/******************************************************************** * Obiview header file * ********************************************************************/ /** * @file obiview.h * @author Celine Mercier (celine.mercier@metabarcoding.org) * @date 16 December 2015 * @brief Header file for the OBIDMS view functions and structures. */ #ifndef OBIVIEW_H_ #define OBIVIEW_H_ #include #include #include #include #include #include #include #include "obidms.h" #include "obidmscolumn.h" #include "obierrno.h" #include "hashtable.h" #include "linked_list.h" #include "obiblob.h" #define OBIVIEW_NAME_MAX_LENGTH (249) /**< The maximum length of an OBIDMS view name, without the extension. */ #define VIEW_TYPE_MAX_LENGTH (1024) /**< The maximum length of the type name of a view. */ #define LINES_COLUMN_NAME "LINES" /**< The name of the column containing the line selections * in all views. */ #define VIEW_TYPE_NUC_SEQS "NUC_SEQS_VIEW" /**< The type name of views based on nucleotide sequences * and their metadata. */ #define NUC_SEQUENCE_COLUMN "NUC_SEQ" /**< The name of the column containing the nucleotide sequences * in NUC_SEQS_VIEW views. */ #define ID_COLUMN "ID" /**< The name of the column containing the sequence identifiers * in NUC_SEQS_VIEW views. */ #define DEFINITION_COLUMN "DEFINITION" /**< The name of the column containing the sequence definitions * in NUC_SEQS_VIEW views. */ #define QUALITY_COLUMN "QUALITY" /**< The name of the column containing the sequence qualities * in NUC_SEQS_VIEW views. */ #define REVERSE_QUALITY_COLUMN "REVERSE_QUALITY" /**< The name of the column containing the sequence qualities * of the reverse read (generated by ngsfilter, used by alignpairedend). */ #define REVERSE_SEQUENCE_COLUMN "REVERSE_SEQUENCE" /**< The name of the column containing the sequence * of the reverse read (generated by ngsfilter, used by alignpairedend). */ #define QUALITY_COLUMN "QUALITY" /**< The name of the column containing the sequence qualities * in NUC_SEQS_VIEW views. */ #define COUNT_COLUMN "COUNT" /**< The name of the column containing the sequence counts * in NUC_SEQS_VIEW views. */ #define SCIENTIFIC_NAME_COLUMN "SCIENTIFIC_NAME" /**< The name of the column containing the taxon scientific name. */ #define TAXID_COLUMN "TAXID" /**< The name of the column containing the taxids. TODO subtype of INT column? */ #define MERGED_TAXID_COLUMN "MERGED_TAXID" /**< The name of the column containing the merged taxids information. */ #define MERGED_PREFIX "MERGED_" /**< The prefix to prepend to column names when merging informations during obi uniq. */ #define TAXID_DIST_COLUMN "TAXID_DIST" /**< The name of the column containing a dictionary of taxid:[list of ids] when merging informations during obi uniq. */ #define MERGED_COLUMN "MERGED" /**< The name of the column containing a list of ids when merging informations during obi uniq. */ #define ID_PREFIX "seq" /**< The default prefix of sequence identifiers in automatic ID columns. */ #define PREDICATE_KEY "predicates" /**< The key used in the json-formatted view comments to store predicates. */ /** * @brief Structure for column aliases. * Column aliases are alternative names used to identify a column in the context of a view. */ typedef struct Alias_column_pair { Column_reference_t column_refs; /**< References (name and version) of the column. */ char alias[OBIDMS_COLUMN_MAX_NAME+1]; /**< Alias of the column in the context of a view. */ } Alias_column_pair_t, *Alias_column_pair_p; /** * @brief Structure for a closed view stored in the view file. * Views are identified by their name. * Once a view has been written in the view file, it can not be modified and can only be read. */ typedef struct Obiview_infos { size_t file_size; /**< View file size in bytes. */ size_t used_size; /**< Used size in bytes. */ time_t creation_date; /**< Time at which the view was created. */ char name[OBIVIEW_NAME_MAX_LENGTH+1]; /**< Name of the view, used to identify it. */ char created_from[OBIVIEW_NAME_MAX_LENGTH+1]; /**< Name of the view from which that view was cloned, if it was cloned. */ char view_type[VIEW_TYPE_MAX_LENGTH+1]; /**< Type of the view if there is one. * Types existing: NUC_SEQS_VIEW. */ bool all_lines; /**< Whether there is a line selection associated with the view. */ Column_reference_t line_selection; /**< The references of the line selection associated with the view if there is one. */ index_t line_count; /**< The number of lines in the view. */ int column_count; /**< The number of columns in the view. */ Alias_column_pair_t column_references[MAX_NB_OPENED_COLUMNS]; /**< References (name, version and alias) for all the columns in the view. */ bool finished; /** Whether the view is finished and can be read. */ char comments[]; /**< Comments, additional informations on the view. */ } Obiview_infos_t, *Obiview_infos_p; /** * @brief Structure for an opened view. */ typedef struct Obiview { Obiview_infos_p infos; /**< A pointer on the mapped view informations. */ OBIDMS_p dms; /**< A pointer on the DMS to which the view belongs. */ bool read_only; /**< Whether the view is read-only or can be modified. */ OBIDMS_column_p line_selection; /**< A pointer on the column containing the line selection * associated with the view if there is one. * This line selection is read-only, and when a line from the view is read, * it is this line selection that is used. */ Linked_list_node_p columns; /**< Double linked chain containing the pointers on all the columns of the view. */ hashtable_p column_dict; /**< Hash table storing the pairs of column names or aliases with the associated * pointers on column pointers (OBIDMS_column_p*). */ int nb_predicates; /**< Number of predicates to test when closing the view. */ char* (**predicate_functions)(struct Obiview* view); /**< Array of pointers on all predicate functions to test when closing the view. */ } Obiview_t, *Obiview_p; /** * Function checking if a view (either finished or unfinished) with a given name already exists in a DMS. * * @param dms The DMS. * @param view_name The name of the view. * * @returns A boolean value indicating whether the view already exists or not. * * @since September 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ bool obi_view_exists(OBIDMS_p dms, const char* view_name); /** * @brief Creates a new view. * * Fails if a view with the same name already exists. * * @param dms A pointer on the OBIDMS. * @param view_name The unique name of the view. Can not be 'taxonomy' (used for URIs). * @param view_to_clone Eventually a pointer on the opened view to clone to create the new one, if there is one. NULL if not. * @param line_selection Eventually a pointer on a list of indexes corresponding to a line selection to use with the view to clone * if there is one. NULL if there is no line selection or no view to clone. * The end of the index array is flagged by a -1 value. * @param comments Eventually, comments to associate with the view. NULL if not. * * @returns A pointer to the newly created view structure. * @retval NULL if an error occurred. * * @since December 2015 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments); /** * @brief Creates a new view by cloning another view written in the view file and identified by its name. * * Note : obi_new_view can clone from a pointer on an opened view, while this function will read the view to clone * from the view file. * * Fails if a view with the same name already exists. * * @param dms A pointer on the OBIDMS. * @param view_name The unique name of the new view. Can not be 'taxonomy' (used for URIs). * @param view_to_clone_name The name of the view to clone stored in the view file of the OBIDMS. * @param line_selection Eventually a pointer on a list of indexes corresponding to a line selection to use with the view to clone * if there is one. NULL if there is no line selection or no view to clone. * @param comments Eventually, comments to associate with the view. NULL if not. * * @returns A pointer to the newly created view structure. * @retval NULL if an error occurred. * * @since December 2015 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments); /** * @brief Creates a new view with the type NUC_SEQ_VIEW, based on nucleotide sequences and their metadata. * * Fails if a view with the same name already exists. * * The obligatory columns specific to the