//**********************************************************************************************************************
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);
+ CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "","",false,false); parameters.push_back(ptempdefault);
+ CommandParameter pdebug("debug", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pdebug);
+ CommandParameter pmodnames("modifynames", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmodnames);
+ CommandParameter pinput("input", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pinput);
+ CommandParameter poutput("output", "String", "", "", "", "", "","",false,false,true); 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); }
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 += "The set.dir command can also be used to run mothur in debug mode.\n";
+ helpString += "The set.dir command can also be used to set the modifynames parameter. Default=t, meaning if your sequence names contain ':' change them to '_' to avoid issues while making trees. modifynames=F will leave sequence names as they are.\n";
+ helpString += "The set.dir command parameters are input, output, tempdefault and debug and one is required.\n";
+ helpString += "To run mothur in debug mode set debug=true. Default debug=false.\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";
tempdefault = validParameter.validFile(parameters, "tempdefault", false);
if (tempdefault == "not found") { tempdefault = ""; }
+
+ bool debug = false;
+ bool nodebug = false;
+ debugOnly = false;
+ string temp = validParameter.validFile(parameters, "debug", false);
+ if (temp == "not found") { debug = false; nodebug=true; }
+ else { debug = m->isTrue(temp); }
+ m->debug = debug;
+
+ bool nomod = false;
+ temp = validParameter.validFile(parameters, "modifynames", false);
+ if (temp == "not found") { modifyNames = true; nomod=true; }
+ else { modifyNames = m->isTrue(temp); }
+ m->modifyNames = modifyNames;
+
+ if (debug) { m->mothurOut("Setting [DEBUG] flag.\n"); }
+
- if ((input == "") && (output == "") && (tempdefault == "")) {
- m->mothurOut("You must provide either an input, output or tempdefault for the set.outdir command."); m->mothurOutEndLine(); abort = true;
- }
+ if ((input == "") && (output == "") && (tempdefault == "") && nodebug && nomod) {
+ m->mothurOut("You must provide either an input, output, tempdefault, debug or modifynames for the set.outdir command."); m->mothurOutEndLine(); abort = true;
+ }else if((input == "") && (output == "") && (tempdefault == "")) { debugOnly = true; }
}
}
catch(exception& e) {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- commandFactory = CommandFactory::getInstance();
-
- m->mothurOut("Mothur's directories:"); m->mothurOutEndLine();
-
- //redirect output
- if ((output == "clear") || (output == "")) { output = ""; commandFactory->setOutputDirectory(output); }
- else if (output == "default") {
- string exepath = m->argv;
- output = exepath.substr(0, (exepath.find_last_of('m')));
-
- m->mothurOut("outputDir=" + 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)
- if (lastChar != "/") { output += "/"; }
- #else
- if (lastChar != "\\") { output += "\\"; }
- #endif
-
- //test to make sure directory exists
- output = m->getFullPathName(output);
- string outTemp = output + "temp";
- ofstream out;
- out.open(outTemp.c_str(), ios::trunc);
- if(!out) {
- m->mothurOut(output + " directory does not exist or is not writable."); m->mothurOutEndLine();
- }else{
- out.close();
- m->mothurRemove(outTemp);
- m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
- commandFactory->setOutputDirectory(output);
- }
- }
-
- //redirect input
- if ((input == "clear") || (input == "")) { input = ""; commandFactory->setInputDirectory(input); }
- else if (input == "default") {
- string exepath = m->argv;
- input = exepath.substr(0, (exepath.find_last_of('m')));
-
- m->mothurOut("inputDir=" + 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)
- if (lastChar != "/") { input += "/"; }
- #else
- if (lastChar != "\\") { input += "\\"; }
- #endif
-
- //test to make sure directory exists
- input = m->getFullPathName(input);
- string inTemp = input + "temp";
- ofstream in;
- in.open(inTemp.c_str(), ios::trunc);
- if(!in) {
- m->mothurOut(input + " directory does not exist or is not writable."); m->mothurOutEndLine();
- }else{
- in.close();
- m->mothurRemove(inTemp);
- m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
- commandFactory->setInputDirectory(input);
- }
- }
-
- //set default
- if (tempdefault == "clear") {
- #ifdef MOTHUR_FILES
- string temp = MOTHUR_FILES;
- m->mothurOut("tempDefault=" + temp); m->mothurOutEndLine();
+ if (debugOnly) { }
+ else {
+ commandFactory = CommandFactory::getInstance();
+
+ m->mothurOut("Mothur's directories:"); m->mothurOutEndLine();
+
+ //redirect output
+ if ((output == "clear") || (output == "")) { output = ""; commandFactory->setOutputDirectory(output); }
+ else if (output == "default") {
+ string exepath = m->argv;
+ output = exepath.substr(0, (exepath.find_last_of('m')));
+
+ m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
+ commandFactory->setOutputDirectory(output);
+ }else {
+ if (m->dirCheck(output)) {
+ m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
+ commandFactory->setOutputDirectory(output);
+ }
+ }
+
+ //redirect input
+ if ((input == "clear") || (input == "")) { input = ""; commandFactory->setInputDirectory(input); }
+ else if (input == "default") {
+ string exepath = m->argv;
+ input = exepath.substr(0, (exepath.find_last_of('m')));
+
+ m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
+ commandFactory->setInputDirectory(input);
+ }else {
+ if (m->dirCheck(input)) {
+ m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
+ commandFactory->setInputDirectory(input);
+ }
+ }
+
+ //set default
+ if (tempdefault == "clear") {
+#ifdef MOTHUR_FILES
+ string temp = MOTHUR_FILES;
+ m->mothurOut("tempDefault=" + temp); m->mothurOutEndLine();
m->setDefaultPath(temp);
- #else
- string temp = "";
- m->mothurOut("No default directory defined at compile time."); m->mothurOutEndLine();
+#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") {
- string exepath = m->argv;
- tempdefault = exepath.substr(0, (exepath.find_last_of('m')));
-
- m->mothurOut("tempDefault=" + 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("tempDefault=" + tempdefault); m->mothurOutEndLine();
- m->setDefaultPath(tempdefault);
- }
-
+#endif
+ }else if (tempdefault == "") { //do nothing
+ }else if (tempdefault == "default") {
+ string exepath = m->argv;
+ tempdefault = exepath.substr(0, (exepath.find_last_of('m')));
+
+ m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();
+ m->setDefaultPath(tempdefault);
+ }else {
+ if (m->dirCheck(tempdefault)) {
+ m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();
+ m->setDefaultPath(tempdefault);
+ }
+ }
+ }
return 0;
}
catch(exception& e) {
projects / mothur.git / blobdiff