source: tags/arb_5.1/ARBDB/adGene.h

Last change on this file was 5768, checked in by westram, 17 years ago
  • rewrote genome importer
  • remove redundant 'translation' entries of genes during import
  • whole code is using
    • 'pos_start' instead of 'pos_begin*'
    • 'pos_stop' instead of 'pos_end*'
    • 'pos_certain' instead of 'pos_uncertain*'
    • 'pos_complement' instead of 'complement'
  • convert gene locations in old genome DBs into new format
  • added several gene functions to ARBDB
    • GEN_create_nonexisting_gene…()
    • GEN_find_or_create_gene..()
    • GEN_global_gene_identifier()
  • added code to handle gene locations into ARBDB (type GEN_position represents every flavour of a Genbank/EMBL feature location)
  • added GBT_write_byte()
  • rewrote GBT_read_gene_sequence() (adding GBT_read_gene_sequence_and_length)
  • changed codon tables according to NCBI code info
    • added start codon(s) for code 3, 9, 13
    • changed code names
  • when importing to a new DB, reset DB type if import fails (before ARB had to be restarted, after one try with wrong genome/non-genome import)
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 2.4 KB
Line 
1/*  ====================================================================  */
2/*                                                                        */
3/*    File      : adGene.h                                                */
4/*    Purpose   : Specific defines for ARB genome                         */
5/*                                                                        */
6/*                                                                        */
7/*  Coded by Ralf Westram (coder@reallysoft.de) in July 2002              */
8/*  Copyright Department of Microbiology (Technical University Munich)    */
9/*                                                                        */
10/*  Visit our web site at: http://www.arb-home.de/                        */
11/*                                                                        */
12/*  ====================================================================  */
13
14#ifndef ADGENE_H
15#define ADGENE_H
16
17#ifndef ARBDB_H
18#include "arbdb.h"
19#endif
20
21#define GENOM_ALIGNMENT "ali_genom"
22#define GENOM_DB_TYPE   "genom_db"  // main flag (true = genom db, false/missing=normal db)
23
24#define ARB_HIDDEN "ARB_display_hidden"
25
26/* GEN_position is interpreted as
27 *
28 * join( complement[0](start_pos[0]..stop_pos[0]),
29 *       complement[1](start_pos[1]..stop_pos[1]),
30 *       complement[2](start_pos[2], stop_pos[2]),
31 *       ... )
32 *
33 * start_pos is always lower than stop_pos
34 * joined genes on complementary strand are normally ordered backwards
35 * (i.e. part with highest positions comes first)
36 */
37
38struct GEN_position {
39    int            parts;
40    GB_BOOL        joinable;    // GB_TRUE = join(...), GB_FALSE = order(...) aka not joinable or unknown
41    size_t        *start_pos;
42    size_t        *stop_pos;
43    unsigned char *complement;  // 0       = normal or 1 = complementary
44
45    // [optional elements]
46
47    // start_uncertain/stop_uncertain contain one char per part (or NULL which means "all positions are certain")
48    // meaning of characters:
49    // '<' = position MIGHT be lower
50    // '=' = position is certain
51    // '>' = position MIGHT be higher
52    // '+' = position is directly BEHIND (but before next base position, i.e. specifies a location between to base positions)
53    // '-' = position is BEFORE
54
55    unsigned char *start_uncertain;
56    unsigned char *stop_uncertain;
57};
58
59#ifndef ARBDB_H
60#include "arbdb.h"
61#endif
62
63
64#else
65#error adGene.h included twice
66#endif /* ADGENE_H */
67
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