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This commit is contained in:
Eric Coissac
2016-12-14 08:44:44 +01:00
parent 06cb7a9a58
commit 04d39c62ab
9 changed files with 649 additions and 297 deletions
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36
python/obitools3/obidms/_obidms.pxd
View File

@ -30,41 +30,6 @@ cdef class OBIDMS_column_line:
cdef index_t _index
cdef class OBIView:
cdef Obiview_p _pointer
cdef dict _columns
cdef Obiview_p _open_or_create_view(self,
OBIDMS dms,
str view_name,
bint new=*,
object view_to_clone=*,
index_t* line_selection_p=*,
str comments=*,
bint quality_column=*,
str view_type=*)
cpdef delete_column(self, str column_name)
cpdef add_column(self,
str column_name,
obiversion_t version_number=*,
str alias=*,
str type=*,
index_t nb_lines=*,
index_t nb_elements_per_line=*,
list elements_names=*,
str indexer_name=*,
str associated_column_name=*,
obiversion_t associated_column_version=*,
str comments=*,
bint create=*
)
cpdef change_column_alias(self, str current_alias, str new_alias)
cpdef update_column_pointers(self)
cpdef close(self)
@staticmethod
cdef object get_view_subclass(str view_type)
cdef class OBIView_line :
@ -85,7 +50,6 @@ cdef class OBIDMS:
cpdef close(self)
cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name)
cpdef OBIView open_view(self, str view_name)
cpdef OBIView new_view(self, str view_name, str view_type=*, bint quality_column=*, str comments=*)
cpdef OBIView clone_view(self, str view_name, object view_to_clone, str comments=*)

