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

Now handling dictionaries with one key

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

2
python/obitools3/commands/cat.pyx
View File

@ -115,7 +115,7 @@ def run(config):
v.close() v.close()
for coln in dict_cols: for coln in dict_cols:
Column.new_column(o_view, coln, dict_cols[coln]['obitype'], Column.new_column(o_view, coln, dict_cols[coln]['obitype'],
nb_elements_per_line=dict_cols[coln]['nbelts'], elements_names=list(dict_cols[coln]['eltnames'])) nb_elements_per_line=dict_cols[coln]['nbelts'], elements_names=list(dict_cols[coln]['eltnames']), dict_column=True)
# Initialize the progress bar # Initialize the progress bar
if not config['obi']['noprogressbar']: if not config['obi']['noprogressbar']:

10
python/obitools3/commands/import.pyx
View File

@ -257,7 +257,8 @@ def run(config):
for tag in dict_dict: for tag in dict_dict:
dcols[tag] = (Column.new_column(view, tag, dict_dict[tag][1], \ dcols[tag] = (Column.new_column(view, tag, dict_dict[tag][1], \
nb_elements_per_line=len(dict_dict[tag][0]), \ nb_elements_per_line=len(dict_dict[tag][0]), \
elements_names=list(dict_dict[tag][0])), \ elements_names=list(dict_dict[tag][0]), \
dict_column=True), \
dict_dict[tag][1]) dict_dict[tag][1])
@ -328,10 +329,13 @@ def run(config):
value_type = type(value) value_type = type(value)
nb_elts = 1 nb_elts = 1
value_obitype = OBI_VOID value_obitype = OBI_VOID
dict_col = False
if value_type == dict or value_type == list : if value_type == dict or value_type == list :
nb_elts = len(value) nb_elts = len(value)
elt_names = list(value) elt_names = list(value)
if value_type == dict :
dict_col = True
else : else :
nb_elts = 1 nb_elts = 1
elt_names = None elt_names = None
@ -339,11 +343,9 @@ def run(config):
value_obitype = get_obitype(value) value_obitype = get_obitype(value)
if value_obitype != OBI_VOID : if value_obitype != OBI_VOID :
dcols[tag] = (Column.new_column(view, tag, value_obitype, nb_elements_per_line=nb_elts, elements_names=elt_names), value_obitype) dcols[tag] = (Column.new_column(view, tag, value_obitype, nb_elements_per_line=nb_elts, elements_names=elt_names, dict_column=dict_col), value_obitype)
# Fill value # Fill value
if value_type == dict and nb_elts == 1: # special case that makes the OBI3 create a 1 elt/line column which won't read a dict value
value = value[list(value.keys())[0]] # The solution is to transform the value in a simple atomic one acceptable by the column
dcols[tag][0][i] = value dcols[tag][0][i] = value
# TODO else log error? # TODO else log error?

5
python/obitools3/commands/test.pyx
View File

@ -302,12 +302,16 @@ def create_random_column(config, infos) :
alias = random.choice([b'', random_unique_name(infos)]) alias = random.choice([b'', random_unique_name(infos)])
tuples = random.choice([True, False]) tuples = random.choice([True, False])
if not tuples : if not tuples :
dict_column = random.choice([True, False])
nb_elements_per_line=random.randint(1, config['test']['maxelts']) nb_elements_per_line=random.randint(1, config['test']['maxelts'])
if nb_elements_per_line > 1:
dict_column = True
elements_names = [] elements_names = []
for i in range(nb_elements_per_line) : for i in range(nb_elements_per_line) :
elements_names.append(random_unique_element_name(config, infos)) elements_names.append(random_unique_element_name(config, infos))
elements_names = random.choice([None, elements_names]) elements_names = random.choice([None, elements_names])
else : else :
dict_column = False
nb_elements_per_line = 1 nb_elements_per_line = 1
elements_names = None elements_names = None
name = random_unique_name(infos) name = random_unique_name(infos)
@ -318,6 +322,7 @@ def create_random_column(config, infos) :
data_type, data_type,
nb_elements_per_line=nb_elements_per_line, nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names, elements_names=elements_names,
dict_column=dict_column,
tuples=tuples, tuples=tuples,
comments=random_comments(config), comments=random_comments(config),
alias=alias alias=alias

