
@@ -182,7 +191,7 @@ int SetDirectoryCommand::execute(){
 			string exepath = m->argv;
 			tempdefault = exepath.substr(0, (exepath.find_last_of('m')));
 			
-			m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();  
+			m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();  
 			m->setDefaultPath(tempdefault);
 		}else {
 			//add / to name if needed
@@ -193,8 +202,19 @@ int SetDirectoryCommand::execute(){
 				if (lastChar != "\\") { tempdefault += "\\"; }	
 			#endif
 			
-			m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();  
-			m->setDefaultPath(tempdefault);
+			//test to make sure directory exists
+			tempdefault = m->getFullPathName(tempdefault);
+			string inTemp = tempdefault + tag + "temp";
+			ofstream in;
+			in.open(inTemp.c_str(), ios::trunc);
+			if(!in) {
+				m->mothurOut(tempdefault + " directory does not exist or is not writable."); m->mothurOutEndLine(); 
+			}else{
+				in.close();
+				m->mothurRemove(inTemp);
+				m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();  
+				m->setDefaultPath(tempdefault);
+			}
 		}
 
 		return 0;