Try for a new API
This commit is contained in:
@ -30,41 +30,6 @@ cdef class OBIDMS_column_line:
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cdef index_t _index
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cdef index_t _index
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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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obiversion_t version_number=*,
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str alias=*,
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str type=*,
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index_t nb_lines=*,
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index_t nb_elements_per_line=*,
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list elements_names=*,
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str indexer_name=*,
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str associated_column_name=*,
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obiversion_t associated_column_version=*,
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str comments=*,
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bint create=*
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)
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cpdef change_column_alias(self, str current_alias, str new_alias)
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cpdef update_column_pointers(self)
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cpdef close(self)
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@staticmethod
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cdef object get_view_subclass(str view_type)
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cdef class OBIView_line :
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cdef class OBIView_line :
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@ -85,7 +50,6 @@ cdef class OBIDMS:
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cpdef close(self)
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cpdef close(self)
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cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name)
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cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name)
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cpdef OBIView open_view(self, str view_name)
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cpdef OBIView new_view(self, str view_name, str view_type=*, bint quality_column=*, str comments=*)
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cpdef OBIView new_view(self, str view_name, str view_type=*, bint quality_column=*, str comments=*)
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cpdef OBIView clone_view(self, str view_name, object view_to_clone, str comments=*)
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cpdef OBIView clone_view(self, str view_name, object view_to_clone, str comments=*)
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@ -76,6 +76,8 @@ from .capi.obiview cimport Obiview_p, \
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from libc.stdlib cimport malloc
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from libc.stdlib cimport malloc
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cdef class OBIDMS_column :
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cdef class OBIDMS_column :
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# Note: should only be initialized through a subclass
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# Note: should only be initialized through a subclass
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@ -266,251 +268,6 @@ cdef class OBIDMS_column_line :
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######################################################################################################
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######################################################################################################
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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, str view_type=""):
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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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if line_selection is not None :
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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 # flagging the end of the array
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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=view_type)
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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=""):
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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 == "" :
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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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else :
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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 == bytes2str(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 :
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raise Exception("View type not recognized")
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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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if view == NULL :
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raise Exception("Error creating/opening a view")
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return view
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def __repr__(self) :
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cdef str s
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s = str(self.name) + "\n" + str(self.comments) + "\n" + str(self.line_count) + " lines\n"
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for column_name in self._columns :
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s = s + repr(self._columns[column_name]) + '\n'
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return s
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cpdef delete_column(self, str column_name) :
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cdef str column_n
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if obi_view_delete_column(self._pointer, str2bytes(column_name)) < 0 :
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raise Exception("Problem deleting a column from a view")
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# Update the dictionary of column objects:
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(self._columns).pop(column_name)
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self.update_column_pointers()
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cpdef add_column(self,
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str column_name,
