obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

The predicates associated with a view are now described in its comments

Browse Source 
field
This commit is contained in:
Celine Mercier
2016-07-19 15:31:21 +02:00
parent 8850e40b6e
commit 56e4848ebd
2 changed files with 172 additions and 43 deletions
Download Patch File Download Diff File Expand all files Collapse all files

213
src/obiview.c
View File

@ -175,12 +175,13 @@ int prepare_to_get_value_from_column(Obiview_p view, index_t* line_nb_p);
*
* @param view The view.
*
* @returns A boolean value indicating whether the view has a NUC_SEQUENCE_COLUMN column.
* @returns A character string describing the predicate.
* @retval NULL if the predicate is false or if there was an error.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
bool view_has_nuc_sequence_column(Obiview_p view);
char* view_has_nuc_sequence_column(Obiview_p view);
/**
@ -191,12 +192,13 @@ bool view_has_nuc_sequence_column(Obiview_p view);
*
* @param view The view.
*
* @returns A boolean value indicating whether the view has a QUALITY_COLUMN column.
* @returns A character string describing the predicate.
* @retval NULL if the predicate is false or if there was an error.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
bool view_has_quality_column(Obiview_p view);
char* view_has_quality_column(Obiview_p view);
/**
@ -207,12 +209,13 @@ bool view_has_quality_column(Obiview_p view);
*
* @param view The view.
*
* @returns A boolean value indicating whether the view has a ID_COLUMN column.
* @returns A character string describing the predicate.
* @retval NULL if the predicate is false or if there was an error.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
bool view_has_id_column(Obiview_p view);
char* view_has_id_column(Obiview_p view);
/**
@ -223,12 +226,13 @@ bool view_has_id_column(Obiview_p view);
*
* @param view The view.
*
* @returns A boolean value indicating whether the view has a DEFINITION_COLUMN column.
* @returns A character string describing the predicate.
* @retval NULL if the predicate is false or if there was an error.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
bool view_has_definition_column(Obiview_p view);
char* view_has_definition_column(Obiview_p view);
/**
@ -239,12 +243,13 @@ bool view_has_definition_column(Obiview_p view);
*
* @param view The view.
*
* @returns A boolean value indicating whether the sequence and quality columns correspond properly.
* @returns A character string describing the predicate.
* @retval NULL if the predicate is false or if there was an error.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
bool view_check_quality_matches_seq_column(Obiview_p view);
char* view_check_quality_matches_seq_column(Obiview_p view);
/**
@ -253,12 +258,13 @@ bool view_check_quality_matches_seq_column(Obiview_p view);
* @param view The view.
* @param predicate_function The predicate function to use.
*
* @returns The boolean value returned by the predicate function.
* @returns A character string describing the predicate.
* @retval NULL if the predicate is false or if there was an error.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
bool view_check_one_predicate(Obiview_p view, bool (*predicate_function)(Obiview_p view));
char* view_check_one_predicate(Obiview_p view, char* (*predicate_function)(Obiview_p view));
/**
@ -266,13 +272,13 @@ bool view_check_one_predicate(Obiview_p view, bool (*predicate_function)(Obiview
*
* @param view The view.
*
* @retval 0 if all the predicates are OK.
* @retval -1 if at least one predicate was found to be false.
* @returns A character string describing all the predicates separated by line breaks.
* @retval NULL if at least one of the predicates is false or if there was an error.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int view_check_all_predicates(Obiview_p view);
char* view_check_all_predicates(Obiview_p view);
/************************************************************************
@ -532,43 +538,91 @@ 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)
char* view_has_nuc_sequence_column(Obiview_p view)
{
char* predicate;
predicate = (char*) malloc((strlen("The view has an associated nucleotide sequence column.") + 1) * sizeof(char));
if (predicate == NULL)
{
obi_set_errno(OBI_MALLOC_ERROR);
obidebug(1, "\nError allocating memory for predicate character string.");
return NULL;
}
strcpy(predicate, "The view has an associated nucleotide sequence column.");
if (obi_view_get_column(view, NUC_SEQUENCE_COLUMN) != NULL)
return true;
return predicate;
else
return false;
return NULL;
}
bool view_has_quality_column(Obiview_p view)
char* view_has_quality_column(Obiview_p view)
{
char* predicate;
predicate = (char*) malloc((strlen("The view has an associated sequence quality column.") + 1) * sizeof(char));
if (predicate == NULL)
{
obi_set_errno(OBI_MALLOC_ERROR);
obidebug(1, "\nError allocating memory for predicate character string.");
return NULL;
}
strcpy(predicate, "The view has an associated sequence quality column.");
if (obi_view_get_column(view, QUALITY_COLUMN) != NULL)
return true;
return predicate;
else
return false;
return NULL;
}
bool view_has_id_column(Obiview_p view)
char* view_has_id_column(Obiview_p view)
{
char* predicate;
predicate = (char*) malloc((strlen("The view has an associated identifier column.") + 1) * sizeof(char));
if (predicate == NULL)
{
obi_set_errno(OBI_MALLOC_ERROR);
obidebug(1, "\nError allocating memory for predicate character string.");