253
python/obitools3/obidms/_obidms.pyx
View File

@ -76,6 +76,8 @@ from .capi.obiview cimport Obiview_p, \
from libc.stdlib cimport malloc
cdef class OBIDMS_column :
# Note: should only be initialized through a subclass
@ -266,251 +268,6 @@ cdef class OBIDMS_column_line :
######################################################################################################
cdef class OBIView :
def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, OBIView_line_selection line_selection=None, str comments="", bint quality_column=False, str view_type=""):
cdef index_t* line_selection_p = NULL
cdef int i
cdef str col_alias
cdef OBIDMS_column_p column_p
cdef object subclass
if line_selection is not None :
# Get the name of the associated view to clone
view_to_clone = line_selection._view_name # TODO discuss. This makes it possible for the view to clone to be closed. If a view to clone was given it is not checked.
# Build the C array corresponding to the line selection
line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array
for i in range(len(line_selection)) :
line_selection_p[i] = line_selection[i]
line_selection_p[len(line_selection)] = -1 # flagging the end of the array
self._pointer = self._open_or_create_view(dms, view_name, new=new, view_to_clone=view_to_clone, line_selection_p=line_selection_p, comments=comments, quality_column=quality_column, view_type=view_type)
# Go through columns to build dictionaries of corresponding python instances # TODO make function?
self._columns = {}
for i in range(self._pointer.infos.column_count) :
col_alias = bytes2str(self._pointer.infos.column_references[i].alias)
column_p = <OBIDMS_column_p> (self._pointer.columns)[i]
subclass = OBIDMS_column.get_subclass_type(column_p)
self._columns[col_alias] = subclass(self, col_alias)
cdef Obiview_p _open_or_create_view(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, index_t* line_selection_p=NULL, str comments="", bint quality_column=False, str view_type=""):
cdef Obiview_p view = NULL
# Create the view if needed, with the right type
if new :
if view_type == "" :
if view_to_clone is not None :
if type(view_to_clone) == str :
view = obi_new_view_cloned_from_name(dms._pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p, str2bytes(comments))
else :
view = obi_new_view(dms._pointer, str2bytes(view_name), (<OBIView> view_to_clone)._pointer, line_selection_p, str2bytes(comments))
else :
view = obi_new_view(dms._pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments))
elif view_type == bytes2str(VIEW_TYPE_NUC_SEQS) :
if view_to_clone is not None :
if type(view_to_clone) == str :
view = obi_new_view_nuc_seqs_cloned_from_name(dms._pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p, str2bytes(comments), quality_column)
else :
view = obi_new_view_nuc_seqs(dms._pointer, str2bytes(view_name), (<OBIView> view_to_clone)._pointer, line_selection_p, str2bytes(comments), quality_column)
else :
view = obi_new_view_nuc_seqs(dms._pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments), quality_column)
else :
raise Exception("View type not recognized")
# Else, open the existing view
else :
view = obi_open_view(dms._pointer, str2bytes(view_name))
if view == NULL :
raise Exception("Error creating/opening a view")
return view
def __repr__(self) :
cdef str s
s = str(self.name) + "\n" + str(self.comments) + "\n" + str(self.line_count) + " lines\n"
for column_name in self._columns :
s = s + repr(self._columns[column_name]) + '\n'
return s
cpdef delete_column(self, str column_name) :
cdef str column_n
if obi_view_delete_column(self._pointer, str2bytes(column_name)) < 0 :
raise Exception("Problem deleting a column from a view")
# Update the dictionary of column objects:
(self._columns).pop(column_name)
self.update_column_pointers()
cpdef add_column(self,
str column_name,
obiversion_t version_number=-1,
str alias='',
str type='',
index_t nb_lines=0,
index_t nb_elements_per_line=1,
list elements_names=None,
str indexer_name="",
str associated_column_name="",
obiversion_t associated_column_version=-1,
str comments="",
bint create=True
) :
cdef bytes column_name_b
cdef bytes elements_names_b
cdef object subclass
cdef OBIDMS_column_p column_p
column_name_b = str2bytes(column_name)
if alias == '' :
alias = column_name
alias_b = column_name_b
else :
alias_b = str2bytes(alias)
if elements_names is None :
elements_names_b = str2bytes("")
else :
elements_names_b = str2bytes(';'.join(elements_names))
if type : # TODO make C function that does that
if type == 'OBI_INT' :
data_type = OBI_INT
elif type == 'OBI_FLOAT' :
data_type = OBI_FLOAT
elif type == 'OBI_BOOL' :
data_type = OBI_BOOL
elif type == 'OBI_CHAR' :
data_type = OBI_CHAR
elif type == 'OBI_QUAL' :
data_type = OBI_QUAL
elif type == 'OBI_STR' :
data_type = OBI_STR
elif type == 'OBI_SEQ' :
data_type = OBI_SEQ
else :
raise Exception("Invalid provided data type")
if (obi_view_add_column(self._pointer, column_name_b, version_number, alias_b,
data_type, nb_lines, nb_elements_per_line,
elements_names_b, str2bytes(indexer_name),
str2bytes(associated_column_name), associated_column_version,
str2bytes(comments), create) < 0) :
raise Exception("Problem adding a column in a view")
# Get the column pointer
column_p = obi_view_get_column(self._pointer, alias_b)
# Open and store the subclass
subclass = OBIDMS_column.get_subclass_type(column_p)
(self._columns)[alias] = subclass(self, alias)
cpdef change_column_alias(self, str current_alias, str new_alias):
cdef OBIDMS_column column
if (obi_view_create_column_alias(self._pointer, str2bytes(current_alias), str2bytes(new_alias)) < 0) :
raise Exception("Problem changing a column alias")
# Update the dictionaries of column objects
self._columns[new_alias] = self._columns[current_alias]
column = self._columns[new_alias]
column._alias = new_alias
(self._columns).pop(current_alias)
cpdef update_column_pointers(self):
cdef str column_n
cdef OBIDMS_column column
for column_n in self._columns :
column = self._columns[column_n]
column._pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self._pointer, str2bytes(column_n))
cpdef close(self) :
if (obi_save_and_close_view(self._pointer) < 0) :
raise Exception("Problem closing a view")
self._pointer = NULL
self._columns = {}
def __iter__(self):
# Iteration on each line of all columns
# Declarations
cdef index_t line_nb
cdef OBIView_line line
# Yield each line
for line_nb in range(self.line_count) :
line = self[line_nb]
yield line
def __getitem__(self, object item) :
if type(item) == str :
return (self._columns)[item]
elif type(item) == int :
return OBIView_line(self, item)
def __contains__(self, str column_name):
return (column_name in self._columns)
def __len__(self):
return(self.line_count)
def __str__(self) :
cdef OBIView_line line
cdef str to_print
to_print = ""
for line in self :
to_print = to_print + str(line) + "\n"
return to_print
# line_count property getter
@property
def line_count(self):
return self._pointer.infos.line_count
# name property getter
@property
def name(self):
return bytes2str(self._pointer.infos.name)
# view type property getter
@property
def type(self): # @ReservedAssignment
return bytes2str(self._pointer.infos.view_type)
# columns property getter
@property
def columns(self):
return self._columns
# comments property getter
@property
def comments(self):
return bytes2str(self._pointer.infos.comments)
# TODO setter that concatenates new comments?
@staticmethod
cdef object get_view_subclass(str view_type) :
cdef object subclass
if view_type == bytes2str(VIEW_TYPE_NUC_SEQS) :
view_class = OBIView_NUC_SEQS
else :
view_class = OBIView
return view_class
######################################################################################################
@ -633,12 +390,6 @@ cdef class OBIDMS :
return OBI_Taxonomy(self, taxo_name)
cpdef OBIView open_view(self, str view_name) :
cdef object view_class
view_class = OBIView.get_view_subclass(self.read_view_infos(view_name)["view_type"])
return view_class(self, view_name)
cpdef OBIView new_view(self, str view_name, str view_type="", bint quality_column=False, str comments="") :
cdef object view_class
# Get right subclass depending on view type

