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First version of alignment functions (imported from suma* programs)

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This commit is contained in:
Celine Mercier
2016-05-11 16:36:23 +02:00
parent 3567681339
commit b3c47809da
27 changed files with 1991 additions and 43 deletions
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18
python/obitools3/obidms/_obidms.pyx
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@ -63,6 +63,7 @@ from .capi.obiview cimport Obiview_p, \
obi_view_delete_column, \
obi_view_add_column, \
obi_view_get_column, \
obi_view_get_column, \
obi_view_get_pointer_on_column_in_view, \
obi_select_line, \
obi_select_lines, \
@ -90,7 +91,7 @@ cdef class OBIDMS_column :
# Fill structure
self.pointer = column_pp
self.dms = view.dms
self.view = view.pointer
self.view = view
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
@ -120,7 +121,7 @@ cdef class OBIDMS_column :
yield self.get_line(line_nb)
cpdef update_pointer(self):
self.pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self.view, str2bytes(self.column_name))
self.pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self.view.pointer, str2bytes(self.column_name))
cpdef list get_elements_names(self):
return self.elements_names
@ -336,7 +337,6 @@ cdef class OBIView :
cdef bytes column_name_b
cdef bytes elements_names_b
cdef object subclass
cdef OBIDMS_column_p* column_pp
cdef OBIDMS_column_p column_p
column_name_b = str2bytes(column_name)
@ -369,10 +369,9 @@ cdef class OBIView :
raise Exception("Problem adding a column in a view")
# Get the column pointer
column_pp = obi_view_get_pointer_on_column_in_view(self.pointer, column_name_b)
column_p = obi_view_get_column(self.pointer, column_name_b)
# Open and store the subclass
column_p = column_pp[0] # TODO ugly cython dereferencing
subclass = OBIDMS_column.get_subclass_type(column_p)
(self.columns)[column_name] = subclass(self, column_name)
@ -495,18 +494,15 @@ cdef class OBIView_NUC_SEQS(OBIView):
cpdef delete_column(self, str column_name) :
cdef int i
cdef Obiview_p view
cdef Obiview_p view_p
cdef OBIDMS_column column
cdef OBIDMS_column_p column_p
cdef OBIDMS_column_header_p header
cdef str column_n
if ((column_name == bytes2str(ID_COLUMN)) or (column_name == bytes2str(NUC_SEQUENCE_COLUMN)) or (column_name == bytes2str(DEFINITION_COLUMN))) :
raise Exception("Can't delete an obligatory column from a NUC_SEQS view")
view = self.pointer
view_p = self.pointer
if obi_view_delete_column(view, str2bytes(column_name)) < 0 :
if obi_view_delete_column(view_p, str2bytes(column_name)) < 0 :
raise Exception("Problem deleting a column from a view")
# Remove instance from the dictionary