Alignment::Alignment(int A) : nCols(A), nRows(A) {
try {
+
+ m = MothurOut::getInstance();
alignment.resize(nRows); // For the Gotoh and Needleman-Wunsch we initialize the dynamic programming
for(int i=0;i<nRows;i++){ // matrix by initializing a matrix that is A x A. By default we will set A
alignment[i].resize(nCols); // at 2000 for 16S rRNA gene sequences
}
}
catch(exception& e) {
- errorOut(e, "Alignment", "Alignment");
+ m->errorOut(e, "Alignment", "Alignment");
exit(1);
}
}
}
}
catch(exception& e) {
- errorOut(e, "Alignment", "resize");
+ m->errorOut(e, "Alignment", "resize");
exit(1);
}
}
seqBend = seqB.length() - seqBend - 1;
}
catch(exception& e) {
- errorOut(e, "Alignment", "traceBack");
+ m->errorOut(e, "Alignment", "traceBack");
exit(1);
}
}
}
}
catch(exception& e) {
- errorOut(e, "Alignment", "~Alignment");
+ m->errorOut(e, "Alignment", "~Alignment");
exit(1);
}
}