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Now handling dictionaries with one key

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This commit is contained in:
Celine Mercier
2021-03-10 16:50:30 +13:00
parent fbf0f7dfb6
commit ad1fd3c341
25 changed files with 115 additions and 64 deletions
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3
src/build_reference_db.c
View File

@ -243,6 +243,7 @@ int build_reference_db(const char* dms_name,
false,
false,
false,
false,
"",
"",
-1,
@ -392,6 +393,7 @@ int build_reference_db(const char* dms_name,
1,
"",
false,
false,
true,
false,
"",
@ -415,6 +417,7 @@ int build_reference_db(const char* dms_name,
1,
"",
false,
false,
true,
false,
"",

12
src/obi_clean.c
View File

@ -88,42 +88,42 @@ static int create_output_columns(Obiview_p o_view,
int sample_count)
{
// Status column
if (obi_view_add_column(o_view, CLEAN_STATUS_COLUMN_NAME, -1, NULL, OBI_CHAR, 0, sample_count, (sample_column->header)->elements_names, true, false, false, NULL, NULL, -1, CLEAN_STATUS_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, CLEAN_STATUS_COLUMN_NAME, -1, NULL, OBI_CHAR, 0, sample_count, (sample_column->header)->elements_names, true, true, false, false, NULL, NULL, -1, CLEAN_STATUS_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", CLEAN_STATUS_COLUMN_NAME);
return -1;
}
// Head column
if (obi_view_add_column(o_view, CLEAN_HEAD_COLUMN_NAME, -1, NULL, OBI_BOOL, 0, 1, NULL, false, false, false, NULL, NULL, -1, CLEAN_HEAD_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, CLEAN_HEAD_COLUMN_NAME, -1, NULL, OBI_BOOL, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, CLEAN_HEAD_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", CLEAN_HEAD_COLUMN_NAME);
return -1;
}
// Sample count column
if (obi_view_add_column(o_view, CLEAN_SAMPLECOUNT_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, CLEAN_SAMPLECOUNT_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, CLEAN_SAMPLECOUNT_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, CLEAN_SAMPLECOUNT_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", CLEAN_SAMPLECOUNT_COLUMN_NAME);
return -1;
}
// Head count column
if (obi_view_add_column(o_view, CLEAN_HEADCOUNT_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, CLEAN_HEADCOUNT_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, CLEAN_HEADCOUNT_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, CLEAN_HEADCOUNT_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", CLEAN_HEADCOUNT_COLUMN_NAME);
return -1;
}
// Internal count column
if (obi_view_add_column(o_view, CLEAN_INTERNALCOUNT_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, CLEAN_INTERNALCOUNT_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, CLEAN_INTERNALCOUNT_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, CLEAN_INTERNALCOUNT_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", CLEAN_INTERNALCOUNT_COLUMN_NAME);
return -1;
}
// Singleton count column
if (obi_view_add_column(o_view, CLEAN_SINGLETONCOUNT_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, CLEAN_SINGLETONCOUNT_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, CLEAN_SINGLETONCOUNT_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, CLEAN_SINGLETONCOUNT_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", CLEAN_SINGLETONCOUNT_COLUMN_NAME);
return -1;