2
python/obitools3/commands/uniq.pyx
View File

@ -378,6 +378,7 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
OBI_INT, OBI_INT,
nb_elements_per_line=merged_infos[merged_col_name]['nb_elts'], nb_elements_per_line=merged_infos[merged_col_name]['nb_elts'],
elements_names=list(merged_infos[merged_col_name]['elt_names']), elements_names=list(merged_infos[merged_col_name]['elt_names']),
dict_column=True,
comments=i_col.comments, comments=i_col.comments,
alias=merged_col_name alias=merged_col_name
) )
@ -400,6 +401,7 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
OBI_INT, OBI_INT,
nb_elements_per_line=len(view), nb_elements_per_line=len(view),
elements_names=[id for id in i_id_col], elements_names=[id for id in i_id_col],
dict_column=True,
alias=TAXID_DIST_COLUMN alias=TAXID_DIST_COLUMN
) )

1
python/obitools3/dms/capi/obidmscolumn.pxd
View File

@ -31,6 +31,7 @@ cdef extern from "obidmscolumn.h" nogil:
const_char_p elements_names const_char_p elements_names
OBIType_t returned_data_type OBIType_t returned_data_type
OBIType_t stored_data_type OBIType_t stored_data_type
bint dict_column
bint tuples bint tuples
bint to_eval bint to_eval
time_t creation_date time_t creation_date

1
python/obitools3/dms/capi/obiview.pxd
View File

@ -95,6 +95,7 @@ cdef extern from "obiview.h" nogil:
index_t nb_elements_per_line, index_t nb_elements_per_line,
char* elements_names, char* elements_names,
bint elt_names_formatted, bint elt_names_formatted,
bint dict_column,
bint tuples, bint tuples,
bint to_eval, bint to_eval,
const_char_p indexer_name, const_char_p indexer_name,

12
python/obitools3/dms/column/column.pyx
View File

@ -90,6 +90,7 @@ cdef class Column(OBIWrapper) :
obitype_t data_type, obitype_t data_type,
index_t nb_elements_per_line=1, index_t nb_elements_per_line=1,
list elements_names=None, list elements_names=None,
bint dict_column=False,
bint tuples=False, bint tuples=False,
bint to_eval=False, bint to_eval=False,
object associated_column_name=b"", object associated_column_name=b"",
@ -152,6 +153,7 @@ cdef class Column(OBIWrapper) :
nb_elements_per_line = nb_elements_per_line, nb_elements_per_line = nb_elements_per_line,
elements_names = elements_names_p, elements_names = elements_names_p,
elt_names_formatted = False, elt_names_formatted = False,
dict_column = dict_column,
tuples = tuples, tuples = tuples,
to_eval = to_eval, to_eval = to_eval,
indexer_name = NULL, indexer_name = NULL,
@ -200,7 +202,7 @@ cdef class Column(OBIWrapper) :
column_p = column_pp[0] column_p = column_pp[0]
column_type = column_p.header.returned_data_type column_type = column_p.header.returned_data_type
column_class = Column.get_column_class(column_type, (column_p.header.nb_elements_per_line > 1), column_p.header.tuples) column_class = Column.get_column_class(column_type, (column_p.header.nb_elements_per_line > 1 or column_p.header.dict_column == True), column_p.header.tuples)
column = OBIWrapper.new_wrapper(column_class, column_pp) column = OBIWrapper.new_wrapper(column_class, column_pp)
column._view = view column._view = view
@ -236,6 +238,7 @@ cdef class Column(OBIWrapper) :
nb_elements_per_line = -1, nb_elements_per_line = -1,
elements_names = NULL, elements_names = NULL,
elt_names_formatted = False, elt_names_formatted = False,
dict_column = False,
tuples = False, tuples = False,
to_eval = False, to_eval = False,
indexer_name = NULL, indexer_name = NULL,
@ -374,6 +377,13 @@ cdef class Column(OBIWrapper) :
raise OBIDeactivatedInstanceError() raise OBIDeactivatedInstanceError()
return self.pointer().header.nb_elements_per_line return self.pointer().header.nb_elements_per_line
# dict_column property getter
@property
def dict_column(self):
if not self.active() :
raise OBIDeactivatedInstanceError()
return self.pointer().header.dict_column
# data_type property getter # data_type property getter
@property @property
def data_type(self): def data_type(self):

