#include "GEN_local.hxx"#include <Translate.hxx>#include <AP_codon_table.hxx>#include <aw_question.hxx>#include <arbdbt.h>
Go to the source code of this file.
Macros | |
| #define | set_result_bit(s) result = GEN_remove_state(result|s) |
Enumerations | |
| enum | GEN_remove_state { GRS_NO_CHANGE = 0, GRS_FAILED = 1, GRS_TRANSLATION_REMOVED = 2, GRS_TRANSLATION_FAILED = 4, GRS_START_CODON_WRONG = 8, GRS_NOTE_ADDED = 16 } |
Functions | |
| static char * | translate_gene_sequence (GBDATA *gb_gene, GB_ERROR &error, int &translated_length, char *startCodon) |
| static GEN_remove_state | remove_redundant_translation (GBDATA *gb_gene, bool ignore_start_codon_error, char *errornousCodon, GB_ERROR &error) |
| GB_ERROR | GEN_testAndRemoveTranslations (GBDATA *gb_gene_data, void(*warn)(AW_CL cd, const char *msg), AW_CL cd, AW_repeated_question *ok_to_ignore_wrong_start_codon) |
Macro Definition Documentation
| #define set_result_bit | ( | s | ) | result = GEN_remove_state(result|s) |
Referenced by remove_redundant_translation().
Enumeration Type Documentation
| enum GEN_remove_state |
| Enumerator | |
|---|---|
| GRS_NO_CHANGE | |
| GRS_FAILED | |
| GRS_TRANSLATION_REMOVED | |
| GRS_TRANSLATION_FAILED | |
| GRS_START_CODON_WRONG | |
| GRS_NOTE_ADDED | |
Definition at line 56 of file GEN_translations.cxx.
Function Documentation
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static |
Definition at line 27 of file GEN_translations.cxx.
References GB_await_error(), GBT_read_gene_sequence_and_length(), NULp, translate_getInfo(), translate_nuc2aa(), and TTIT_embl2arb().
Referenced by remove_redundant_translation().
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static |
Definition at line 65 of file GEN_translations.cxx.
References GB_delete(), GB_entry(), GB_read_char_pntr(), GBS_global_string(), GBS_global_string_copy(), GBT_write_byte(), GBT_write_string(), GRS_FAILED, GRS_NO_CHANGE, GRS_NOTE_ADDED, GRS_START_CODON_WRONG, GRS_TRANSLATION_FAILED, GRS_TRANSLATION_REMOVED, NULp, result, set_result_bit, and translate_gene_sequence().
Referenced by GEN_testAndRemoveTranslations().
| GB_ERROR GEN_testAndRemoveTranslations | ( | GBDATA * | gb_gene_data, |
| void(*)(AW_CL cd, const char *msg) | warn, | ||
| AW_CL | cd, | ||
| AW_repeated_question * | ok_to_ignore_wrong_start_codon | ||
| ) |
Definition at line 157 of file GEN_translations.cxx.
References error(), GB_entry(), GB_IGNORE_CASE, GB_nextEntry(), GBS_create_hash(), GBS_free_hash(), GBS_global_string(), GBS_hashtab_2_string(), GBS_incr_hash(), gen_assert, GRS_FAILED, GRS_NO_CHANGE, GRS_NOTE_ADDED, GRS_START_CODON_WRONG, GRS_TRANSLATION_FAILED, GRS_TRANSLATION_REMOVED, NULp, and remove_redundant_translation().
