X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=maligner.h;h=6ddd6acebdff359294deda6b4cc1b4c2c5ae788f;hb=d8ed98e71c2da5b39b8a778e2c694a4ddff677eb;hp=13aa917afb5b39ac238dda69b6032bb509e1345e;hpb=81276c241b984898f8d30ad123c00592ee6db7b8;p=mothur.git

diff --git a/maligner.h b/maligner.h
index 13aa917..6ddd6ac 100644
--- a/maligner.h
+++ b/maligner.h
@@ -47,13 +47,15 @@ class Maligner {
 		
 		vector< vector<score_struct> > buildScoreMatrix(int, int);
 		void fillScoreMatrix(vector<vector<score_struct> >&, vector<Sequence*>, int);
-		vector<score_struct> extractHighestPath(vector<vector<score_struct> >);
+		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*>);
 		float computePercentID(string, string);
 		string chimeraMaligner(int, DeCalculator*);
 		vector<Sequence*> getBlastSeqs(Sequence*, int);
 		vector<Sequence*> getKmerSeqs(Sequence*, int);
+		MothurOut* m;
 		
 };