When a new view is created with a line selection, the view to clone is
automatically found + compacted redundant code + fixed potential bug when cloning a NUC_SEQS view by name
This commit is contained in:
Celine Mercier
@ -35,6 +35,16 @@ cdef class OBIView:
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cdef Obiview_p _pointer
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cdef dict _columns
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cdef Obiview_p _open_or_create_view(self,
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OBIDMS dms,
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str view_name,
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bint new=*,
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object view_to_clone=*,
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index_t* line_selection_p=*,
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str comments=*,
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bint quality_column=*,
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str view_type=*)
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cpdef delete_column(self, str column_name)
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cpdef add_column(self,
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str column_name,
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@ -273,27 +273,41 @@ cdef class OBIDMS_column_line :
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cdef class OBIView :
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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):
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# TODO quality_column is only here because it's needed for OBIView_NUC_SEQS views, not clean?
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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=None):
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cdef Obiview_p view = NULL
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cdef index_t* line_selection_p
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cdef index_t* line_selection_p = NULL
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cdef int i
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cdef str col_alias
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cdef OBIDMS_column_p column_p
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cdef object subclass
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# Create the C array for the line selection if needed
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if line_selection is not None :
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line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))
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# Get the name of the associated view to clone
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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.
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# Build the C array corresponding to the line selection
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line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array
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for i in range(len(line_selection)) :
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line_selection_p[i] = line_selection[i]
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line_selection_p[len(line_selection)] = -1
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else :
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line_selection_p = NULL
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line_selection_p[len(line_selection)] = -1 # flagging the end of the array
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# Create the view if needed
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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=None)
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# Go through columns to build dictionaries of corresponding python instances # TODO make function?
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self._columns = {}
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for i in range(self._pointer.infos.column_count) :
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col_alias = bytes2str(self._pointer.infos.column_references[i].alias)
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column_p = <OBIDMS_column_p> (self._pointer.columns)[i]
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subclass = OBIDMS_column.get_subclass_type(column_p)
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self._columns[col_alias] = subclass(self, col_alias)
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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=None):
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cdef Obiview_p view = NULL
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# Create the view if needed, with the right type
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if new :
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if view_type is None :
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if view_to_clone is not None :
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if type(view_to_clone) == str :
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view = obi_new_view_cloned_from_name(dms._pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p, str2bytes(comments))
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@ -301,6 +315,15 @@ cdef class OBIView :
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view = obi_new_view(dms._pointer, str2bytes(view_name), (<OBIView> view_to_clone)._pointer, line_selection_p, str2bytes(comments))
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else :
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view = obi_new_view(dms._pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments))
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elif view_type == VIEW_TYPE_NUC_SEQS :
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if view_to_clone is not None :
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if type(view_to_clone) == str :
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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)
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else :
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view = obi_new_view_nuc_seqs(dms._pointer, str2bytes(view_name), (<OBIView> view_to_clone)._pointer, line_selection_p, str2bytes(comments), quality_column)
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else :
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view = obi_new_view_nuc_seqs(dms._pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments), quality_column)
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# Else, open the existing view
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else :
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view = obi_open_view(dms._pointer, str2bytes(view_name))
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@ -308,15 +331,7 @@ cdef class OBIView :
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if view == NULL :
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raise Exception("Error creating/opening a view")
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self._pointer = view
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# Go through columns to build dictionaries of corresponding python instances # TODO make function?
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self._columns = {}
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for i in range(view.infos.column_count) :
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col_alias = bytes2str(view.infos.column_references[i].alias)
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column_p = <OBIDMS_column_p> (view.columns)[i]
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subclass = OBIDMS_column.get_subclass_type(column_p)
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self._columns[col_alias] = subclass(self, col_alias)
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return view
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def __repr__(self) :
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@ -491,59 +506,6 @@ cdef class OBIView :
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cdef class OBIView_NUC_SEQS(OBIView):
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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):
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cdef Obiview_p view = NULL
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cdef index_t* line_selection_p
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cdef int i
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cdef str col_alias
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cdef OBIDMS_column_p column_p
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cdef object subclass
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if line_selection is not None :
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# Check that the line selection is associated with the view to clone
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if view_to_clone is None :
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raise Exception("Error creating a view: there is a new line selection but no associated view to clone")
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if type(view_to_clone) == str :
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if line_selection._view_name != view_to_clone :
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raise Exception("Error creating a view: the new line selection isn't associated with the view to clone")
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elif line_selection._view != view_to_clone :
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raise Exception("Error creating a view: the new line selection isn't associated with the view to clone")
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# Build the C array corresponding to the line selection
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line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array
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for i in range(len(line_selection)) :
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line_selection_p[i] = line_selection[i]
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line_selection_p[len(line_selection)] = -1 # flagging the end of the array
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else :
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line_selection_p = NULL
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if new :
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if view_to_clone is not None :
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if type(view_to_clone) == str :
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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)
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else :
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view = obi_new_view_nuc_seqs(dms._pointer, str2bytes(view_name), (<OBIView> view_to_clone)._pointer, line_selection_p, str2bytes(comments), quality_column)
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elif view_to_clone is None :
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view = obi_new_view_nuc_seqs(dms._pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments), quality_column)
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elif not new :
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if view_name is not None :
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view = obi_open_view(dms._pointer, str2bytes(view_name))
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elif view_name is None :
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view = obi_open_view(dms._pointer, NULL)
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if view == NULL :
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raise Exception("Error creating/opening view")
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self._pointer = view
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# Go through columns to build dictionaries of corresponding python instances # TODO make function?
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self._columns = {}
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for i in range(view.infos.column_count) :
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col_alias = bytes2str(view.infos.column_references[i].alias)
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column_p = <OBIDMS_column_p> (view.columns)[i]
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subclass = OBIDMS_column.get_subclass_type(column_p)
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self._columns[col_alias] = subclass(self, col_alias)
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def __getitem__(self, object item) :
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if type(item) == str :
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@ -551,6 +513,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
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elif type(item) == int :
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return OBI_Nuc_Seq_Stored(self, item)
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def __setitem__(self, index_t line_idx, OBI_Nuc_Seq sequence_obj) :
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for key in sequence_obj :
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self[line_idx][key] = sequence_obj[key]
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@ -753,11 +716,12 @@ cdef class OBIDMS :
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view_class = OBIView
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# Check the type of the view to clone if there is one # TODO make generic for future other view types
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if view_to_clone is not None and \
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((type(view_to_clone) == str and self.read_view_infos(view_to_clone)["view_type"] == VIEW_TYPE_NUC_SEQS) or \
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((type(view_to_clone) == str and self.read_view_infos(view_to_clone)["view_type"] == bytes2str(VIEW_TYPE_NUC_SEQS)) or \
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isinstance(view_to_clone, OBIView_NUC_SEQS)) :
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view_type = bytes2str(VIEW_TYPE_NUC_SEQS)
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view_class = OBIView_NUC_SEQS
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return view_class(self, view_name, new=True, view_to_clone=view_to_clone, line_selection=line_selection, comments=comments, quality_column=quality_column)
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return view_class(self, view_name, new=True, view_to_clone=view_to_clone, line_selection=line_selection, comments=comments, quality_column=quality_column, view_type=view_type)
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cpdef dict read_view_infos(self, str view_name) :
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