- void fillScoreMatrix(vector<vector<score_struct> >&, vector<Sequence*>, int);
- vector<trace_struct> extractHighestPath(vector<vector<score_struct> >);
- vector<trace_struct> mapTraceRegionsToAlignment(vector<score_struct>, vector<Sequence*>);
- string constructChimericSeq(vector<trace_struct>, vector<Sequence*>);
- string constructAntiChimericSeq(vector<trace_struct>, vector<Sequence*>);
+ void fillScoreMatrix(vector<vector<score_struct> >&, vector<Sequence>, int);
+ vector<score_struct> extractHighestPath(vector<vector<score_struct> >);
+ vector<trace_struct> mapTraceRegionsToAlignment(vector<score_struct>);
+ string constructChimericSeq(vector<trace_struct>, vector<Sequence>);
+ string constructAntiChimericSeq(vector<trace_struct>, vector<Sequence>);