Inheritance diagram for Aligner:
Collaboration diagram for Aligner:
Public Member Functions | |
| Aligner (GBDATA *gb_main_, FA_alignTarget alignWhat_, GB_CSTR alignment_, GB_CSTR toalign_, Aligner_get_first_selected_species get_first_selected_species_, Aligner_get_next_selected_species get_next_selected_species_, GB_CSTR reference_, Aligner_get_consensus_func get_consensus_, SearchRelativeParams &relSearch_, FA_turn turnAllowed_, const AlignParams &ali_params_, int maxProtection_, bool continue_on_error_, FA_errorAction error_action_) | |
| ARB_ERROR | run () |
Detailed Description
Definition at line 1820 of file fast_aligner.cxx.
Constructor & Destructor Documentation
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inline |
Definition at line 1874 of file fast_aligner.cxx.
References gb_assert.
Member Function Documentation
| ARB_ERROR Aligner::run | ( | ) |
Definition at line 2075 of file fast_aligner.cxx.
References aw_message(), aw_message_if(), LooseBases::clear(), ClustalV_exit(), error(), fa_assert(), FA_MARK_ALIGNED, FA_NO_ACTION, FA_TURN_NEVER, GB_append_exportedError(), GB_AT_DNA, GB_AT_RNA, GB_AT_UNKNOWN, GB_end_transaction(), GB_get_transaction_level(), GB_push_transaction(), GB_write_flag(), GBS_global_string(), GBT_get_alignment_len(), GBT_get_alignment_type(), GBT_get_species_data(), GBT_mark_all(), global_alignmentType, PosRange::is_part(), SearchRelativeParams::pt_server_alignment, AlignParams::range, and ta.
The documentation for this class was generated from the following file:
- SL/FAST_ALIGNER/fast_aligner.cxx
