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/********************************************************************
* 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 <stdlib.h>
#include <errno.h>
#include <stdio.h>
#include <stdbool.h>
#include <time.h>
#include <math.h>
#include "obidms.h"
#include "obidmscolumn.h"
#include "obierrno.h"
#define OBIVIEW_NAME_MAX_LENGTH (1000) /**< The maximum length of an OBIDMS view name.
*/
#define OBIVIEW_COMMENTS_MAX_LENGTH (10000) /**< The maximum length of the comments associated
* with a view.
*/
#define VIEW_TYPE_MAX_LENGTH (1024) /**< The maximum length of the type name of a view.
*/
#define OBIVIEW_FILE_NAME "obiviews" /**< The default name of a view file.
*/
#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 NUC_SEQUENCE_INDEXER "NUC_SEQ_INDEXER" /**< The name of the indexer 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 ID_INDEXER "ID_INDEXER" /**< The name of the indexer 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 DEFINITION_INDEXER "DEFINITION_INDEXER" /**< The name of the indexer containing the sequence definitions
* in NUC_SEQS_VIEW views.
*/
/**
* @brief Structure for an opened view.
*/
typedef struct Obiview {
OBIDMS_p dms; /**< A pointer on the DMS to which the view belongs.
*/
char name[OBIVIEW_NAME_MAX_LENGTH+1]; /**< Name of the view.
*/
char created_from[OBIVIEW_NAME_MAX_LENGTH+1]; /**< Name of the view from which that view was cloned if the view was cloned.
*/
char view_type[VIEW_TYPE_MAX_LENGTH+1]; /**< Type of the view if there is one.
* Types existing: NUC_SEQS_VIEW.
*/
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.
*/
OBIDMS_column_p new_line_selection; /**< A pointer on the column containing the new line selection being built
* to associate with the view, if there is one.
* When a line is selected with obi_select_line() or obi_select_lines(),
* it is recorded in this line selection.
*/
index_t line_count; /**< The number of lines in the view. Refers to the number of lines in each
* column of the view if line_selection is NULL, or to the line count of
* line_selection if it is not NULL.
*/
int column_count; /**< The number of columns in the view.
*/
OBIDMS_column_p columns[MAX_NB_OPENED_COLUMNS]; /**< Array of pointers on all the columns of the view.
*/
char comments[OBIVIEW_COMMENTS_MAX_LENGTH+1]; /**< Comments, additional informations on the view.
*/
} Obiview_t, *Obiview_p;
/**
* @brief Structure referencing a column by its name and its version.
*/
typedef struct Column_reference {
char column_name[OBIDMS_COLUMN_MAX_NAME+1]; /**< Name of the column.
*/
obiversion_t version; /**< Version of the column.
*/
} Column_reference_t, *Column_reference_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 {
int view_number; /**< Number of the view in the view file.
*/
time_t creation_date; /**< Time at which the view was written in the view file.
*/
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; /**< Whether there is a line selection associated with the view.
*/
index_t line_count; /**< The number of lines in the view.
*/
int column_count; /**< The number of columns in the view.
*/
Column_reference_t column_references[MAX_NB_OPENED_COLUMNS]; /**< References (name and version) for all the columns in the view.
*/
char comments[OBIVIEW_COMMENTS_MAX_LENGTH+1]; /**< Comments, additional informations on the view.
*/
} Obiview_infos_t, *Obiview_infos_p;
// TODO : Combine the common elements of the Obiview_infos and Obiview structures in one structure used by both?
/**
* @brief Structure for the header of view files.
*/
typedef struct Obiviews_header {
size_t header_size; /**< Size of the header in bytes.
*/
size_t views_size; /**< Size of the views in bytes.
*/
int view_count; /**< Number of views saved.
*/
} Obiviews_header_t, *Obiviews_header_p;
/**
* @brief Structure for the information stored in view files.
*/
typedef struct Obiviews_infos_all {
Obiviews_header_p header; /**< Pointer on the header of the view file.
*/
Obiview_infos_p view_infos; /**< Pointer on the beginning (first view) of the informations on views.
*/
} Obiviews_infos_all_t, *Obiviews_infos_all_p;
/**
* @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.
* @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.
*
* @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.
* @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
*
* @param dms A pointer on the OBIDMS.
* @param view_name The unique name of the view.
* @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.
*
* @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);
/**
* @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
*
* @param dms A pointer on the OBIDMS.
* @param view_name The unique name of the new view.
* @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 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.
*
* @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 data_type The OBIType code of the data.
* @param nb_lines The number of lines to be stored.
