source: tags/svn.1.5.4/RNACMA/Analyser.h

Last change on this file was 7896, checked in by westram, 14 years ago
  • removed disabled-code leftover from changes
File size: 1.5 KB
Line 
1/**
2 * Analyser.h
3 *
4 * This class is the main entry point to this package.
5 * The analyser object is responsible for interacting with the Cma code and Arb.
6 *
7 * The alphabet used is also defined in this class. Please check the implementation
8 * of the constructor.
9 *
10 * If you are looking for information on Cma computations, please check the
11 * comments in the Cma class.
12 *
13 *  Created on: Feb 15, 2010
14 *      Author: Breno Faria
15 */
16
17#ifndef ANALYSER_H_
18#define ANALYSER_H_
19
20#include <arbdb.h>
21#include <arbdbt.h>
22
23#include "Analyser.h"
24#include "AlignedSequenceLoader.h"
25#include "Cma.h"
26
27class Analyser {
28
29private:
30    /**
31     * The sequence loader. This object is an interface to Arb's DB.
32     */
33    AlignedSequenceLoader *loader;
34
35    /**
36     * The correlated mutation analysis computation is done by this object.
37     */
38    Cma *cma;
39
40public:
41    /**
42     * Returns a reference to the Cma object.
43     */
44    Cma* getCma();
45
46    /**
47     * Saves the clustering result as SAI in the ARB DB.
48     */
49    GB_ERROR saveSAI(vector<size_t> clusters, double threshold);
50    static const char *getSAIname() { return "cma_clusters"; }
51
52    /**
53     * Gives the clusters sensible names.
54     */
55    vector<char> normalizeClusters(vector<size_t> clusters);
56
57    /**
58     * Returns reference to the loader object.
59     */
60    AlignedSequenceLoader* getLoader();
61
62    /**
63     * Constructor.
64     */
65    Analyser();
66
67    /**
68     * Desctructor.
69     */
70    virtual ~Analyser();
71
72};
73
74#endif /* ANALYSER_H_ */
Note: See TracBrowser for help on using the repository browser.