added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / alignmentdb.h

diff --git a/alignmentdb.h b/alignmentdb.h
index d665f788764f6ea228ad70bb99867602820a16c5..a69b917388fcabb052ab453a4c9e8e93e55e3fb6 100644 (file)
--- a/alignmentdb.h
+++ b/alignmentdb.h
@@ -21,15 +21,18 @@ class AlignmentDB {
 public:
 
        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;