exit(1);
}
}
+//**********************************************************************************************************************
+string ClusterFragmentsCommand::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 = "fragclust.fasta"; }
+ else if (type == "name") { outputFileName = "fragclust.names"; }
+ 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, "ClusterFragmentsCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
ClusterFragmentsCommand::ClusterFragmentsCommand(){
try {
// ...at some point should added some additional type checking...
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not found") { namefile = ""; }
- else if (namefile == "not open") { abort = true; }
+ else if (namefile == "not open") { namefile = ""; abort = true; }
else { readNameFile(); m->setNameFile(namefile); }
string temp;
temp = validParameter.validFile(parameters, "diffs", false); if (temp == "not found"){ temp = "0"; }
- convert(temp, diffs);
+ m->mothurConvert(temp, diffs);
temp = validParameter.validFile(parameters, "percent", false); if (temp == "not found"){ temp = "0"; }
- convert(temp, percent);
+ m->mothurConvert(temp, percent);
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
}
string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
- string newFastaFile = fileroot + "fragclust.fasta";
- string newNamesFile = fileroot + "names";
+ string newFastaFile = fileroot + getOutputFileNameTag("fasta");
+ string newNamesFile = fileroot + getOutputFileNameTag("name");
if (m->control_pressed) { return 0; }
m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
- if (m->control_pressed) { remove(newFastaFile.c_str()); remove(newNamesFile.c_str()); return 0; }
+ if (m->control_pressed) { m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();