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obiversion_t version_number=-1,
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str alias='',
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str type='',
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index_t nb_lines=0,
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index_t nb_elements_per_line=1,
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list elements_names=None,
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str indexer_name="",
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str associated_column_name="",
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obiversion_t associated_column_version=-1,
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str comments="",
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bint create=True
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) :
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cdef bytes column_name_b
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cdef bytes elements_names_b
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cdef object subclass
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cdef OBIDMS_column_p column_p
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column_name_b = str2bytes(column_name)
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if alias == '' :
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alias = column_name
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alias_b = column_name_b
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else :
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alias_b = str2bytes(alias)
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if elements_names is None :
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elements_names_b = str2bytes("")
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else :
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elements_names_b = str2bytes(';'.join(elements_names))
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if type : # TODO make C function that does that
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if type == 'OBI_INT' :
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data_type = OBI_INT
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elif type == 'OBI_FLOAT' :
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data_type = OBI_FLOAT
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elif type == 'OBI_BOOL' :
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data_type = OBI_BOOL
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elif type == 'OBI_CHAR' :
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data_type = OBI_CHAR
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elif type == 'OBI_QUAL' :
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data_type = OBI_QUAL
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elif type == 'OBI_STR' :
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data_type = OBI_STR
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elif type == 'OBI_SEQ' :
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data_type = OBI_SEQ
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else :
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raise Exception("Invalid provided data type")
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if (obi_view_add_column(self._pointer, column_name_b, version_number, alias_b,
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data_type, nb_lines, nb_elements_per_line,
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elements_names_b, str2bytes(indexer_name),
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str2bytes(associated_column_name), associated_column_version,
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str2bytes(comments), create) < 0) :
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raise Exception("Problem adding a column in a view")
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# Get the column pointer
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column_p = obi_view_get_column(self._pointer, alias_b)
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# Open and store the subclass
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subclass = OBIDMS_column.get_subclass_type(column_p)
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(self._columns)[alias] = subclass(self, alias)
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cpdef change_column_alias(self, str current_alias, str new_alias):
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cdef OBIDMS_column column
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if (obi_view_create_column_alias(self._pointer, str2bytes(current_alias), str2bytes(new_alias)) < 0) :
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raise Exception("Problem changing a column alias")
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# Update the dictionaries of column objects
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self._columns[new_alias] = self._columns[current_alias]
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column = self._columns[new_alias]
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column._alias = new_alias
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(self._columns).pop(current_alias)
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cpdef update_column_pointers(self):
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cdef str column_n
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cdef OBIDMS_column column
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for column_n in self._columns :
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column = self._columns[column_n]
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column._pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self._pointer, str2bytes(column_n))
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cpdef close(self) :
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if (obi_save_and_close_view(self._pointer) < 0) :
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raise Exception("Problem closing a view")
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self._pointer = NULL
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self._columns = {}
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def __iter__(self):
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# Iteration on each line of all columns
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# Declarations
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cdef index_t line_nb
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cdef OBIView_line line
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# Yield each line
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for line_nb in range(self.line_count) :
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line = self[line_nb]
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yield line
