source: tags/ms_r16q2/RNACMA/AlignedSequenceLoader.h

Last change on this file was 8940, checked in by westram, 10 years ago
  • added MBI copyright
  • fixed include wrappers
  • fixed cppcheck warning
File size: 1.5 KB
Line 
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
26class AlignedSequenceLoader : virtual Noncopyable {
27
28private:
29    /**
30     * The aligned sequences (see Cma.h for the definition of VecVecType).
31     */
32    VecVecType *seqs;
33    /**
34     * The positions map between cleaned-up alignment and original one.
35     */
36    vector<size_t> *position_map;
37    /**
38     * The length of the multiple sequence alignment.
39     */
40    size_t MSA_len;
41    /**
42     * Cleans-up the MSA, removing positions with no base occurrence.
43     */
44    void cleanSeqs(size_t* occurrences, long len);
45
46public:
47
48    /**
49     * Returns the MSA length.
50     */
51    size_t getMsaLen();
52
53    /**
54     * Returns the position map.
55     */
56    vector<size_t> * getPositionMap();
57
58    /**
59     * Returns the aligned sequences.
60     */
61    VecVecType* getSequences();
62
63    /**
64     * Constructor.
65     */
66    AlignedSequenceLoader();
67
68    /**
69     * Destructor.
70     */
71    virtual ~AlignedSequenceLoader();
72};
73
74#else
75#error AlignedSequenceLoader.h included twice
76#endif // ALIGNEDSEQUENCELOADER_H
Note: See TracBrowser for help on using the repository browser.