X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignment.hpp;h=3a2e84de5a8e24cf744ef3544d44df9e3e5dc722;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=b3175560af7f16aa7a4e6fe4d8e87a2a081ae7cf;hpb=74c78f9abd9e733f0c2f812efec97a76632fcbf8;p=mothur.git

diff --git a/alignment.hpp b/alignment.hpp
index b317556..3a2e84d 100644
--- a/alignment.hpp
+++ b/alignment.hpp
@@ -23,17 +23,24 @@ class Alignment {
 public:
 	Alignment(int);
 	Alignment();
+	virtual ~Alignment();
 	virtual void align(string, string) = 0;
+    virtual void alignPrimer(string, string) {}
 	
-	float getAlignmentScore();
+	
+//	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:
@@ -45,6 +52,9 @@ protected:
 	int pairwiseLength;
 	int nRows, nCols, lA, lB;
 	vector<vector<AlignmentCell> > alignment;
+    map<int, int> ABaseMap;
+    map<int, int> BBaseMap;
+	MothurOut* m;
 };
 
 /**************************************************************************************************/