added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / alignment.hpp

diff --git a/alignment.hpp b/alignment.hpp
index c033d62cbd8aa94d8ce6b7bc0b429015fd5c3d50..7a943fd0037430991a7baab418474e78a496d403 100644 (file)
--- a/alignment.hpp
+++ b/alignment.hpp
@@ -23,8 +23,10 @@ class Alignment {
 public:
        Alignment(int);
        Alignment();
+       virtual ~Alignment();
        virtual void align(string, string) = 0;
        
+       
 //     float getAlignmentScore();
        string getSeqAAln();
        string getSeqBAln();
@@ -32,8 +34,10 @@ public:
        int getCandidateEndPos();
        int getTemplateStartPos();
        int getTemplateEndPos();
-
+       
        int getPairwiseLength();
+       void resize(int);
+       int getnRows() { return nRows; }
 //     int getLongestTemplateGap();
 
 protected:
@@ -45,6 +49,7 @@ protected:
        int pairwiseLength;
        int nRows, nCols, lA, lB;
        vector<vector<AlignmentCell> > alignment;
+       MothurOut* m;
 };
 
 /**************************************************************************************************/