view type are created too and opened: * - NUC_SEQUENCE_COLUMN where nucleotide sequences are stored * - ID_COLUMN where sequence identifiers are stored * - DEFINITION_COLUMN where sequence definitions are stored * And, if quality_column is True: * - QUALITY_COLUMN where sequence qualities are stored * * @param dms A pointer on the OBIDMS. * @param view_name The unique name of the view. Can not be 'taxonomy' (used for URIs). * @param view_to_clone Eventually a pointer on the opened view to clone to create the new one, if there is one. NULL if not. * @param line_selection Eventually a pointer on a list of indexes corresponding to a line selection to use with the view to clone * if there is one. NULL if there is no line selection or no view to clone. * @param comments Eventually, comments to associate with the view. NULL if not. * @param quality_column Whether or not a sequence quality column is associated with the view. * @param create_default_columns Whether to create the default columns associated with the view type (false when importing all columns from a view for example). * * @returns A pointer to the newly created view structure. * @retval NULL if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments, bool quality_column, bool create_default_columns); /** * @brief Creates a new view with the type NUC_SEQ_VIEW, based on nucleotide sequences and their metadata, * by cloning another NUC_SEQ_VIEW view written in the view file and identified by its name. * * Note : obi_new_view_nuc_seqs can clone from a pointer on an opened view, while this function will read the view to clone * from the view file. * * Fails if a view with the same name already exists. * Fails if the view to clone doesn't have the type NUC_SEQ_VIEW. * * The obligatory columns specific to the view type are created too and opened: * - NUC_SEQUENCE_COLUMN where nucleotide sequences are stored * - ID_COLUMN where sequence identifiers are stored * - DEFINITION_COLUMN where sequence definitions are stored * And, if quality_column is True: * - QUALITY_COLUMN where sequence qualities are stored * * @param dms A pointer on the OBIDMS. * @param view_name The unique name of the new view. Can not be 'taxonomy' (used for URIs). * @param view_to_clone_name The name of the view to clone stored in the view file of the OBIDMS. * @param line_selection Eventually a pointer on a list of indexes corresponding to a line selection to use with the view to clone * if there is one. NULL if there is no line selection or no view to clone. * @param comments Eventually, comments to associate with the view. NULL if not. * * @returns A pointer to the newly created view structure. * @retval NULL if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments); /** * @brief Clones a view using a pointer on the view to clone. * * The new view has the same type as the cloned one. * Fails if a view with the same name already exists. * * @param dms A pointer on the OBIDMS. * @param view_to_clone A pointer on the opened view to clone to create the new one. * @param view_name The unique name of the new view. Can not be 'taxonomy' (used for URIs). * @param line_selection Eventually a pointer on a list of indexes corresponding to a line selection to use with the view to clone * if there is one. NULL if there is no line selection or no view to clone. * @param comments Eventually, comments to associate with the view. NULL if not. * * @returns A pointer to the newly created view structure. * @retval NULL if an error occurred. * * @since April 2017 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ Obiview_p obi_clone_view(OBIDMS_p dms, Obiview_p view_to_clone, const char* view_name, index_t* line_selection, const char* comments); /** * @brief Clones a view using the name of the view to clone. * * The new view has the same type as the cloned one. * Fails if a view with the same name already exists. * * @param dms A pointer on the OBIDMS. * @param view_to_clone_name The name of the view to clone. * @param view_name The unique name of the new view. Can not be 'taxonomy' (used for URIs). * @param line_selection Eventually a pointer on a list of indexes corresponding to a line selection to use with the view to clone * if there is one. NULL if there is no line selection or no view to clone. * @param comments Eventually, comments to associate with the view. NULL if not. * * @returns A pointer to the newly created view structure. * @retval NULL if an error occurred. * * @since April 2017 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Maps a view file and returns the mapped structure stored in it. * * @param dms A pointer on the OBIDMS. * @param view_name The unique name identifying the view. * @param finished Whether the view is finished or not. * * @returns A pointer on the mapped view infos structure. * @retval NULL if an error occurred. * * @since June 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name, bool finished); /** * @brief Unmaps a view file. * * @param dms A pointer on the OBIDMS. * @param view_infos A pointer on the mapped view infos structure. * * @returns A value indicating the success of the operation. * @retval 0 if the operation was successfully completed. * @retval -1 if an error occurred. * * @since June 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_view_unmap_file(OBIDMS_p dms, Obiview_infos_p view_infos); /** * @brief Opens a view identified by its name stored in the view file. * * When opening a view, all the columns and eventually the line selection belonging to it are opened with it. * * @warning The opened view is read-only. * * @param dms A pointer on the OBIDMS. * @param view_name The unique name identifying the view. * * @returns A pointer on the opened view structure. * @retval NULL if an error occurred. * * @since December 2015 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name); /** * @brief Adds a column to a view. * * - If there is a line selection: * - The column's lines_used attribute must be at least the view's line count * - If there is no line selection: * - If it's the first column in the view: * - The view's line count is set to the column's lines_used attribute * - If it's not the first column in the view: * - The column's lines_used attribute must be equal to the view's line count * * @warning The view must be writable. * * @param view A pointer on the view. * @param column_name The name of the column. * @param version_number The version of the column if it should be opened and not created * (if -1, the latest version is retrieved). * @param alias The unique name used to identify the column in the context of this view. * If NULL or "", column_name is used. * @param data_type The OBIType code of the data, if the column is created. * @param nb_lines The number of lines to be stored (can be 0 if not known), if the column is created. * @param nb_elements_per_line The number of elements per line, if the column is created. * @param elements_names The names of the elements with ';' as separator (no terminal ';'), * if the column is created; NULL or "" if the default names are to be used ("0\01\02\0...