| 1 | // ================================================================ // |
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| 2 | // // |
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| 3 | // File : DBwriter.h // |
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| 4 | // Purpose : // |
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| 5 | // // |
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| 6 | // Coded by Ralf Westram (coder@reallysoft.de) in November 2006 // |
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| 7 | // Institute of Microbiology (Technical University Munich) // |
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| 8 | // http://www.arb-home.de/ // |
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| 9 | // // |
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| 10 | // ================================================================ // |
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| 11 | |
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| 12 | #ifndef DBWRITER_H |
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| 13 | #define DBWRITER_H |
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| 14 | |
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| 15 | #ifndef METAINFO_H |
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| 16 | #include "MetaInfo.h" |
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| 17 | #endif |
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| 18 | #ifndef FEATURE_H |
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| 19 | #include "Feature.h" |
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| 20 | #endif |
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| 21 | #ifndef SEQUENCEBUFFER_H |
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| 22 | #include "SequenceBuffer.h" |
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| 23 | #endif |
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| 24 | #ifndef IMPORTER_H |
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| 25 | #include "Importer.h" |
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| 26 | #endif |
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| 27 | #ifndef GENOMEIMPORT_H |
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| 28 | #include "GenomeImport.h" |
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| 29 | #endif |
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| 30 | |
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| 31 | class UniqueNameDetector; |
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| 32 | |
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| 33 | class DBerror { |
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| 34 | // error class used for DB errors |
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| 35 | |
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| 36 | string err; // error message |
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| 37 | |
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| 38 | void init(const string& msg, GB_ERROR gberror); |
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| 39 | |
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| 40 | public: |
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| 41 | DBerror(); |
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| 42 | DBerror(const char *msg); |
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| 43 | DBerror(const string& msg); |
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| 44 | DBerror(const char *msg, GB_ERROR gberror); |
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| 45 | DBerror(const string& msg, GB_ERROR gberror); |
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| 46 | |
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| 47 | const string& getMessage() const { return err; } |
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| 48 | }; |
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| 49 | |
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| 50 | typedef std::map<std::string, int> NameCounter; |
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| 51 | struct Translator; |
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| 52 | |
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| 53 | class DBwriter : virtual Noncopyable { |
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| 54 | const char *ali_name; |
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| 55 | ImportSession& session; |
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| 56 | |
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| 57 | // following data is valid for one organism write : |
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| 58 | GBDATA *gb_organism; // current organism |
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| 59 | GBDATA *gb_gene_data; // current gene data |
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| 60 | NameCounter generatedGenes; // helper to create unique gene names (key = name, value = count occurrences) |
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| 61 | |
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| 62 | void testAndRemoveTranslations(Importer& importer); // test and delete translations (if test was ok). warns via Importer |
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| 63 | void hideUnwantedGenes(); |
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| 64 | |
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| 65 | static Translator *unreserve; |
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| 66 | static const string& getUnreservedQualifier(const string& qualifier); |
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| 67 | |
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| 68 | public: |
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| 69 | DBwriter(ImportSession& session_, const char *Ali_name) |
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| 70 | // : gb_species_data(Gb_species_data) |
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| 71 | : ali_name(Ali_name) |
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| 72 | // , UND_species(Und_species) |
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| 73 | , session(session_) |
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| 74 | , gb_organism(0) |
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| 75 | , gb_gene_data(0) |
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| 76 | {} |
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| 77 | |
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| 78 | void createOrganism(const string& flatfile, const char *importerTag); |
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| 79 | |
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| 80 | void writeFeature(const Feature& feature, long seqLength); |
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| 81 | void writeSequence(const SequenceBuffer& seqData); |
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| 82 | |
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| 83 | void renumberDuplicateGenes(); |
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| 84 | void finalizeOrganism(const MetaInfo& meta, const References& refs, Importer& importer); |
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| 85 | |
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| 86 | static void deleteStaticData(); |
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| 87 | }; |
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| 88 | |
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| 89 | |
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| 90 | #else |
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| 91 | #error DBwriter.h included twice |
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| 92 | #endif // DBWRITER_H |
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| 93 | |
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| 94 | |
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| 95 | |
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