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Reworked and commented a bit the cython layer for dms, columns and views

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This commit is contained in:
Celine Mercier
2016-05-02 15:16:06 +02:00
parent 872071b104
commit bc12360490
1 changed files with 46 additions and 53 deletions
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99
python/obitools3/obidms/_obidms.pyx
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@ -90,7 +90,7 @@ cdef class OBIDMS_column :
# Fill structure
self.pointer = column_pp
self.dms = view.dms
self.view = view.pointer # TODO pointer or instance?
self.view = view.pointer
self.data_type = bytes2str(name_data_type((column_p.header).returned_data_type))
self.column_name = bytes2str((column_p.header).name)
self.nb_elements_per_line = (column_p.header).nb_elements_per_line
@ -137,12 +137,15 @@ cdef class OBIDMS_column :
cpdef str get_comments(self):
return bytes2str((self.pointer)[0].header.comments)
def __repr__(self) :
def __str__(self) :
cdef str to_print
to_print = ''
for line in self :
to_print = to_print + str(line) + "\n"
return to_print
def __repr__(self) :
return (self.column_name + ", version " + str((self.pointer)[0].header.version) + ", data type: " + self.data_type)
cpdef close(self):
if obi_close_column((self.pointer)[0]) < 0 :
@ -248,14 +251,16 @@ cdef class OBIView :
self.dms = dms
# Create the C array for the line selection if needed
if line_selection is not None :
line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))
for i in range(len(line_selection)) :
line_selection_p[i] = line_selection[i] # TODO type problem?
line_selection_p[i] = line_selection[i]
line_selection_p[len(line_selection)] = -1
else :
line_selection_p = NULL
# Create the view if needed
if new :
if view_to_clone is not None :
if type(view_to_clone) == str :
@ -264,31 +269,27 @@ cdef class OBIView :
view = obi_new_view(dms.pointer, str2bytes(view_name), (<OBIView> view_to_clone).pointer, line_selection_p, str2bytes(comments))
elif view_to_clone is None :
view = obi_new_view(dms.pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments))
# Else, open the existing view
elif not new :
if view_name is not None :
view = obi_open_view(dms.pointer, str2bytes(view_name))
elif view_name is None :
view = obi_open_view(dms.pointer, NULL)
view = obi_open_view(dms.pointer, NULL) # TODO discuss
if view == NULL :
raise Exception("Error creating/opening view")
raise Exception("Error creating/opening a view")
self.pointer = view
self.name = bytes2str(view.name)
# go through columns to build list and open python object (TODO make separate function?)
# Go through columns to build list of corresponding python instances
self.columns = {}
i = 0
while i < view.column_count :
column_p = <OBIDMS_column_p> (view.columns)[i]
header = (column_p).header
col_name = bytes2str(header.name)
subclass = OBIDMS_column.get_subclass_type(column_p)
for i in range(view.column_count) :
column_p = <OBIDMS_column_p> (view.columns)[i]
header = (column_p).header
col_name = bytes2str(header.name)
subclass = OBIDMS_column.get_subclass_type(column_p)
self.columns[col_name] = subclass(self, col_name)
i+=1
def __repr__(self) :
@ -298,11 +299,9 @@ cdef class OBIView :
cdef OBIDMS_column_p column_p
s = self.name
s = s + ", " + self.comments + ", " + str(self.pointer.line_count) + " lines"
for column_name in self.columns : # TODO make function in OBIDMS_column class
column = self.columns[column_name]
column_p = (column.pointer)[0]
s = s + "\n" + column_name + ", version " + str(column_p.header.version) + ", data type: " + column.data_type
s = s + ", " + self.comments + ", " + str(self.pointer.line_count) + " lines\n"
for column_name in self.columns :
s = s + self.columns[column_name].__repr__() + '\n'
return s
@ -332,11 +331,11 @@ cdef class OBIView :
obiversion_t version_number=-1,
str type='',
index_t nb_lines=0,
index_t nb_elements_per_line=1, # TODO 1?
index_t nb_elements_per_line=1,
list elements_names=None,
str indexer_name="",
str comments="",
bint create=True # TODO
bint create=True
) :
cdef bytes column_name_b
@ -368,7 +367,7 @@ cdef class OBIView :
else :
raise Exception("Invalid provided data type")
if (obi_view_add_column(self.pointer, column_name_b, version_number, # should return pointer on column?
