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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 | |
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17 | #ifndef ANALYSER_H_ |
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18 | #define ANALYSER_H_ |
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19 | |
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20 | #include <arbdb.h> |
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21 | #include <arbdbt.h> |
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22 | |
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23 | #include "Analyser.h" |
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24 | #include "AlignedSequenceLoader.h" |
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25 | #include "Cma.h" |
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26 | |
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27 | class Analyser { |
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28 | |
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29 | private: |
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30 | /** |
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31 | * The sequence loader. This object is an interface to Arb's DB. |
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32 | */ |
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33 | AlignedSequenceLoader *loader; |
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34 | |
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35 | /** |
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36 | * The correlated mutation analysis computation is done by this object. |
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37 | */ |
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38 | Cma *cma; |
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39 | |
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40 | public: |
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41 | /** |
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42 | * Returns a reference to the Cma object. |
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43 | */ |
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44 | Cma* getCma(); |
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45 | |
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46 | /** |
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47 | * Saves the clustering result as SAI in the ARB DB. |
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48 | */ |
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49 | GB_ERROR saveSAI(vector<size_t> clusters, double threshold); |
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50 | static const char *getSAIname() { return "cma_clusters"; } |
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51 | |
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52 | /** |
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53 | * Gives the clusters sensible names. |
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54 | */ |
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55 | vector<char> normalizeClusters(vector<size_t> clusters); |
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56 | |
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57 | /** |
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58 | * Returns reference to the loader object. |
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59 | */ |
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60 | AlignedSequenceLoader* getLoader(); |
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61 | |
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62 | /** |
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63 | * Constructor. |
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64 | */ |
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65 | Analyser(); |
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66 | |
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67 | /** |
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68 | * Desctructor. |
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69 | */ |
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70 | virtual ~Analyser(); |
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71 | |
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72 | }; |
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73 | |
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74 | #endif /* ANALYSER_H_ */ |
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