55
python/obitools3/obidms/_obiseq.pyx
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@ -6,6 +6,7 @@ from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
ID_COLUMN, \
DEFINITION_COLUMN, \
QUALITY_COLUMN
from docutils.nodes import definition
cdef str __str__ID_COLUMN__ = bytes2str(ID_COLUMN)
@ -16,14 +17,23 @@ cdef str __str__NUC_SEQUENCE_COLUMN__ = bytes2str(NUC_SEQUENCE_COLUMN)
cdef class OBI_Seq(dict) :
def __init__(self, str id,
def __init__(self, str id,
object seq,
str definition=None,
dict attributes=None) :
self.id = id
self.seq = seq
str definition=None,
dict tags=None) :
if tags is not None:
self.update(tags)
self._id = id
self._seq = seq
if definition is not None :
self.definition = definition
self._definition = definition
else:
self._definition = None
def __getitem__(self,str key):
if key == __str__ID_COLUMN__:
@ -33,6 +43,14 @@ cdef class OBI_Seq(dict) :
else:
return dict.__getitem__(self,key)
def __setitem__(self,str key,object value):
if key == __str__ID_COLUMN__:
self._id=value
elif key == __str__DEFINITION_COLUMN__:
self._definition=value
else:
dict.__setitem__(self,key,value)
# sequence id property getter and setter
@property
def id(self): # @ReservedAssignment
@ -61,14 +79,37 @@ cdef class OBI_Seq(dict) :
cdef class OBI_Nuc_Seq(OBI_Seq) :
def __init__(self, str id,
object seq,
str quality=None,
str definition=None,
dict tags=None) :
OBI_Seq.__init__(self,id,seq,tags)
if quality is not None:
self._quality=quality
else:
self._quality=None
def __getitem__(self,str key):
if key == __str__NUC_SEQUENCE_COLUMN__:
return self._id
return self._seq
elif key == __str__QUALITY_COLUMN__:
return self._quality
else:
return OBI_Seq.__getitem__(self,key)
def __setitem__(self,str key, object value):
if key == __str__NUC_SEQUENCE_COLUMN__:
self._seq = value
elif key == __str__QUALITY_COLUMN__:
self._quality=value
else:
OBI_Seq.__setitem__(self,key,value)
cpdef object get_str_quality(self) : # TODO not ideal. Make quality_int and quality_str properties
return self._quality

