mods to trim.seqs

[mothur.git] / setdircommand.cpp

diff --git a/setdircommand.cpp b/setdircommand.cpp
index 001ae235dd11ff0f015ebeba76de10ee3bcb2dbf..a76db24282e2c00032ec747de2d1d5decf20e095 100644 (file)
--- a/setdircommand.cpp
+++ b/setdircommand.cpp
@@ -9,14 +9,48 @@
 
 #include "setdircommand.h"
 
+//**********************************************************************************************************************
+vector<string> SetDirectoryCommand::getValidParameters(){      
+       try {
+               string Array[] =  {"output","input","tempdefault","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SetDirectoryCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> SetDirectoryCommand::getRequiredParameters(){   
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SetDirectoryCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> SetDirectoryCommand::getRequiredFiles(){        
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SetDirectoryCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 
 SetDirectoryCommand::SetDirectoryCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -60,8 +94,11 @@ 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");
@@ -80,13 +117,20 @@ SetDirectoryCommand::~SetDirectoryCommand(){}
 int SetDirectoryCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                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)
@@ -96,7 +140,7 @@ int SetDirectoryCommand::execute(){
                        #endif
                        
                        //test to make sure directory exists
-                       output = getFullPathName(output);
+                       output = m->getFullPathName(output);
                        string outTemp = output + "temp";
                        ofstream out;
                        out.open(outTemp.c_str(), ios::trunc);
@@ -112,7 +156,14 @@ 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)
@@ -122,7 +173,7 @@ int SetDirectoryCommand::execute(){
                        #endif
                        
                        //test to make sure directory exists
-                       input = getFullPathName(input);
+                       input = m->getFullPathName(input);
                        string inTemp = input + "temp";
                        ofstream in;
                        in.open(inTemp.c_str(), ios::trunc);
@@ -148,6 +199,13 @@ 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);