+ 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);
+ }
+}
+//**********************************************************************************************************************
+string AlignCheckCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "aligncheck") { outputFileName = "align.check"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "getOutputFileNameTag");
+ 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);
+ }
+}
+//**********************************************************************************************************************
+
+AlignCheckCommand::AlignCheckCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+ haderror = 0;
+