\0n"). * @param elt_names_formatted Whether the separator for the elements names is ';' (false), or '\0' (true, as formatted by format_elements_names()). * @param dict_column Whether the column contains dictionary-like values. * @param tuples A boolean indicating whether the column should contain indices referring to indexed tuples. * @param to_eval A boolean indicating whether the column contains expressions that should be evaluated * (typically OBI_STR columns containing character strings to be evaluated by Python). * @param indexer_name The name of the indexer if there is one associated with the column, if the column is created. * If NULL or "", the indexer name is set as the column name. * @param associated_column_name The name of the associated column if there is one (otherwise NULL or ""), if the column is created. * @param associated_column_version The version of the associated column if there is one (otherwise -1), if the column is created. * @param comments Optional comments associated with the column if it is created (NULL or "" if no comments associated). * @param create Whether the column should be created (create == true) or already exists (create == false). * * @returns A value indicating the success of the operation. * @retval 0 if the operation was successfully completed. * @retval -1 if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_view_add_column(Obiview_p view, char* column_name, obiversion_t version_number, const char* alias, OBIType_t data_type, index_t nb_lines, index_t nb_elements_per_line, char* elements_names, bool elt_names_formatted, bool dict_column, bool tuples, bool to_eval, const char* indexer_name, const char* associated_column_name, obiversion_t associated_column_version, const char* comments, bool create); /** * @brief Deletes a column from a view. * * @warning The view must be writable. * * @param view A pointer on the view. * @param column_name The name of the column that should be deleted from the view. * @param delete_file Whether the column file should be deleted. Use carefully re: dependencies. * * @returns A value indicating the success of the operation. * @retval 0 if the operation was successfully completed. * @retval -1 if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_view_delete_column(Obiview_p view, const char* column_name, bool delete_file); /** * @brief Gets the pointer on a column from its name in a view. * * @param view A pointer on the view. * @param column_name The name of the column in the view. * * @returns A pointer on the column. * @retval NULL if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ OBIDMS_column_p obi_view_get_column(Obiview_p view, const char* column_name); /** * @brief Checks if a column exists in a view. * * @param view A pointer on the view. * @param column_name The name of the column in the view. * * @returns A boolean indicating whether or not the column exists in the view. * * @since July 2017 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ bool obi_view_column_exists(Obiview_p view, const char* column_name); /** * @brief Gets the pointer on the pointer on a column from its name in a view. * * Note: This is used to replace old cloned columns with new ones in views in layers above the C layer. * * @param view A pointer on the view. * @param column_name The name of the column in the view. * * @returns A pointer on the pointer on the column. * @retval NULL if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const char* column_name); /** * @brief Changes the name that identifies a column in the context of a view. * * In the context of a view, each column is identified by a name that is unique in this view. * * @warning The view must be writable. * * @param view A pointer on the view. * @param current_name The current name that identifies the column in this view. * @param alias The new name that should be used to identify the column in this view. * * @returns A value indicating the success of the operation. * @retval 0 if the operation was successfully completed. * @retval -1 if an error occurred. * * @since July 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_view_create_column_alias(Obiview_p view, const char* current_name, const char* alias); /** * @brief Returns the informations of a view with a human readable format (view name, date created, line count, column informations, comments). * * @warning The returned pointer has to be freed by the caller. * * @param column A pointer on a view. * @param detailed Whether the informations should contain view comments. * * @returns A pointer on a character array where the formatted view informations are stored. * @retval NULL if an error occurred. * * @since September 2020 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ char* obi_view_formatted_infos(Obiview_p view, bool detailed); /** * @brief Returns the informations of a view with a human readable format on one line (view name, date created, line count). * * @warning The returned pointer has to be freed by the caller. * * @param column A pointer on a view. * * @returns A pointer on a character array where the formatted view informations are stored. * @retval NULL if an error occurred. * * @since September 2020 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ char* obi_view_formatted_infos_one_line(Obiview_p view); /** * @brief Internal function writing new comments in a view file. * * The new comments replace the pre-existing ones. * The view file is enlarged if necessary. * * @param view A pointer on the view. * @param comments The new comments that should be written. * * @retval 0 if the operation was successfully completed. * @retval -1 if an error occurred. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_view_write_comments(Obiview_p view, const char* comments); /** * @brief Adds comments to a view file. * * This reads the comments in the JSON format and adds the key value pair. * If the key already exists, the value format is turned into an array and the new value is appended * if it is not already in the array. * * @param column A pointer on an OBIDMS column. * @param key The key. * @param value The value associated with the key. * * @retval 0 if the operation was successfully completed. * @retval -1 if an error occurred. * * @since August 2018 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_view_add_comment(Obiview_p view, const char* key, const char* value); /** * @brief Closes an opened view, and saves it if it is not read-only (meaning it is not already saved in the view file). * * The predicates associated with the view are checked before saving it, and -1 is returned if at * least one predicate is not respected. * * @param view A pointer on the view. * * @returns A value indicating the success of the operation. * @retval 0 if the operation was successfully completed. * @retval -1 if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_save_and_close_view(Obiview_p view); /** * @brief Goes through all the view files of a DMS and checks for views that have * not been flagged as finished (file extension renamed from '.obiview_unfinished' * to '.obiview' and finished boolean set to true in the file, done by finish_view()). * * @param dms A pointer on an OBIDMS. * * @returns A boolean indicating whether unfinished views were found. * * @since September 2019 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_dms_has_unfinished_views(OBIDMS_p dms); /** * @brief Goes through all the view files of a DMS and deletes views that have * not been flagged as finished (file extension renamed from '.obiview_unfinished' * to '.obiview' and finished boolean set to true in the file, done by finish_view()). * * @param dms A pointer on an OBIDMS. * * @returns A value indicating the success of the operation. * @retval 0 if the operation was successfully completed. * @retval -1 if an error occurred. * * @since October 2017 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_clean_unfinished_views(OBIDMS_p dms); /** * @brief Frees and deletes an opened, writable view and the columns it created. * * The view and column files are deleted and the structures are freed. * * @warning The view pointer becomes invalid, as well as the pointers on * the columns created by the view. * * @param view A pointer on the writable view to rollback. * * @returns A value indicating the success of the operation. * @retval 0 if the operation was successfully completed. * @retval -1 if an error occurred. * * @since October 2017 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_rollback_view(Obiview_p view); /** * @brief Deletes a finished view file. * * Only the view informations file is deleted. * This function should only be used to delete 'temporary views' not meant to appear in the DMS history. * * @warning The view needs to be closed. The function checks that the view exists and is finished, but not that it is closed. * If it was not closed, memory errors will be generated when the system tries to read the deleted file. * // TODO maybe take opened view as argument in order to close it? but doesn't guarantee that it isn't open elsewhere. * * @param dms A pointer on the DMS to which the view belongs. * @param view_name The name of the view to delete. * * @returns A value indicating the success of the operation. * @retval 0 if the operation was successfully completed. * @retval -1 if an error occurred. * * @since October 2018 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_delete_view(OBIDMS_p dms, const char* view_name); /** * @brief Creates an OBI_INT column with the line count of the view it belongs to, and sets all