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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