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