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A first version of predicate functions that are checked when a new view

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is saved and closed
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Celine Mercier
2016-07-12 14:54:11 +02:00
parent 000b9999ad
commit 8ee85c3005
2 changed files with 262 additions and 26 deletions
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248
src/obiview.c
View File

@ -129,7 +129,7 @@ OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name);
/**
* Internal function preparing to set a value in a column, in the context of a view.
* @brief Internal function preparing to set a value in a column, in the context of a view.
*
* The function checks that the view is not read-only, clones the column or all columns if needed,
* and updates the line count if needed.
@ -148,7 +148,7 @@ int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* column_pp, i
/**
* Internal function preparing to get a value from a column, in the context of a view.
* @brief Internal function preparing to get a value from a column, in the context of a view.
*
* The function checks that the line index is not beyond the current line count of the view,
* and modifies it if there is a line selection associated with the view.
@ -165,6 +165,116 @@ int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* column_pp, i
int prepare_to_get_value_from_column(Obiview_p view, index_t* line_nb_p);
/****** PREDICATE FUNCTIONS *******/
/**
* @brief Internal function checking if a view has a NUC_SEQUENCE_COLUMN column.
*
* The function checks that the view has a column with the name attributed to obligatory
* nucleotide sequence columns.
*
* @param view The view.
*
* @returns A boolean value indicating whether the view has a NUC_SEQUENCE_COLUMN column.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
bool view_has_nuc_sequence_column(Obiview_p view);
/**
* @brief Internal function checking if a view has a QUALITY_COLUMN column.
*
* The function checks that the view has a column with the name attributed to obligatory
* quality columns.
*
* @param view The view.
*
* @returns A boolean value indicating whether the view has a QUALITY_COLUMN column.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
bool view_has_quality_column(Obiview_p view);
/**
* @brief Internal function checking if a view has a ID_COLUMN column.
*
* The function checks that the view has a column with the name attributed to obligatory
* id columns.
*
* @param view The view.
*
* @returns A boolean value indicating whether the view has a ID_COLUMN column.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
bool view_has_id_column(Obiview_p view);
/**
* @brief Internal function checking if a view has a DEFINITION_COLUMN column.
*
* The function checks that the view has a column with the name attributed to obligatory
* definition columns.
*
* @param view The view.
*
* @returns A boolean value indicating whether the view has a DEFINITION_COLUMN column.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
bool view_has_definition_column(Obiview_p view);
/**
* @brief Internal function checking that the quality column of a view and the sequence column associated to it
* correspond properly:
* - when a line is defined for either column, it must also be defined for the other column
* - when a line is defined, the lengths of the sequence and of the quality must be equal
*
* @param view The view.
*
* @returns A boolean value indicating whether the sequence and quality columns correspond properly.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
bool view_check_quality_matches_seq_column(Obiview_p view);
/**
* @brief Internal function checking one predicate function on a view.
*
* @param view The view.
* @param predicate_function The predicate function to use.
*
* @returns The boolean value returned by the predicate function.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
bool view_check_one_predicate(Obiview_p view, bool (*predicate_function)(Obiview_p view));
/**
* @brief Internal function checking all the predicates associated with a view.
*
* @param view The view.
*
* @retval 0 if all the predicates are OK.
* @retval -1 if at least one predicate was found to be false.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int view_check_all_predicates(Obiview_p view);
/************************************************************************
*
* D E F I N I T I O N O F T H E P R I V A T E F U N C T I O N S
@ -229,11 +339,11 @@ int create_obiview_file(OBIDMS_p dms, const char* view_name)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError creating an obiview file");
// free(file_name); TODO
// free(file_name);
return -1;
}
//free(file_name); TODO
//free(file_name);
// Truncate file to the right size
file_size = get_platform_view_file_size();