44
src/obi_ecopcr.c
View File

@ -150,49 +150,49 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
{
// Original length column
if (obi_view_add_column(o_view, ECOPCR_SEQLEN_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_SEQLEN_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_SEQLEN_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_SEQLEN_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_SEQLEN_COLUMN_NAME);
return -1;
}
// Amplicon length column
if (obi_view_add_column(o_view, ECOPCR_AMPLICONLEN_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_AMPLICONLEN_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_AMPLICONLEN_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_AMPLICONLEN_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_AMPLICONLEN_COLUMN_NAME);
return -1;
}
// Taxid column
if (obi_view_add_column(o_view, TAXID_COLUMN, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, TAXID_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, TAXID_COLUMN, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, TAXID_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", TAXID_COLUMN);
return -1;
}
// Taxonomic rank column
if (obi_view_add_column(o_view, ECOPCR_RANK_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_RANK_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_RANK_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_RANK_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_RANK_COLUMN_NAME);
return -1;
}
// Species taxid column
if (obi_view_add_column(o_view, ECOPCR_SPECIES_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_SPECIES_TAXID_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_SPECIES_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_SPECIES_TAXID_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_SPECIES_TAXID_COLUMN_NAME);
return -1;
}
// Genus taxid column
if (obi_view_add_column(o_view, ECOPCR_GENUS_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_GENUS_TAXID_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_GENUS_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_GENUS_TAXID_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_GENUS_TAXID_COLUMN_NAME);
return -1;
}
// Family taxid column
if (obi_view_add_column(o_view, ECOPCR_FAMILY_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_FAMILY_TAXID_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_FAMILY_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_FAMILY_TAXID_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_FAMILY_TAXID_COLUMN_NAME);
return -1;
@ -201,7 +201,7 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
if (kingdom_mode)
{
// Kingdom taxid column
if (obi_view_add_column(o_view, ECOPCR_KINGDOM_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_KINGDOM_TAXID_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_KINGDOM_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_KINGDOM_TAXID_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_KINGDOM_TAXID_COLUMN_NAME);
return -1;
@ -210,7 +210,7 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
else
{
// Superkingdom taxid column
if (obi_view_add_column(o_view, ECOPCR_SUPERKINGDOM_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_SUPERKINGDOM_TAXID_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_SUPERKINGDOM_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_SUPERKINGDOM_TAXID_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_SUPERKINGDOM_TAXID_COLUMN_NAME);
return -1;
@ -218,28 +218,28 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
}
// Scientific name column
if (obi_view_add_column(o_view, ECOPCR_SCIENTIFIC_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_SCIENTIFIC_NAME_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_SCIENTIFIC_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_SCIENTIFIC_NAME_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_SCIENTIFIC_NAME_COLUMN_NAME);
return -1;
}
// Species name column
if (obi_view_add_column(o_view, ECOPCR_SPECIES_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_SPECIES_NAME_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_SPECIES_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_SPECIES_NAME_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_SPECIES_NAME_COLUMN_NAME);
return -1;
}
// Genus name column
if (obi_view_add_column(o_view, ECOPCR_GENUS_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_GENUS_NAME_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_GENUS_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_GENUS_NAME_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_GENUS_NAME_COLUMN_NAME);
return -1;
}
// Family name column
if (obi_view_add_column(o_view, ECOPCR_FAMILY_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_FAMILY_NAME_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_FAMILY_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_FAMILY_NAME_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_FAMILY_NAME_COLUMN_NAME);
return -1;
@ -248,7 +248,7 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
if (kingdom_mode)
{
// Kingdom name column
if (obi_view_add_column(o_view, ECOPCR_KINGDOM_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_KINGDOM_NAME_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_KINGDOM_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_KINGDOM_NAME_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_KINGDOM_NAME_COLUMN_NAME);
return -1;
@ -257,7 +257,7 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
else
{
// Superkingdom name column
if (obi_view_add_column(o_view, ECOPCR_SUPERKINGDOM_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_SUPERKINGDOM_NAME_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_SUPERKINGDOM_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_SUPERKINGDOM_NAME_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_SUPERKINGDOM_NAME_COLUMN_NAME);
return -1;
@ -265,49 +265,49 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
}
// Strand column
if (obi_view_add_column(o_view, ECOPCR_STRAND_COLUMN_NAME, -1, NULL, OBI_CHAR, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_STRAND_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_STRAND_COLUMN_NAME, -1, NULL, OBI_CHAR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_STRAND_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_STRAND_COLUMN_NAME);
return -1;
}
// Primer 1 column
if (obi_view_add_column(o_view, ECOPCR_PRIMER1_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_PRIMER1_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_PRIMER1_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_PRIMER1_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_PRIMER1_COLUMN_NAME);
return -1;
}
// Primer 2 column
if (obi_view_add_column(o_view, ECOPCR_PRIMER2_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_PRIMER2_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_PRIMER2_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_PRIMER2_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_PRIMER2_COLUMN_NAME);
return -1;
}
// Error 1 column
if (obi_view_add_column(o_view, ECOPCR_ERROR1_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_ERROR1_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_ERROR1_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_ERROR1_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_ERROR1_COLUMN_NAME);
return -1;
}
// Error 2 column
if (obi_view_add_column(o_view, ECOPCR_ERROR2_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_ERROR2_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_ERROR2_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_ERROR2_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_ERROR2_COLUMN_NAME);
return -1;
}
// Temperature 1 column
if (obi_view_add_column(o_view, ECOPCR_TEMP1_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_TEMP1_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_TEMP1_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_TEMP1_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_TEMP1_COLUMN_NAME);
return -1;
}
// Temperature 2 column
if (obi_view_add_column(o_view, ECOPCR_TEMP2_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, false, false, false, NULL, NULL, -1, ECOPCR_TEMP2_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(o_view, ECOPCR_TEMP2_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ECOPCR_TEMP2_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the %s column", ECOPCR_TEMP2_COLUMN_NAME);
return -1;