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def __getitem__(self, object item) :
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if type(item) == str :
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return (self._columns)[item]
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elif type(item) == int :
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return OBIView_line(self, item)
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def __contains__(self, str column_name):
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return (column_name in self._columns)
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def __len__(self):
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return(self.line_count)
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def __str__(self) :
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cdef OBIView_line line
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cdef str to_print
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to_print = ""
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for line in self :
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to_print = to_print + str(line) + "\n"
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return to_print
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# line_count property getter
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@property
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def line_count(self):
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return self._pointer.infos.line_count
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# name property getter
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@property
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def name(self):
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return bytes2str(self._pointer.infos.name)
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# view type property getter
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@property
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def type(self): # @ReservedAssignment
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return bytes2str(self._pointer.infos.view_type)
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# columns property getter
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@property
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def columns(self):
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return self._columns
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# comments property getter
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@property
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def comments(self):
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return bytes2str(self._pointer.infos.comments)
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# TODO setter that concatenates new comments?
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@staticmethod
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cdef object get_view_subclass(str view_type) :
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cdef object subclass
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if view_type == bytes2str(VIEW_TYPE_NUC_SEQS) :
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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
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######################################################################################################
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######################################################################################################
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@ -633,12 +390,6 @@ cdef class OBIDMS :
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return OBI_Taxonomy(self, taxo_name)
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return OBI_Taxonomy(self, taxo_name)
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cpdef OBIView open_view(self, str view_name) :
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cdef object view_class
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view_class = OBIView.get_view_subclass(self.read_view_infos(view_name)["view_type"])
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return view_class(self, view_name)
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cpdef OBIView new_view(self, str view_name, str view_type="", bint quality_column=False, str comments="") :
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cpdef OBIView new_view(self, str view_name, str view_type="", bint quality_column=False, str comments="") :
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cdef object view_class
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cdef object view_class
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# Get right subclass depending on view type
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# Get right subclass depending on view type
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@ -6,6 +6,7 @@ from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
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ID_COLUMN, \
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ID_COLUMN, \
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DEFINITION_COLUMN, \
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DEFINITION_COLUMN, \
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QUALITY_COLUMN
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QUALITY_COLUMN
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from docutils.nodes import definition
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cdef str __str__ID_COLUMN__ = bytes2str(ID_COLUMN)
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cdef str __str__ID_COLUMN__ = bytes2str(ID_COLUMN)
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@ -19,11 +20,20 @@ cdef class OBI_Seq(dict) :
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def __init__(self, str id,
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def __init__(self, str id,
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object seq,
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object seq,
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str definition=None,
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str definition=None,
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dict attributes=None) :
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dict tags=None) :
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self.id = id
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self.seq = seq
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if tags is not None:
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self.update(tags)
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self._id = id
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self._seq = seq
