X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignment.hpp;h=3a2e84de5a8e24cf744ef3544d44df9e3e5dc722;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hp=7a943fd0037430991a7baab418474e78a496d403;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git diff --git a/alignment.hpp b/alignment.hpp index 7a943fd..3a2e84d 100644 --- a/alignment.hpp +++ b/alignment.hpp @@ -25,11 +25,14 @@ public: Alignment(); virtual ~Alignment(); virtual void align(string, string) = 0; + virtual void alignPrimer(string, string) {} // float getAlignmentScore(); string getSeqAAln(); string getSeqBAln(); + map getSeqAAlnBaseMap(); + map getSeqBAlnBaseMap(); int getCandidateStartPos(); int getCandidateEndPos(); int getTemplateStartPos(); @@ -49,6 +52,8 @@ protected: int pairwiseLength; int nRows, nCols, lA, lB; vector > alignment; + map ABaseMap; + map BBaseMap; MothurOut* m; };