+//**********************************************************************************************************************
+vector<string> ChimeraCcodeCommand::getValidParameters(){
+ try {
+ string AlignArray[] = {"fasta", "filter", "processors", "window", "template", "mask", "numwanted", "outputdir","inputdir" };
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraCcodeCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ChimeraCcodeCommand::ChimeraCcodeCommand(){
+ try {
+ vector<string> tempOutNames;
+ outputTypes["chimera"] = tempOutNames;
+ outputTypes["mapinfo"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraCcodeCommand", "ChimeraCcodeCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ChimeraCcodeCommand::getRequiredParameters(){
+ try {
+ string AlignArray[] = {"template","fasta"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraCcodeCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ChimeraCcodeCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraCcodeCommand", "getRequiredFiles");
+ exit(1);
+ }
+}