added filter.shared command. fixed lci and uci for thetayc calc

[mothur.git] / alignment.hpp

diff --git a/alignment.hpp b/alignment.hpp
index 6dd7f0aed42938bd94a50bc6d4ebf88eda1c2b40..9d2197f5eaa7248b9bb8490c87c804f85931d095 100644 (file)
--- a/alignment.hpp
+++ b/alignment.hpp
@@ -30,6 +30,8 @@ public:
 //     float getAlignmentScore();
        string getSeqAAln();
        string getSeqBAln();
+    map<int, int> getSeqAAlnBaseMap();
+    map<int, int> getSeqBAlnBaseMap();
        int getCandidateStartPos();
        int getCandidateEndPos();
        int getTemplateStartPos();
@@ -49,6 +51,9 @@ protected:
        int pairwiseLength;
        int nRows, nCols, lA, lB;
        vector<vector<AlignmentCell> > alignment;
+    map<int, int> ABaseMap;
+    map<int, int> BBaseMap;
+       MothurOut* m;
 };
 
 /**************************************************************************************************/