return NULL;
}
strcpy(predicate, "The view has an associated identifier column.");
if (obi_view_get_column(view, ID_COLUMN) != NULL)
return true;
return predicate;
else
return false;
return NULL;
}
bool view_has_definition_column(Obiview_p view)
char* view_has_definition_column(Obiview_p view)
{
char* predicate;
predicate = (char*) malloc((strlen("The view has an associated definition column.") + 1) * sizeof(char));
if (predicate == NULL)
{
obi_set_errno(OBI_MALLOC_ERROR);
obidebug(1, "\nError allocating memory for predicate character string.");
return NULL;
}
strcpy(predicate, "The view has an associated definition column.");
if (obi_view_get_column(view, DEFINITION_COLUMN) != NULL)
return true;
return predicate;
else
return false;
return NULL;
}
bool view_check_quality_matches_seq_column(Obiview_p view) // TODO Print error if there is one?
char* 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;
@ -577,10 +631,21 @@ bool view_check_quality_matches_seq_column(Obiview_p view) // TODO Print error i
char* seq;
OBIDMS_column_p qual_column;
OBIDMS_column_p seq_column;
char* predicate;
predicate = (char*) malloc((strlen("The sequences and sequence quality arrays match.") + 1) * sizeof(char));
if (predicate == NULL)
{
obi_set_errno(OBI_MALLOC_ERROR);
obidebug(1, "\nError allocating memory for predicate character string.");
return NULL;
}
strcpy(predicate, "The sequences and sequence quality arrays match.");
qual_column = obi_view_get_column(view, QUALITY_COLUMN);
if (qual_column == NULL)
return false;
return NULL;
seq_column = obi_view_get_column(view, ((qual_column->header)->associated_column).column_name);
//seq_column = obi_open_column(view->dms, ((qual_column->header)->associated_column).column_name, ((qual_column->header)->associated_column).version);
@ -588,12 +653,12 @@ bool view_check_quality_matches_seq_column(Obiview_p view) // TODO Print error i
// TODO if outside of view, make function that opens a column from a column reference structure?
if (seq_column == NULL)
return false;
return NULL;
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;
return NULL;
for (i=0; i < (view->infos)->line_count; i++)
{
@ -605,36 +670,91 @@ bool view_check_quality_matches_seq_column(Obiview_p view) // TODO Print error i
{
// Test that the lengths of the quality and the sequence are equal
if (qual_len != (int)strlen(seq))
return false;
return NULL;
}
// 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 NULL;
}
}
//obi_close_column(seq_column);
return true;
return predicate;
}
bool view_check_one_predicate(Obiview_p view, bool (*predicate_function)(Obiview_p view))
char* view_check_one_predicate(Obiview_p view, char* (*predicate_function)(Obiview_p view))
{
return predicate_function(view);
}
int view_check_all_predicates(Obiview_p view)
char* view_check_all_predicates(Obiview_p view)
{
int i;
int i, j;
size_t size_to_allocate;
char* predicate = NULL;
char* all_predicates_string = NULL;
char** all_predicates = NULL;
size_to_allocate = 0;
// Allocate memory for predicate array
all_predicates = (char**) malloc((view->nb_predicates) * sizeof(char*));
if (all_predicates == NULL)
{
obi_set_errno(OBI_MALLOC_ERROR);
obidebug(1, "\nError allocating memory for predicate array.");
return NULL;
}
for (i=0; i < view->nb_predicates; i++)
{
if (view_check_one_predicate(view, (view->predicate_functions)[i]) == false)
return -1;
// Initialize predicate in predicate array
all_predicates[i] = NULL;
// Check the predicate
predicate = view_check_one_predicate(view, (view->predicate_functions)[i]);
if (predicate == NULL)
{
// TODO discuss
for (j=0; j<=i; j++)
free(all_predicates[j]);
free(all_predicates);
return NULL;
}
else
{
all_predicates[i] = predicate;
size_to_allocate = size_to_allocate + strlen(predicate) + 1; // +1 for '\n'
}
}
return 0;
size_to_allocate += 1; // +1 for '\0'
all_predicates_string = (char*) malloc(size_to_allocate * sizeof(char));
if (all_predicates_string == NULL)
{
obi_set_errno(OBI_MALLOC_ERROR);
obidebug(1, "\nError allocating memory for predicate character string.");
return NULL;
}
// Build the character string with all the predicates
strcpy(all_predicates_string, all_predicates[0]);
for (i=1; i < view->nb_predicates; i++)
{
strcat(all_predicates_string, "\n");
strcat(all_predicates_string, all_predicates[i]);
}
// Free everything
for (i=0; i < view->nb_predicates; i++)
free(all_predicates[i]);
free(all_predicates);
return all_predicates_string;
}
@ -894,7 +1014,7 @@ 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 = malloc((view->nb_predicates) * sizeof(char* (*) (bool)));
(view->predicate_functions)[0] = view_has_nuc_sequence_column;
(view->predicate_functions)[1] = view_has_quality_column;
@ -1398,10 +1518,19 @@ int obi_close_view(Obiview_p view)
int obi_save_and_close_view(Obiview_p view)
{
char* predicates;
if (!(view->read_only))
{
if (view_check_all_predicates(view) < 0)
predicates = view_check_all_predicates(view);
if (predicates == NULL)
return -1; // TODO reverse view (delete files)
else
{
// TODO check size and grow file if needed
strcpy((view->infos)->comments, predicates);
free(predicates);
}
if (obi_save_view(view) < 0)
return -1;
}

2
src/obiview.h
View File

@ -108,7 +108,7 @@ typedef struct Obiview {
*/
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.
char* (**predicate_functions)(struct Obiview* view); /**< Array of pointers on all predicate functions to test when closing the view.
*/
} Obiview_t, *Obiview_p;