12
src/obi_ecotag.c
View File

@ -104,42 +104,42 @@ int print_assignment_result(Obiview_p output_view, index_t line,
static int create_output_columns(Obiview_p o_view)
{
// Score column
if (obi_view_add_column(o_view, ECOTAG_SCORE_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, false, false, false, NULL, NULL, -1, "{}", true) < 0)
if (obi_view_add_column(o_view, ECOTAG_SCORE_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, "{}", true) < 0)
{
obidebug(1, "\nError creating the column for the score in ecotag");
return -1;
}
// Assigned taxid column
if (obi_view_add_column(o_view, ECOTAG_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, NULL, NULL, -1, "{}", true) < 0)
if (obi_view_add_column(o_view, ECOTAG_TAXID_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, "{}", true) < 0)
{
obidebug(1, "\nError creating the column for the assigned taxid in ecotag");
return -1;
}
// Assigned scientific name column
if (obi_view_add_column(o_view, ECOTAG_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, NULL, NULL, -1, "{}", true) < 0)
if (obi_view_add_column(o_view, ECOTAG_NAME_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, "{}", true) < 0)
{
obidebug(1, "\nError creating the column for the assigned scientific name in ecotag");
return -1;
}
// Assignement status column
if (obi_view_add_column(o_view, ECOTAG_STATUS_COLUMN_NAME, -1, NULL, OBI_BOOL, 0, 1, NULL, false, false, false, NULL, NULL, -1, "{}", true) < 0)
if (obi_view_add_column(o_view, ECOTAG_STATUS_COLUMN_NAME, -1, NULL, OBI_BOOL, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, "{}", true) < 0)
{
obidebug(1, "\nError creating the column for the assignment status in ecotag");
return -1;
}
// Column for array of best match ids
if (obi_view_add_column(o_view, ECOTAG_BEST_MATCH_IDS_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, true, false, NULL, NULL, -1, "{}", true) < 0)
if (obi_view_add_column(o_view, ECOTAG_BEST_MATCH_IDS_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, true, false, NULL, NULL, -1, "{}", true) < 0)
{
obidebug(1, "\nError creating the column for the array of ids of best matches in ecotag");
return -1;
}
// Column for array of best match taxids
if (obi_view_add_column(o_view, ECOTAG_BEST_MATCH_TAXIDS_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, true, false, NULL, NULL, -1, "{}", true) < 0)
if (obi_view_add_column(o_view, ECOTAG_BEST_MATCH_TAXIDS_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, true, false, NULL, NULL, -1, "{}", true) < 0)
{
obidebug(1, "\nError creating the column for the array of taxids of best matches in ecotag");
return -1;

24
src/obi_lcs.c
View File

@ -155,35 +155,35 @@ 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, false, false, false, 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, false, false, 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, false, false, false, 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, false, false, 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, false, false, false, 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, false, false, 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, false, false, false, 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, false, false, 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, false, false, false, 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, false, false, false, NULL, NULL, -1, LCS_LENGTH_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the column for the LCS length when aligning");
return -1;
@ -192,7 +192,7 @@ 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, false, false, false, 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, false, false, false, NULL, NULL, -1, ALI_LENGTH_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the column for the alignment length when aligning");
return -1;
@ -201,7 +201,7 @@ 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, false, false, false, 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, false, false, false, NULL, NULL, -1, SCORE_COLUMN_NAME, true) < 0)
{
obidebug(1, "\nError creating the column for the score when aligning");
return -1;
@ -209,7 +209,7 @@ 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, false, false, false, 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, false, false, false, NULL, NULL, -1, SCORE_COLUMN_NAME, true) < 0)
{
obidebug(1, "\nError creating the column for the score when aligning");
return -1;
@ -219,14 +219,14 @@ 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, false, false, false, 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, false, false, 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, false, false, false, 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, false, false, 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;
@ -235,14 +235,14 @@ static int create_alignment_output_columns(Obiview_p output_view,
if (print_count)
{
// 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, false, false, false, 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, false, false, 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, false, false, false, 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, false, false, false, NULL, NULL, -1, COUNT2_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the second column for the sequence counts when aligning");
return -1;

5
src/obidms.c
View File

@ -1575,8 +1575,8 @@ 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->tuples,
header_1->to_eval, new_avl_name, (header_1->associated_column).column_name,
header_1->nb_elements_per_line, header_1->elements_names, true, header_1->dict_column,
header_1->tuples, header_1->to_eval, new_avl_name, (header_1->associated_column).column_name,
(header_1->associated_column).version, header_1->comments);
if (column_2 == NULL)
@ -1813,6 +1813,7 @@ int obi_import_view(const char* dms_path_1, const char* dms_path_2, const char*
false,
false,
false,
false,
NULL,
NULL,
-1,

