#include <TranslateRealign.h>#include <Translate.hxx>#include <AP_codon_table.hxx>#include <AP_pro_a_nucs.hxx>#include <aw_question.hxx>#include <arb_progress.h>#include <arb_global_defs.h>#include <arbdbt.h>#include <arb_defs.h>#include <string>
Go to the source code of this file.
Classes | |
| class | BufferPtr< T > |
| class | SizedBufferPtr< T > |
| class | Distributor |
| class | FailedAt |
| class | RealignAttempt |
| class | Realigner |
| struct | Data |
Macros | |
| #define | ali_assert(cond) arb_assert(cond) |
Typedefs | |
| typedef SizedBufferPtr< const char > | SizedReadBuffer |
| typedef SizedBufferPtr< char > | SizedWriteBuffer |
Functions | |
| bool | legal_ORF_pos (int p) |
| GB_ERROR | ALI_translate_marked (GBDATA *gb_main, bool use_entries, bool save_entries, int selected_startpos, bool translate_all, const char *ali_source, const char *ali_dest) |
| bool | isGap (char c) |
| static GB_ERROR | distribute_xdata (SizedReadBuffer &dna, size_t xcount, char *xtarget_, bool gap_before, bool gap_after, const TransTables &allowed, TransTables &remaining) |
| char * | unalign (const char *data, size_t len, size_t &compressed_len) |
| GB_ERROR | ALI_realign_marked (GBDATA *gb_main, const char *ali_source, const char *ali_dest, size_t &neededLength, bool unmark_succeeded, bool cutoff_dna) |
Macro Definition Documentation
| #define ali_assert | ( | cond | ) | arb_assert(cond) |
Definition at line 22 of file TranslateRealign.cxx.
Referenced by FailedAt::add_prefix(), ALI_realign_marked(), ALI_translate_marked(), distribute_xdata(), FailedAt::FailedAt(), BufferPtr< char >::inc(), BufferPtr< char >::operator[](), Distributor::operator[](), Realigner::realign_seq(), RealignAttempt::RealignAttempt(), SizedBufferPtr< char >::restLength(), Distributor::translates_to_Xs(), and SizedBufferPtr< char >::~SizedBufferPtr().
Typedef Documentation
| typedef SizedBufferPtr<const char> SizedReadBuffer |
Definition at line 73 of file TranslateRealign.cxx.
| typedef SizedBufferPtr<char> SizedWriteBuffer |
Definition at line 74 of file TranslateRealign.cxx.
Function Documentation
|
inline |
Definition at line 79 of file TranslateRealign.cxx.
Referenced by ALI_translate_marked().
| GB_ERROR ALI_translate_marked | ( | GBDATA * | gb_main, |
| bool | use_entries, | ||
| bool | save_entries, | ||
| int | selected_startpos, | ||
| bool | translate_all, | ||
| const char * | ali_source, | ||
| const char * | ali_dest | ||
| ) |
Definition at line 81 of file TranslateRealign.cxx.
References ali_assert, ARB_strdup(), AUTODETECT_STARTPOS, aw_ask_sure(), AWAR_PROTEIN_TYPE, AWT_CODON_TABLES, error(), GB_await_error(), GB_clear_error(), GB_entry(), GB_print_error(), GB_read_string(), GB_read_string_count(), GB_STRING, GB_warning(), GB_write_string(), GBS_global_string(), GBS_global_string_copy(), GBT_add_alignment_changekeys(), GBT_add_data(), GBT_count_marked_species(), GBT_create_alignment(), GBT_first_marked_species(), GBT_get_alignment(), GBT_get_alignment_len(), GBT_next_marked_species(), GBT_read_int(), arb_progress::inc_and_check_user_abort(), legal_ORF_pos(), NULp, translate_getInfo(), translate_nuc2aa(), translate_saveInfo(), and TTIT_arb2embl().
Referenced by transpro_event().
|
inline |
Definition at line 441 of file TranslateRealign.cxx.
References GAP::is_std_gap().
Referenced by BaseFrequencies::build_consensus_string_to(), export_sequence_data::detectVerticalGaps(), distribute_xdata(), export_sequence_data::get_export_sequence(), and unalign().
|
static |
distributes 'dna' to marked X-positions
- Parameters
-
xtarget destination buffer (target positions are marked with '!') xcount number of X's encountered gap_before true if resulting realignment has a gap or the start of alignment before the X-positions gap_after analog to 'gap_before' allowed allowed translation tables remaining remaining allowed translation tables (with those tables disabled for which no distribution possible)
- Returns
- error if dna distribution wasn't possible
Definition at line 511 of file TranslateRealign.cxx.
References ali_assert, BufferPtr< T >::copy(), error(), FALLTHROUGH, BufferPtr< T >::get(), Distributor::get_score(), BufferPtr< T >::inc(), TransTables::is_subset_of(), isGap(), SizedBufferPtr< T >::length(), Distributor::mayFailTranslation(), NULp, BufferPtr< T >::offset(), BufferPtr< T >::put(), Distributor::size(), tree_defaults::SPREAD, Distributor::translates_to_Xs(), and SizedBufferPtr< T >::valid().
Definition at line 820 of file TranslateRealign.cxx.
References isGap().
Referenced by Realigner::realign_seq().
| GB_ERROR ALI_realign_marked | ( | GBDATA * | gb_main, |
| const char * | ali_source, | ||
| const char * | ali_dest, | ||
| size_t & | neededLength, | ||
| bool | unmark_succeeded, | ||
| bool | cutoff_dna | ||
| ) |
realigns DNA alignment of marked sequences according to their protein alignment
- Parameters
-
ali_source protein source alignment ali_dest modified DNA alignment neededLength result: minimum alignment length needed in ali_dest (if too short) or 0 if long enough unmark_succeeded unmark all species that were successfully realigned
Definition at line 1004 of file TranslateRealign.cxx.
References ali_assert, TransTables::any(), AP_initialize_codon_tables(), arb_progress::auto_subtitles(), buffer, Realigner::clear_failure(), Data::data, arb_progress::done(), error(), Data::error, TransTables::explicit_table(), Realigner::failure(), TransTables::forbidAllBut(), GB_append_exportedError(), GB_AT_AA, GB_AT_DNA, Data::gb_data, GB_get_transaction_level(), GB_warning(), GB_warningf(), GB_write_flag(), GB_write_string(), GBS_global_string(), GBT_check_data(), GBT_count_marked_species(), GBT_first_marked_species(), GBT_get_alignment(), GBT_get_alignment_len(), GBT_get_alignment_type(), GBT_get_name_or_description(), GBT_next_marked_species(), Realigner::get_needed_dest_alilen(), arb_progress::inc_and_check_user_abort(), Data::len, NULp, Realigner::realign_seq(), Realigner::set_failure(), ta, translate_getInfo(), and translate_saveInfo().
Referenced by realign_event().
