}
}
//**********************************************************************************************************************
+string BinSeqCommand::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 = "fasta"; }
+ 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, "BinSeqCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
BinSeqCommand::BinSeqCommand(){
try {
abort = true; calledHelp = true;
}
namesfile = validParameter.validFile(parameters, "name", true);
- if (namesfile == "not open") { abort = true; }
+ if (namesfile == "not open") { namesfile = ""; abort = true; }
else if (namesfile == "not found") { namesfile = ""; }
else { m->setNameFile(namesfile); }
else if (groupfile == "not found") { groupfile = ""; }
else { m->setGroupFile(groupfile); }
+ if (namesfile == ""){
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
+
}
}
catch(exception& e) {
try {
string binnames, name, sequence;
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".fasta";
- m->openOutputFile(outputFileName, out);
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + getOutputFileNameTag("fasta");
+ m->openOutputFile(outputFileName, out);
//save to output list of output file names
outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);