}
}
//**********************************************************************************************************************
+string FilterSeqsCommand::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 = "filter.fasta"; }
+ else if (type == "filter") { outputFileName = "filter"; }
+ 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, "FilterSeqsCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
FilterSeqsCommand::FilterSeqsCommand(){
try {
abort = true; calledHelp = true;
fasta = validParameter.validFile(parameters, "fasta", false);
if (fasta == "not found") {
fasta = m->getFastaFile();
- if (fasta != "") { fastafileNames.push_back(fasta); m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ if (fasta != "") {
+ fastafileNames.push_back(fasta);
+ m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine();
+ string simpleName = m->getSimpleName(fasta);
+ filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
+ }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else {
//prevent giantic file name
string filterFile;
- if (fastafileNames.size() > 3) { filterFile = outputDir + "merge.filter"; }
- else { filterFile = outputDir + filterFileName + ".filter"; }
+ if (fastafileNames.size() > 3) { filterFile = outputDir + "merge." + getOutputFileNameTag("filter"); }
+ else { filterFile = outputDir + filterFileName + "." + getOutputFileNameTag("filter"); }
m->openOutputFile(filterFile, outFilter);
outFilter << filter << endl;
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
- string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
+ string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + getOutputFileNameTag("fasta");
#ifdef USE_MPI
int pid, numSeqsPerProcessor, num;
int tag = 2001;