427 lines
14 KiB
Cython
427 lines
14 KiB
Cython
#cython: language_level=3
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from obitools3.utils cimport bytes2str, str2bytes
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from .capi.obitypes cimport OBI_INT, \
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OBI_FLOAT, \
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OBI_BOOL, \
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OBI_CHAR, \
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OBI_QUAL, \
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OBI_STR, \
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OBI_SEQ, \
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only_ATGC
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from .capi.obiview cimport Obiview_p, \
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obi_new_view, \
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obi_open_view, \
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obi_view_delete_column, \
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obi_view_add_column, \
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obi_view_create_column_alias, \
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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_save_and_close_view
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from .capi.obidmscolumn cimport OBIDMS_column_p
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from ._obidms cimport OBIDMS, \
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OBIDMS_column
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from libc.stdlib cimport malloc
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cdef class OBIView :
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def __init__(self,int __internalCall__):
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if __internalCall__!=987654:
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raise RuntimeError('OBIView constructor cannot be called directly')
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self._pointer = NULL
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self._columns = {}
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cdef __init_columns__(self):
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cdef size_t i
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cdef str col_alias
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cdef OBIDMS_column_p column_p
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cdef Obiview_p pointer = self._pointer
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self._columns = {}
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for i in range(pointer.infos.column_count) :
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col_alias = bytes2str(pointer.infos.column_references[i].alias)
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column_p = <OBIDMS_column_p> (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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cpdef OBIView clone(self,
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str view_name,
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str comments=""):
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cdef OBIView view = OBIView(987654)
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view._pointer = obi_new_view(self._pointer.dms,
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str2bytes(view_name),
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self._pointer,
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NULL,
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str2bytes(comments))
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if view._pointer == NULL :
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raise RuntimeError("Error : Cannot clone view %s into view %s"
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% (str(self.name),
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view_name)
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)
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view.__init_columns__()
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return view
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@staticmethod
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cdef OBIView new(OBIDMS dms,
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str view_name,
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str comments=""):
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cdef OBIView view = OBIView(987654) # @DuplicatedSignature
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view._pointer = obi_new_view(dms._pointer,
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str2bytes(view_name),
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NULL,
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NULL,
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str2bytes(comments))
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if view._pointer == NULL :
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raise RuntimeError("Error : Cannot create view %s" % view_name)
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view.__init_columns__()
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return view
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@staticmethod
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cdef OBIView open(OBIDMS dms,
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str view_name):
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cdef OBIView view = OBIView(987654) # @DuplicatedSignature
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view._pointer = obi_open_view(dms._pointer,
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str2bytes(view_name))
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if view._pointer == NULL :
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raise RuntimeError("Error : Cannot open view %s" % view_name)
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view.__init_columns__()
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return view
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def __dealloc__(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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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 OBIView_line_selection new_selection(self,list lines=None):
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return OBIView_line_selection(self,lines)
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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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cdef class OBIView_line :
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def __init__(self, OBIView view, index_t line_nb) :
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self._index = line_nb
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self._view = view
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def __getitem__(self, str column_name) :
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return ((self._view)._columns)[column_name][self._index]
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def __setitem__(self, str column_name, object value):
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# TODO detect multiple elements (dict type)? put somewhere else? but more risky (in get)
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# TODO OBI_QUAL ?
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cdef type value_type
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cdef str value_obitype
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cdef bytes value_b
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if column_name not in self._view :
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if value == None :
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raise Exception("Trying to create a column from a None value (can't guess type)")
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value_type = type(value)
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if value_type == int :
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value_obitype = 'OBI_INT'
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elif value_type == float :
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value_obitype = 'OBI_FLOAT'
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elif value_type == bool :
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value_obitype = 'OBI_BOOL'
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elif value_type == str or value_type == bytes :
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if value_type == str :
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value_b = str2bytes(value)
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else :
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value_b = value
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if only_ATGC(value_b) : # TODO detect IUPAC
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value_obitype = 'OBI_SEQ'
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elif len(value) == 1 :
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value_obitype = 'OBI_CHAR'
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elif (len(value) > 1) :
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value_obitype = 'OBI_STR'
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else :
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raise Exception("Could not guess the type of a value to create a new column")
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self._view.add_column(column_name, type=value_obitype)
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(((self._view)._columns)[column_name]).set_line(self._index, value)
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def __iter__(self):
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for column_name in ((self._view)._columns) :
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yield column_name
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def __contains__(self, str column_name):
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return (column_name in self._view._columns)
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def __repr__(self):
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cdef dict line
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cdef str column_name
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line = {}
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for column_name in self._view._columns :
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line[column_name] = self[column_name]
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return str(line)
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cdef class OBIView_line_selection(list):
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def __init__(self, OBIView view, lines=None) :
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if view._pointer == NULL:
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raise Exception("Error: trying to create a line selection with an invalidated view")
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self._view = view
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self._view_name = view.name
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if lines is not None:
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self.extend(lines)
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def extend(self, iterable):
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cdef index_t i
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cdef index_t max_i = self._view.line_count
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for i in iterable:
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if i > max_i:
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raise RuntimeError("Error: trying to select line %d beyond the line count %d of view %s" %
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(i,
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max_i,
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self._view_name)
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)
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list.append(self,i)
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def append(self, index_t idx) :
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if idx >= self._view.line_count :
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raise RuntimeError("Error: trying to select line %d beyond the line count %d of view %s" %
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(idx,
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self._view.line_count,
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self._view_name)
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)
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list.append(self,idx)
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cdef index_t* __build_binary_list__(self):
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cdef index_t* line_selection_p = NULL
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cdef int i
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cdef size_t len_selection = len(self)
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line_selection_p = <index_t*> malloc((len_selection + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array
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for i in range(len_selection) :
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line_selection_p[i] = self[i]
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line_selection_p[len_selection] = -1 # flagging the end of the array
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return line_selection_p
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cpdef OBIView materialize(self,
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str view_name,
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str comments=""):
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cdef OBIView view = OBIView(987654)
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view._pointer = obi_new_view(self._view._pointer.dms,
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str2bytes(view_name),
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self._view._pointer,
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self.__build_binary_list__(),
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str2bytes(comments))
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if view._pointer == NULL :
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raise RuntimeError("Error: Cannot clone view %s into view %s"
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% (str(self.name),
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view_name)
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)
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view.__init_columns__()
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return view
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