alignmentdb.h

   1 #ifndef ALIGNMENTDB_H
   2 #define ALIGNMENTDB_H
   3
   4 /*
   5  *  alignmentdb.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 11/4/09.
   9  *  Copyright 2009 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "sequence.hpp"
  15 #include "database.hpp"
  16
  17 /**************************************************************************************************/
  18
  19 class AlignmentDB {
  20
  21 public:
  22
  23         AlignmentDB(string, string, int, float, float, float, float, int);  //reads fastafile passed in and stores sequences
  24         AlignmentDB(string);
  25         ~AlignmentDB();
  26
  27         Sequence findClosestSequence(Sequence*);
  28         float getSearchScore()  {  return search->getSearchScore();  }
  29         int getLongestBase()    {  return longest;  }
  30
  31 private:
  32         int numSeqs, longest, threadID;
  33         string method;
  34
  35         Database* search;
  36         vector<Sequence> templateSequences;
  37         Sequence emptySequence;
  38         MothurOut* m;
  39 };
  40
  41 /**************************************************************************************************/
  42
  43 #endif
  44