Sequence* findClosest(Sequence*, vector<Sequence*>);
set<int> getPos() { return h; }
void setMask(string);
void setAlignmentLength(int l) { alignLength = l; }
void runMask(Sequence*);
void trimSeqs(Sequence*, Sequence*, map<int, int>&);
Sequence* findClosest(Sequence*, vector<Sequence*>);
set<int> getPos() { return h; }
void setMask(string);
void setAlignmentLength(int l) { alignLength = l; }
void runMask(Sequence*);
void trimSeqs(Sequence*, Sequence*, map<int, int>&);