#include "systemcommand.h"
+//**********************************************************************************************************************
+vector<string> SystemCommand::getValidParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SystemCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SystemCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SystemCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SystemCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SystemCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
-SystemCommand::SystemCommand(string option){
+SystemCommand::SystemCommand(string option) {
try {
abort = false;
if(option == "help") { help(); abort = true; }
else {
- if (option == "") { mothurOut("You must enter a command to run."); mothurOutEndLine(); abort = true; }
+ if (option == "") { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
else {
//check for outputdir and inputdir parameters
int commaPos = option.find_first_of(',');
}
catch(exception& e) {
- errorOut(e, "SystemCommand", "SystemCommand");
+ m->errorOut(e, "SystemCommand", "SystemCommand");
exit(1);
}
}
void SystemCommand::help(){
try {
- mothurOut("The system command allows you to execute a system command from within mothur.\n");
- mothurOut("The system has no parameters.\n");
- mothurOut("The system command should be in the following format: system(yourCommand).\n");
- mothurOut("Example system(clear).\n");
+ m->mothurOut("The system command allows you to execute a system command from within mothur.\n");
+ m->mothurOut("The system has no parameters.\n");
+ m->mothurOut("The system command should be in the following format: system(yourCommand).\n");
+ m->mothurOut("Example system(clear).\n");
}
catch(exception& e) {
- errorOut(e, "SystemCommand", "help");
+ m->errorOut(e, "SystemCommand", "help");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "SystemCommand", "execute");
+ m->errorOut(e, "SystemCommand", "execute");
exit(1);
}
}