added modify names parameter to set.dir

[mothur.git] / alignment.hpp

diff --git a/alignment.hpp b/alignment.hpp
index 6dd7f0aed42938bd94a50bc6d4ebf88eda1c2b40..3a2e84de5a8e24cf744ef3544d44df9e3e5dc722 100644 (file)
--- a/alignment.hpp
+++ b/alignment.hpp
@@ -25,11 +25,14 @@ public:
        Alignment();
        virtual ~Alignment();
        virtual void align(string, string) = 0;
+    virtual void alignPrimer(string, string) {}
        
        
 //     float getAlignmentScore();
        string getSeqAAln();
        string getSeqBAln();
+    map<int, int> getSeqAAlnBaseMap();
+    map<int, int> getSeqBAlnBaseMap();
        int getCandidateStartPos();
        int getCandidateEndPos();
        int getTemplateStartPos();
@@ -49,6 +52,9 @@ protected:
        int pairwiseLength;
        int nRows, nCols, lA, lB;
        vector<vector<AlignmentCell> > alignment;
+    map<int, int> ABaseMap;
+    map<int, int> BBaseMap;
+       MothurOut* m;
 };
 
 /**************************************************************************************************/