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Added tuple columns containing immutable indexed data arrays of any type

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This commit is contained in:
Celine Mercier
2017-11-15 13:48:59 +01:00
parent 1684f96b79
commit 9a50803c00
32 changed files with 1097 additions and 284 deletions
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73
src/array_indexer.c Normal file
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@ -0,0 +1,73 @@
/****************************************************************************
* Array indexing functions *
****************************************************************************/
/**
* @file array_indexer.c
* @author Celine Mercier
* @date October 5th 2017
* @brief Functions handling the indexing and retrieval of arrays of any type.
*/
#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>
#include <math.h>
#include "obiblob.h"
#include "obiblob_indexer.h"
#include "obidebug.h"
#include "obitypes.h"
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
index_t obi_index_array(Obi_indexer_p indexer, const void* value, uint8_t elt_size, int value_length)
{
Obi_blob_p value_b;
index_t idx;
int32_t length_bytes;
// fprintf(stderr, "\nelt size in C: %u", elt_size);
// for (int i=0; i<value_length; i++)
// fprintf(stderr, "\nvalue %d", ((obibool_t*)value)[i]);
length_bytes = value_length * elt_size;
// Encode value
value_b = obi_blob((byte_t*)value, elt_size, length_bytes, length_bytes);
if (value_b == NULL)
return -1;
// for (int i=0; i<value_length; i++)
// fprintf(stderr, "\nin blob: value %d", ((obibool_t*)(value_b->value))[i]);
// Add in the indexer
idx = obi_indexer_add(indexer, value_b);
free(value_b);
return idx;
}
const void* obi_retrieve_array(Obi_indexer_p indexer, index_t idx, int* value_length_p)
{
Obi_blob_p value_b;
// Get encoded value
value_b = obi_indexer_get(indexer, idx);
// Store array length
*value_length_p = (value_b->length_decoded_value) / (value_b->element_size);
// for (int i=0; i<*value_length_p; i++)
// fprintf(stderr, "\nvalue %d", ((obibool_t*)(value_b->value))[i]);
// Return pointer on mapped array
return ((void*) (value_b->value));
}

60
src/array_indexer.h Normal file
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@ -0,0 +1,60 @@
/****************************************************************************
* Array indexer header file *
****************************************************************************/
/**
* @file array_indexer.h
* @author Celine Mercier
* @date October 5th 2017
* @brief Header file for the functions handling the indexing of arrays of any type.
*/
#ifndef ARRAY_INDEXER_H_
#define ARRAY_INDEXER_H_
#include <stdlib.h>
#include <stdio.h>
#include "obidms.h"
#include "obitypes.h"
#include "obiblob.h"
#include "obiblob_indexer.h"
/**
* @brief Stores an array of elements of any type in an indexer and returns the index.
*
* @param indexer The indexer structure.
* @param value The array to index.
* @param elt_size The size in bits of one element.
* @param value_length The length (number of elements) of the array to index.
*
* @returns The index referring to the stored array in the indexer.
*
* @since October 2017
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
index_t obi_index_array(Obi_indexer_p indexer, const void* value, uint8_t elt_size, int32_t value_length);
/**
* @brief Retrieves an array from an indexer.
*
* @warning The array returned is mapped.
*
* @param indexer The indexer structure.
* @param idx The index referring to the array to retrieve in the indexer.
* @param value_length A pointer on an integer to store the length of the array retrieved.
*
* @returns A pointer on the array.
*
* @since October 2017
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
const void* obi_retrieve_array(Obi_indexer_p indexer, index_t idx, int32_t* value_length_p);
#endif /* ARRAY_INDEXER_H_ */

