added modify names parameter to set.dir

[mothur.git] / alignment.hpp

diff --git a/alignment.hpp b/alignment.hpp
index 336781244b5a3370c37a7ad6f369cd9553f31618..3a2e84de5a8e24cf744ef3544d44df9e3e5dc722 100644 (file)
--- 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 +23,24 @@ 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:
@@ -46,6 +52,9 @@ protected:
        int pairwiseLength;
        int nRows, nCols, lA, lB;
        vector<vector<AlignmentCell> > alignment;
+    map<int, int> ABaseMap;
+    map<int, int> BBaseMap;
+       MothurOut* m;
 };
 
 /**************************************************************************************************/