| 1 | // =============================================================== // |
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| 2 | // // |
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| 3 | // File : ali_arbdb.cxx // |
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| 4 | // Purpose : // |
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| 5 | // // |
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| 6 | // Institute of Microbiology (Technical University Munich) // |
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| 7 | // http://www.arb-home.de/ // |
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| 8 | // // |
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| 9 | // =============================================================== // |
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| 10 | |
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| 11 | #include "ali_sequence.hxx" |
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| 12 | #include "ali_arbdb.hxx" |
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| 13 | |
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| 14 | |
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| 15 | #define HELIX_PAIRS "helix_pairs" |
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| 16 | #define HELIX_LINE "helix_line" |
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| 17 | |
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| 18 | |
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| 19 | ALI_ARBDB::~ALI_ARBDB() { |
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| 20 | if (gb_main) GB_close(gb_main); |
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| 21 | freenull(alignment); |
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| 22 | } |
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| 23 | |
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| 24 | int ALI_ARBDB::open(char *name, char *use_alignment) { |
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| 25 | gb_main = GB_open(name, "rt"); |
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| 26 | if (!gb_main) { |
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| 27 | GB_print_error(); |
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| 28 | return 1; |
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| 29 | } |
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| 30 | |
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| 31 | if (use_alignment) { |
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| 32 | alignment = ARB_strdup(use_alignment); |
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| 33 | } |
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| 34 | else { |
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| 35 | GB_begin_transaction(gb_main); |
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| 36 | alignment = GBT_get_default_alignment(gb_main); |
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| 37 | GB_commit_transaction(gb_main); |
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| 38 | |
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| 39 | if (!alignment) { |
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| 40 | GB_print_error(); |
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| 41 | return 1; |
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| 42 | } |
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| 43 | } |
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| 44 | |
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| 45 | return 0; |
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| 46 | } |
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| 47 | |
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| 48 | void ALI_ARBDB::close() { |
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| 49 | GB_close(gb_main); |
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| 50 | freenull(alignment); |
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| 51 | } |
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| 52 | |
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| 53 | char *ALI_ARBDB::get_sequence_string(char *name, int and_mark) { |
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| 54 | char *sequence = NULp; |
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| 55 | GBDATA *gb_species_data; |
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| 56 | GBDATA *gb_seq; |
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| 57 | |
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| 58 | gb_species_data = GBT_get_species_data(gb_main); |
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| 59 | |
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| 60 | gb_seq = GB_find_string(gb_species_data, "name", name, GB_IGNORE_CASE, SEARCH_GRANDCHILD); |
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| 61 | if (gb_seq) { |
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| 62 | if (and_mark) GB_write_flag(GB_get_father(gb_seq), 1); |
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| 63 | gb_seq = GB_brother(gb_seq, alignment); |
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| 64 | if (gb_seq) { |
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| 65 | gb_seq = GB_entry(gb_seq, "data"); |
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| 66 | if (gb_seq) |
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| 67 | sequence = GB_read_string(gb_seq); |
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| 68 | } |
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| 69 | } |
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| 70 | |
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| 71 | return sequence; |
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| 72 | } |
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| 73 | |
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| 74 | ALI_SEQUENCE *ALI_ARBDB::get_sequence(char *name, int and_mark) { |
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| 75 | ALI_SEQUENCE *ali_seq; |
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| 76 | char *sequence = NULp; |
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| 77 | GBDATA *gb_species_data; |
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| 78 | GBDATA *gb_seq; |
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| 79 | |
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| 80 | gb_species_data = GBT_get_species_data(gb_main); |
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| 81 | |
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| 82 | gb_seq = GB_find_string(gb_species_data, "name", name, GB_IGNORE_CASE, SEARCH_GRANDCHILD); |
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| 83 | if (gb_seq) { |
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| 84 | if (and_mark) GB_write_flag(GB_get_father(gb_seq), 1); |