4
python/obitools3/dms/column/typed_column/bool.pyx
View File

@ -38,11 +38,13 @@ cdef class Column_bool(Column):
object column_name, object column_name,
index_t nb_elements_per_line=1, index_t nb_elements_per_line=1,
object elements_names=None, object elements_names=None,
bint dict_column=False,
bint tuples=False, bint tuples=False,
object comments={}): object comments={}):
return Column.new_column(view, column_name, OBI_BOOL, return Column.new_column(view, column_name, OBI_BOOL,
nb_elements_per_line=nb_elements_per_line, nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names, elements_names=elements_names,
dict_column=dict_column,
tuples=tuples, tuples=tuples,
comments=comments) comments=comments)

2
python/obitools3/dms/column/typed_column/char.pyx
View File

@ -36,12 +36,14 @@ cdef class Column_char(Column):
object column_name, object column_name,
index_t nb_elements_per_line=1, index_t nb_elements_per_line=1,
object elements_names=None, object elements_names=None,
bint dict_column=False,
bint tuples=False, bint tuples=False,
object comments={}): object comments={}):
return Column.new_column(view, column_name, OBI_CHAR, return Column.new_column(view, column_name, OBI_CHAR,
nb_elements_per_line=nb_elements_per_line, nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names, elements_names=elements_names,
dict_column=dict_column,
tuples=tuples, tuples=tuples,
comments=comments) comments=comments)

2
python/obitools3/dms/column/typed_column/float.pyx
View File

@ -36,12 +36,14 @@ cdef class Column_float(Column):
object column_name, object column_name,
index_t nb_elements_per_line=1, index_t nb_elements_per_line=1,
object elements_names=None, object elements_names=None,
bint dict_column=False,
bint tuples=False, bint tuples=False,
object comments={}): object comments={}):
return Column.new_column(view, column_name, OBI_FLOAT, return Column.new_column(view, column_name, OBI_FLOAT,
nb_elements_per_line=nb_elements_per_line, nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names, elements_names=elements_names,
dict_column=dict_column,
tuples=tuples, tuples=tuples,
comments=comments) comments=comments)

2
python/obitools3/dms/column/typed_column/int.pyx
View File

@ -38,12 +38,14 @@ cdef class Column_int(Column):
object column_name, object column_name,
index_t nb_elements_per_line=1, index_t nb_elements_per_line=1,
object elements_names=None, object elements_names=None,
bint dict_column=False,
bint tuples=False, bint tuples=False,
object comments={}): object comments={}):
return Column.new_column(view, column_name, OBI_INT, return Column.new_column(view, column_name, OBI_INT,
nb_elements_per_line=nb_elements_per_line, nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names, elements_names=elements_names,
dict_column=dict_column,
tuples=tuples, tuples=tuples,
comments=comments) comments=comments)

2
python/obitools3/dms/column/typed_column/qual.pyx
View File

@ -38,6 +38,7 @@ cdef class Column_qual(Column_idx):
object column_name, object column_name,
index_t nb_elements_per_line=1, index_t nb_elements_per_line=1,
object elements_names=None, object elements_names=None,
bint dict_column=False,
object associated_column_name=b"", object associated_column_name=b"",
int associated_column_version=-1, int associated_column_version=-1,
object comments={}): object comments={}):
@ -45,6 +46,7 @@ cdef class Column_qual(Column_idx):
return Column.new_column(view, column_name, OBI_QUAL, return Column.new_column(view, column_name, OBI_QUAL,
nb_elements_per_line=nb_elements_per_line, nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names, elements_names=elements_names,
dict_column=dict_column,
tuples=False, tuples=False,
associated_column_name=associated_column_name, associated_column_name=associated_column_name,
associated_column_version=associated_column_name, associated_column_version=associated_column_name,

2
python/obitools3/dms/column/typed_column/seq.pyx
View File

@ -39,12 +39,14 @@ cdef class Column_seq(Column_idx):
object column_name, object column_name,
index_t nb_elements_per_line=1, index_t nb_elements_per_line=1,
object elements_names=None, object elements_names=None,
bint dict_column=False,
bint tuples=False, bint tuples=False,
object comments={}): object comments={}):
return Column.new_column(view, column_name, OBI_SEQ, return Column.new_column(view, column_name, OBI_SEQ,
nb_elements_per_line=nb_elements_per_line, nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names, elements_names=elements_names,
dict_column=dict_column,
tuples=tuples, tuples=tuples,
comments=comments) comments=comments)