24
src/obi_align.c
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@ -154,35 +154,35 @@ static int create_alignment_output_columns(Obiview_p output_view,
bool normalize, int reference, bool similarity_mode)
{
// Create the column for the ids of the 1st sequence aligned
if (obi_view_add_column(output_view, ID1_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, id1_indexer_name, NULL, -1, ID1_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(output_view, ID1_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, id1_indexer_name, NULL, -1, ID1_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the first column for the sequence ids when aligning");
return -1;
}
// Create the column for the ids of the 2nd sequence aligned
if (obi_view_add_column(output_view, ID2_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, id2_indexer_name, NULL, -1, ID2_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(output_view, ID2_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, id2_indexer_name, NULL, -1, ID2_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the second column for the sequence ids when aligning");
return -1;
}
// Create the column for the index (in the input view) of the first sequences aligned
if (obi_view_add_column(output_view, IDX1_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, NULL, NULL, -1, IDX1_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(output_view, IDX1_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, NULL, NULL, -1, IDX1_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the first column for the sequence indices when aligning");
return -1;
}
// Create the column for the index (in the input view) of the second sequences aligned
if (obi_view_add_column(output_view, IDX2_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, NULL, NULL, -1, IDX2_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(output_view, IDX2_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, NULL, NULL, -1, IDX2_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the second column for the sequence indices when aligning");
return -1;
}
// Create the column for the LCS length
if (obi_view_add_column(output_view, LCS_LENGTH_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, NULL, NULL, -1, LCS_LENGTH_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(output_view, LCS_LENGTH_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, NULL, NULL, -1, LCS_LENGTH_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the column for the LCS length when aligning");
return -1;
@ -191,7 +191,7 @@ static int create_alignment_output_columns(Obiview_p output_view,
// Create the column for the alignment length if it is computed
if ((reference == ALILEN) && (normalize || !similarity_mode))
{
if (obi_view_add_column(output_view, ALI_LENGTH_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, NULL, NULL, -1, ALI_LENGTH_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(output_view, ALI_LENGTH_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, NULL, NULL, -1, ALI_LENGTH_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the column for the alignment length when aligning");
return -1;
@ -200,7 +200,7 @@ static int create_alignment_output_columns(Obiview_p output_view,
// Create the column for the alignment score
if (normalize)
{
if (obi_view_add_column(output_view, SCORE_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, NULL, NULL, -1, SCORE_COLUMN_NAME, true) < 0)
if (obi_view_add_column(output_view, SCORE_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, false, NULL, NULL, -1, SCORE_COLUMN_NAME, true) < 0)
{
obidebug(1, "\nError creating the column for the score when aligning");
return -1;
@ -208,7 +208,7 @@ static int create_alignment_output_columns(Obiview_p output_view,
}
else
{
if (obi_view_add_column(output_view, SCORE_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, NULL, NULL, -1, SCORE_COLUMN_NAME, true) < 0)
if (obi_view_add_column(output_view, SCORE_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, NULL, NULL, -1, SCORE_COLUMN_NAME, true) < 0)
{
obidebug(1, "\nError creating the column for the score when aligning");
return -1;
@ -218,14 +218,14 @@ static int create_alignment_output_columns(Obiview_p output_view,
if (print_seq)
{
// Create the column for the first sequences aligned
if (obi_view_add_column(output_view, SEQ1_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, seq1_indexer_name, NULL, -1, SEQ1_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(output_view, SEQ1_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, false, seq1_indexer_name, NULL, -1, SEQ1_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the first column for the sequences when aligning");
return -1;
}
// Create the column for the second sequences aligned
if (obi_view_add_column(output_view, SEQ2_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, seq2_indexer_name, NULL, -1, SEQ2_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(output_view, SEQ2_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, false, seq2_indexer_name, NULL, -1, SEQ2_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the second column for the sequences when aligning");
return -1;
@ -234,14 +234,14 @@ static int create_alignment_output_columns(Obiview_p output_view,
// if (print_count) // TODO count columns not implemented yet
// {
// // Create the column for the count of the first sequences aligned
// if (obi_view_add_column(output_view, COUNT1_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, NULL, NULL, -1, COUNT1_COLUMN_COMMENTS, true) < 0)
// if (obi_view_add_column(output_view, COUNT1_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, NULL, NULL, -1, COUNT1_COLUMN_COMMENTS, true) < 0)
// {
// obidebug(1, "\nError creating the first column for the sequence counts when aligning");
// return -1;
// }
//
// // Create the column for the count of the second sequences aligned
// if (obi_view_add_column(output_view, COUNT2_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, NULL, NULL, -1, COUNT2_COLUMN_COMMENTS, true) < 0)
// if (obi_view_add_column(output_view, COUNT2_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, NULL, NULL, -1, COUNT2_COLUMN_COMMENTS, true) < 0)
// {
// obidebug(1, "\nError creating the second column for the sequence counts when aligning");
// return -1;

3
src/obidms.c
View File

@ -924,7 +924,7 @@ obiversion_t obi_import_column(const char* dms_path_1, const char* dms_path_2, c
// Create new column
column_2 = obi_create_column(dms_2, column_name, header_1->returned_data_type, header_1->line_count,
header_1->nb_elements_per_line, header_1->elements_names, true,
header_1->nb_elements_per_line, header_1->elements_names, true, header_1->tuples,
new_avl_name, (header_1->associated_column).column_name, (header_1->associated_column).version,
header_1->comments);
@ -1142,6 +1142,7 @@ int obi_import_view(const char* dms_path_1, const char* dms_path_2, const char*
0,
0,
NULL,
false,
NULL,
NULL,
-1,