54
python/obitools3/obidms/_obiview.pxd Normal file
View File

@ -0,0 +1,54 @@
#cython: language_level=3
cdef class OBIView:
cdef Obiview_p _pointer
cdef dict _columns
cdef __init_columns__(self):
cpdef OBIView clone(self,
str view_name,
OBIView_line_selection line_selection=*,
str comments=*)
@staticmethod
cpdef OBIView new(OBIDMS dms,
str view_name,
str comments=*)
@staticmethod
cpdef OBIView open(OBIDMS dms,
str view_name)
cpdef delete_column(self, str column_name)
cpdef add_column(self,
str column_name,
obiversion_t version_number=*,
str alias=*,
str type=*,
index_t nb_lines=*,
index_t nb_elements_per_line=*,
list elements_names=*,
str indexer_name=*,
str associated_column_name=*,
obiversion_t associated_column_version=*,
str comments=*,
bint create=*
)
cpdef change_column_alias(self, str current_alias, str new_alias)
cpdef update_column_pointers(self)
cpdef OBIView_line_selection new_selection(self,
list lines=*)
cdef class OBIView_line_selection(list):
cdef OBIView _view
cdef str _view_name
cdef index_t* __build_binary_list__(self)
cpdef OBIView materialize(self,
str view_name,
str comments=*)

