Added Obiviews specialized for the handling of nucleotide sequences
This commit is contained in:
Celine Mercier
@ -64,6 +64,15 @@ cdef class OBIView:
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cpdef save_and_close(self)
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cdef class OBIView_NUC_SEQS(OBIView):
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cdef OBIDMS_column ids
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cdef OBIDMS_column sequences
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cdef OBIDMS_column descriptions
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cpdef delete_column(self, str column_name)
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cdef class OBIView_line :
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cdef index_t index
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@ -77,5 +86,7 @@ cdef class OBIDMS:
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cpdef close(self)
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cpdef OBIView open_view(self, str view_name)
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cpdef OBIView new_view(self, str view_name, object view_to_clone=*, list line_selection=*)
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cpdef OBIView new_view(self, str view_name, object view_to_clone=*, list line_selection=*, str view_type=*)
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cpdef dict read_view_infos(self, str view_name)
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cpdef dict read_views(self)
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@ -48,16 +48,26 @@ from ._obidmscolumn_seq cimport OBIDMS_column_seq, \
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from ._obidms cimport OBIView, OBIView_line
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from .capi.obiview cimport Obiview_p, \
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Obiviews_infos_all_p, \
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Obiview_infos_p, \
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Column_reference_p, \
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obi_new_view_nuc_seqs, \
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obi_new_view, \
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obi_new_view_cloned_from_name, \
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obi_new_view_nuc_seqs_cloned_from_name, \
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obi_open_view, \
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obi_read_views, \
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obi_view_delete_column, \
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obi_view_add_column, \
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obi_view_get_column, \
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obi_view_get_pointer_on_column_in_view, \
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obi_select_line, \
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obi_select_lines, \
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obi_save_and_close_view
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obi_save_and_close_view, \
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VIEW_TYPE_NUC_SEQS, \
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NUC_SEQUENCE_COLUMN, \
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ID_COLUMN, \
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DESCRIPTION_COLUMN
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from libc.stdlib cimport malloc
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from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
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@ -380,7 +390,6 @@ cdef class OBIView :
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raise Exception("Problem adding a column in a view")
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# Store the column pointer
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column_pp = obi_view_get_pointer_on_column_in_view(self.pointer, column_name_b)
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if column_pp == NULL :
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raise Exception("Problem getting a column in a view")
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@ -451,6 +460,112 @@ cdef class OBIView :
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#############################################
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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, list line_selection=None):
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cdef Obiview_p view = NULL
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cdef int i
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cdef list col_list
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cdef str col_name
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cdef OBIDMS_column column
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cdef OBIDMS_column_p column_p
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cdef OBIDMS_column_p* column_pp
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cdef OBIDMS_column_header_p header
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cdef index_t* line_selection_p
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self.dms = dms
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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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for i in range(len(line_selection)) :
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line_selection_p[i] = line_selection[i] # TODO type problem?
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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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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)
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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)
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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)
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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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self.name = bytes2str(view.name)
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# go through columns to build list and open python object (TODO make separate function?)
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self.columns = {}
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self.columns_pp = {}
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i = 0
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while i < view.column_count :
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column_pp = <OBIDMS_column_p*> ((view.columns)+i)
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column_p = <OBIDMS_column_p> (view.columns)[i]
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header = (column_p).header
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col_name = bytes2str(header.name)
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col_capsule = PyCapsule_New(column_pp, NULL, NULL) # TODO discuss
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(self.columns_pp)[col_name] = col_capsule
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subclass = OBIDMS_column.get_subclass_type(column_p)
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self.columns[col_name] = subclass(self, col_name)
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i+=1
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self.ids = self.columns[bytes2str(ID_COLUMN)]
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self.sequences = self.columns[bytes2str(NUC_SEQUENCE_COLUMN)]
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self.descriptions = self.columns[bytes2str(DESCRIPTION_COLUMN)]
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cpdef delete_column(self, str column_name) :
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cdef int i
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cdef Obiview_p view
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cdef OBIDMS_column column
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cdef OBIDMS_column_p column_p
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cdef OBIDMS_column_p* column_pp
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cdef OBIDMS_column_header_p header
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cdef str column_n
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if ((column_name == bytes2str(ID_COLUMN)) or (column_name == bytes2str(NUC_SEQUENCE_COLUMN)) or (column_name == bytes2str(DESCRIPTION_COLUMN))) :
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raise Exception("Can't delete an obligatory column from a NUC_SEQS view")
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view = self.pointer
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if obi_view_delete_column(view, str2bytes(column_name)) < 0 :
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raise Exception("Problem deleting a column from a view")
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# Update the dictionaries of column pointers and column objects, and update pointers in column objects (make function?):
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(self.columns).pop(column_name)
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(self.columns_pp).pop(column_name)
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i = 0
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while i < view.column_count :
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column_pp = <OBIDMS_column_p*> ((view.columns)+i)
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column_p = <OBIDMS_column_p> (view.columns)[i]
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header = (column_p).header
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col_name = bytes2str(header.name)
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col_capsule = PyCapsule_New(column_pp, NULL, NULL)
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(self.columns_pp)[col_name] = col_capsule
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i+=1
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for column_n in self.columns :
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(self.columns[column_n]).update_pointer()
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#############################################
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cdef class OBIView_line :
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def __init__(self, OBIView view, index_t line_nb) :
