X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=setdircommand.cpp;h=1bc78bdf13cd69ee3be268bef006fc74d69dce9e;hb=fbaa6c7ac44f857c1ece7c8199e9e7e09b4bbe74;hp=238ffa5ff227eb85bae8dff594a7d1f97d357280;hpb=5df1b242d9c2b604eb414da44b28de81d52567d7;p=mothur.git

diff --git a/setdircommand.cpp b/setdircommand.cpp
index 238ffa5..1bc78bd 100644
--- a/setdircommand.cpp
+++ b/setdircommand.cpp
@@ -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);
@@ -37,9 +37,12 @@ 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 == "")) {	
-				m->mothurOut("You must provide either an input or output for the set.outdir command."); m->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;
 			}
 		}
 	}
@@ -54,10 +57,12 @@ void SetDirectoryCommand::help(){
 	try {
 		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 parameter is output and is required.\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 same directory as the mothur.exe you may enter: input=clear.\n");
-		m->mothurOut("The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory).\n");
+		m->mothurOut("To return the tempdefault to the default you provided at compile time you may enter: tempdefault=clear.\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");
 	}
@@ -130,6 +135,42 @@ int SetDirectoryCommand::execute(){
 				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 {
+			//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
+			
+			//test to make sure directory exists
+			tempdefault = getFullPathName(tempdefault);
+			string inTemp = tempdefault + "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();
+				remove(inTemp.c_str());
+				m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();  
+				m->setDefaultPath(tempdefault);
+			}
+		}
 
 		return 0;
 	}