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| 85 | gb_seq = GB_brother(gb_seq, alignment); |
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| 86 | if (gb_seq) { |
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| 87 | gb_seq = GB_entry(gb_seq, "data"); |
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| 88 | if (gb_seq) |
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| 89 | sequence = GB_read_string(gb_seq); |
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| 90 | } |
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| 91 | } |
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| 92 | |
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| 93 | if (!sequence) |
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| 94 | return NULp; |
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| 95 | |
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| 96 | ali_seq = new ALI_SEQUENCE(name, sequence); |
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| 97 | |
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| 98 | return ali_seq; |
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| 99 | } |
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| 100 | |
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| 101 | char *ALI_ARBDB::get_SAI(char *name) { |
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| 102 | char *extended = NULp; |
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| 103 | GBDATA *gb_sai_data = GBT_get_SAI_data(gb_main); |
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| 104 | GBDATA *gb_sai = GB_find_string(gb_sai_data, "name", name, GB_IGNORE_CASE, SEARCH_GRANDCHILD); |
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| 105 | |
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| 106 | if (gb_sai) { |
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| 107 | gb_sai = GB_brother(gb_sai, alignment); |
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| 108 | if (gb_sai) { |
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| 109 | gb_sai = GB_entry(gb_sai, "data"); |
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| 110 | if (gb_sai) |
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| 111 | extended = GB_read_string(gb_sai); |
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| 112 | } |
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| 113 | } |
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| 114 | |
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| 115 | return extended; |
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| 116 | } |
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| 117 | |
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| 118 | |
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| 119 | int ALI_ARBDB::put_sequence_string(char *name, char *sequence) { |
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| 120 | GB_securityLevel raised(gb_main, 6); |
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| 121 | |
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| 122 | GBDATA *gb_species_data = GBT_get_species_data(gb_main); |
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| 123 | GBDATA *gb_seq = GB_find_string(gb_species_data, "name", name, GB_IGNORE_CASE, SEARCH_GRANDCHILD); |
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| 124 | if (gb_seq) { |
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| 125 | GBDATA *gb_ali = GB_brother(gb_seq, alignment); |
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| 126 | if (gb_ali) { |
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| 127 | GBDATA *gb_data = GB_search(gb_ali, "data", GB_STRING); |
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| 128 | GB_write_string(gb_data, sequence); |
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| 129 | free(sequence); |
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| 130 | } |
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| 131 | } |
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| 132 | |
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| 133 | return 0; |
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| 134 | } |
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| 135 | |
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| 136 | int ALI_ARBDB::put_sequence(char *name, ALI_SEQUENCE *sequence) { |
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| 137 | GB_securityLevel raised(gb_main, 6); |
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| 138 | |
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| 139 | GBDATA *gb_species_data = GBT_get_species_data(gb_main); |
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| 140 | GBDATA *gb_seq = GB_find_string(gb_species_data, "name", name, GB_IGNORE_CASE, SEARCH_GRANDCHILD); |
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| 141 | if (gb_seq) { |
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| 142 | GBDATA *gb_ali = GB_brother(gb_seq, alignment); |
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| 143 | if (gb_ali) { |
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| 144 | GBDATA *gb_data = GB_search(gb_ali, "data", GB_STRING); |
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| 145 | char *String = sequence->string(); |
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| 146 | GB_write_string(gb_data, String); |
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| 147 | free(String); |
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| 148 | } |
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| 149 | } |
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| 150 | |
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| 151 | return 0; |
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| 152 | } |
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| 153 | |
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| 154 | |
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| 155 | int ALI_ARBDB::put_SAI(const char *name, char *sequence) { |
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| 156 | GB_securityLevel raised(gb_main, 6); |
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| 157 | |
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| 158 | GBDATA *gb_extended = GBT_find_or_create_SAI(gb_main, name); |
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| 159 | GBDATA *gb_data = GBT_add_data(gb_extended, alignment, "data", GB_STRING); |
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| 160 | GB_write_string(gb_data, sequence); |
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| 161 | |
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| 162 | return 0; |
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| 163 | } |
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