9
src/obidmscolumn.c
View File

@ -890,6 +890,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
index_t nb_elements_per_line,
char* elements_names,
bool elt_names_formatted,
bool tuples,
const char* indexer_name,
const char* associated_column_name,
obiversion_t associated_column_version,
@ -957,7 +958,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
}
// Build the indexer name if needed
if ((data_type == OBI_STR) || (data_type == OBI_SEQ) || (data_type == OBI_QUAL))
if ((data_type == OBI_STR) || (data_type == OBI_SEQ) || (data_type == OBI_QUAL) || tuples)
{
if ((indexer_name == NULL) || (*indexer_name == 0))
{
@ -973,7 +974,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
}
returned_data_type = data_type;
if ((data_type == OBI_STR) || (data_type == OBI_SEQ) || (data_type == OBI_QUAL))
if ((data_type == OBI_STR) || (data_type == OBI_SEQ) || (data_type == OBI_QUAL) || tuples)
// stored data is indices referring to data stored elsewhere
stored_data_type = OBI_IDX;
else
@ -1105,6 +1106,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
header->nb_elements_per_line = nb_elements_per_line;
header->stored_data_type = stored_data_type;
header->returned_data_type = returned_data_type;
header->tuples = tuples;
header->creation_date = time(NULL);
header->version = version_number;
header->cloned_from = -1;
@ -1146,7 +1148,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
}
// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated obi_indexer is opened or created
if ((returned_data_type == OBI_STR) || (returned_data_type == OBI_SEQ) || (returned_data_type == OBI_QUAL))
if ((returned_data_type == OBI_STR) || (returned_data_type == OBI_SEQ) || (returned_data_type == OBI_QUAL) || tuples)
{
new_column->indexer = obi_indexer(dms, final_indexer_name);
if (new_column->indexer == NULL)
@ -1377,6 +1379,7 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
nb_elements_per_line,
(column_to_clone->header)->elements_names,
true,
(column_to_clone->header)->tuples,
(column_to_clone->header)->indexer_name,
((column_to_clone->header)->associated_column).column_name,
((column_to_clone->header)->associated_column).version,

6
src/obidmscolumn.h
View File

@ -86,6 +86,8 @@ typedef struct OBIDMS_column_header {
OBIType_t stored_data_type; /**< Type of the data that is actually stored in the data
* part of the column.
*/
bool tuples; /**< A boolean indicating whether the column contains indices referring to indexed tuples.
*/
time_t creation_date; /**< Date of creation of the file.
*/
obiversion_t version; /**< Version of the column.
@ -100,7 +102,7 @@ typedef struct OBIDMS_column_header {
*/
Column_reference_t associated_column; /**< If there is one, the reference to the associated column.
*/
bool finished; /**< A boolean indicating whether the column was properly closed by the view that created it. TODO
bool finished; /**< A boolean indicating whether the column was properly closed by the view that created it.
*/
char comments[COMMENTS_MAX_LENGTH+1]; /**< Comments stored as a classical zero end C string.
*/
@ -239,6 +241,7 @@ size_t obi_get_platform_header_size();
* @param elements_names The names of the elements with ';' as separator (no terminal ';'),
* 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 tuples A boolean indicating whether the column should contain indices referring to indexed tuples.
* @param indexer_name The name of the indexer if there is one associated with the column.
* 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 "").
@ -258,6 +261,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
index_t nb_elements_per_line,
char* elements_names,
bool elt_names_formatted,
bool tuples,
const char* indexer_name,
const char* associated_column_name,
obiversion_t associated_column_version,

