modified the engine to extract the path of mothur executable if argv does not contain...

[mothur.git] / setdircommand.cpp

diff --git a/setdircommand.cpp b/setdircommand.cpp
index 001ae235dd11ff0f015ebeba76de10ee3bcb2dbf..043c0acc8ec524c1b510da28c36c149d300f215a 100644 (file)
--- 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);