added count.groups command and paralellized align.seqs for windows

[mothur.git] / sequence.hpp

diff --git a/sequence.hpp b/sequence.hpp
index 94d7d29b6117da80862e9fc8b3d0855c4adb8edd..b4337405a811545d4c3b2f64dc8771d42898d1fc 100644 (file)
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -25,6 +25,8 @@ public:
        Sequence(string, string);
        Sequence(ifstream&);
        Sequence(istringstream&);
+       Sequence(const Sequence& se) : name(se.name), unaligned(se.unaligned), aligned(se.aligned), pairwise(se.pairwise), numBases(se.numBases), startPos(se.startPos), endPos(se.endPos),
+                                                                       alignmentLength(se.alignmentLength), isAligned(se.isAligned), longHomoPolymer(se.longHomoPolymer), ambigBases(se.ambigBases) { m = MothurOut::getInstance(); }
        
        //these constructors just set the unaligned string to save space
        Sequence(string, string, string);