}
}
//**********************************************************************************************************************
+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;
m->openInputFile(fastafile, in);
ofstream out;
- string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "align.check";
+ string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("aligncheck");
m->openOutputFile(outfile, out);