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First version for the association of one column to another. Closes #55

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This commit is contained in:
Celine Mercier
2016-07-15 15:38:49 +02:00
parent 8ee85c3005
commit 38718320f9
4 changed files with 110 additions and 63 deletions
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31
src/obiview.c
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@ -582,7 +582,11 @@ bool view_check_quality_matches_seq_column(Obiview_p view) // TODO Print error i
if (qual_column == NULL)
return false;
seq_column = obi_view_get_column(view, NUC_SEQUENCE_COLUMN); // TODO Get associated nuc column
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);
// TODO discuss the fact that it's opened outside of the context of the view or not
// TODO if outside of view, make function that opens a column from a column reference structure?
if (seq_column == NULL)
return false;
@ -608,6 +612,9 @@ bool view_check_quality_matches_seq_column(Obiview_p view) // TODO Print error i
return false;
}
}
//obi_close_column(seq_column);
return true;
}
@ -714,7 +721,7 @@ 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, LINES_COLUMN_NAME, NULL, NULL);
view->line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL, -1, NULL);
if ((view->line_selection) == NULL)
{
obidebug(1, "\nError creating a column corresponding to a line selection");
@ -836,7 +843,8 @@ Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, con
Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments)
{
Obiview_p view;
Obiview_p view;
OBIDMS_column_p associated_nuc_column;
if (view_to_clone != NULL)
{ // Check that the view to clone is already a NUC_SEQS view (TODO discuss possibility of transforming type of a view)
@ -857,25 +865,26 @@ 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, OBI_SEQ, 0, 1, NUC_SEQUENCE_COLUMN, "", "Nucleotide sequences", true) < 0)
if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, OBI_SEQ, 0, 1, NUC_SEQUENCE_COLUMN, "", NULL, -1, "Nucleotide sequences", true) < 0)
{
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, OBI_STR, 0, 1, ID_COLUMN, "", "Ids", true) < 0)
if (obi_view_add_column(view, ID_COLUMN, -1, OBI_STR, 0, 1, ID_COLUMN, "", NULL, -1, "Ids", 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, OBI_STR, 0, 1, DEFINITION_COLUMN, "", "Definitions", true) < 0)
if (obi_view_add_column(view, DEFINITION_COLUMN, -1, OBI_STR, 0, 1, DEFINITION_COLUMN, "", NULL, -1, "Definitions", true) < 0)
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
}
// Adding quality column
if (obi_view_add_column(view, QUALITY_COLUMN, -1, OBI_QUAL, 0, 1, QUALITY_COLUMN, "", "Sequence qualities", true) < 0)
associated_nuc_column = obi_view_get_column(view, NUC_SEQUENCE_COLUMN);
if (obi_view_add_column(view, QUALITY_COLUMN, -1, OBI_QUAL, 0, 1, QUALITY_COLUMN, "", (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;
@ -1062,6 +1071,8 @@ int obi_view_add_column(Obiview_p view,
index_t nb_elements_per_line,
const char* elements_names,
const char* indexer_name,
const char* associated_column_name,
obiversion_t associated_column_version,
const char* comments,
bool create) // all infos for creation or open
{
@ -1131,7 +1142,7 @@ 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, indexer_name, comments);
column = obi_create_column(view->dms, column_name, data_type, nb_lines, nb_elements_per_line, elements_names, indexer_name, associated_column_name, associated_column_version, comments);
}
else
{ // Open column
@ -1241,7 +1252,7 @@ int obi_select_line(Obiview_p view, index_t line_nb)
// If the column for line selection doesn't already exists, create it and store its informations
if ((view->new_line_selection) == NULL)
{
view->new_line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL);
view->new_line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL, -1, NULL);
if ((view->new_line_selection) == NULL)
{
obidebug(1, "\nError creating a column corresponding to a line selection");
@ -1276,7 +1287,7 @@ int obi_select_lines(Obiview_p view, index_t* line_nbs)
// If column for line selection doesn't already exists, create it and store its informations
if ((view->new_line_selection) == NULL)
{
view->new_line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL);
view->new_line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL, -1, NULL);
if ((view->new_line_selection) == NULL)
{
obidebug(1, "\nError creating a column corresponding to a line selection");