Nast::Nast(Alignment* method, Sequence* cand, Sequence* temp) : alignment(method), candidateSeq(cand), templateSeq(temp) {
try {
+ m = MothurOut::getInstance();
maxInsertLength = 0;
pairwiseAlignSeqs(); // This is part A in Fig. 2 of DeSantis et al.
regapSequences(); // This is parts B-F in Fig. 2 of DeSantis et al.
-
}
catch(exception& e) {
- errorOut(e, "Nast", "Nast");
+ m->errorOut(e, "Nast", "Nast");
exit(1);
}
-
}
/**************************************************************************************************/
try {
alignment->align(candidateSeq->getUnaligned(), templateSeq->getUnaligned());
-
+
string candAln = alignment->getSeqAAln();
string tempAln = alignment->getSeqBAln();
-
+
if(candAln == ""){
candidateSeq->setPairwise("");
candidateSeq->setPairwise(candAln); // set the pairwise sequences in the Sequence objects for
templateSeq->setPairwise(tempAln); // the candidate and template sequences
-
}
catch(exception& e) {
- errorOut(e, "Nast", "pairwiseAlignSeqs");
+ m->errorOut(e, "Nast", "pairwiseAlignSeqs");
exit(1);
}
}
}
}
catch(exception& e) {
- errorOut(e, "Nast", "removeExtraGaps");
+ m->errorOut(e, "Nast", "removeExtraGaps");
exit(1);
}
}
// would skip the gaps and not progress through full alignment sequence
// not tested yet
- mothurOut("We're into D " + toString(fullAlignIndex) + " " + toString(pairwiseAlignIndex)); mothurOutEndLine();
+ m->mothurOut("We're into D " + toString(fullAlignIndex) + " " + toString(pairwiseAlignIndex)); m->mothurOutEndLine();
pairwiseAlignIndex++;
}
else{
// everything has a gap - not possible
// not tested yet
- mothurOut("We're into F " + toString(fullAlignIndex) + " " + toString(pairwiseAlignIndex)); mothurOutEndLine();
+ m->mothurOut("We're into F " + toString(fullAlignIndex) + " " + toString(pairwiseAlignIndex)); m->mothurOutEndLine();
pairwiseAlignIndex++;
fullAlignIndex++;
}
candidateSeq->setAligned(candAln);
}
catch(exception& e) {
- errorOut(e, "Nast", "regapSequences");
+ m->errorOut(e, "Nast", "regapSequences");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "Nast", "getSimilarityScore");
+ m->errorOut(e, "Nast", "getSimilarityScore");
exit(1);
}
}