lines to 1. * * @warning The number of lines set corresponds to the line count of the view. * * @param view A pointer on the view. * * @returns A value indicating the success of the operation. * @retval 0 if the operation was successfully completed. * @retval -1 if an error occurred. * * @since July 2017 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_create_auto_count_column(Obiview_p view); /** * @brief Creates an OBI_STR column with the line count of the view it belongs to, and sets all lines with automatic identifiers * with the form prefix_index. * * @warning The number of lines set corresponds to the line count of the view. * * @param view A pointer on the view. * @param prefix The prefix of automatic ids. The ids have the form prefix_index. If NULL, the default ID_PREFIX is used. * * @returns A value indicating the success of the operation. * @retval 0 if the operation was successfully completed. * @retval -1 if an error occurred. * * @since July 2017 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_create_auto_id_column(Obiview_p view, const char* prefix); /** * @brief Recovers an obiblob from an OBIDMS column containing indices referring to obiblobs, * using the index of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * * @returns The recovered obiblob. * @retval OBIBlob_NA the NA value of the type if an error occurred and obi_errno is set. * * @since November 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ Obi_blob_p obi_get_blob_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx); /** * @brief Recovers an obiblob from an OBIDMS column containing indices referring to obiblobs, * using the index of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * * @returns The recovered obiblob. * @retval OBIBlob_NA the NA value of the type if an error occurred and obi_errno is set. * * @since November 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ Obi_blob_p obi_get_blob_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx); /** * @brief Recovers an obiblob from an OBIDMS column containing indices referring to obiblobs, * using the name of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * * @returns The recovered obiblob. * @retval OBIBlob_NA the NA value of the type if an error occurred and obi_errno is set. * * @since November 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ Obi_blob_p obi_get_blob_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const char* element_name); /** * @brief Recovers an obiblob from an OBIDMS column containing indices referring to obiblobs, * using the name of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * * @returns The recovered obiblob. * @retval OBIBlob_NA the NA value of the type if an error occurred and obi_errno is set. * * @since November 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ Obi_blob_p obi_get_blob_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL, * using the index of the element in the line, and the column pointer, in the context of a view. * * Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned. * * @param view A pointer on the opened writable view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be set. * @param element_idx The index of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL, * using the index of the element in the line, and the column name, in the context of a view. * * Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned. * * @param view A pointer on the opened writable view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be set. * @param element_idx The index of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_set_bool_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, obibool_t value); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL, * using the index of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL, * using the index of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ obibool_t obi_get_bool_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL, * using the name of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened writable view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be set. * @param element_name The name of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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* element_name, obibool_t value); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL, * using the name of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened writable view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be set. * @param element_name The name of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_set_bool_with_elt_name_and_column_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, obibool_t value); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL, * using the name of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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* element_name); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL, * using the name of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ obibool_t obi_get_bool_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR, * using the index of the element in the line, and the column pointer, in the context of a view. * * Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned. * * @param view A pointer on the opened writable view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be set. * @param element_idx The index of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR, * using the index of the element in the line, and the column name, in the context of a view. * * Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned. * * @param view A pointer on the opened writable view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be set. * @param element_idx The index of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_set_char_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, obichar_t value); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR, * using the index of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIChar_NA the NA value of the type if an error occurred and obi_errno is set. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR, * using the index of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIChar_NA the NA value of the type if an error occurred and obi_errno is set. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ obichar_t obi_get_char_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR, * using the name of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened writable view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be set. * @param element_name The name of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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* element_name, obichar_t value); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR, * using the name of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened writable view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be set. * @param element_name The name of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_set_char_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, obichar_t value); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR, * using the name of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIChar_NA the NA value of the type if an error occurred and obi_errno is set. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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* element_name); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR, * using the name of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIChar_NA the NA value of the type if an error occurred and obi_errno is set. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ obichar_t obi_get_char_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT, * using the index of the element in the line, and the column pointer, in the context of a view. * * Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned. * * @param view A pointer on the opened writable view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be set. * @param element_idx The index of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT, * using the index of the element in the line, and the column name, in the context of a view. * * Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned. * * @param view A pointer on the opened writable view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be set. * @param element_idx The index of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_set_float_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, obifloat_t value); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT, * using the index of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIFloat_NA the NA value of the type if an error occurred and obi_errno is set. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT, * using the index of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIFloat_NA the NA value of the type if an error occurred and obi_errno is set. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ obifloat_t obi_get_float_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT, * using the name of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened writable view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be set. * @param element_name The name of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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* element_name, obifloat_t value); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT, * using the name of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened writable view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be set. * @param element_name The name of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_set_float_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, obifloat_t value); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT, * using the name of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIFloat_NA the NA value of the type if an error occurred and obi_errno is set. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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* element_name); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT, * using the name of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIFloat_NA the NA value of the type if an error occurred and obi_errno is set. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ obifloat_t obi_get_float_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_INT, * using the index of the element in the line, and the column pointer, in the context of a view. * * Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned. * * @param view A pointer on the opened writable view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be set. * @param element_idx The index of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_INT, * using the index of the element in the line, and the column name, in the context of a view. * * Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned. * * @param view A pointer on the opened writable view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be set. * @param element_idx The index of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_set_int_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, obiint_t value); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT, * using the index of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIInt_NA the NA value of the type if an error occurred and obi_errno is set. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT, * using the index of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIInt_NA the NA value of the type if an error occurred and obi_errno is set. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ obiint_t obi_get_int_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_INT, * using the index of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened writable view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be set. * @param element_name The name of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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* element_name, obiint_t value); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_INT, * using the index of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened writable view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be set. * @param element_name The name of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_set_int_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, obiint_t value); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT, * using the name of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIInt_NA the NA value of the type if an error occurred and obi_errno is set. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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* element_name); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT, * using the name of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIInt_NA the NA value of the type if an error occurred and obi_errno is set. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ obiint_t obi_get_int_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name); /** * @brief Sets a value in an OBIDMS column containing data in the form of indices referring * to sequence qualities handled by an indexer (OBI_QUAL data type), * using the index of the element in the line, and the column pointer, in the context of a view. * * This function is for qualities in the character string format. * * @warning Pointers returned by obi_open_column() don't allow writing. * * @param view A pointer on the opened view. * @param column_p A pointer as returned by obi_create_column() or obi_clone_column(). * @param line_nb The number of the line where the value should be set. * @param element_idx The index of the element that should be set in the line. * @param value The value that should be set, in the character string format. * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers * and the other way around. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since May 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Sets a value in an OBIDMS column containing data in the form of indices referring * to sequence qualities handled by an indexer (OBI_QUAL data type), * using the index of the element in the line, and the column name, in the context of a view. * * This function is for qualities in the character string format. * * @warning Pointers returned by obi_open_column() don't allow writing. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be set. * @param element_idx The index of the element that should be set in the line. * @param value The value that should be set, in the character string format. * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers * and the other way around. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_set_qual_char_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, const char* value, int offset); /** * @brief Sets a value in an OBIDMS column containing data in the form of indices referring * to sequence qualities handled by an indexer (OBI_QUAL data type), * using the index of the element in the line, and the column pointer, in the context of a view. * * This function is for qualities in the integer array format. * * @warning Pointers returned by obi_open_column() don't allow writing. * * @param view A pointer on the opened view. * @param column_p A pointer as returned by obi_create_column() or obi_clone_column(). * @param line_nb The number of the line where the value should be set. * @param element_idx The index of the element that should be set in the line. * @param value The value that should be set, in the integer array format. * @param value_length The length of the integer array. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since May 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Sets a value in an OBIDMS column containing data in the form of indices referring * to sequence qualities handled by an indexer (OBI_QUAL data type), * using the index of the element in the line, and the column name, in the context of a view. * * This function is for qualities in the integer array format. * * @warning Pointers returned by obi_open_column() don't allow writing. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be set. * @param element_idx The index of the element that should be set in the line. * @param value The value that should be set, in the integer array format. * @param value_length The length of the integer array. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_set_qual_int_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, const uint8_t* value, int value_length); /** * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring * to sequence qualities handled by an indexer (OBI_QUAL data type), * using the index of the element in the line, and the column pointer, in the context of a view. * * This function returns quality scores in the character string format. * * @param view A pointer on the opened view. * @param column_p A pointer as returned by obi_create_column(). * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers * and the other way around. * * @returns The recovered value, in the character string format. * @retval OBIQual_char_NA the NA value of the type if an error occurred and obi_errno is set. * * @since May 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring * to sequence qualities handled by an indexer (OBI_QUAL data type), * using the index of the element in the line, and the column name, in the context of a view. * * This function returns quality scores in the character string format. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers * and the other way around. * * @returns The recovered value, in the character string format. * @retval OBIQual_char_NA the NA value of the type if an error occurred and obi_errno is set. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ char* obi_get_qual_char_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, int offset); /** * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring * to sequence qualities handled by an indexer (OBI_QUAL data type), * using the index of the element in the line, and the column pointer, in the context of a view. * * This function returns quality scores in the integer array format. * * @param view A pointer on the opened view. * @param column_p A pointer as returned by obi_create_column(). * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * @param value_length A pointer on an integer to store the length of the integer array recovered. * * @returns The recovered value, in the integer array format. * @retval OBIQual_int_NA the NA value of the type if an error occurred and obi_errno is set. * * @since May 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring * to sequence qualities handled by an indexer (OBI_QUAL data type), * using the index of the element in the line, and the column name, in the context of a view. * * This function returns quality scores in the integer array format. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * @param value_length A pointer on an integer to store the length of the integer array recovered. * * @returns The recovered value, in the integer array format. * @retval OBIQual_int_NA the NA value of the type if an error occurred and obi_errno is set. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ const uint8_t* obi_get_qual_int_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, int* value_length); /** * @brief Sets a value in an OBIDMS column containing data in the form of indices referring * to sequence qualities handled by an indexer (OBI_QUAL data type), * using the name of the element in the line, and the column pointer, in the context of a view. * * This function is for quality scores in the character string format. * * @warning Pointers returned by obi_open_column() don't allow writing. * * @param view A pointer on the opened view. * @param column_p A pointer as returned by obi_create_column() or obi_clone_column(). * @param line_nb The number of the line where the value should be set. * @param element_name The name of the element that should be set in the line. * @param value The value that should be set, in the character string format. * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers * and the other way around. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since May 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Sets a value in an OBIDMS column containing data in the form of indices referring * to sequence qualities handled by an indexer (OBI_QUAL data type), * using the name of the element in the line, and the column name, in the context of a view. * * This function is for quality scores in the character string format. * * @warning Pointers returned by obi_open_column() don't allow writing. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be set. * @param element_name The name of the element that should be set in the line. * @param value The value that should be set, in the character string format. * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers * and the other way around. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_set_qual_char_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, const char* value, int offset); /** * @brief Sets a value in an OBIDMS column containing data in the form of indices referring * to sequence qualities handled by an indexer (OBI_QUAL data type), * using the name of the element in the line, and the column pointer, in the context of a view. * * This function is for quality scores in the integer array format. * * @warning Pointers returned by obi_open_column() don't allow writing. * * @param view A pointer on the opened view. * @param column_p A pointer as returned by obi_create_column() or obi_clone_column(). * @param line_nb The number of the line where the value should be set. * @param element_name The name of the element that should be set in the line. * @param value The value that should be set, in the integer format. * @param value_length The length of the integer array. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since May 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Sets a value in an OBIDMS column containing data in the form of indices referring * to sequence qualities handled by an indexer (OBI_QUAL data type), * using the name of the element in the line, and the column name, in the context of a view. * * This function is for quality scores in the integer array format. * * @warning Pointers returned by obi_open_column() don't allow writing. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be set. * @param element_name The name of the element that should be set in the line. * @param value The value that should be set, in the integer format. * @param value_length The length of the integer array. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_set_qual_int_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, const uint8_t* value, int value_length); /** * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring * to sequence qualities handled by an indexer (OBI_QUAL data type), * using the name of the element in the line, and the column pointer, in the context of a view. * * This function returns quality scores in the character string format. * * @param view A pointer on the opened view. * @param column_p A pointer as returned by obi_create_column() or obi_clone_column(). * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers * and the other way around. * * @returns The recovered value, in the character string format. * @retval OBIQual_char_NA the NA value of the type if an error occurred and obi_errno is set. * * @since May 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring * to sequence qualities handled by an indexer (OBI_QUAL data type), * using the name of the element in the line, and the column name, in the context of a view. * * This function returns quality scores in the character string format. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * @param offset The ASCII base of sequence quality, used to convert sequence qualities from characters to integers * and the other way around. * * @returns The recovered value, in the character string format. * @retval OBIQual_char_NA the NA value of the type if an error occurred and obi_errno is set. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ char* obi_get_qual_char_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, int offset); /** * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring * to sequence qualities handled by an indexer (OBI_QUAL data type), * using the name of the element in the line, and the column pointer, in the context of a view. * * This function returns quality scores in the integer array format. * * @param view A pointer on the opened view. * @param column_p A pointer as returned by obi_create_column() or obi_clone_column(). * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * @param value_length A pointer on an integer to store the length of the integer array recovered. * * @returns The recovered value, in the integer format. * @retval OBIQual_int_NA the NA value of the type if an error occurred and obi_errno is set. * * @since May 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring * to sequence qualities handled by an indexer (OBI_QUAL data type), * using the name of the element in the line, and the column name, in the context of a view. * * This function returns quality scores in the integer array format. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * @param value_length A pointer on an integer to store the length of the integer array recovered. * * @returns The recovered value, in the integer format. * @retval OBIQual_int_NA the NA value of the type if an error occurred and obi_errno is set. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ const uint8_t* obi_get_qual_int_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, int* value_length); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_SEQ, * using the index of the element in the line, and the column pointer, in the context of a view. * * Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned. * * @param view A pointer on the opened writable view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be set. * @param element_idx The index of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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* value); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_SEQ, * using the index of the element in the line, and the column name, in the context of a view. * * Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned. * * @param view A pointer on the opened writable view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be set. * @param element_idx The index of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_set_seq_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, const char* value); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_SEQ, * using the index of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBISeq_NA the NA value of the type if an error occurred and obi_errno is set. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_SEQ, * using the index of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBISeq_NA the NA value of the type if an error occurred and obi_errno is set. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ char* obi_get_seq_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_SEQ, * using the name of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened writable view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be set. * @param element_name The name of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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* element_name, const char* value); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_SEQ, * using the name of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened writable view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be set. * @param element_name The name of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_set_seq_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, const char* value); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_SEQ, * using the name of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBISeq_NA the NA value of the type if an error occurred and obi_errno is set. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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* element_name); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_SEQ, * using the name of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBISeq_NA the NA value of the type if an error occurred and obi_errno is set. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ char* obi_get_seq_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_STR, * using the index of the element in the line, and the column pointer, in the context of a view. * * Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned. * * @param view A pointer on the opened writable view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be set. * @param element_idx The index of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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* value); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_STR, * using the index of the element in the line, and the column name, in the context of a view. * * Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned. * * @param view A pointer on the opened writable view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be set. * @param element_idx The index of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_set_str_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, const char* value); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_STR, * using the index of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIStr_NA the NA value of the type if an error occurred and obi_errno is set. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ const char* 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); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_STR, * using the index of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIStr_NA the NA value of the type if an error occurred and obi_errno is set. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ const char* obi_get_str_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_STR, * using the name of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened writable view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be set. * @param element_name The name of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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* element_name, const char* value); /** * @brief Sets a value in an OBIDMS column containing data with the type OBI_STR, * using the name of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened writable view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be set. * @param element_name The name of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_set_str_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, const char* value); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_STR, * using the name of the element in the line, and the column pointer, in the context of a view. * * @param view A pointer on the opened view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIStr_NA the NA value of the type if an error occurred and obi_errno is set. * * @since February 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ const char* 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* element_name); /** * @brief Recovers a value in an OBIDMS column containing data with the type OBI_STR, * using the name of the element in the line, and the column name, in the context of a view. * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIStr_NA the NA value of the type if an error occurred and obi_errno is set. * * @since August 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ const char* obi_get_str_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name); /** * @brief Sets a value in an OBIDMS column containing indices (stored data type: OBI_IDX), * using the index of the element in the line, and the column pointer, in the context of a view. * * Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned. * * Note: Columns containing indices refer to data stored elsewhere, for example lines in other columns, * or data stored in indexers. * * In the case of columns referring to values stored in indexers, this allows to directly set already-known * indices without going through the time-consuming step of indexing the value. * * @param view A pointer on the opened writable view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be set. * @param element_idx The index of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since November 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Sets a value in an OBIDMS column containing indices (stored data type: OBI_IDX), * using the index of the element in the line, and the column name, in the context of a view. * * Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned. * * Note: Columns containing indices refer to data stored elsewhere, for example lines in other columns, * or data