@ -419,6 +529,111 @@ int prepare_to_get_value_from_column(Obiview_p view, index_t* line_nb_p)
}
/****** PREDICATE FUNCTIONS *******/
bool view_has_nuc_sequence_column(Obiview_p view)
{
if (obi_view_get_column(view, NUC_SEQUENCE_COLUMN) != NULL)
return true;
else
return false;
}
bool view_has_quality_column(Obiview_p view)
{
if (obi_view_get_column(view, QUALITY_COLUMN) != NULL)
return true;
else
return false;
}
bool view_has_id_column(Obiview_p view)
{
if (obi_view_get_column(view, ID_COLUMN) != NULL)
return true;
else
return false;
}
bool view_has_definition_column(Obiview_p view)
{
if (obi_view_get_column(view, DEFINITION_COLUMN) != NULL)
return true;
else
return false;
}
bool view_check_quality_matches_seq_column(Obiview_p view) // TODO Print error if there is one?
{
index_t i, j;
index_t nb_elements_per_line;
int qual_len;
const uint8_t* qual;
char* seq;
OBIDMS_column_p qual_column;
OBIDMS_column_p seq_column;
qual_column = obi_view_get_column(view, QUALITY_COLUMN);
if (qual_column == NULL)
return false;
seq_column = obi_view_get_column(view, NUC_SEQUENCE_COLUMN); // TODO Get associated nuc column
if (seq_column == NULL)
return false;
nb_elements_per_line = (qual_column->header)->nb_elements_per_line;
// Check that the quality and the sequence columns have the same number of elements per line
if (nb_elements_per_line != (seq_column->header)->nb_elements_per_line)
return false;
for (i=0; i < (view->infos)->line_count; i++)
{
for (j=0; j < nb_elements_per_line; j++)
{
qual = obi_column_get_obiqual_int_with_elt_idx(qual_column, i, j, &qual_len);
seq = obi_column_get_obiseq_with_elt_idx(seq_column, i, j);
if ((qual != OBIQual_int_NA) && (seq != OBISeq_NA))
{
// Test that the lengths of the quality and the sequence are equal
if (qual_len != (int)strlen(seq))
return false;
}
// Test if one value is NA and not the other
else if (((qual == OBIQual_int_NA) && (seq != OBISeq_NA)) || ((qual != OBIQual_int_NA) && (seq == OBISeq_NA)))
return false;
}
}
return true;
}
bool view_check_one_predicate(Obiview_p view, bool (*predicate_function)(Obiview_p view))
{
return predicate_function(view);
}
int view_check_all_predicates(Obiview_p view)
{
int i;
for (i=0; i < view->nb_predicates; i++)
{
if (view_check_one_predicate(view, (view->predicate_functions)[i]) == false)
return -1;
}
return 0;
}
// TODO predicate function that goes through each line / each elements
/**********************************************************************
*
* 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
@ -581,6 +796,8 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
strcpy((view->infos)->comments, comments);
(view->infos)->creation_date = time(NULL);
view->read_only = 0;
view->nb_predicates = 0;
view->predicate_functions = NULL;
// Store reference for line selection
if (view->line_selection == NULL)
@ -665,6 +882,17 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
}
}
// Add predicate functions of the view type
view->nb_predicates = 5; // TODO macro?
view->predicate_functions = malloc((view->nb_predicates) * sizeof(bool (*) (bool)));
(view->predicate_functions)[0] = view_has_nuc_sequence_column;
(view->predicate_functions)[1] = view_has_quality_column;
(view->predicate_functions)[2] = view_has_id_column;
(view->predicate_functions)[3] = view_has_definition_column;
(view->predicate_functions)[4] = view_check_quality_matches_seq_column;
return view;
}
@ -704,11 +932,11 @@ Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError opening an obiview file");
// free(file_name); TODO
// free(file_name);
return NULL;
}
//free(file_name); TODO
//free(file_name);
// Map the view infos structure
file_size = get_platform_view_file_size();
@ -750,11 +978,11 @@ int obi_view_unmap_file(OBIDMS_p dms, Obiview_infos_p view_infos)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError opening an obiview file");
// free(file_name); TODO
// free(file_name);
return -1;
}
//free(file_name); TODO
//free(file_name);
// Unmap the view infos structure
file_size = get_platform_view_file_size();
@ -819,6 +1047,8 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name)
view->dms = dms;
view->new_line_selection = NULL;
view->read_only = true;
view->nb_predicates = 0;
view->predicate_functions = NULL;
return view;
}
@ -1159,6 +1389,8 @@ int obi_save_and_close_view(Obiview_p view)
{
if (!(view->read_only))
{
if (view_check_all_predicates(view) < 0)
return -1; // TODO reverse view (delete files)
if (obi_save_view(view) < 0)
return -1;
}

4
src/obiview.h
View File

@ -117,6 +117,10 @@ typedef struct Obiview {
*/
OBIDMS_column_p columns[MAX_NB_OPENED_COLUMNS]; /**< Array of pointers on all the columns of the view.
*/
int nb_predicates; /**< Number of predicates to test when closing the view.
*/
bool (**predicate_functions)(struct Obiview* view); /**< Array of pointers on all predicate functions to test when closing the view.
*/
} Obiview_t, *Obiview_p;