exit(1);
}
}
+//**********************************************************************************************************************
+string ShhhSeqsCommand::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 == "fasta") { outputFileName = "shhh_seqs.fasta"; }
+ else if (type == "name") { outputFileName = "shhh_seqs.names"; }
+ else if (type == "map") { outputFileName = "shhh_seqs.map"; }
+ 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, "ShhhSeqsCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
ShhhSeqsCommand::ShhhSeqsCommand(){
if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (outputDir == "") { outputDir = m->hasPath(fastafile); }//if user entered a file with a path then preserve it
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.fasta";
- string nameFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.names";
- string mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.map";
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta");
+ string nameFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("name");
+ string mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("map");
if (groupfile != "") {
//Parse sequences by group