X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignment.hpp;h=6dd7f0aed42938bd94a50bc6d4ebf88eda1c2b40;hb=5f44783e6d74a9c207492ac244210c915cadc272;hp=336781244b5a3370c37a7ad6f369cd9553f31618;hpb=526a868606faa50caf86e7399f7554c0335b39e5;p=mothur.git

diff --git a/alignment.hpp b/alignment.hpp
index 3367812..6dd7f0a 100644
--- a/alignment.hpp
+++ b/alignment.hpp
@@ -12,7 +12,6 @@
  *	As of 12/18/08 these included alignments based on blastn, needleman-wunsch, and the	Gotoh algorithms
  * 
  */
-using namespace std;
 
 #include "mothur.h"
 #include "alignmentcell.hpp"
@@ -24,17 +23,21 @@ class Alignment {
 public:
 	Alignment(int);
 	Alignment();
+	virtual ~Alignment();
 	virtual void align(string, string) = 0;
 	
-	float getAlignmentScore();
+	
+//	float getAlignmentScore();
 	string getSeqAAln();
 	string getSeqBAln();
 	int getCandidateStartPos();
 	int getCandidateEndPos();
 	int getTemplateStartPos();
 	int getTemplateEndPos();
-
+	
 	int getPairwiseLength();
+	void resize(int);
+	int getnRows() { return nRows; }
 //	int getLongestTemplateGap();
 
 protected: