| 1 | /** |
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| 2 | * Analyser.h |
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| 3 | * |
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| 4 | * This class is the main entry point to this package. |
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| 5 | * The analyser object is responsible for interacting with the Cma code and Arb. |
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| 6 | * |
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| 7 | * The alphabet used is also defined in this class. Please check the implementation |
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| 8 | * of the constructor. |
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| 9 | * |
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| 10 | * If you are looking for information on Cma computations, please check the |
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| 11 | * comments in the Cma class. |
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| 12 | * |
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| 13 | * Created on: Feb 15, 2010 |
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| 14 | * Author: Breno Faria |
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| 15 | * |
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| 16 | * Institute of Microbiology (Technical University Munich) |
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| 17 | * http://www.arb-home.de/ |
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| 18 | */ |
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| 19 | |
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| 20 | #ifndef ANALYSER_H |
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| 21 | #define ANALYSER_H |
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| 22 | |
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| 23 | #ifndef ARBDBT_H |
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| 24 | #include <arbdbt.h> |
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| 25 | #endif |
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| 26 | #ifndef ALIGNEDSEQUENCELOADER_H |
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| 27 | #include "AlignedSequenceLoader.h" |
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| 28 | #endif |
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| 29 | #ifndef CMA_H |
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| 30 | #include "Cma.h" |
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| 31 | #endif |
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| 32 | |
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| 33 | class Analyser FINAL_TYPE : virtual Noncopyable { |
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| 34 | |
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| 35 | /** |
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| 36 | * The sequence loader. This object is an interface to Arb's DB. |
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| 37 | */ |
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| 38 | AlignedSequenceLoader *loader; |
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| 39 | |
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| 40 | /** |
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| 41 | * The correlated mutation analysis computation is done by this object. |
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| 42 | */ |
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| 43 | Cma *cma; |
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| 44 | |
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| 45 | public: |
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| 46 | /** |
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| 47 | * Returns a reference to the Cma object. |
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| 48 | */ |
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| 49 | Cma* getCma(); |
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| 50 | |
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| 51 | /** |
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| 52 | * Saves the clustering result as SAI in the ARB DB. |
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| 53 | */ |
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| 54 | GB_ERROR saveSAI(GBDATA *gb_main, vector<size_t> clusters, double threshold); |
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| 55 | static const char *getSAIname() { return "cma_clusters"; } |
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| 56 | |
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| 57 | /** |
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| 58 | * Gives the clusters sensible names. |
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| 59 | */ |
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| 60 | vector<char> normalizeClusters(vector<size_t> clusters); |
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| 61 | |
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| 62 | /** |
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| 63 | * Returns reference to the loader object. |
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| 64 | */ |
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| 65 | AlignedSequenceLoader* getLoader(); |
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| 66 | |
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| 67 | GB_ERROR get_error() const { return loader->get_error(); } |
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| 68 | bool has_error() const { return get_error(); } |
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| 69 | |
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| 70 | /** |
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| 71 | * Constructor. |
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| 72 | */ |
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| 73 | Analyser(class GBDATA *gb_main); |
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| 74 | |
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| 75 | /** |
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| 76 | * Desctructor. |
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| 77 | */ |
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| 78 | virtual ~Analyser(); |
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| 79 | |
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| 80 | }; |
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| 81 | |
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| 82 | #else |
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| 83 | #error Analyser.h included twice |
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| 84 | #endif // ANALYSER_H |
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