X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignment.hpp;h=9d2197f5eaa7248b9bb8490c87c804f85931d095;hb=e339f9008daa7d37c9a9034829565620a6abe783;hp=7a943fd0037430991a7baab418474e78a496d403;hpb=15b252e317fde72ce0a5de8776cb88112e0ed2b6;p=mothur.git

diff --git a/alignment.hpp b/alignment.hpp
index 7a943fd..9d2197f 100644
--- a/alignment.hpp
+++ b/alignment.hpp
@@ -30,6 +30,8 @@ public:
 //	float getAlignmentScore();
 	string getSeqAAln();
 	string getSeqBAln();
+    map<int, int> getSeqAAlnBaseMap();
+    map<int, int> getSeqBAlnBaseMap();
 	int getCandidateStartPos();
 	int getCandidateEndPos();
 	int getTemplateStartPos();
@@ -49,6 +51,8 @@ protected:
 	int pairwiseLength;
 	int nRows, nCols, lA, lB;
 	vector<vector<AlignmentCell> > alignment;
+    map<int, int> ABaseMap;
+    map<int, int> BBaseMap;
 	MothurOut* m;
 };