//**********************************************************************************************************************
-SetDirectoryCommand::SetDirectoryCommand(string option){
+SetDirectoryCommand::SetDirectoryCommand(string option) {
try {
abort = false;
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);
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 == "")) {
- mothurOut("You must provide either an input or output for the set.outdir command."); 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;
}
}
}
catch(exception& e) {
- errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
+ m->errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
exit(1);
}
}
void SetDirectoryCommand::help(){
try {
- 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");
- mothurOut("The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n");
- mothurOut("The set.dir command parameter is output and is required.\n");
- mothurOut("To return the output to the same directory as the input files you may enter: output=clear.\n");
- mothurOut("To return the input to the same directory as the mothur.exe you may enter: input=clear.\n");
- mothurOut("The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory).\n");
- mothurOut("Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n");
- mothurOut("Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n\n");
+ 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 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 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");
}
catch(exception& e) {
- errorOut(e, "SetDirectoryCommand", "help");
+ m->errorOut(e, "SetDirectoryCommand", "help");
exit(1);
}
}
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)
ofstream out;
out.open(outTemp.c_str(), ios::trunc);
if(!out) {
- mothurOut(output + " directory does not exist or is not writable."); mothurOutEndLine();
+ m->mothurOut(output + " directory does not exist or is not writable."); m->mothurOutEndLine();
}else{
+ out.close();
remove(outTemp.c_str());
- mothurOut("Changing output directory to " + output); mothurOutEndLine();
+ m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();
commandFactory->setOutputDirectory(output);
}
}
//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)
ofstream in;
in.open(inTemp.c_str(), ios::trunc);
if(!in) {
- mothurOut(input + " directory does not exist or is not writable."); mothurOutEndLine();
+ m->mothurOut(input + " directory does not exist or is not writable."); m->mothurOutEndLine();
}else{
+ in.close();
remove(inTemp.c_str());
- mothurOut("Changing input directory to " + input); mothurOutEndLine();
+ m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();
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 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);
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if (lastChar != "/") { tempdefault += "/"; }
+ #else
+ if (lastChar != "\\") { tempdefault += "\\"; }
+ #endif
+
+ m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();
+ m->setDefaultPath(tempdefault);
+ }
return 0;
}
catch(exception& e) {
- errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
+ m->errorOut(e, "SetDirectoryCommand", "execute");
exit(1);
}
}
projects / mothur.git / blobdiff