X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignment.hpp;h=7a943fd0037430991a7baab418474e78a496d403;hb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;hp=215e4b32f77e1fc21df19ffd61b493b84d89acc6;hpb=02909d6cae9963ba00dc746969a370fa8ca934fc;p=mothur.git

diff --git a/alignment.hpp b/alignment.hpp
index 215e4b3..7a943fd 100644
--- a/alignment.hpp
+++ b/alignment.hpp
@@ -26,6 +26,7 @@ public:
 	virtual ~Alignment();
 	virtual void align(string, string) = 0;
 	
+	
 //	float getAlignmentScore();
 	string getSeqAAln();
 	string getSeqBAln();
@@ -33,8 +34,10 @@ public:
 	int getCandidateEndPos();
 	int getTemplateStartPos();
 	int getTemplateEndPos();
-
+	
 	int getPairwiseLength();
+	void resize(int);
+	int getnRows() { return nRows; }
 //	int getLongestTemplateGap();
 
 protected:
@@ -46,6 +49,7 @@ protected:
 	int pairwiseLength;
 	int nRows, nCols, lA, lB;
 	vector<vector<AlignmentCell> > alignment;
+	MothurOut* m;
 };
 
 /**************************************************************************************************/