if (obi_view_add_column(self.pointer, column_name_b, version_number, # TODO should return pointer on column?
data_type, nb_lines, nb_elements_per_line,
elements_names_b, str2bytes(indexer_name),
str2bytes(comments), create) < 0) :
@ -392,11 +391,11 @@ cdef class OBIView :
# iter on each line of all columns
# Declarations
cdef index_t lines_used
cdef index_t line_nb
cdef OBIView_line line # TODO for NUC SEQS View
cdef index_t lines_used
cdef index_t line_nb
cdef OBIView_line line # TODO Check that this works for NUC SEQ views
# Yield each line TODO line class
# Yield each line
lines_used = (self.pointer).line_count
for line_nb in range(lines_used) :
@ -407,7 +406,7 @@ cdef class OBIView :
def __getitem__(self, object item) :
if type(item) == str :
return (self.columns)[item]
elif type(item) == int : # TODO int?
elif type(item) == int :
return OBIView_line(self, item)
@ -420,7 +419,7 @@ cdef class OBIView :
cdef index_t* line_selection_p
line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))
for i in range(len(line_selection)) :
line_selection_p[i] = line_selection[i] # TODO type problem?
line_selection_p[i] = line_selection[i]
line_selection_p[len(line_selection)] = -1
if obi_select_lines(self.pointer, line_selection_p) < 0 :
raise Exception("Problem selecting a list of lines")
@ -444,21 +443,21 @@ cdef class OBIView_NUC_SEQS(OBIView):
def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, list line_selection=None, str comments=""):
cdef Obiview_p view = NULL
cdef int i
cdef list col_list
cdef str col_name
cdef OBIDMS_column column
cdef OBIDMS_column_p column_p
cdef Obiview_p view = NULL
cdef int i
cdef list col_list
cdef str col_name
cdef OBIDMS_column column
cdef OBIDMS_column_p column_p
cdef OBIDMS_column_header_p header
cdef index_t* line_selection_p
cdef index_t* line_selection_p
self.dms = dms
if line_selection is not None :
line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))
for i in range(len(line_selection)) :
line_selection_p[i] = line_selection[i] # TODO type problem?
line_selection_p[i] = line_selection[i]
line_selection_p[len(line_selection)] = -1
else :
line_selection_p = NULL
@ -484,20 +483,14 @@ cdef class OBIView_NUC_SEQS(OBIView):
self.name = bytes2str(view.name)
self.comments = bytes2str(view.comments)
# go through columns to build list and open python object (TODO make separate function?)
# Go through columns to build list of corresponding python instances
self.columns = {}
i = 0
while i < view.column_count :
column_p = <OBIDMS_column_p> (view.columns)[i]
header = (column_p).header
col_name = bytes2str(header.name)
subclass = OBIDMS_column.get_subclass_type(column_p)
for i in range(view.column_count) :
column_p = <OBIDMS_column_p> (view.columns)[i]
header = (column_p).header
col_name = bytes2str(header.name)
subclass = OBIDMS_column.get_subclass_type(column_p)
self.columns[col_name] = subclass(self, col_name)
i+=1
self.ids = self.columns[bytes2str(ID_COLUMN)]
self.sequences = self.columns[bytes2str(NUC_SEQUENCE_COLUMN)]
@ -521,7 +514,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
if obi_view_delete_column(view, str2bytes(column_name)) < 0 :
raise Exception("Problem deleting a column from a view")
# Update the dictionaries of column pointers and column objects, and update pointers in column objects (make function?):
# Remove instance from the dictionary
(self.columns).pop(column_name)
for column_n in self.columns :
@ -531,7 +524,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
def __getitem__(self, object item) :
if type(item) == str :
return (self.columns)[item]
elif type(item) == int : # TODO int? (range problem)
elif type(item) == int :
return OBI_Nuc_Seq_Stored(self, item)
@ -650,7 +643,7 @@ cdef class OBIDMS :
return all_views[view_name]
cpdef dict read_views(self) : # TODO function that prints the dic nicely and function that prints 1 view. Add column type in col ref
cpdef dict read_views(self) : # TODO function that prints the dic nicely and function that prints 1 view nicely. Add column type in col ref
cdef Obiviews_infos_all_p all_views_p
cdef Obiview_infos_p view_p