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if definition is not None :
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if definition is not None :
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self.definition = definition
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self._definition = definition
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else:
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self._definition = None
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def __getitem__(self,str key):
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def __getitem__(self,str key):
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if key == __str__ID_COLUMN__:
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if key == __str__ID_COLUMN__:
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@ -33,6 +43,14 @@ cdef class OBI_Seq(dict) :
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else:
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else:
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return dict.__getitem__(self,key)
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return dict.__getitem__(self,key)
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def __setitem__(self,str key,object value):
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if key == __str__ID_COLUMN__:
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self._id=value
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elif key == __str__DEFINITION_COLUMN__:
|
||||||
|
self._definition=value
|
||||||
|
else:
|
||||||
|
dict.__setitem__(self,key,value)
|
||||||
|
|
||||||
# sequence id property getter and setter
|
# sequence id property getter and setter
|
||||||
@property
|
@property
|
||||||
def id(self): # @ReservedAssignment
|
def id(self): # @ReservedAssignment
|
||||||
@ -61,14 +79,37 @@ cdef class OBI_Seq(dict) :
|
|||||||
|
|
||||||
cdef class OBI_Nuc_Seq(OBI_Seq) :
|
cdef class OBI_Nuc_Seq(OBI_Seq) :
|
||||||
|
|
||||||
|
def __init__(self, str id,
|
||||||
|
object seq,
|
||||||
|
str quality=None,
|
||||||
|
str definition=None,
|
||||||
|
dict tags=None) :
|
||||||
|
OBI_Seq.__init__(self,id,seq,tags)
|
||||||
|
if quality is not None:
|
||||||
|
self._quality=quality
|
||||||
|
else:
|
||||||
|
self._quality=None
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def __getitem__(self,str key):
|
def __getitem__(self,str key):
|
||||||
if key == __str__NUC_SEQUENCE_COLUMN__:
|
if key == __str__NUC_SEQUENCE_COLUMN__:
|
||||||
return self._id
|
return self._seq
|
||||||
elif key == __str__QUALITY_COLUMN__:
|
elif key == __str__QUALITY_COLUMN__:
|
||||||
return self._quality
|
return self._quality
|
||||||
else:
|
else:
|
||||||
return OBI_Seq.__getitem__(self,key)
|
return OBI_Seq.__getitem__(self,key)
|
||||||
|
|
||||||
|
def __setitem__(self,str key, object value):
|
||||||
|
if key == __str__NUC_SEQUENCE_COLUMN__:
|
||||||
|
self._seq = value
|
||||||
|
elif key == __str__QUALITY_COLUMN__:
|
||||||
|
self._quality=value
|
||||||
|
else:
|
||||||
|
OBI_Seq.__setitem__(self,key,value)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
cpdef object get_str_quality(self) : # TODO not ideal. Make quality_int and quality_str properties
|
cpdef object get_str_quality(self) : # TODO not ideal. Make quality_int and quality_str properties
|
||||||
return self._quality
|
return self._quality
|
||||||
|
|
||||||
|
|||||||
54
python/obitools3/obidms/_obiview.pxd
Normal file
54
python/obitools3/obidms/_obiview.pxd
Normal file
@ -0,0 +1,54 @@
|
|||||||
|
#cython: language_level=3
|
||||||
|
|
||||||
|
cdef class OBIView:
|
||||||
|
|
||||||
|
cdef Obiview_p _pointer
|
||||||
|
cdef dict _columns
|
||||||
|
|
||||||
|
cdef __init_columns__(self):
|
||||||
|
|
||||||
|
cpdef OBIView clone(self,
|
||||||
|
str view_name,
|
||||||
|
OBIView_line_selection line_selection=*,
|
||||||
|
str comments=*)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
cpdef OBIView new(OBIDMS dms,
|
||||||
|
str view_name,
|
||||||
|
str comments=*)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
cpdef OBIView open(OBIDMS dms,
|
||||||
|
str view_name)
|
||||||
|
|
||||||
|
cpdef delete_column(self, str column_name)
|
||||||
|
cpdef add_column(self,
|
||||||
|
str column_name,
|
||||||
|
obiversion_t version_number=*,
|
||||||
|
str alias=*,
|
||||||
|
str type=*,
|
||||||
|
index_t nb_lines=*,
|
||||||
|
index_t nb_elements_per_line=*,
|
||||||
|
list elements_names=*,
|
||||||
|
str indexer_name=*,
|
||||||
|
str associated_column_name=*,
|
||||||
|
obiversion_t associated_column_version=*,
|
||||||
|
str comments=*,
|
||||||
|
bint create=*
|
||||||
|
)
|
||||||
|
cpdef change_column_alias(self, str current_alias, str new_alias)
|
||||||
|
cpdef update_column_pointers(self)
|
||||||
|
|
||||||
|
cpdef OBIView_line_selection new_selection(self,
|
||||||
|
list lines=*)
|
||||||
|
|
||||||
|
cdef class OBIView_line_selection(list):
|
||||||
|
|
||||||
|
cdef OBIView _view
|
||||||
|
cdef str _view_name
|
||||||
|
|
||||||
|
cdef index_t* __build_binary_list__(self)
|
||||||
|
cpdef OBIView materialize(self,
|
||||||
|
str view_name,
|
||||||
|
str comments=*)
|
||||||
|
|
||||||
324
python/obitools3/obidms/_obiview.pyx
Normal file
324
python/obitools3/obidms/_obiview.pyx
Normal file
@ -0,0 +1,324 @@
|
|||||||
|
#cython: language_level=3
|
||||||
|
|
||||||
|
|
||||||
|
cdef class OBIView :
|
||||||
|
|
||||||
|
def __init__(self,int __internalCall__):
|
||||||
|
if __internalCall__!=987654:
|
||||||
|
raise RuntimeError('OBIView constructor cannot be called directly')
|
||||||
|
self._pointer = NULL
|
||||||
|
self._columns = {}
|
||||||
|
|
||||||
|
cdef __init_columns__(self):
|
||||||
|
cdef size_t i
|
||||||
|
cdef str col_alias
|
||||||
|
cdef OBIDMS_column_p column_p
|
||||||
|
cdef Obiview_p pointer = self._pointer
|
||||||
|
|
||||||
|
self._columns = {}
|
||||||
|
|
||||||
|
for i in range(pointer.infos.column_count) :
|
||||||
|
col_alias = bytes2str(pointer.infos.column_references[i].alias)
|
||||||
|
column_p = <OBIDMS_column_p> (pointer.columns)[i]
|
||||||
|
subclass = OBIDMS_column.get_subclass_type(column_p)
|
||||||
|
self._columns[col_alias] = subclass(self, col_alias)
|
||||||
|
|
||||||
|
|
||||||
|
cpdef OBIView clone(self,
|
||||||
|
str view_name,
|
||||||
|
str comments=""):
|
||||||
|
|
||||||
|
cdef OBIView view = OBIView(987654)
|
||||||
|
|
||||||
|
view._pointer = obi_new_view(self._pointer.dms,
|
||||||
|
str2bytes(view_name),
|
||||||
|
self._pointer,
|
||||||
|
NULL,
|
||||||
|
str2bytes(comments))
|
||||||
|
|
||||||
|
if view._pointer == NULL :
|
||||||
|
raise RuntimeError("Error : Cannot clone view %s into view %s"
|
||||||
|
% (str(self.name),
|
||||||
|
view_name)
|
||||||
|
)
|
||||||
|
|
||||||
|
view.__init_columns__(self)
|
||||||
|
|
||||||
|
return view
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
cpdef OBIView new(OBIDMS dms,
|
||||||
|
str view_name,
|
||||||
|
str comments=""):