324
python/obitools3/obidms/_obiview.pyx Normal file
View File

@ -0,0 +1,324 @@
#cython: language_level=3
cdef class OBIView :
def __init__(self,int __internalCall__):
if __internalCall__!=987654:
raise RuntimeError('OBIView constructor cannot be called directly')
self._pointer = NULL
self._columns = {}
cdef __init_columns__(self):
cdef size_t i
cdef str col_alias
cdef OBIDMS_column_p column_p
cdef Obiview_p pointer = self._pointer
self._columns = {}
for i in range(pointer.infos.column_count) :
col_alias = bytes2str(pointer.infos.column_references[i].alias)
column_p = <OBIDMS_column_p> (pointer.columns)[i]
subclass = OBIDMS_column.get_subclass_type(column_p)
self._columns[col_alias] = subclass(self, col_alias)
cpdef OBIView clone(self,
str view_name,
str comments=""):
cdef OBIView view = OBIView(987654)
view._pointer = obi_new_view(self._pointer.dms,
str2bytes(view_name),
self._pointer,
NULL,
str2bytes(comments))
if view._pointer == NULL :
raise RuntimeError("Error : Cannot clone view %s into view %s"
% (str(self.name),
view_name)
)
view.__init_columns__(self)
return view
@staticmethod
cpdef OBIView new(OBIDMS dms,
str view_name,
str comments=""):
cdef OBIView view = OBIView(987654) # @DuplicatedSignature
view._pointer = obi_new_view(dms._pointer,
str2bytes(view_name),
NULL,
NULL,
str2bytes(comments))
if view._pointer == NULL :
raise RuntimeError("Error : Cannot create view %s" % view_name)
view.__init_columns__(self)
return view
@staticmethod
cpdef OBIView open(OBIDMS dms,
str view_name):
cdef OBIView view = OBIView(987654) # @DuplicatedSignature
view._pointer = obi_open_view(dms._pointer,
str2bytes(view_name))
if view._pointer == NULL :
raise RuntimeError("Error : Cannot open view %s" % view_name)
view.__init_columns__(self)
return view
def __dealloc__(self):
if (obi_save_and_close_view(self._pointer) < 0) :
raise Exception("Problem closing a view")
def __repr__(self) :
cdef str s
s = str(self.name) + "\n" + str(self.comments) + "\n" + str(self.line_count) + " lines\n"
for column_name in self._columns :
s = s + repr(self._columns[column_name]) + '\n'
return s
cpdef delete_column(self, str column_name) :
cdef str column_n
if obi_view_delete_column(self._pointer, str2bytes(column_name)) < 0 :
raise Exception("Problem deleting a column from a view")
# Update the dictionary of column objects:
(self._columns).pop(column_name)
self.update_column_pointers()
cpdef add_column(self,
str column_name,
obiversion_t version_number=-1,
str alias='',
str type='',
index_t nb_lines=0,
index_t nb_elements_per_line=1,
list elements_names=None,
str indexer_name="",
str associated_column_name="",
obiversion_t associated_column_version=-1,
str comments="",
bint create=True
) :
cdef bytes column_name_b
cdef bytes elements_names_b
cdef object subclass
cdef OBIDMS_column_p column_p
column_name_b = str2bytes(column_name)
if alias == '' :
alias = column_name
alias_b = column_name_b
else :
alias_b = str2bytes(alias)
if elements_names is None :
elements_names_b = str2bytes("")
else :
elements_names_b = str2bytes(';'.join(elements_names))
if type : # TODO make C function that does that
if type == 'OBI_INT' :
data_type = OBI_INT
elif type == 'OBI_FLOAT' :
data_type = OBI_FLOAT
elif type == 'OBI_BOOL' :
data_type = OBI_BOOL
elif type == 'OBI_CHAR' :
data_type = OBI_CHAR
elif type == 'OBI_QUAL' :
data_type = OBI_QUAL
elif type == 'OBI_STR' :
data_type = OBI_STR
elif type == 'OBI_SEQ' :
data_type = OBI_SEQ
else :
raise Exception("Invalid provided data type")
if (obi_view_add_column(self._pointer, column_name_b, version_number, alias_b,
data_type, nb_lines, nb_elements_per_line,
elements_names_b, str2bytes(indexer_name),
str2bytes(associated_column_name), associated_column_version,
str2bytes(comments), create) < 0) :
raise Exception("Problem adding a column in a view")
# Get the column pointer
column_p = obi_view_get_column(self._pointer, alias_b)
# Open and store the subclass
subclass = OBIDMS_column.get_subclass_type(column_p)
(self._columns)[alias] = subclass(self, alias)
cpdef change_column_alias(self, str current_alias, str new_alias):
cdef OBIDMS_column column
if (obi_view_create_column_alias(self._pointer, str2bytes(current_alias), str2bytes(new_alias)) < 0) :
raise Exception("Problem changing a column alias")
# Update the dictionaries of column objects
self._columns[new_alias] = self._columns[current_alias]
column = self._columns[new_alias]
column._alias = new_alias
(self._columns).pop(current_alias)
cpdef update_column_pointers(self):
cdef str column_n
cdef OBIDMS_column column
for column_n in self._columns :
column = self._columns[column_n]
column._pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self._pointer, str2bytes(column_n))
cpdef OBIView_line_selection new_selection(self,list lines=None):
return OBIView_line_selection(self,lines)
def __iter__(self):
# Iteration on each line of all columns
# Declarations
cdef index_t line_nb
cdef OBIView_line line
# Yield each line
for line_nb in range(self.line_count) :
line = self[line_nb]
yield line
def __getitem__(self, object item) :
if type(item) == str :
return (self._columns)[item]
elif type(item) == int :
return OBIView_line(self, item)
def __contains__(self, str column_name):
return (column_name in self._columns)
def __len__(self):
return(self.line_count)
def __str__(self) :
cdef OBIView_line line
cdef str to_print
to_print = ""
for line in self :
to_print = to_print + str(line) + "\n"
return to_print
# line_count property getter
@property
def line_count(self):
return self._pointer.infos.line_count
# name property getter
@property
def name(self):
return bytes2str(self._pointer.infos.name)
# view type property getter
@property
def type(self): # @ReservedAssignment
return bytes2str(self._pointer.infos.view_type)
# columns property getter
@property
def columns(self):
return self._columns
# comments property getter
@property
def comments(self):
return bytes2str(self._pointer.infos.comments)
# TODO setter that concatenates new comments?
cdef class OBIView_line_selection(list):
def __init__(self, OBIView view, lines=None) :
if view._pointer == NULL:
raise Exception("Error: trying to create a line selection with an invalidated view")
self._view = view
self._view_name = view.name
if lines is not None:
self.extend(lines)
def extend(self, iterable):
cdef index_t i
cdef index_t max_i = self._view.line_count
for i in iterable:
if i > max_i:
raise RuntimeError("Error: trying to select line %d beyond the line count %d of view %s" %
(i,
max_i,
self._view_name)
)
list.append(self,i)
def append(self, index_t idx) :
if idx >= self._view.line_count :
raise RuntimeError("Error: trying to select line %d beyond the line count %d of view %s" %
(i,
max_i,
self._view_name)
)
list.append(self,idx)
cdef index_t* __build_binary_list__(self):
cdef index_t* line_selection_p = NULL
cdef int i
cdef size_t l_selection = len(self)
line_selection_p = <index_t*> malloc((l_selection + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array
for i in range(l_selection) :
line_selection_p[i] = line_selection[i]
line_selection_p[l_selection] = -1 # flagging the end of the array
return line_selection_p
cpdef OBIView materialize(self,
str view_name,
str comments=""):
cdef OBIView view = OBIView(987654)
view._pointer = obi_new_view(self._view._pointer.dms,
str2bytes(view_name),
self._view._pointer,
self.__build_binary_list__(),
str2bytes(comments))
if view._pointer == NULL :
raise RuntimeError("Error : Cannot clone view %s into view %s"
% (str(self.name),
view_name)
)
view.__init_columns__(self)
return view

