+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter pmap("map", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pmap);
+ 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, "AlignCheckCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string AlignCheckCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The align.check command reads a fasta file and map file.\n";
+ helpString += "It outputs a file containing the secondary structure matches in the .align.check file.\n";
+ helpString += "The align.check command parameters are fasta and map, both are required.\n";
+ helpString += "The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n";
+ helpString += "Example align.check(map=silva.ss.map, fasta=amazon.fasta).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+AlignCheckCommand::AlignCheckCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["aligncheck"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
+ exit(1);
+ }
+}