stored in indexers. * * In the case of columns referring to values stored in indexers, this allows to directly set already-known * indices without going through the time-consuming step of indexing the value. * * @param view A pointer on the opened writable view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be set. * @param element_idx The index of the element that should be set in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since November 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_set_index_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, index_t value); /** * @brief Recovers a value in an OBIDMS column containing indices (stored data type: OBI_IDX), * using the index of the element in the line, and the column pointer, in the context of a view. * * This enables to recover the indexes in columns containing any type of indexed data (OBI_SEQ, OBI_STR...), for example to quickly test if * the values are identical (same index in the same indexer). * * @param view A pointer on the opened view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIIdx_NA the NA value of the type if an error occurred and obi_errno is set. * * @since November 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Recovers a value in an OBIDMS column containing indices (stored data type: OBI_IDX), * using the index of the element in the line, and the column name, in the context of a view. * * This enables to recover the indexes in columns containing any type of indexed data (OBI_SEQ, OBI_STR...), for example to quickly test if * the values are identical (same index in the same indexer). * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_idx The index of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIIdx_NA the NA value of the type if an error occurred and obi_errno is set. * * @since November 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ index_t obi_get_index_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx); /** * @brief Sets a value in an OBIDMS column containing indices (stored data type: OBI_IDX), * using the name of the element in the line, and the column pointer, in the context of a view. * * Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned. * * Note: Columns containing indices refer to data stored elsewhere, for example lines in other columns, * or data stored in indexers. * * In the case of columns referring to values stored in indexers, this allows to directly set already-known * indices without going through the time-consuming step of indexing the value. * * @param view A pointer on the opened writable view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be set. * @param element_name The name of the element that should be recovered in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since November 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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* element_name, index_t value); /** * @brief Sets a value in an OBIDMS column containing indices (stored data type: OBI_IDX), * using the name of the element in the line, and the column name, in the context of a view. * * Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned. * * Note: Columns containing indices refer to data stored elsewhere, for example lines in other columns, * or data stored in indexers. * * In the case of columns referring to values stored in indexers, this allows to directly set already-known * indices without going through the time-consuming step of indexing the value. * * @param view A pointer on the opened writable view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be set. * @param element_name The name of the element that should be recovered in the line. * @param value The value that should be set. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since November 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ int obi_set_index_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, index_t value); /** * @brief Recovers a value in an OBIDMS column containing indices (stored data type: OBI_IDX), * using the name of the element in the line, and the column pointer, in the context of a view. * * This enables to recover the indexes in columns containing any type of indexed data (OBI_SEQ, OBI_STR...), for example to quickly test if * the values are identical (same index in the same indexer). * * @param view A pointer on the opened view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIIdx_NA the NA value of the type if an error occurred and obi_errno is set. * * @since November 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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* element_name); /** * @brief Recovers a value in an OBIDMS column containing indices (stored data type: OBI_IDX), * using the name of the element in the line, and the column name, in the context of a view. * * This enables to recover the indexes in columns containing any type of indexed data (OBI_SEQ, OBI_STR...), for example to quickly test if * the values are identical (same index in the same indexer). * * @param view A pointer on the opened view. * @param column_name The alias of the column in the view. * @param line_nb The number of the line where the value should be recovered. * @param element_name The name of the element that should be recovered in the line. * * @returns The recovered value. * @retval OBIIdx_NA the NA value of the type if an error occurred and obi_errno is set. * * @since November 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ index_t obi_get_index_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name); /*********** FOR ARRAY COLUMNS ***********/ /** * @brief Sets a value in an OBIDMS column containing indices referring to indexed arrays, * using the column pointer, in the context of a view. * * Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned. * * @param view A pointer on the opened writable view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be set. * @param value The value that should be set. * @param elt_size The size in bits of one element. * @param value_length The length (number of elements) of the array to index. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since October 2017 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Recovers a value in an OBIDMS column containing indices referring to indexed arrays, * using the column pointer, in the context of a view. * * @param view A pointer on the opened view. * @param column_p A pointer on the column. * @param line_nb The number of the line where the value should be recovered. * @param value_length_p A pointer on an int where the length of the value (number of elements in the array) will be stored. * * @returns The recovered value. * @retval OBITuple_NA the NA value of the type if an error occurred and obi_errno is set. * * @since October 2017 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Sets a value in an OBIDMS column containing indices referring to indexed arrays, * using the column name, in the context of a view. * * Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned. * * @param view A pointer on the opened writable view. * @param column_name The name of the column. * @param line_nb The number of the line where the value should be set. * @param value The value that should be set. * @param elt_size The size in bits of one element. * @param value_length The length (number of elements) of the array to index. * * @returns An integer value indicating the success of the operation. * @retval 0 on success. * @retval -1 if an error occurred. * * @since October 2017 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); /** * @brief Recovers a value in an OBIDMS column containing indices referring to indexed arrays, * using the column name, in the context of a view. * * @param view A pointer on the opened view. * @param column_name The name of the column. * @param line_nb The number of the line where the value should be recovered. * @param value_length_p A pointer on an int where the length of the value (number of elements in the array) will be stored. * * @returns The recovered value. * @retval OBITuple_NA the NA value of the type if an error occurred and obi_errno is set. * * @since October 2017 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ 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); #endif /* OBIVIEW_H_ */