|
||||||
|
|
||||||
|
cdef OBIView view = OBIView(987654) # @DuplicatedSignature
|
||||||
|
|
||||||
|
view._pointer = obi_new_view(dms._pointer,
|
||||||
|
str2bytes(view_name),
|
||||||
|
NULL,
|
||||||
|
NULL,
|
||||||
|
str2bytes(comments))
|
||||||
|
|
||||||
|
if view._pointer == NULL :
|
||||||
|
raise RuntimeError("Error : Cannot create view %s" % view_name)
|
||||||
|
|
||||||
|
view.__init_columns__(self)
|
||||||
|
|
||||||
|
return view
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
cpdef OBIView open(OBIDMS dms,
|
||||||
|
str view_name):
|
||||||
|
|
||||||
|
cdef OBIView view = OBIView(987654) # @DuplicatedSignature
|
||||||
|
|
||||||
|
view._pointer = obi_open_view(dms._pointer,
|
||||||
|
str2bytes(view_name))
|
||||||
|
|
||||||
|
if view._pointer == NULL :
|
||||||
|
raise RuntimeError("Error : Cannot open view %s" % view_name)
|
||||||
|
|
||||||
|
view.__init_columns__(self)
|
||||||
|
|
||||||
|
return view
|
||||||
|
|
||||||
|
def __dealloc__(self):
|
||||||
|
if (obi_save_and_close_view(self._pointer) < 0) :
|
||||||
|
raise Exception("Problem closing a view")
|
||||||
|
|
||||||
|
|
||||||
|
def __repr__(self) :
|
||||||
|
cdef str s
|
||||||
|
s = str(self.name) + "\n" + str(self.comments) + "\n" + str(self.line_count) + " lines\n"
|
||||||
|
for column_name in self._columns :
|
||||||
|
s = s + repr(self._columns[column_name]) + '\n'
|
||||||
|
return s
|
||||||
|
|
||||||
|
|
||||||
|
cpdef delete_column(self, str column_name) :
|
||||||
|
cdef str column_n
|
||||||
|
if obi_view_delete_column(self._pointer, str2bytes(column_name)) < 0 :
|
||||||
|
raise Exception("Problem deleting a column from a view")
|
||||||
|
# Update the dictionary of column objects:
|
||||||
|
(self._columns).pop(column_name)
|
||||||
|
self.update_column_pointers()
|
||||||
|
|
||||||
|
|
||||||
|
cpdef add_column(self,
|
||||||
|
str column_name,
|
||||||
|
obiversion_t version_number=-1,
|
||||||
|
str alias='',
|
||||||
|
str type='',
|
||||||
|
index_t nb_lines=0,
|
||||||
|
index_t nb_elements_per_line=1,
|
||||||
|
list elements_names=None,
|
||||||
|
str indexer_name="",
|
||||||
|
str associated_column_name="",
|
||||||
|
obiversion_t associated_column_version=-1,
|
||||||
|
str comments="",
|
||||||
|
bint create=True
|
||||||
|
) :
|
||||||
|
|
||||||
|
cdef bytes column_name_b
|
||||||
|
cdef bytes elements_names_b
|
||||||
|
cdef object subclass
|
||||||
|
cdef OBIDMS_column_p column_p
|
||||||
|
|
||||||
|
column_name_b = str2bytes(column_name)
|
||||||
|
if alias == '' :
|
||||||
|
alias = column_name
|
||||||
|
alias_b = column_name_b
|
||||||
|
else :
|
||||||
|
alias_b = str2bytes(alias)
|
||||||
|
|
||||||
|
if elements_names is None :
|
||||||
|
elements_names_b = str2bytes("")
|
||||||
|
else :
|
||||||
|
elements_names_b = str2bytes(';'.join(elements_names))
|
||||||
|
|
||||||
|
if type : # TODO make C function that does that
|
||||||
|
if type == 'OBI_INT' :
|
||||||
|
data_type = OBI_INT
|
||||||
|
elif type == 'OBI_FLOAT' :
|
||||||
|
data_type = OBI_FLOAT
|
||||||
|
elif type == 'OBI_BOOL' :
|
||||||
|
data_type = OBI_BOOL
|
||||||
|
elif type == 'OBI_CHAR' :
|
||||||
|
data_type = OBI_CHAR
|
||||||
|
elif type == 'OBI_QUAL' :
|
||||||
|
data_type = OBI_QUAL
|
||||||
|
elif type == 'OBI_STR' :
|
||||||
|
data_type = OBI_STR
|
||||||
|
elif type == 'OBI_SEQ' :
|
||||||
|
data_type = OBI_SEQ
|
||||||
|
else :
|
||||||
|
raise Exception("Invalid provided data type")
|
||||||
|
|
||||||
|
if (obi_view_add_column(self._pointer, column_name_b, version_number, alias_b,
|
||||||
|
data_type, nb_lines, nb_elements_per_line,
|
||||||
|
elements_names_b, str2bytes(indexer_name),
|
||||||
|
str2bytes(associated_column_name), associated_column_version,
|
||||||
|
str2bytes(comments), create) < 0) :
|
||||||
|
raise Exception("Problem adding a column in a view")
|
||||||
|
|
||||||
|
# Get the column pointer
|
||||||
|
column_p = obi_view_get_column(self._pointer, alias_b)
|
||||||
|
|
||||||
|
# Open and store the subclass
|
||||||
|
subclass = OBIDMS_column.get_subclass_type(column_p)
|
||||||
|
(self._columns)[alias] = subclass(self, alias)
|
||||||
|
|
||||||
|
|
||||||
|
cpdef change_column_alias(self, str current_alias, str new_alias):
|
||||||
|
cdef OBIDMS_column column
|
||||||
|
if (obi_view_create_column_alias(self._pointer, str2bytes(current_alias), str2bytes(new_alias)) < 0) :
|
||||||
|
raise Exception("Problem changing a column alias")
|
||||||
|
# Update the dictionaries of column objects
|
||||||
|
self._columns[new_alias] = self._columns[current_alias]
|
||||||
|
column = self._columns[new_alias]
|
||||||
|
column._alias = new_alias
|
||||||
|
(self._columns).pop(current_alias)
|
||||||
|
|
||||||
|
|
||||||
|
cpdef update_column_pointers(self):
|
||||||
|
cdef str column_n
|
||||||
|
cdef OBIDMS_column column
|
||||||
|
for column_n in self._columns :
|
||||||
|
column = self._columns[column_n]
|
||||||
|
column._pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self._pointer, str2bytes(column_n))
|
||||||
|
|
||||||
|
cpdef OBIView_line_selection new_selection(self,list lines=None):
|
||||||
|
return OBIView_line_selection(self,lines)
|
||||||
|
|
||||||
|
def __iter__(self):
|
||||||
|
# Iteration on each line of all columns
|
||||||
|
|
||||||
|
# Declarations
|
||||||
|
cdef index_t line_nb
|
||||||
|
cdef OBIView_line line
|
||||||
|
|
||||||
|
# Yield each line
|
||||||
|
for line_nb in range(self.line_count) :
|
||||||
|
line = self[line_nb]
|
||||||
|
yield line
|
||||||
|
|
||||||
|
|
||||||
|
def __getitem__(self, object item) :
|
||||||
|
if type(item) == str :
|
||||||
|
return (self._columns)[item]
|
||||||
|
elif type(item) == int :
|
||||||
|
return OBIView_line(self, item)
|
||||||
|
|
||||||
|
|
||||||
|
def __contains__(self, str column_name):
|
||||||
|
return (column_name in self._columns)
|
||||||
|
|
||||||
|
|
||||||
|
def __len__(self):
|
||||||
|
return(self.line_count)
|
||||||
|
|
||||||
|
|
||||||
|
def __str__(self) :
|
||||||
|
cdef OBIView_line line
|
||||||
|
cdef str to_print
|
||||||
|
to_print = ""
|
||||||
|
for line in self :
|
||||||
|
to_print = to_print + str(line) + "\n"
|
||||||
|
return to_print
|
||||||
|
|
||||||
|
|
||||||
|
# line_count property getter
|
||||||
|
@property
|
||||||
|
def line_count(self):
|
||||||
|
return self._pointer.infos.line_count
|
||||||
|
|
||||||
|
# name property getter
|
||||||
|
@property
|
||||||
|
def name(self):
|
||||||
|
return bytes2str(self._pointer.infos.name)
|
||||||
|
|
||||||
|
# view type property getter
|
||||||
|
@property
|
||||||
|
def type(self): # @ReservedAssignment
|
||||||
|
return bytes2str(self._pointer.infos.view_type)
|
||||||
|
|
||||||
|
# columns property getter
|
||||||
|
@property
|
||||||
|
def columns(self):
|
||||||
|
return self._columns
|
||||||
|
|
||||||
|
# comments property getter
|
||||||
|
@property
|
||||||
|
def comments(self):
|
||||||
|
return bytes2str(self._pointer.infos.comments)