2
python/obitools3/dms/column/typed_column/str.pyx
View File

@ -38,12 +38,14 @@ cdef class Column_str(Column_idx):
object column_name, object column_name,
index_t nb_elements_per_line=1, index_t nb_elements_per_line=1,
object elements_names=None, object elements_names=None,
bint dict_column=False,
bint tuples=False, bint tuples=False,
object comments={}): object comments={}):
return Column.new_column(view, column_name, OBI_STR, return Column.new_column(view, column_name, OBI_STR,
nb_elements_per_line=nb_elements_per_line, nb_elements_per_line=nb_elements_per_line,
elements_names=elements_names, elements_names=elements_names,
dict_column=dict_column,
tuples=tuples, tuples=tuples,
comments=comments) comments=comments)

3
python/obitools3/dms/view/view.pyx
View File

@ -343,7 +343,7 @@ cdef class View(OBIWrapper) :
new_column = Column.new_column(self, old_column.pointer().header.name, new_data_type, new_column = Column.new_column(self, old_column.pointer().header.name, new_data_type,
nb_elements_per_line=new_nb_elements_per_line, elements_names=new_elements_names, nb_elements_per_line=new_nb_elements_per_line, elements_names=new_elements_names,
comments=old_column.comments, alias=column_name_b+tobytes('___new___')) dict_column=(new_nb_elements_per_line>1), comments=old_column.comments, alias=column_name_b+tobytes('___new___'))
switch_to_dict = old_column.nb_elements_per_line == 1 and new_nb_elements_per_line > 1 switch_to_dict = old_column.nb_elements_per_line == 1 and new_nb_elements_per_line > 1
ori_key = old_column._elements_names[0] ori_key = old_column._elements_names[0]
@ -404,6 +404,7 @@ cdef class View(OBIWrapper) :
col.data_type_int, col.data_type_int,
nb_elements_per_line = col.nb_elements_per_line, nb_elements_per_line = col.nb_elements_per_line,
elements_names = col._elements_names, elements_names = col._elements_names,
dict_column = col.dict_column,
tuples = col.tuples, tuples = col.tuples,
to_eval = col.to_eval, to_eval = col.to_eval,
comments = col.comments, comments = col.comments,

