exit(1);
}
}
+//**********************************************************************************************************************
+string AlignCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string tag = "";
+ 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") { tag = "align"; }
+ else if (type == "alignreport") { tag = "align.report"; }
+ else if (type == "accnos") { tag = "flip.accnos"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return tag;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCommand", "getOutputFileName");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
AlignCommand::AlignCommand(){
try {
m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
if (outputDir == "") { outputDir += m->hasPath(candidateFileNames[s]); }
- string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align";
- string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report";
- string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos";
+ string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("fasta");
+ string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("alignreport");
+ string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("accnos");
bool hasAccnos = true;
int numFastaSeqs = 0;
if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
alignment->resize(candidateSeq->getUnaligned().length()+1);
}
-
Sequence temp = templateDB->findClosestSequence(candidateSeq);
Sequence* templateSeq = &temp;