#include "nast.hpp"
//***************************************************************************************************************
-ChimeraReAligner::ChimeraReAligner(vector<Sequence*> t, int m, int mm) : match(m), misMatch(mm) { templateSeqs = t; }
+ChimeraReAligner::ChimeraReAligner(vector<Sequence*> t, int ms, int mm) : match(ms), misMatch(mm) { templateSeqs = t; m = MothurOut::getInstance(); }
//***************************************************************************************************************
ChimeraReAligner::~ChimeraReAligner() {}
//***************************************************************************************************************
}
catch(exception& e) {
- errorOut(e, "ChimeraReAligner", "reAlign");
+ m->errorOut(e, "ChimeraReAligner", "reAlign");
exit(1);
}
}
}
}
- if(spot == -1) { mothurOut("Error: Could not find sequence."); mothurOutEndLine(); return NULL; }
+ if(spot == -1) { m->mothurOut("Error: Could not find sequence."); m->mothurOutEndLine(); return NULL; }
temp = new Sequence(templateSeqs[spot]->getName(), templateSeqs[spot]->getAligned());
return temp;
}
catch(exception& e) {
- errorOut(e, "ChimeraReAligner", "getSequence");
+ m->errorOut(e, "ChimeraReAligner", "getSequence");
exit(1);
}
}