|
||||||
|
# TODO setter that concatenates new comments?
|
||||||
|
|
||||||
|
|
||||||
|
cdef class OBIView_line_selection(list):
|
||||||
|
|
||||||
|
def __init__(self, OBIView view, lines=None) :
|
||||||
|
if view._pointer == NULL:
|
||||||
|
raise Exception("Error: trying to create a line selection with an invalidated view")
|
||||||
|
self._view = view
|
||||||
|
self._view_name = view.name
|
||||||
|
|
||||||
|
if lines is not None:
|
||||||
|
self.extend(lines)
|
||||||
|
|
||||||
|
def extend(self, iterable):
|
||||||
|
cdef index_t i
|
||||||
|
cdef index_t max_i = self._view.line_count
|
||||||
|
|
||||||
|
for i in iterable:
|
||||||
|
if i > max_i:
|
||||||
|
raise RuntimeError("Error: trying to select line %d beyond the line count %d of view %s" %
|
||||||
|
(i,
|
||||||
|
max_i,
|
||||||
|
self._view_name)
|
||||||
|
)
|
||||||
|
list.append(self,i)
|
||||||
|
|
||||||
|
def append(self, index_t idx) :
|
||||||
|
if idx >= self._view.line_count :
|
||||||
|
raise RuntimeError("Error: trying to select line %d beyond the line count %d of view %s" %
|
||||||
|
(i,
|
||||||
|
max_i,
|
||||||
|
self._view_name)
|
||||||
|
)
|
||||||
|
list.append(self,idx)
|
||||||
|
|
||||||
|
cdef index_t* __build_binary_list__(self):
|
||||||
|
cdef index_t* line_selection_p = NULL
|
||||||
|
cdef int i
|
||||||
|
cdef size_t l_selection = len(self)
|
||||||
|
|
||||||
|
line_selection_p = <index_t*> malloc((l_selection + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array
|
||||||
|
for i in range(l_selection) :
|
||||||
|
line_selection_p[i] = line_selection[i]
|
||||||
|
line_selection_p[l_selection] = -1 # flagging the end of the array
|
||||||
|
|
||||||
|
return line_selection_p
|
||||||
|
|
||||||
|
cpdef OBIView materialize(self,
|
||||||
|
str view_name,
|
||||||
|
str comments=""):
|
||||||
|
|
||||||
|
cdef OBIView view = OBIView(987654)
|
||||||
|
|
||||||
|
view._pointer = obi_new_view(self._view._pointer.dms,
|
||||||
|
str2bytes(view_name),
|
||||||
|
self._view._pointer,
|
||||||
|
self.__build_binary_list__(),
|
||||||
|
str2bytes(comments))
|
||||||
|
|
||||||
|
if view._pointer == NULL :
|
||||||
|
raise RuntimeError("Error : Cannot clone view %s into view %s"
|
||||||
|
% (str(self.name),
|
||||||
|
view_name)
|
||||||
|
)
|
||||||
|
|
||||||
|
view.__init_columns__(self)
|
||||||
|
|
||||||
|
return view
|
||||||
|
|
||||||
|
|
||||||
@ -4,5 +4,22 @@ from ._obidms cimport OBIView
|
|||||||
from ._obiseq cimport OBI_Nuc_Seq, OBI_Nuc_Seq_Stored
|
from ._obiseq cimport OBI_Nuc_Seq, OBI_Nuc_Seq_Stored
|
||||||
|
|
||||||
|
|
||||||
cdef class OBIView_NUC_SEQS(OBIView):
|
cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS):
|
||||||
pass
|
cpdef OBIView clone(self,
|
||||||
|
str view_name,
|
||||||
|
OBIView_line_selection line_selection=*,
|
||||||
|
str comments=*)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
cpdef OBIView new(OBIDMS dms,
|
||||||
|
str view_name,
|
||||||
|
str comments=*)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
cpdef OBIView open(OBIDMS dms,
|
||||||
|
str view_name)
|
||||||
|
|
||||||
|
cdef class OBIView_NUC_SEQS_line_selection(OBIView_line_selection):
|
||||||
|
cpdef OBIView materialize(self,
|
||||||
|
str view_name,
|
||||||
|
str comments=*)
|
||||||
|
|||||||
@ -5,6 +5,68 @@ from .capi.obitypes cimport index_t
|
|||||||
|
|
||||||
cdef class OBIView_NUC_SEQS(OBIView):
|
cdef class OBIView_NUC_SEQS(OBIView):
|
||||||
|
|
||||||
|
cpdef OBIView clone(self,
|
