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Revision 8301, 1.2 KB
(checked in by westram, 5 months ago)
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- fixed some realigner bugs
- when species did not contain transl_table and codon_start, the realigner inserted only codon_start.
- the next realignment/translation failed since it expected BOTH or NONE of the two fields.
- now the realigner
- either writes both fields (if used transl_table is well-defined)
- deletes both fields
- when some/all species did not contain data in source and/or destination alignment, the realigner silently skipped them
- now prints a message about skipped species
- errors during realignment (e.g. protection errors) were not shown
Note: grml .. similar patch was already in trunk as [6600]
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Author Date Id Revision
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| 1 | // =============================================================== // |
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| 2 | // // |
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| 3 | // File : awt_translate.hxx // |
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| 4 | // Purpose : // |
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| 5 | // // |
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| 6 | // Coded by Ralf Westram (coder@reallysoft.de) in June 2006 // |
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| 7 | // Institute of Microbiology (Technical University Munich) // |
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| 8 | // http://www.arb-home.de/ // |
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| 9 | // // |
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| 10 | // =============================================================== // |
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| 11 | #ifndef AWT_TRANSLATE_HXX |
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| 12 | #define AWT_TRANSLATE_HXX |
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| 13 | |
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| 14 | GB_ERROR AWT_getTranslationInfo(GBDATA *gb_species, int& arb_transl_table, int &codon_start); |
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| 15 | GB_ERROR AWT_saveTranslationInfo(GBDATA *gb_species, int arb_transl_table, int codon_start); |
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| 16 | GB_ERROR AWT_removeTranslationInfo(GBDATA *gb_species); |
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| 17 | |
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| 18 | int AWT_pro_a_nucs_convert(int arb_code_nr, char *data, size_t size, size_t pos, bool translate_all, bool create_start_codon, bool append_stop_codon, int *translatedSize); |
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| 19 | |
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| 20 | #else |
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| 21 | #error awt_translate.hxx included twice |
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| 22 | #endif // AWT_TRANSLATE_HXX |
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