ARB
AlignedSequenceLoader.h
Go to the documentation of this file.
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 ARB_CORE_H
23 #include <arb_core.h>
24 #endif
25 #ifndef ARBTOOLS_H
26 #include <arbtools.h>
27 #endif
28 
29 class AlignedSequenceLoader FINAL_TYPE : virtual Noncopyable {
30 
35  VecVecType *seqs;
39  vector<size_t> position_map;
43  size_t MSA_len;
47  void cleanSeqs(const size_t * occurrences, long len);
48 
49  public:
50 
54  size_t getMsaLen();
55 
59  const vector<size_t>& getPositionMap();
60 
64  VecVecType* getSequences();
65 
66  GB_ERROR get_error() const { return error; }
67  bool has_error() const { return get_error(); }
68 
72  AlignedSequenceLoader(class GBDATA *gb_main);
73 
77  ~AlignedSequenceLoader();
78 };
79 
80 #else
81 #error AlignedSequenceLoader.h included twice
82 #endif // ALIGNEDSEQUENCELOADER_H
GB_ERROR get_error() const
static void error(const char *msg)
Definition: mkptypes.cxx:96
vector< vector< string > > VecVecType
Definition: Cma.h:60
xml element
bool has_error() const
GBDATA * gb_main
Definition: adname.cxx:33