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Columns: elements names informations are now kept in a memory arena of

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adapted size in the header, and added a boolean in the header indicating
whether the values should be evaluated (typically character strings to
be evaluated in Python)
This commit is contained in:
Celine Mercier
2017-12-13 22:46:50 +01:00
parent 2df5932b67
commit 1fd3323372
10 changed files with 177 additions and 111 deletions
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20
src/obiview.c
View File

@@ -1646,7 +1646,7 @@ 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, false, NULL, NULL, -1, NULL);
view->line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, NULL, false, false, false, NULL, NULL, -1, NULL);
if ((view->line_selection) == NULL)
{
obidebug(1, "\nError creating a column corresponding to a line selection");
@@ -1799,6 +1799,8 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
0,
NULL,
false,
false,
false,
NULL,
NULL,
-1,
@@ -1866,19 +1868,19 @@ 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, false, 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, false, 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, false, NULL, NULL, -1, "Sequence identifiers", true) < 0)
if (obi_view_add_column(view, ID_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, false, false, 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, false, NULL, NULL, -1, "Definitions", true) < 0)
if (obi_view_add_column(view, DEFINITION_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, "Definitions", true) < 0)
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
@@ -1887,7 +1889,7 @@ 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, false, 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, false, 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;
@@ -2215,7 +2217,9 @@ int obi_view_add_column(Obiview_p view,
index_t nb_lines,
index_t nb_elements_per_line,
char* elements_names,
bool elt_names_formatted,
bool tuples,
bool to_eval,
const char* indexer_name,
const char* associated_column_name,
obiversion_t associated_column_version,
@@ -2294,7 +2298,7 @@ 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, tuples, 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, elt_names_formatted, tuples, to_eval, indexer_name, associated_column_name, associated_column_version, comments);
if (column == NULL)
{
obidebug(1, "\nError creating a column to add to a view");
@@ -2801,7 +2805,7 @@ 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, false, NULL, NULL, -1, "Sequence counts", true) < 0)
if (obi_view_add_column(view, COUNT_COLUMN, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, "Sequence counts", true) < 0)
{
obidebug(1, "Error adding an automatic count column in a view");
return -1;
@@ -2853,7 +2857,7 @@ 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, false, NULL, NULL, -1, "Sequence identifiers", true) < 0)
if (obi_view_add_column(view, ID_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, "Sequence identifiers", true) < 0)
{
obidebug(1, "Error adding an automatic ID column in a view");
return -1;