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@ -520,12 +635,81 @@ cdef class OBIDMS :
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cpdef close(self) :
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if (obi_close_dms(self.pointer)) < 0 :
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raise Exception("Problem closing an OBIDMS")
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cpdef OBIView open_view(self, str view_name) :
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return OBIView(self, view_name)
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cpdef OBIView new_view(self, str view_name, object view_to_clone=None, list line_selection=None) :
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return OBIView(self, view_name, new=True, view_to_clone=view_to_clone, line_selection=line_selection)
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cpdef OBIView open_view(self, str view_name) :
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cdef object view_class
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cdef dict view_infos
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view_infos = self.read_view_infos(view_name)
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if view_infos["view_type"] == bytes2str(VIEW_TYPE_NUC_SEQS) : # TODO not gonna work
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view_class = OBIView_NUC_SEQS
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else :
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view_class = OBIView
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return view_class(self, view_name)
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cpdef OBIView new_view(self, str view_name, object view_to_clone=None, list line_selection=None, str view_type=None) :
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cdef object view_class
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if view_type is not None :
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if view_type == bytes2str(VIEW_TYPE_NUC_SEQS) : # TODO not gonna work
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view_class = OBIView_NUC_SEQS
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else :
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view_class = OBIView
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return view_class(self, view_name, new=True, view_to_clone=view_to_clone, line_selection=line_selection)
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cpdef dict read_view_infos(self, str view_name) :
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all_views = self.read_views()
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return all_views[view_name]
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cpdef dict read_views(self) : # TODO function that gets 1 view with name, function that prints the dic and function that prints 1 view. Add column type in col ref
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cdef Obiviews_infos_all_p all_views_p
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cdef Obiview_infos_p view_p
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cdef Column_reference_p column_refs
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cdef int nb_views
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cdef int i, j
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cdef str view_name
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cdef str column_name
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cdef dict views
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cdef bytes name_b
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views = {}
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all_views_p = obi_read_views(self.pointer)
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nb_views = <int> (all_views_p.header).view_count
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for i in range(nb_views) :
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view_p = (<Obiview_infos_p> (all_views_p.view_infos)) + i
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view_name = bytes2str(view_p.name)
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views[view_name] = {}
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views[view_name]["view_type"] = bytes2str(view_p.view_type)
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views[view_name]["column_count"] = <int> view_p.column_count
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views[view_name]["line_count"] = <int> view_p.line_count
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views[view_name]["view_number"] = <int> view_p.view_number
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views[view_name]["created_from"] = bytes2str(view_p.created_from)
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views[view_name]["creation_date"] = bytes2str(obi_column_format_date(view_p.creation_date)) # TODO move this function in utils or somethings
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if (view_p.all_lines) :
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views[view_name]["line_selection"] = None
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else :
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views[view_name]["line_selection"] = {}
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views[view_name]["line_selection"]["column_name"] = bytes2str((view_p.line_selection).column_name)
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views[view_name]["line_selection"]["version"] = <int> (view_p.line_selection).version
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views[view_name]["column_references"] = {}
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column_refs = view_p.column_references
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for j in range(views[view_name]["column_count"]) :
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column_name = bytes2str((column_refs[j]).column_name)
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views[view_name]["column_references"][column_name] = {}
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views[view_name]["column_references"][column_name]["version"] = column_refs[j].version
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return views
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@ -3,15 +3,21 @@
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from .obitypes cimport const_char_p, \
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OBIType_t, \
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obiversion_t, \
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index_t
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index_t, \
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time_t
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from ..capi.obidms cimport OBIDMS_p
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from ..capi.obidmscolumn cimport OBIDMS_column_p
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cdef extern from "obiview.h" nogil:
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extern const_char_p VIEW_TYPE_NUC_SEQS
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extern const_char_p NUC_SEQUENCE_COLUMN
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extern const_char_p ID_COLUMN
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extern const_char_p DESCRIPTION_COLUMN
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struct Column_reference_t :
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char column_name
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const_char_p column_name
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obiversion_t version
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ctypedef Column_reference_t* Column_reference_p
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@ -31,12 +37,48 @@ cdef extern from "obiview.h" nogil:
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ctypedef Obiview_t* Obiview_p
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struct Obiview_infos_t :
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int view_number
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int column_count
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index_t line_count
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const_char_p name
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const_char_p created_from
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time_t creation_date
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bint all_lines
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Column_reference_t line_selection
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Column_reference_p column_references
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const_char_p view_type
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ctypedef Obiview_infos_t* Obiview_infos_p
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struct Obiviews_header_t :
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size_t header_size
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size_t views_size
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int view_count
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ctypedef Obiviews_header_t* Obiviews_header_p
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struct Obiviews_infos_all_t :
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Obiviews_header_p header
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Obiview_infos_p view_infos
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ctypedef Obiviews_infos_all_t* Obiviews_infos_all_p
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Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection)
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Obiview_p obi_new_view(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection)
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Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection)
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Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection)
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Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection)
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Obiview_p obi_open_view(OBIDMS_p dms, const_char_p view_name)
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Obiviews_infos_all_p obi_read_views(OBIDMS_p dms)
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int obi_view_add_column(Obiview_p view,
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const_char_p column_name,
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obiversion_t version_number,
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