21
python/obitools3/obidms/_obiview_nuc_seq.pxd
View File

@ -4,5 +4,22 @@ from ._obidms cimport OBIView
from ._obiseq cimport OBI_Nuc_Seq, OBI_Nuc_Seq_Stored
cdef class OBIView_NUC_SEQS(OBIView):
pass
cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS):
cpdef OBIView clone(self,
str view_name,
OBIView_line_selection line_selection=*,
str comments=*)
@staticmethod
cpdef OBIView new(OBIDMS dms,
str view_name,
str comments=*)
@staticmethod
cpdef OBIView open(OBIDMS dms,
str view_name)
cdef class OBIView_NUC_SEQS_line_selection(OBIView_line_selection):
cpdef OBIView materialize(self,
str view_name,
str comments=*)

86
python/obitools3/obidms/_obiview_nuc_seq.pyx
View File

@ -5,6 +5,68 @@ from .capi.obitypes cimport index_t
cdef class OBIView_NUC_SEQS(OBIView):
cpdef OBIView clone(self,
str view_name,
str comments=""):
cdef OBIView view = OBIView_NUC_SEQS(987654)
view._pointer = obi_new_view_nuc_seqs(self._pointer.dms,
str2bytes(view_name),
self._pointer,
NULL,
str2bytes(comments),
False)
if view._pointer == NULL :
raise RuntimeError("Error : Cannot clone view %s into view %s"
% (str(self.name),
view_name)
)
view.__init_columns__(self)
return view
@staticmethod
cpdef OBIView new(OBIDMS dms,
str view_name,
str comments=""):
cdef OBIView view = OBIView_NUC_SEQS(987654) # @DuplicatedSignature
view._pointer = obi_new_view_nuc_seqs(dms._pointer,
str2bytes(view_name),
NULL,
NULL,
str2bytes(comments),
False)
if view._pointer == NULL :
raise RuntimeError("Error : Cannot create view %s" % view_name)
view.__init_columns__(self)
return view
@staticmethod
cpdef OBIView open(OBIDMS dms,
str view_name):
cdef OBIView view = OBIView_NUC_SEQS(987654) # @DuplicatedSignature
view._pointer = obi_open_view(dms._pointer,
str2bytes(view_name))
if view._pointer == NULL :
raise RuntimeError("Error : Cannot open view %s" % view_name)
view.__init_columns__(self)
return view
cpdef OBIView_line_selection new_selection(self,list lines=None):
return OBIView_NUC_SEQS_line_selection(self,lines)
def __getitem__(self, object item) :
if type(item) == str :
@ -17,3 +79,27 @@ cdef class OBIView_NUC_SEQS(OBIView):
for key in sequence_obj :
self[line_idx][key] = sequence_obj[key]
cdef class OBIView_NUC_SEQS_line_selection(OBIView_line_selection):
cpdef OBIView materialize(self,
str view_name,
str comments=""):
cdef OBIView view = OBIView_NUC_SEQS(987654)
view._pointer = obi_new_view(self._view._pointer.dms,
str2bytes(view_name),
self._view._pointer,
self.__build_binary_list__(),
str2bytes(comments))
if view._pointer == NULL :
raise RuntimeError("Error : Cannot clone view %s into view %s"
% (str(self.name),
view_name)
)
view.__init_columns__(self)
return view

