#include "getcurrentcommand.h"
-
//**********************************************************************************************************************
-vector<string> GetCurrentCommand::getValidParameters(){
+vector<string> GetCurrentCommand::setParameters(){
try {
- string Array[] = {"outputdir","inputdir","clear"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pclear("clear", "String", "", "", "", "", "",false,false); parameters.push_back(pclear);
+ 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, "GetCurrentCommand", "getValidParameters");
+ m->errorOut(e, "GetCurrentCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-GetCurrentCommand::GetCurrentCommand(){
+string GetCurrentCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
+ string helpString = "";
+ helpString += "The get.current command outputs the current files saved by mothur.\n";
+ helpString += "The get.current command has one parameter: clear.\n";
+ helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
+ helpString += "The get.current command should be in the following format: \n";
+ helpString += "get.current() or get.current(clear=fasta-name-accnos)\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "GetCurrentCommand", "GetCurrentCommand");
+ m->errorOut(e, "GetCurrentCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> GetCurrentCommand::getRequiredParameters(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "GetCurrentCommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> GetCurrentCommand::getRequiredFiles(){
+GetCurrentCommand::GetCurrentCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
}
catch(exception& e) {
- m->errorOut(e, "GetCurrentCommand", "getRequiredFiles");
+ m->errorOut(e, "GetCurrentCommand", "GetCurrentCommand");
exit(1);
}
}
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"outputdir","inputdir","clear"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
}
//**********************************************************************************************************************
-void GetCurrentCommand::help(){
- try {
- m->mothurOut("The get.current command outputs the current files saved by mothur.\n");
- m->mothurOut("The get.current command has one parameter: clear.\n");
- m->mothurOut("The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n");
- m->mothurOut("The get.current command should be in the following format: \n");
- m->mothurOut("get.current() or get.current(clear=fasta-name-accnos)\n");
-
- }
- catch(exception& e) {
- m->errorOut(e, "GetCurrentCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-GetCurrentCommand::~GetCurrentCommand(){}
-//**********************************************************************************************************************
-
int GetCurrentCommand::execute(){
try {
}else if (types[i] == "accnos") {
m->setAccnosFile("");
}else if (types[i] == "taxonomy") {
- m->setTaxonomyFile("");
+ m->setTaxonomyFile("");
+ }else if (types[i] == "flow") {
+ m->setFlowFile("");
+ }else if (types[i] == "biom") {
+ m->setBiomFile("");
+ }else if (types[i] == "processors") {
+ m->setProcessors("1");
}else if (types[i] == "all") {
m->clearCurrentFiles();
}else {
}
}
- m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
- m->printCurrentFiles();
+ if (m->hasCurrentFiles()) {
+ m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
+ m->printCurrentFiles();
+ }
return 0;
}