3
src/build_reference_db.c
View File

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

12
src/obi_clean.c
View File

@ -88,42 +88,42 @@ static int create_output_columns(Obiview_p o_view,
int sample_count) int sample_count)
{ {
// Status column // 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); obidebug(1, "\nError creating the %s column", CLEAN_STATUS_COLUMN_NAME);
return -1; return -1;
} }
// Head column // 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); obidebug(1, "\nError creating the %s column", CLEAN_HEAD_COLUMN_NAME);
return -1; return -1;
} }
// Sample count column // 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); obidebug(1, "\nError creating the %s column", CLEAN_SAMPLECOUNT_COLUMN_NAME);
return -1; return -1;
} }
// Head count column // 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); obidebug(1, "\nError creating the %s column", CLEAN_HEADCOUNT_COLUMN_NAME);
return -1; return -1;
} }
// Internal count column // 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); obidebug(1, "\nError creating the %s column", CLEAN_INTERNALCOUNT_COLUMN_NAME);
return -1; return -1;
} }
// Singleton count column // 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); obidebug(1, "\nError creating the %s column", CLEAN_SINGLETONCOUNT_COLUMN_NAME);
return -1; 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) static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
{ {
// Original length column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_SEQLEN_COLUMN_NAME);
return -1; return -1;
} }
// Amplicon length column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_AMPLICONLEN_COLUMN_NAME);
return -1; return -1;
} }
// Taxid column // 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); obidebug(1, "\nError creating the %s column", TAXID_COLUMN);
return -1; return -1;
} }
// Taxonomic rank column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_RANK_COLUMN_NAME);
return -1; return -1;
} }
// Species taxid column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_SPECIES_TAXID_COLUMN_NAME);
return -1; return -1;
} }
// Genus taxid column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_GENUS_TAXID_COLUMN_NAME);
return -1; return -1;
} }
// Family taxid column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_FAMILY_TAXID_COLUMN_NAME);
return -1; return -1;
@ -201,7 +201,7 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
if (kingdom_mode) if (kingdom_mode)
{ {
// Kingdom taxid column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_KINGDOM_TAXID_COLUMN_NAME);
return -1; return -1;
@ -210,7 +210,7 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
else else
{ {
// Superkingdom taxid column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_SUPERKINGDOM_TAXID_COLUMN_NAME);
return -1; return -1;
@ -218,28 +218,28 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
} }
// Scientific name column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_SCIENTIFIC_NAME_COLUMN_NAME);
return -1; return -1;
} }
// Species name column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_SPECIES_NAME_COLUMN_NAME);
return -1; return -1;
} }
// Genus name column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_GENUS_NAME_COLUMN_NAME);
return -1; return -1;
} }
// Family name column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_FAMILY_NAME_COLUMN_NAME);
return -1; return -1;
@ -248,7 +248,7 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
if (kingdom_mode) if (kingdom_mode)
{ {
// Kingdom name column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_KINGDOM_NAME_COLUMN_NAME);
return -1; return -1;
@ -257,7 +257,7 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
else else
{ {
// Superkingdom name column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_SUPERKINGDOM_NAME_COLUMN_NAME);
return -1; return -1;
@ -265,49 +265,49 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode)
} }
// Strand column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_STRAND_COLUMN_NAME);
return -1; return -1;
} }
// Primer 1 column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_PRIMER1_COLUMN_NAME);
return -1; return -1;
} }
// Primer 2 column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_PRIMER2_COLUMN_NAME);
return -1; return -1;
} }
// Error 1 column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_ERROR1_COLUMN_NAME);
return -1; return -1;
} }
// Error 2 column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_ERROR2_COLUMN_NAME);
return -1; return -1;
} }
// Temperature 1 column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_TEMP1_COLUMN_NAME);
return -1; return -1;
} }
// Temperature 2 column // 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); obidebug(1, "\nError creating the %s column", ECOPCR_TEMP2_COLUMN_NAME);
return -1; 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) static int create_output_columns(Obiview_p o_view)
{ {
// Score column // 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"); obidebug(1, "\nError creating the column for the score in ecotag");
return -1; return -1;
} }
// Assigned taxid column // 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"); obidebug(1, "\nError creating the column for the assigned taxid in ecotag");
return -1; return -1;
} }
// Assigned scientific name column // 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"); obidebug(1, "\nError creating the column for the assigned scientific name in ecotag");
return -1; return -1;
} }
// Assignement status column // 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"); obidebug(1, "\nError creating the column for the assignment status in ecotag");
return -1; return -1;
} }
// Column for array of best match ids // 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"); obidebug(1, "\nError creating the column for the array of ids of best matches in ecotag");
return -1; return -1;
} }
// Column for array of best match taxids // 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"); obidebug(1, "\nError creating the column for the array of taxids of best matches in ecotag");
return -1; 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) bool normalize, int reference, bool similarity_mode)
{ {
// Create the column for the ids of the 1st sequence aligned // 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"); obidebug(1, "\nError creating the first column for the sequence ids when aligning");
return -1; return -1;
} }
// Create the column for the ids of the 2nd sequence aligned // 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"); obidebug(1, "\nError creating the second column for the sequence ids when aligning");
return -1; return -1;
} }
// Create the column for the index (in the input view) of the first sequences aligned // 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"); obidebug(1, "\nError creating the first column for the sequence indices when aligning");
return -1; return -1;
} }
// Create the column for the index (in the input view) of the second sequences aligned // 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"); obidebug(1, "\nError creating the second column for the sequence indices when aligning");
return -1; return -1;
} }
// Create the column for the LCS length // 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"); obidebug(1, "\nError creating the column for the LCS length when aligning");
return -1; 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 // Create the column for the alignment length if it is computed
if ((reference == ALILEN) && (normalize || !similarity_mode)) 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"); obidebug(1, "\nError creating the column for the alignment length when aligning");