3
src/obidmscolumn.c
View File

@ -1024,6 +1024,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
index_t nb_elements_per_line,
char* elements_names,
bool elt_names_formatted,
bool dict_column,
bool tuples,
bool to_eval,
const char* indexer_name,
@ -1282,6 +1283,7 @@ 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->dict_column = dict_column;
header->tuples = tuples;
header->to_eval = to_eval;
header->creation_date = time(NULL);
@ -1611,6 +1613,7 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
nb_elements_per_line,
(column_to_clone->header)->elements_names,
true,
(column_to_clone->header)->dict_column,
(column_to_clone->header)->tuples,
(column_to_clone->header)->to_eval,
(column_to_clone->header)->indexer_name,

4
src/obidmscolumn.h
View File

@ -77,6 +77,8 @@ 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 dict_column; /**< Whether the column contains dictionary-like values.
*/
bool tuples; /**< A boolean indicating whether the column contains indices referring to indexed tuples.
*/
bool to_eval; /**< A boolean indicating whether the column contains expressions that should be evaluated
@ -249,6 +251,7 @@ size_t obi_calculate_header_size(index_t nb_elements_per_line, int64_t elts_name
* @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 dict_column A boolean indicating whether the column should contain dictionary-like values.
* @param tuples A boolean indicating whether the column should contain indices referring to indexed tuples.
* @param to_eval A boolean indicating whether the column contains expressions that should be evaluated
* (typically OBI_STR columns containing character strings to be evaluated by Python).
@ -271,6 +274,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
index_t nb_elements_per_line,
char* elements_names,
bool elt_names_formatted,
bool dict_column,
bool tuples,
bool to_eval,
const char* indexer_name,

18
src/obiview.c
View File

@ -1712,7 +1712,7 @@ 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, false, NULL, NULL, -1, NULL);
view->line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, NULL);
if ((view->line_selection) == NULL)
{
obidebug(1, "\nError creating a column corresponding to a line selection");
@ -1862,6 +1862,7 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
false,
false,
false,
false,
NULL,
NULL,
-1,
@ -1930,19 +1931,19 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
if ((view_to_clone == NULL) && create_default_columns)
{
// Adding sequence column
if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, NULL, OBI_SEQ, 0, 1, NULL, false, false, false, NULL, NULL, -1, "{}", 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, false, NULL, NULL, -1, "{}", 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, false, false, NULL, NULL, -1, "{}", true) < 0)
if (obi_view_add_column(view, ID_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, "{}", 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, false, false, NULL, NULL, -1, "{}", true) < 0)
if (obi_view_add_column(view, DEFINITION_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, "{}", true) < 0)
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
@ -1951,7 +1952,7 @@ 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, false, false, NULL, (associated_nuc_column->header)->name, (associated_nuc_column->header)->version, "{}", true) < 0) // TODO discuss automatic association
if (obi_view_add_column(view, QUALITY_COLUMN, -1, NULL, OBI_QUAL, 0, 1, NULL, false, false, false, false, NULL, (associated_nuc_column->header)->name, (associated_nuc_column->header)->version, "{}", true) < 0) // TODO discuss automatic association
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
@ -2284,6 +2285,7 @@ int obi_view_add_column(Obiview_p view,
index_t nb_elements_per_line,
char* elements_names,
bool elt_names_formatted,
bool dict_column,
bool tuples,
bool to_eval,
const char* indexer_name,
@ -2366,7 +2368,7 @@ 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, elt_names_formatted, tuples, to_eval, 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, dict_column, 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");
@ -3230,7 +3232,7 @@ 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, false, false, NULL, NULL, -1, "{}", true) < 0)
if (obi_view_add_column(view, COUNT_COLUMN, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, "{}", true) < 0)
{
obidebug(1, "Error adding an automatic count column in a view");
return -1;
@ -3282,7 +3284,7 @@ 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, false, false, NULL, NULL, -1, "{}", true) < 0)
if (obi_view_add_column(view, ID_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, "{}", true) < 0)
{
obidebug(1, "Error adding an automatic ID column in a view");
return -1;

2
src/obiview.h
View File

@ -400,6 +400,7 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name);
* @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 elt_names_formatted Whether the separator for the elements names is ';' (false), or '\0' (true, as formatted by format_elements_names()).
* @param dict_column Whether the column contains dictionary-like values.
* @param tuples A boolean indicating whether the column should contain indices referring to indexed tuples.
* @param to_eval A boolean indicating whether the column contains expressions that should be evaluated
* (typically OBI_STR columns containing character strings to be evaluated by Python).
@ -426,6 +427,7 @@ int obi_view_add_column(Obiview_p view,
index_t nb_elements_per_line,
char* elements_names,
bool elt_names_formatted,
bool dict_column,
bool tuples,
bool to_eval,
const char* indexer_name,