created mothurOut class to handle logfiles

[mothur.git] / alignment.hpp

diff --git a/alignment.hpp b/alignment.hpp
index 215e4b32f77e1fc21df19ffd61b493b84d89acc6..7a943fd0037430991a7baab418474e78a496d403 100644 (file)
--- 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;
 };
 
 /**************************************************************************************************/