25
python/obitools3/obidms/_obiview_nuc_seq_qual.pxd Normal file
View File

@ -0,0 +1,25 @@
#cython: language_level=3
from ._obidms cimport OBIView
from ._obiseq cimport OBI_Nuc_Seq, OBI_Nuc_Seq_Stored
cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS):
cpdef OBIView clone(self,
str view_name,
OBIView_line_selection line_selection=*,
str comments=*)
@staticmethod
cpdef OBIView new(OBIDMS dms,
str view_name,
str comments=*)
@staticmethod
cpdef OBIView open(OBIDMS dms,
str view_name)
cdef class OBIView_NUC_SEQS_QUAL_line_selection(OBIView_NUC_SEQS_line_selection):
cpdef OBIView materialize(self,
str view_name,
str comments=*)

90
python/obitools3/obidms/_obiview_nuc_seq_qual.pyx Normal file
View File

@ -0,0 +1,90 @@
#cython: language_level=3
from .capi.obitypes cimport index_t
cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS):
cpdef OBIView clone(self,
str view_name,
str comments=""):
cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654)
view._pointer = obi_new_view_nuc_seqs(self._pointer.dms,
str2bytes(view_name),
self._pointer,
NULL,
str2bytes(comments),
True)
if view._pointer == NULL :
raise RuntimeError("Error : Cannot clone view %s into view %s"
% (str(self.name),
view_name)
)
view.__init_columns__(self)
return view
@staticmethod
cpdef OBIView new(OBIDMS dms,
str view_name,
str comments=""):
cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654) # @DuplicatedSignature
view._pointer = obi_new_view_nuc_seqs(dms._pointer,
str2bytes(view_name),
NULL,
NULL,
str2bytes(comments),
True)
if view._pointer == NULL :
raise RuntimeError("Error : Cannot create view %s" % view_name)
view.__init_columns__(self)
return view
@staticmethod
cpdef OBIView open(OBIDMS dms,
str view_name):
cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654) # @DuplicatedSignature
view._pointer = obi_open_view(dms._pointer,
str2bytes(view_name))
if view._pointer == NULL :
raise RuntimeError("Error : Cannot open view %s" % view_name)
view.__init_columns__(self)
return view
cdef class OBIView_NUC_SEQS_QUAL_line_selection(OBIView_NUC_SEQS_line_selection):
cpdef OBIView materialize(self,
str view_name,
str comments=""):
cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654)
view._pointer = obi_new_view(self._view._pointer.dms,
str2bytes(view_name),
self._view._pointer,
self.__build_binary_list__(),
str2bytes(comments))
if view._pointer == NULL :
raise RuntimeError("Error : Cannot clone view %s into view %s"
% (str(self.name),
view_name)
)
view.__init_columns__(self)
return view