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Column rewriter and optimized View getter

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This commit is contained in:
Celine Mercier
2017-07-05 17:49:05 +02:00
parent 3bbc2ae469
commit 535fc2af83
2 changed files with 56 additions and 14 deletions
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10
python/obitools3/dms/view/view.pxd
View File

@ -3,12 +3,14 @@
from ..capi.obiview cimport Obiview_p
from ..capi.obitypes cimport index_t
from ..capi.obitypes cimport index_t, obitype_t
from ..object cimport OBIWrapper
from ..dms cimport DMS
from ..column.column cimport Column
cdef dict __OBIDMS_VIEW_CLASS__
@ -26,6 +28,12 @@ cdef class View(OBIWrapper):
object current_name,
object new_name)
cpdef Column rewrite_column_with_diff_attributes(self,
object column_name,
obitype_t new_data_type=*,
index_t new_nb_elements_per_line=*,
list new_elements_names=*)
cpdef Line_selection new_selection(self,
list lines=*)

54
python/obitools3/dms/view/view.pyx
View File

@ -17,7 +17,6 @@ from ..capi.obiview cimport Alias_column_pair_p, \
from ..capi.obidmscolumn cimport OBIDMS_column_p
from ..capi.obidms cimport OBIDMS_p
from ..capi.obitypes cimport obitype_t
from obitools3.utils cimport tobytes, \
str2bytes, \
@ -25,11 +24,10 @@ from obitools3.utils cimport tobytes, \
from ..object cimport OBIObjectClosedInstance
from ..column.column cimport Column
from obitools3.dms.view import typed_view
from ..capi.obitypes cimport only_ATGC, \
from ..capi.obitypes cimport is_a_DNA_seq, \
OBI_VOID, \
OBI_BOOL, \
OBI_CHAR, \
OBI_FLOAT, \
@ -216,8 +214,6 @@ cdef class View(OBIWrapper) :
bytes2str(column_name_b))
cpdef rename_column(self,
object current_name,
object new_name):
@ -237,6 +233,44 @@ cdef class View(OBIWrapper) :
bytes2str(new_name_b)))
# TODO warning, not multithreading compliant
cpdef Column rewrite_column_with_diff_attributes(self,
object column_name,
obitype_t new_data_type=<obitype_t>OBI_VOID,
index_t new_nb_elements_per_line=0,
list new_elements_names=None) :
cdef Column old_column
cdef Column new_column
cdef index_t length = len(self)
old_column = self.get_column(column_name)
if new_data_type == 0 :
new_data_type = old_column.data_type
if new_nb_elements_per_line == 0 :
new_nb_elements_per_line = old_column.nb_elements_per_line
if new_elements_names is None :
new_elements_names = old_column.elements_names
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,
comments=old_column.comments, alias=tobytes(column_name)+tobytes('___new___'))
for i in range(length) :
new_column[i] = old_column[i]
# Remove old column from view
self.delete_column(column_name)
# Rename new
new_column.name = column_name
return new_column
cpdef Line_selection new_selection(self,list lines=None):
return Line_selection(self, lines)
@ -255,10 +289,10 @@ cdef class View(OBIWrapper) :
def __getitem__(self, object item) :
if type(item) == str :
return self.get_column(item) # TODO hyper lent dans la pratique
elif type(item) == int :
if type(item) == int :
return Line(self, item)
else : # TODO assume str or bytes for optimization?
return self.get_column(item) # TODO hyper lent dans la pratique
def __contains__(self, str column_name):
@ -341,7 +375,7 @@ cdef class Line :
value_b = str2bytes(value)
else :
value_b = value
if only_ATGC(value_b) : # TODO detect IUPAC
if is_a_DNA_seq(value_b) :
value_obitype = OBI_SEQ
elif len(value) == 1 :
value_obitype = OBI_CHAR