* @param nb_elements_per_line The number of elements per line.
* @param elements_names The names of the elements with ';' as separator.
* @param indexer_name The name of the indexer if there is one associated with the column.
* @param comments Optional comments associated with the column.
* @param create Whether the column should be created (create == true) or opened (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,
const char* column_name,
obiversion_t version_number,
OBIType_t data_type,
index_t nb_lines,
index_t nb_elements_per_line,
const char* elements_names,
const char* indexer_name,
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.
*
* @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);
/**
* @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 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 Selects a line in the context of a view.
*
* If no line selection exists for the view, it will be created.
*
* @warning The view must be writable.
* @warning The new line index will be simply added at the end of the current
* new line selection.
*
* @param view A pointer on the view.
* @param line_nb The index of the line that should be added in the selection.
*
* @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_select_line(Obiview_p view, index_t line_nb);
/**
* @brief Selects a list of line in the context of a view.
*
* If no line selection exists for the view, it will be created.
*
* @warning The view must be writable.
* @warning The new line indexes will be simply added at the end of the current
* new line selection.
*
* @param view A pointer on the view.
* @param line_nbs A pointer on an array of indexes corresponding to the lines that
* should be added in the selection.
*
* @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_select_lines(Obiview_p view, index_t* line_nbs);
/**
* @brief Saves a view, writing it in the view file.
*
* The view is written at the end of the view file, following the latest written view.
*
* @warning The view must be writable.
*
* @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_view(Obiview_p view);
/**
* @brief Closes an opened view.
*
* @warning Use obi_save_and_close_view() to automatically save the view if it's not already saved in the view file.
*
* @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_close_view(Obiview_p view);
/**
* @brief Closes an opened view, and saves it if it is not read-only (meaning it is not already saved in the view file).
*
* @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 Opens the structure containing all the informations written in the view file.
*
* @param dms A pointer on the OBIDMS to which the view file belongs.
*
* @returns A pointer on the view informations structure.
* @retval NULL if an error occurred.
*
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
Obiviews_infos_all_p obi_read_view_infos(OBIDMS_p dms);
/**
* @brief Closes the structure containing all the informations written in the view file.
*
* @param views A pointer on the view informations 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 February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_close_view_infos(Obiviews_infos_all_p views);
// TODO in following functions would it be better to use column names instead of column pointers?
// check if it would be a gain or loss of time
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL, using the index of the element in the line,
* 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 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_column_set_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, 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, in the context of a view.
*
* @param view A pointer on the opened view.
* @param column 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_column_get_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, 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, in the context of a view.
*
* @param view A pointer on the opened writable view.
* @param column 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_column_set_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, 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, in the context of a view.
*
* @param view A pointer on the opened view.
* @param column 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_column_get_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, 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,
* 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 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_column_set_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, 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, in the context of a view.
*
* @param view A pointer on the opened view.
* @param column 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_column_get_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, 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, in the context of a view.
*
* @param view A pointer on the opened writable view.
* @param column 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_column_set_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, 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, in the context of a view.
*
* @param view A pointer on the opened view.
* @param column 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_column_get_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, 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,
* 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 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_column_set_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, 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, in the context of a view.
*
* @param view A pointer on the opened view.
* @param column 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_column_get_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, 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, in the context of a view.
*
* @param view A pointer on the opened writable view.
* @param column 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_column_set_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, 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, in the context of a view.
*
* @param view A pointer on the opened view.
* @param column 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_column_get_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, 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,
* 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 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_column_set_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, 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, in the context of a view.
*
* @param view A pointer on the opened view.
* @param column 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_column_get_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, 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 name of the element in the line, in the context of a view.
*
* @param view A pointer on the opened writable view.
* @param column 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_column_set_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, 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, in the context of a view.
*
* @param view A pointer on the opened view.
* @param column 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_column_get_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_SEQ, using the index of the element in the line,
* 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 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_column_set_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, 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, in the context of a view.
*
* @param view A pointer on the opened view.
* @param column 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_column_get_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, 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, in the context of a view.
*
* @param view A pointer on the opened writable view.
* @param column 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_column_set_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, 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, in the context of a view.
*
* @param view A pointer on the opened view.
* @param column 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_column_get_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, 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,
* 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 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_column_set_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, 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, in the context of a view.
*
* @param view A pointer on the opened view.
* @param column 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_column_get_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, 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, in the context of a view.
*
* @param view A pointer on the opened writable view.
* @param column 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_column_set_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, 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, in the context of a view.
*
* @param view A pointer on the opened view.
* @param column 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_column_get_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
#endif /* OBIVIEW_H_ */
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