ARB
AlignedSequenceLoader.h
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1 /*
2  * AlignedSequenceLoader.h
3  *
4  * Interface to Arb's DB.
5  * This class loads aligned sequences from Arb's DB and allows the other
6  * code in this package to access it in a standard way.
7  *
8  * Created on: Feb 15, 2010
9  * Author: Breno Faria
10  *
11  * Institute of Microbiology (Technical University Munich)
12  * http://www.arb-home.de/
13  */
14 
15 
16 #ifndef ALIGNEDSEQUENCELOADER_H
17 #define ALIGNEDSEQUENCELOADER_H
18 
19 #ifndef CMA_H
20 #include "Cma.h"
21 #endif
22 #ifndef ARBTOOLS_H
23 #include <arbtools.h>
24 #endif
25 
26 class AlignedSequenceLoader FINAL_TYPE : virtual Noncopyable {
27 
28 private:
32  VecVecType *seqs;
36  vector<size_t> *position_map;
40  size_t MSA_len;
44  void cleanSeqs(size_t* occurrences, long len);
45 
46 public:
47 
51  size_t getMsaLen();
52 
56  vector<size_t> * getPositionMap();
57 
61  VecVecType* getSequences();
62 
66  AlignedSequenceLoader();
67 
71  virtual ~AlignedSequenceLoader();
72 };
73 
74 #else
75 #error AlignedSequenceLoader.h included twice
76 #endif // ALIGNEDSEQUENCELOADER_H
vector< vector< string > > VecVecType
Definition: Cma.h:60
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