+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta","map", "outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+AlignCheckCommand::AlignCheckCommand(){
+ try {
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["aligncheck"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta","map"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "getRequiredFiles");
+ exit(1);
+ }
+}