1 | #ifndef GENBANK_H |
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2 | #define GENBANK_H |
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3 | |
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4 | #ifndef REFS_H |
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5 | #include "refs.h" |
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6 | #endif |
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7 | #ifndef PARSER_H |
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8 | #include "parser.h" |
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9 | #endif |
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10 | |
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11 | struct GenbankRef { |
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12 | char *ref; |
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13 | char *author; |
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14 | char *title; |
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15 | char *journal; |
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16 | char *standard; |
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17 | |
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18 | GenbankRef() |
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19 | : ref(no_content()), |
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20 | author(no_content()), |
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21 | title(no_content()), |
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22 | journal(no_content()), |
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23 | standard(no_content()) |
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24 | {} |
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25 | GenbankRef(const GenbankRef& other) |
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26 | : ref(strdup(other.ref)), |
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27 | author(strdup(other.author)), |
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28 | title(strdup(other.title)), |
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29 | journal(strdup(other.journal)), |
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30 | standard(strdup(other.standard)) |
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31 | {} |
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32 | ~GenbankRef() { |
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33 | free(standard); |
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34 | free(journal); |
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35 | free(title); |
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36 | free(author); |
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37 | free(ref); |
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38 | } |
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39 | DECLARE_ASSIGNMENT_OPERATOR(GenbankRef); |
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40 | }; |
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41 | |
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42 | class GenBank : public InputFormat, public RefContainer<GenbankRef> { // derived from a Noncopyable |
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43 | char *create_id() const OVERRIDE { |
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44 | char buf[TOKENSIZE]; |
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45 | genbank_key_word(locus, 0, buf); |
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46 | return strdup(buf); |
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47 | } |
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48 | public: |
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49 | char *locus; |
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50 | char *definition; |
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51 | char *accession; |
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52 | char *keywords; |
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53 | char *source; |
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54 | char *organism; |
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55 | |
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56 | RDP_comments comments; |
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57 | |
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58 | GenBank() { |
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59 | locus = no_content(); |
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60 | definition = no_content(); |
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61 | accession = no_content(); |
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62 | keywords = no_content(); |
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63 | source = no_content(); |
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64 | organism = no_content(); |
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65 | } |
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66 | virtual ~GenBank() OVERRIDE { |
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67 | freenull(locus); |
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68 | freenull(definition); |
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69 | freenull(accession); |
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70 | freenull(keywords); |
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71 | freenull(source); |
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72 | freenull(organism); |
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73 | } |
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74 | |
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75 | bool locus_contains_date() const { return str0len(locus) >= 60; } |
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76 | |
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77 | char *get_date() const { |
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78 | if (locus_contains_date()) return strndup(locus+50, 11); |
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79 | return strdup(genbank_date(today_date())); |
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80 | } |
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81 | |
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82 | // InputFormat interface |
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83 | void reinit() OVERRIDE { INPLACE_RECONSTRUCT(GenBank, this); } |
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84 | Format format() const OVERRIDE { return GENBANK; } |
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85 | }; |
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86 | |
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87 | class GenbankReader : public SimpleFormatReader { |
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88 | GenBank data; |
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89 | public: |
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90 | GenbankReader(const char *inf) : SimpleFormatReader(inf) {} |
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91 | |
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92 | const char *get_key_word(int offset) { |
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93 | char key[TOKENSIZE]; |
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94 | genbank_key_word(line() + offset, 0, key); |
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95 | return shorttimecopy(key); |
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96 | } |
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97 | bool read_one_entry(Seq& seq) OVERRIDE __ATTR__USERESULT; |
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98 | InputFormat& get_data() OVERRIDE { return data; } |
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99 | }; |
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100 | |
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101 | // ---------------------- |
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102 | // GenbankParser |
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103 | |
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104 | class GenbankParser : public Parser { |
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105 | GenBank& gbk; |
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106 | |
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107 | void parse_keyed_section(const char *key); |
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108 | public: |
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109 | GenbankParser(GenBank& gbk_, Seq& seq_, GenbankReader& reader_) : Parser(seq_, reader_), gbk(gbk_) {} |
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110 | void parse_section() OVERRIDE; |
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111 | |
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112 | const GenBank& get_data() const OVERRIDE { return gbk; } |
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113 | }; |
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114 | |
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115 | #else |
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116 | #error genbank.h included twice |
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117 | #endif // GENBANK_H |
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