#cython: language_level=3 from .obitypes cimport const_char_p, \ OBIType_t, \ obiversion_t, \ obiint_t, \ obibool_t, \ obichar_t, \ obifloat_t, \ index_t, \ time_t from ..capi.obidms cimport OBIDMS_p from ..capi.obidmscolumn cimport OBIDMS_column_p, \ Column_reference_t, \ Column_reference_p from libc.stdint cimport uint8_t, int32_t cdef extern from "obiview.h" nogil: extern const_char_p VIEW_TYPE_NUC_SEQS extern const_char_p NUC_SEQUENCE_COLUMN extern const_char_p ID_COLUMN extern const_char_p DEFINITION_COLUMN extern const_char_p QUALITY_COLUMN extern const_char_p COUNT_COLUMN extern const_char_p TAXID_COLUMN extern const_char_p MERGED_TAXID_COLUMN extern const_char_p MERGED_PREFIX extern const_char_p TAXID_DIST_COLUMN extern const_char_p MERGED_COLUMN struct Alias_column_pair_t : Column_reference_t column_refs const_char_p alias ctypedef Alias_column_pair_t* Alias_column_pair_p struct Obiview_infos_t : time_t creation_date const_char_p name const_char_p created_from const_char_p view_type bint all_lines Column_reference_t line_selection index_t line_count int column_count Alias_column_pair_p column_references const_char_p comments ctypedef Obiview_infos_t* Obiview_infos_p struct Obiview_t : Obiview_infos_p infos OBIDMS_p dms bint read_only OBIDMS_column_p line_selection OBIDMS_column_p columns int nb_predicates # TODO declarations for column dictionary and predicate function array? ctypedef Obiview_t* Obiview_p Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection, const_char_p comments, bint quality_column, bint create_default_columns) Obiview_p obi_new_view(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection, const_char_p comments) Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments) Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments) Obiview_p obi_clone_view(OBIDMS_p dms, Obiview_p view_to_clone, const char* view_name, index_t* line_selection, const char* comments) Obiview_p obi_clone_view_from_name(OBIDMS_p dms, const char* view_to_clone_name, const char* view_name, index_t* line_selection, const char* comments) Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name, bint finished) int obi_view_unmap_file(OBIDMS_p dms, Obiview_infos_p view_infos) Obiview_p obi_open_view(OBIDMS_p dms, const_char_p view_name) int obi_view_add_column(Obiview_p view, const_char_p column_name, obiversion_t version_number, const_char_p alias, OBIType_t data_type, index_t nb_lines, index_t nb_elements_per_line, char* elements_names, bint elt_names_formatted, bint tuples, bint to_eval, const_char_p indexer_name, const_char_p associated_column_name, obiversion_t associated_column_version, const_char_p comments, bint create) int obi_view_delete_column(Obiview_p view, const_char_p column_name) OBIDMS_column_p obi_view_get_column(Obiview_p view, const_char_p column_name) OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const_char_p column_name) int obi_view_create_column_alias(Obiview_p view, const_char_p current_name, const_char_p alias) int obi_view_write_comments(Obiview_p view, const_char_p comments) int obi_view_add_comment(Obiview_p view, const_char_p key, const_char_p value) int obi_save_and_close_view(Obiview_p view) int obi_clean_unfinished_views(OBIDMS_p dms) int obi_rollback_view(Obiview_p view) int obi_delete_view(OBIDMS_p dms, const char* view_name) # OBI_INT int obi_set_int_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const_char_p element_name, obiint_t value) int obi_set_int_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx, obiint_t value) obiint_t obi_get_int_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const_char_p element_name) obiint_t obi_get_int_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx) # OBI_BOOL int obi_set_bool_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const_char_p element_name, obibool_t value) int obi_set_bool_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx, obibool_t value) obibool_t obi_get_bool_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const_char_p element_name) obibool_t obi_get_bool_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx) # OBI_CHAR int obi_set_char_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const_char_p element_name, obichar_t value) int obi_set_char_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx, obichar_t value) obichar_t obi_get_char_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const_char_p element_name) obichar_t obi_get_char_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx) # OBI_FLOAT int obi_set_float_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const_char_p element_name, obifloat_t value) int obi_set_float_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx, obifloat_t value) obifloat_t obi_get_float_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const_char_p element_name) obifloat_t obi_get_float_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx) # OBI_QUAL int obi_set_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx, const char* value, int offset) int obi_set_qual_int_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx, const uint8_t* value, int value_length) char* obi_get_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx, int offset) const uint8_t* obi_get_qual_int_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx, int* value_length) int obi_set_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const char* element_name, const char* value, int offset) int obi_set_qual_int_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const char* element_name, const uint8_t* value, int value_length) char* obi_get_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const char* element_name, int offset) const uint8_t* obi_get_qual_int_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const char* element_name, int* value_length) # OBI_STR int obi_set_str_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const_char_p element_name, const_char_p value) int obi_set_str_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx, const_char_p value) const_char_p obi_get_str_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const_char_p element_name) const_char_p obi_get_str_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx) # OBI_SEQ int obi_set_seq_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const_char_p element_name, const_char_p value) int obi_set_seq_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx, const_char_p value) char* obi_get_seq_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const_char_p element_name) char* obi_get_seq_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx) # OBI_IDX int obi_set_index_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const_char_p element_name, index_t value) int obi_set_index_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx, index_t value) index_t obi_get_index_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const_char_p element_name) index_t obi_get_index_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx) # ARRAY int obi_set_array_with_col_p_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const void* value, uint8_t elt_size, int32_t value_length) const void* obi_get_array_with_col_p_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, int32_t* value_length_p) int obi_set_array_with_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const void* value, uint8_t elt_size, int32_t value_length) const void* obi_get_array_with_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, int32_t* value_length_p)