||||||
|
str view_name,
|
||||||
|
str comments=""):
|
||||||
|
|
||||||
|
cdef OBIView view = OBIView_NUC_SEQS(987654)
|
||||||
|
|
||||||
|
view._pointer = obi_new_view_nuc_seqs(self._pointer.dms,
|
||||||
|
str2bytes(view_name),
|
||||||
|
self._pointer,
|
||||||
|
NULL,
|
||||||
|
str2bytes(comments),
|
||||||
|
False)
|
||||||
|
|
||||||
|
if view._pointer == NULL :
|
||||||
|
raise RuntimeError("Error : Cannot clone view %s into view %s"
|
||||||
|
% (str(self.name),
|
||||||
|
view_name)
|
||||||
|
)
|
||||||
|
|
||||||
|
view.__init_columns__(self)
|
||||||
|
|
||||||
|
return view
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
cpdef OBIView new(OBIDMS dms,
|
||||||
|
str view_name,
|
||||||
|
str comments=""):
|
||||||
|
|
||||||
|
cdef OBIView view = OBIView_NUC_SEQS(987654) # @DuplicatedSignature
|
||||||
|
|
||||||
|
view._pointer = obi_new_view_nuc_seqs(dms._pointer,
|
||||||
|
str2bytes(view_name),
|
||||||
|
NULL,
|
||||||
|
NULL,
|
||||||
|
str2bytes(comments),
|
||||||
|
False)
|
||||||
|
|
||||||
|
if view._pointer == NULL :
|
||||||
|
raise RuntimeError("Error : Cannot create view %s" % view_name)
|
||||||
|
|
||||||
|
view.__init_columns__(self)
|
||||||
|
|
||||||
|
return view
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
cpdef OBIView open(OBIDMS dms,
|
||||||
|
str view_name):
|
||||||
|
|
||||||
|
cdef OBIView view = OBIView_NUC_SEQS(987654) # @DuplicatedSignature
|
||||||
|
|
||||||
|
view._pointer = obi_open_view(dms._pointer,
|
||||||
|
str2bytes(view_name))
|
||||||
|
|
||||||
|
if view._pointer == NULL :
|
||||||
|
raise RuntimeError("Error : Cannot open view %s" % view_name)
|
||||||
|
|
||||||
|
view.__init_columns__(self)
|
||||||
|
|
||||||
|
return view
|
||||||
|
|
||||||
|
cpdef OBIView_line_selection new_selection(self,list lines=None):
|
||||||
|
return OBIView_NUC_SEQS_line_selection(self,lines)
|
||||||
|
|
||||||
def __getitem__(self, object item) :
|
def __getitem__(self, object item) :
|
||||||
if type(item) == str :
|
if type(item) == str :
|
||||||
@ -17,3 +79,27 @@ cdef class OBIView_NUC_SEQS(OBIView):
|
|||||||
for key in sequence_obj :
|
for key in sequence_obj :
|
||||||
self[line_idx][key] = sequence_obj[key]
|
self[line_idx][key] = sequence_obj[key]
|
||||||
|
|
||||||
|
|
||||||
|
cdef class OBIView_NUC_SEQS_line_selection(OBIView_line_selection):
|
||||||
|
|
||||||
|
cpdef OBIView materialize(self,
|
||||||
|
str view_name,
|
||||||
|
str comments=""):
|
||||||
|
|
||||||
|
cdef OBIView view = OBIView_NUC_SEQS(987654)
|
||||||
|
|
||||||
|
view._pointer = obi_new_view(self._view._pointer.dms,
|
||||||
|
str2bytes(view_name),
|
||||||
|
self._view._pointer,
|
||||||
|
self.__build_binary_list__(),
|
||||||
|
str2bytes(comments))
|
||||||
|
|
||||||
|
if view._pointer == NULL :
|
||||||
|
raise RuntimeError("Error : Cannot clone view %s into view %s"
|
||||||
|
% (str(self.name),
|
||||||
|
view_name)
|
||||||
|
)
|
||||||
|
|
||||||
|
view.__init_columns__(self)
|
||||||
|
|
||||||
|
return view
|
||||||
|
|||||||
25
python/obitools3/obidms/_obiview_nuc_seq_qual.pxd
Normal file
25
python/obitools3/obidms/_obiview_nuc_seq_qual.pxd
Normal file
@ -0,0 +1,25 @@
|
|||||||
|
#cython: language_level=3
|
||||||
|
|
||||||
|
from ._obidms cimport OBIView
|
||||||
|
from ._obiseq cimport OBI_Nuc_Seq, OBI_Nuc_Seq_Stored
|
||||||
|
|
||||||
|
|
||||||
|
cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS):
|
||||||
|
cpdef OBIView clone(self,
|
||||||
|
str view_name,
|
||||||
