X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignment.hpp;h=3a2e84de5a8e24cf744ef3544d44df9e3e5dc722;hb=541bab1dac00688b4c3a8c4a95ab464412663c50;hp=6dd7f0aed42938bd94a50bc6d4ebf88eda1c2b40;hpb=1244c4907c07baea86b0f0676d098a29d2e95a39;p=mothur.git

diff --git a/alignment.hpp b/alignment.hpp
index 6dd7f0a..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<int, int> getSeqAAlnBaseMap();
+    map<int, int> getSeqBAlnBaseMap();
 	int getCandidateStartPos();
 	int getCandidateEndPos();
 	int getTemplateStartPos();
@@ -49,6 +52,9 @@ protected:
 	int pairwiseLength;
 	int nRows, nCols, lA, lB;
 	vector<vector<AlignmentCell> > alignment;
+    map<int, int> ABaseMap;
+    map<int, int> BBaseMap;
+	MothurOut* m;
 };
 
 /**************************************************************************************************/