worked on trim.seqs

[mothur.git] / alignmentdb.h

diff --git a/alignmentdb.h b/alignmentdb.h
index 339f46ff65f423dc0366064181e690e25420b1f0..a69b917388fcabb052ab453a4c9e8e93e55e3fb6 100644 (file)
--- a/alignmentdb.h
+++ b/alignmentdb.h
@@ -20,20 +20,24 @@ class AlignmentDB {
 
 public:
 
-       AlignmentDB(string, string, int, int, int, int, int);  //reads fastafile passed in and stores sequences
+       AlignmentDB(string, string, int, float, float, float, float);  //reads fastafile passed in and stores sequences
+       AlignmentDB(string);
        ~AlignmentDB();
        
        Sequence findClosestSequence(Sequence*);
        float getSearchScore()  {  return search->getSearchScore();  }
        int getLongestBase()    {  return longest;  }
+       int MPISend(int);
+       int MPIRecv(int);
        
 private:
        int numSeqs, longest;
-       float searchScore;
+       string method;
        
        Database* search;
        vector<Sequence> templateSequences;
        Sequence emptySequence;
+       MothurOut* m;
 };
 
 /**************************************************************************************************/