#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(){
+vector<string> SetDirectoryCommand::setParameters(){
try {
+ CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "",false,false); parameters.push_back(ptempdefault);
+ CommandParameter pinput("input", "String", "", "", "", "", "",false,false); parameters.push_back(pinput);
+ CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "SetDirectoryCommand", "getRequiredParameters");
+ m->errorOut(e, "SetDirectoryCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> SetDirectoryCommand::getRequiredFiles(){
+string SetDirectoryCommand::getHelpString(){
try {
- vector<string> myArray;
- return myArray;
+ string helpString = "";
+ helpString += "The set.dir command can be used to direct the output files generated by mothur to a specific place, the directory must exist.\n";
+ helpString += "The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n";
+ helpString += "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";
+ helpString += "The set.dir command parameters are input, output and tempdefault and one is required.\n";
+ helpString += "To return the output to the same directory as the input files you may enter: output=clear.\n";
+ helpString += "To return the input to the current working directory you may enter: input=clear.\n";
+ helpString += "To set the output to the directory where mothur.exe is located you may enter: output=default.\n";
+ helpString += "To set the input to the directory where mothur.exe is located you may enter: input=default.\n";
+ helpString += "To return the tempdefault to the default you provided at compile time you may enter: tempdefault=clear.\n";
+ 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";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "SetDirectoryCommand", "getRequiredFiles");
+ m->errorOut(e, "SetDirectoryCommand", "getHelpString");
exit(1);
}
}
}
//**********************************************************************************************************************
-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 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) {
- m->errorOut(e, "SetDirectoryCommand", "help");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-SetDirectoryCommand::~SetDirectoryCommand(){}
-
-//**********************************************************************************************************************
-
int SetDirectoryCommand::execute(){
try {
//redirect output
if ((output == "clear") || (output == "")) { output = ""; commandFactory->setOutputDirectory(output); }
else if (output == "default") {
- GlobalData* globaldata = GlobalData::getInstance();
- string exepath = globaldata->argv;
+ string exepath = m->argv;
output = exepath.substr(0, (exepath.find_last_of('m')));
m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();
//redirect input
if ((input == "clear") || (input == "")) { input = ""; commandFactory->setInputDirectory(input); }
else if (input == "default") {
- GlobalData* globaldata = GlobalData::getInstance();
- string exepath = globaldata->argv;
+ string exepath = m->argv;
input = exepath.substr(0, (exepath.find_last_of('m')));
m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();
#endif
}else if (tempdefault == "") { //do nothing
}else if (tempdefault == "default") {
- GlobalData* globaldata = GlobalData::getInstance();
- string exepath = globaldata->argv;
+ string exepath = m->argv;
tempdefault = exepath.substr(0, (exepath.find_last_of('m')));
m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();
projects / mothur.git / blobdiff