return -1; return -1;
@ -201,7 +201,7 @@ static int create_alignment_output_columns(Obiview_p output_view,
// Create the column for the alignment score // Create the column for the alignment score
if (normalize) 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"); obidebug(1, "\nError creating the column for the score when aligning");
return -1; return -1;
@ -209,7 +209,7 @@ static int create_alignment_output_columns(Obiview_p output_view,
} }
else 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"); obidebug(1, "\nError creating the column for the score when aligning");
return -1; return -1;
@ -219,14 +219,14 @@ static int create_alignment_output_columns(Obiview_p output_view,
if (print_seq) if (print_seq)
{ {
// Create the column for the first sequences aligned // 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"); obidebug(1, "\nError creating the first column for the sequences when aligning");
return -1; return -1;
} }
// Create the column for the second sequences aligned // 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"); obidebug(1, "\nError creating the second column for the sequences when aligning");
return -1; return -1;
@ -235,14 +235,14 @@ static int create_alignment_output_columns(Obiview_p output_view,
if (print_count) if (print_count)
{ {
// Create the column for the count of the first sequences aligned // 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"); obidebug(1, "\nError creating the first column for the sequence counts when aligning");
return -1; return -1;
} }
// Create the column for the count of the second sequences aligned // 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"); obidebug(1, "\nError creating the second column for the sequence counts when aligning");
return -1; 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 // Create new column
column_2 = obi_create_column(dms_2, column_name, header_1->returned_data_type, header_1->line_count, 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->nb_elements_per_line, header_1->elements_names, true, header_1->dict_column,
header_1->to_eval, new_avl_name, (header_1->associated_column).column_name, header_1->tuples, header_1->to_eval, new_avl_name, (header_1->associated_column).column_name,
(header_1->associated_column).version, header_1->comments); (header_1->associated_column).version, header_1->comments);
if (column_2 == NULL) 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,
false, false,
false,
NULL, NULL,
NULL, NULL,
-1, -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, index_t nb_elements_per_line,
char* elements_names, char* elements_names,
bool elt_names_formatted, bool elt_names_formatted,
bool dict_column,
bool tuples, bool tuples,
bool to_eval, bool to_eval,
const char* indexer_name, 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->nb_elements_per_line = nb_elements_per_line;
header->stored_data_type = stored_data_type; header->stored_data_type = stored_data_type;
header->returned_data_type = returned_data_type; header->returned_data_type = returned_data_type;
header->dict_column = dict_column;
header->tuples = tuples; header->tuples = tuples;
header->to_eval = to_eval; header->to_eval = to_eval;
header->creation_date = time(NULL); header->creation_date = time(NULL);
@ -1611,6 +1613,7 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
nb_elements_per_line, nb_elements_per_line,
(column_to_clone->header)->elements_names, (column_to_clone->header)->elements_names,
true, true,
(column_to_clone->header)->dict_column,
(column_to_clone->header)->tuples, (column_to_clone->header)->tuples,
(column_to_clone->header)->to_eval, (column_to_clone->header)->to_eval,
(column_to_clone->header)->indexer_name, (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 OBIType_t stored_data_type; /**< Type of the data that is actually stored in the data
* part of the column. * 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 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 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 ';'), * @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"). * 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 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 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 * @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). * (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, index_t nb_elements_per_line,
char* elements_names, char* elements_names,
bool elt_names_formatted, bool elt_names_formatted,
bool dict_column,
bool tuples, bool tuples,
bool to_eval, bool to_eval,
const char* indexer_name, 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 // 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) 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) if ((view->line_selection) == NULL)
{ {
obidebug(1, "\nError creating a column corresponding to a line selection"); 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,
false, false,
false,
NULL, NULL,
NULL, NULL,
-1, -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) if ((view_to_clone == NULL) && create_default_columns)
{ {
// Adding sequence column // 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"); obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL; return NULL;
} }
// Adding id column // 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"); obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL; return NULL;
} }
// Adding definition column // 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"); obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL; 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) if (quality_column)
{ {
associated_nuc_column = obi_view_get_column(view, NUC_SEQUENCE_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"); obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL; return NULL;
@ -2284,6 +2285,7 @@ int obi_view_add_column(Obiview_p view,
index_t nb_elements_per_line, index_t nb_elements_per_line,
char* elements_names, char* elements_names,
bool elt_names_formatted, bool elt_names_formatted,
bool dict_column,
bool tuples, bool tuples,
bool to_eval, bool to_eval,
const char* indexer_name, const char* indexer_name,
@ -2366,7 +2368,7 @@ int obi_view_add_column(Obiview_p view,
// Open or create the column // Open or create the column
if (create) if (create)
{ // Create column { // 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) if (column == NULL)
{ {
obidebug(1, "\nError creating a column to add to a view"); 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; 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"); obidebug(1, "Error adding an automatic count column in a view");
return -1; return -1;
@ -3282,7 +3284,7 @@ int obi_create_auto_id_column(Obiview_p view, const char* prefix)
} }
// Create the new ID column // 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"); obidebug(1, "Error adding an automatic ID column in a view");
return -1; 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 ';'), * @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"). * 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 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 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 * @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). * (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, index_t nb_elements_per_line,
char* elements_names, char* elements_names,
bool elt_names_formatted, bool elt_names_formatted,
bool dict_column,
bool tuples, bool tuples,
bool to_eval, bool to_eval,
const char* indexer_name, const char* indexer_name,