85
src/obidmscolumn_array.c Normal file
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@ -0,0 +1,85 @@
/****************************************************************************
* OBIDMS_column_array functions *
****************************************************************************/
/**
* @file obidsmcolumn_array.c
* @author Celine Mercier
* @date October 27th 2017
* @brief Functions handling OBIColumns containing data arrays of any type.
*/
#include <stdlib.h>
#include <stdio.h>
#include "obidmscolumn.h"
#include "obitypes.h"
#include "array_indexer.h"
/**********************************************************************
*
* D E F I N I T I O N O F T H E P U B L I C F U N C T I O N S
*
**********************************************************************/
int obi_column_set_array(OBIDMS_column_p column, index_t line_nb, const void* value, uint8_t elt_size, int32_t value_length)
{
index_t idx;
if (obi_column_prepare_to_set_value(column, line_nb, 0) < 0)
return -1;
if (value == OBITuple_NA)
{
idx = OBIIdx_NA;
}
else
{
// Add the value in the indexer
idx = obi_index_array(column->indexer, value, elt_size, value_length);
if (idx == -1) // An error occurred
{
if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR)
{
// If the error is that the indexer is read-only, clone it
if (obi_clone_column_indexer(column) < 0)
return -1;
obi_set_errno(0);
// Add the value in the new indexer
idx = obi_index_array(column->indexer, value, elt_size, value_length);
if (idx == -1)
return -1;
}
else
return -1;
}
}
// Add the value's index in the column
*(((index_t*) (column->data)) + line_nb) = idx;
return 0;
}
const void* obi_column_get_array(OBIDMS_column_p column, index_t line_nb, int32_t* value_length_p)
{
index_t idx;
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
return OBITuple_NA;
idx = *(((index_t*) (column->data)) + line_nb);
// Check NA
if (idx == OBIIdx_NA)
return OBITuple_NA;
return obi_retrieve_array(column->indexer, idx, value_length_p);
}

64
src/obidmscolumn_array.h Normal file
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@ -0,0 +1,64 @@
/****************************************************************************
* Array columns header file *
****************************************************************************/
/**
* @file obidsmcolumn_array.h
* @author Celine Mercier
* @date October 30th 2017
* @brief Header file for the functions handling OBIColumns containing data in the form of indices referring to data arrays.
*/
#ifndef OBIDMSCOLUMN_ARRAY_H_
#define OBIDMSCOLUMN_ARRAY_H_
#include <stdlib.h>
#include <stdio.h>
#include "obidmscolumn.h"
#include "obitypes.h"
/**
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
* to arrays handled by an indexer.
*
* @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 A pointer on the array.
* @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_column_set_array(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 data in the form of indices referring
* to arrays handled by an indexer.
*
* @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 value_length A pointer on an integer to store the length of the array retrieved.
*
* @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_column_get_array(OBIDMS_column_p column, index_t line_nb, int32_t* value_length_p);
#endif /* OBIDMSCOLUMN_ARRAY_H_ */

2
src/obitypes.h
View File

@ -27,7 +27,7 @@
#define OBIBlob_NA (NULL) /**< NA value for the type Obiblobs */ // TODO discuss
#define OBIQual_char_NA (NULL) /**< NA value for the type OBI_QUAL if the quality is in character string format */
#define OBIQual_int_NA (NULL) /**< NA value for the type OBI_QUAL if the quality is in integer format */
#define OBITuple_NA (NULL) /**< NA value for tuples of any type */
/**
* @brief enum for the boolean OBIType.

58
src/obiview.c
View File

@ -28,6 +28,7 @@
#include "obidmscolumn_qual.h"
#include "obidmscolumn_seq.h"
#include "obidmscolumn_str.h"
#include "obidmscolumn_array.h"
#include "obierrno.h"
#include "obidebug.h"
#include "obilittlebigman.h"
@ -1643,7 +1644,7 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
// If there is a new line selection, build it by combining it with the one from the view to clone if there is one
else if (line_selection != NULL)
{
view->line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, NULL, false, NULL, NULL, -1, NULL);
view->line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, NULL, false, false, NULL, NULL, -1, NULL);
if ((view->line_selection) == NULL)
{
obidebug(1, "\nError creating a column corresponding to a line selection");
@ -1795,6 +1796,7 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
0,
0,
NULL,
false,
NULL,
NULL,
-1,
@ -1862,19 +1864,19 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
if (view_to_clone == NULL)
{
// Adding sequence column
if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, NULL, OBI_SEQ, 0, 1, NULL, NULL, NULL, -1, "Nucleotide sequences", true) < 0) // discuss using same indexer "NUC_SEQ_INDEXER"
if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, NULL, OBI_SEQ, 0, 1, NULL, false, NULL, NULL, -1, "Nucleotide sequences", true) < 0) // discuss using same indexer "NUC_SEQ_INDEXER"
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
}
// Adding id column
if (obi_view_add_column(view, ID_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, NULL, NULL, -1, "Sequence identifiers", true) < 0)
if (obi_view_add_column(view, ID_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, false, NULL, NULL, -1, "Sequence identifiers", true) < 0)
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
}
// Adding definition column
if (obi_view_add_column(view, DEFINITION_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, NULL, NULL, -1, "Definitions", true) < 0)
if (obi_view_add_column(view, DEFINITION_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, false, NULL, NULL, -1, "Definitions", true) < 0)
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
@ -1883,7 +1885,7 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
if (quality_column)
{
associated_nuc_column = obi_view_get_column(view, NUC_SEQUENCE_COLUMN);
if (obi_view_add_column(view, QUALITY_COLUMN, -1, NULL, OBI_QUAL, 0, 1, NULL, NULL, (associated_nuc_column->header)->name, (associated_nuc_column->header)->version, "Sequence qualities", true) < 0) // TODO discuss automatic association
if (obi_view_add_column(view, QUALITY_COLUMN, -1, NULL, OBI_QUAL, 0, 1, NULL, false, NULL, (associated_nuc_column->header)->name, (associated_nuc_column->header)->version, "Sequence qualities", true) < 0) // TODO discuss automatic association
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
@ -2211,6 +2213,7 @@ int obi_view_add_column(Obiview_p view,
index_t nb_lines,
index_t nb_elements_per_line,
char* elements_names,
bool tuples,
const char* indexer_name,
const char* associated_column_name,
obiversion_t associated_column_version,
@ -2289,7 +2292,7 @@ int obi_view_add_column(Obiview_p view,
// Open or create the column
if (create)
{ // Create column
column = obi_create_column(view->dms, column_name, data_type, nb_lines, nb_elements_per_line, elements_names, false, indexer_name, associated_column_name, associated_column_version, comments);
column = obi_create_column(view->dms, column_name, data_type, nb_lines, nb_elements_per_line, elements_names, false, tuples, indexer_name, associated_column_name, associated_column_version, comments);
if (column == NULL)
{
obidebug(1, "\nError creating a column to add to a view");
@ -2796,7 +2799,7 @@ int obi_create_auto_count_column(Obiview_p view)
return -1;
}
if (obi_view_add_column(view, COUNT_COLUMN, -1, NULL, OBI_INT, 0, 1, NULL, NULL, NULL, -1, "Sequence counts", true) < 0)
if (obi_view_add_column(view, COUNT_COLUMN, -1, NULL, OBI_INT, 0, 1, NULL, false, NULL, NULL, -1, "Sequence counts", true) < 0)
{
obidebug(1, "Error adding an automatic count column in a view");
return -1;
@ -2848,7 +2851,7 @@ int obi_create_auto_id_column(Obiview_p view, const char* prefix)
}
// Create the new ID column
if (obi_view_add_column(view, ID_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, NULL, NULL, -1, "Sequence identifiers", true) < 0)
if (obi_view_add_column(view, ID_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, false, NULL, NULL, -1, "Sequence identifiers", true) < 0)
{
obidebug(1, "Error adding an automatic ID column in a view");
return -1;
@ -3623,3 +3626,42 @@ index_t obi_get_index_with_elt_name_and_col_name_in_view(Obiview_p view, const c
/****************************************/
/*********** FOR ARRAY COLUMNS ***********/
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)
{
if (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
return -1;
return obi_column_set_array(column, line_nb, value, elt_size, value_length);
}
const void* obi_get_array_with_col_p_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, int32_t* value_length_p)
{
if (prepare_to_get_value_from_column(view, &line_nb) < 0)
return OBITuple_NA;
return obi_column_get_array(column, line_nb, value_length_p);
}
int obi_set_array_with_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const void* value, uint8_t elt_size, int32_t value_length)
{
OBIDMS_column_p column_p;
column_p = obi_view_get_column(view, column_name);
if (column_p == NULL)
return -1;
return obi_set_array_with_col_p_in_view(view, column_p, line_nb, value, elt_size, value_length);
}
const void* obi_get_array_with_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, int32_t* value_length_p)
{
OBIDMS_column_p column_p;
column_p = obi_view_get_column(view, column_name);
if (column_p == NULL)
return OBITuple_NA;
return obi_get_array_with_col_p_in_view(view, column_p, line_nb, value_length_p);
}
/****************************************/

86
src/obiview.h
View File

@ -361,6 +361,7 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name);
* @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 tuples A boolean indicating whether the column should contain indices referring to indexed tuples.
* @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.
@ -383,6 +384,7 @@ int obi_view_add_column(Obiview_p view,
index_t nb_lines,
index_t nb_elements_per_line,
char* elements_names,
bool tuples,
const char* indexer_name,
const char* associated_column_name,
obiversion_t associated_column_version,
@ -2207,4 +2209,88 @@ index_t obi_get_index_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_col
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_ */