|
OBIView_line_selection line_selection=*,
|
||||||
|
str comments=*)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
cpdef OBIView new(OBIDMS dms,
|
||||||
|
str view_name,
|
||||||
|
str comments=*)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
cpdef OBIView open(OBIDMS dms,
|
||||||
|
str view_name)
|
||||||
|
|
||||||
|
cdef class OBIView_NUC_SEQS_QUAL_line_selection(OBIView_NUC_SEQS_line_selection):
|
||||||
|
cpdef OBIView materialize(self,
|
||||||
|
str view_name,
|
||||||
|
str comments=*)
|
||||||
90
python/obitools3/obidms/_obiview_nuc_seq_qual.pyx
Normal file
90
python/obitools3/obidms/_obiview_nuc_seq_qual.pyx
Normal file
@ -0,0 +1,90 @@
|
|||||||
|
#cython: language_level=3
|
||||||
|
|
||||||
|
from .capi.obitypes cimport index_t
|
||||||
|
|
||||||
|
|
||||||
|
cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS):
|
||||||
|
|
||||||
|
cpdef OBIView clone(self,
|
||||||
|
str view_name,
|
||||||
|
str comments=""):
|
||||||
|
|
||||||
|
cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654)
|
||||||
|
|
||||||
|
view._pointer = obi_new_view_nuc_seqs(self._pointer.dms,
|
||||||
|
str2bytes(view_name),
|
||||||
|
self._pointer,
|
||||||
|
NULL,
|
||||||
|
str2bytes(comments),
|
||||||
|
True)
|
||||||
|
|
||||||
|
if view._pointer == NULL :
|
||||||
|
raise RuntimeError("Error : Cannot clone view %s into view %s"
|
||||||
|
% (str(self.name),
|
||||||
|
view_name)
|
||||||
|
)
|
||||||
|
|
||||||
|
view.__init_columns__(self)
|
||||||
|
|
||||||
|
return view
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
cpdef OBIView new(OBIDMS dms,
|
||||||
|
str view_name,
|
||||||
|
str comments=""):
|
||||||
|
|
||||||
|
cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654) # @DuplicatedSignature
|
||||||
|
|
||||||
|
view._pointer = obi_new_view_nuc_seqs(dms._pointer,
|
||||||
|
str2bytes(view_name),
|
||||||
|
NULL,
|
||||||
|
NULL,
|
||||||
|
str2bytes(comments),
|
||||||
|
True)
|
||||||
|
|
||||||
|
if view._pointer == NULL :
|
||||||
|
raise RuntimeError("Error : Cannot create view %s" % view_name)
|
||||||
|
|
||||||
|
view.__init_columns__(self)
|
||||||
|
|
||||||
|
return view
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
cpdef OBIView open(OBIDMS dms,
|
||||||
|
str view_name):
|
||||||
|
|
||||||
|
cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654) # @DuplicatedSignature
|
||||||
|
|
||||||
|
view._pointer = obi_open_view(dms._pointer,
|
||||||
|
str2bytes(view_name))
|
||||||
|
|
||||||
|
if view._pointer == NULL :
|
||||||
|
raise RuntimeError("Error : Cannot open view %s" % view_name)
|
||||||
|
|
||||||
|
view.__init_columns__(self)
|
||||||
|
|
||||||
|
return view
|
||||||
|
|
||||||
|
cdef class OBIView_NUC_SEQS_QUAL_line_selection(OBIView_NUC_SEQS_line_selection):
|
||||||
|
|
||||||
|
cpdef OBIView materialize(self,
|
||||||
|
str view_name,
|
||||||
|
str comments=""):
|
||||||
|
|
||||||
|
cdef OBIView view = OBIView_NUC_SEQS_QUAL(987654)
|
||||||
|
|
||||||
|
view._pointer = obi_new_view(self._view._pointer.dms,
|
||||||
|
str2bytes(view_name),
|
||||||
|
self._view._pointer,
|
||||||
|
self.__build_binary_list__(),
|
||||||
|
str2bytes(comments))
|
||||||
|
|
||||||
|
if view._pointer == NULL :
|
||||||
|
raise RuntimeError("Error : Cannot clone view %s into view %s"
|
||||||
|
% (str(self.name),
|
||||||
|
view_name)
|
||||||
|
)
|
||||||
|
|
||||||
|
view.__init_columns__(self)
|
||||||
|
|
||||||
|
return view
|
||||||
Reference in New Issue
Block a user