+vector<string> RemoveLineageCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta","name", "group", "alignreport", "taxon", "dups", "list","taxonomy","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+RemoveLineageCommand::RemoveLineageCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["taxonomy"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["alignreport"] = tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> RemoveLineageCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"taxonomy"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> RemoveLineageCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************