Commit 4ad8c16a by Celine Mercier

Finished adding all the functions to directly set and get indices in

columns containing indices referring to any type of data.
parent 6f609968
......@@ -24,33 +24,34 @@
**********************************************************************/
int obi_column_set_index(OBIDMS_column_p column, index_t line_nb, index_t value)
int obi_column_set_index_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, index_t value)
{
if (obi_column_prepare_to_set_value(column, line_nb) < 0)
return -1;
// Set the value
*(((index_t*) (column->data)) + line_nb) = value;
*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
return 0;
}
index_t obi_column_get_index(OBIDMS_column_p column, index_t line_nb)
index_t obi_column_get_index_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
return OBIIdx_NA;
return *(((index_t*) (column->data)) + line_nb);
return *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
}
index_t obi_column_get_index_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
int obi_column_set_index_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, index_t value)
{
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
return OBIIdx_NA;
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
return *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
return obi_column_set_index_with_elt_idx(column, line_nb, element_idx, value);
}
......
......@@ -6,10 +6,10 @@
* @file obidsmcolumn_idx.h
* @author Celine Mercier
* @date February 14th 2016
* @brief Header file for the functions handling OBIColumns containing data with the OBIType OBI_IDX.
* @brief Header file for the functions handling OBIColumns containing indices (stored data type: OBI_IDX).
*
* Note: OBI_IDX columns contain indices referring to data stored elsewhere
* (for example lines in other columns) and contain only one element (index) per line.
* Note: Columns containing indices refer to data stored elsewhere, for example lines in other columns,
* or data stored in indexers.
*/
......@@ -25,65 +25,90 @@
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_IDX.
* @brief Sets a value in an OBIDMS column containing indices (stored data type: OBI_IDX),
* using the index of the element in the line.
*
* Note: OBI_IDX columns contain indices referring to data stored elsewhere
* (for example lines in other columns) and contain only one element (index) per line.
* 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.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column 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 value The value that should be set.
* @param element_idx The index of the element that should be set in the line.
* @param value The index 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
* @since November 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_index(OBIDMS_column_p column, index_t line_nb, index_t value);
int obi_column_set_index_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, index_t value);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_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.
*
* Note: OBI_IDX columns contain indices referring to data stored elsewhere
* (for example lines in other columns) and contain only one element (index) per line.
* Note: Columns containing indices refer to data stored elsewhere, for example lines in other columns,
* or data stored in indexers.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
* The value recovered is the index itself and not the data it is referring to.
*
* @param column 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.
*
* @returns The recovered value.
* @retval OBIIdx_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @since February 2016
* @since November 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
index_t obi_column_get_index(OBIDMS_column_p column, index_t line_nb);
index_t obi_column_get_index_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_IDX.
* @brief Sets a value in an OBIDMS column containing indices (stored data type: OBI_IDX),
* using the index of the element in the line.
*
* @param column 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.
* Note: Columns containing indices refer to data stored elsewhere, for example lines in other columns,
* or data stored in indexers.
*
* @returns The recovered value.
* @retval OBIIdx_NA the NA value of the type if an error occurred and obi_errno is set.
* 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.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column 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 index 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)
*/
index_t obi_column_get_index_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
int obi_column_set_index_with_elt_name(OBIDMS_column_p column, index_t line_nb, index_t element_idx, index_t value);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_IDX,
* @brief Recovers a value in an OBIDMS column containing indices (stored data type: OBI_IDX),
* using the name of the element in the line.
*
* Note: Columns containing indices refer to data stored elsewhere, for example lines in other columns,
* or data stored in indexers.
*
* The value recovered is the index itself and not the data it is referring to.
*
* @param column 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.
......
......@@ -1263,9 +1263,9 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
}
if (view_to_clone->line_selection != NULL)
line_nb = obi_column_get_index(view_to_clone->line_selection, line_nb);
line_nb = obi_column_get_index_with_elt_idx(view_to_clone->line_selection, line_nb, 0);
if (obi_column_set_index(view->line_selection, ((view->line_selection)->header)->lines_used, line_nb) < 0)
if (obi_column_set_index_with_elt_idx(view->line_selection, ((view->line_selection)->header)->lines_used, 0, line_nb) < 0)
{
obi_close_column(view->line_selection);
obi_view_unmap_file(view->dms, view->infos);
......@@ -2724,6 +2724,15 @@ const char* obi_get_str_with_elt_name_and_col_name_in_view(Obiview_p view, const
/*********** FOR COLUMNS WITH INDEXED VALUES ***********/
int obi_set_index_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, index_t value)
{
if (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
return -1;
return obi_column_set_index_with_elt_idx(column, line_nb, element_idx, value);
}
index_t obi_get_index_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
if (prepare_to_get_value_from_column(view, &line_nb) < 0)
......@@ -2732,6 +2741,15 @@ index_t obi_get_index_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_colu
}
int obi_set_index_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, index_t value)
{
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
return obi_set_index_with_elt_idx_and_col_p_in_view(view, column, line_nb, element_idx, value);
}
index_t obi_get_index_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
......@@ -2741,6 +2759,26 @@ index_t obi_get_index_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_col
}
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)
{
OBIDMS_column_p column_p;
column_p = obi_view_get_column(view, column_name);
if (column_p == NULL)
return -1;
return obi_set_index_with_elt_name_and_col_p_in_view(view, column_p, line_nb, element_name, value);
}
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)
{
OBIDMS_column_p column_p;
column_p = obi_view_get_column(view, column_name);
if (column_p == NULL)
return -1;
return obi_set_index_with_elt_idx_and_col_p_in_view(view, column_p, line_nb, element_idx, value);
}
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)
{
OBIDMS_column_p column_p;
......
......@@ -1315,6 +1315,38 @@ const char* obi_get_str_with_elt_name_and_col_name_in_view(Obiview_p view, const
/**
* @brief Sets a value in an OBIDMS column containing indices, 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.
*
* 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 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);
// TODO
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 indexes, 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
......@@ -1339,6 +1371,38 @@ index_t obi_get_index_with_elt_idx_and_col_name_in_view(Obiview_p view, const ch
/**
* @brief Sets a value in an OBIDMS column containing indices, 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.
*
* 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 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);
// TODO
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 indexes,
* using the name of the element in the line, in the context of a view.
*
......
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