X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=alignment.hpp;h=3a2e84de5a8e24cf744ef3544d44df9e3e5dc722;hp=215e4b32f77e1fc21df19ffd61b493b84d89acc6;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=02909d6cae9963ba00dc746969a370fa8ca934fc

diff --git a/alignment.hpp b/alignment.hpp
index 215e4b3..3a2e84d 100644
--- a/alignment.hpp
+++ b/alignment.hpp
@@ -25,16 +25,22 @@ 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();
 	int getTemplateEndPos();
-
+	
 	int getPairwiseLength();
+	void resize(int);
+	int getnRows() { return nRows; }
 //	int getLongestTemplateGap();
 
 protected:
@@ -46,6 +52,9 @@ protected:
 	int pairwiseLength;
 	int nRows, nCols, lA, lB;
 	vector<vector<AlignmentCell> > alignment;
+    map<int, int> ABaseMap;
+    map<int, int> BBaseMap;
+	MothurOut* m;
 };
 
 /**************************************************************************************************/