675 lines
25 KiB
Cython
675 lines
25 KiB
Cython
#cython: language_level=3
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from obitools3.utils cimport bytes2str, str2bytes
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from .capi.obidms cimport obi_dms, \
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obi_close_dms
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from .capi.obidmscolumn cimport obi_close_column, \
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OBIDMS_column_p, \
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OBIDMS_column_header_p
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from .capi.obiutils cimport obi_format_date
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from .capi.obitypes cimport const_char_p, \
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OBIType_t, \
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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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name_data_type, \
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only_ATGC # discuss
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from ._obidms cimport OBIDMS, \
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OBIDMS_column, \
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OBIView, \
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OBIView_line
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from ._obitaxo cimport OBI_Taxonomy
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from ._obiseq cimport OBI_Nuc_Seq, OBI_Nuc_Seq_Stored
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from ._obidmscolumn_int cimport OBIDMS_column_int, \
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OBIDMS_column_multi_elts_int
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from ._obidmscolumn_float cimport OBIDMS_column_float, \
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OBIDMS_column_multi_elts_float
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from ._obidmscolumn_bool cimport OBIDMS_column_bool, \
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OBIDMS_column_multi_elts_bool
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from ._obidmscolumn_char cimport OBIDMS_column_char, \
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OBIDMS_column_multi_elts_char
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from ._obidmscolumn_qual cimport OBIDMS_column_qual, \
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OBIDMS_column_multi_elts_qual
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from ._obidmscolumn_str cimport OBIDMS_column_str, \
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OBIDMS_column_multi_elts_str
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from ._obidmscolumn_seq cimport OBIDMS_column_seq, \
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OBIDMS_column_multi_elts_seq
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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_view_infos, \
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obi_close_view_infos, \
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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_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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VIEW_TYPE_NUC_SEQS, \
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NUC_SEQUENCE_COLUMN, \
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ID_COLUMN, \
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DEFINITION_COLUMN, \
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QUALITY_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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cdef class OBIDMS_column :
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# Should only be initialized through a subclass
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def __init__(self, OBIView view, str column_name):
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cdef OBIDMS_column_p column_p
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cdef OBIDMS_column_p* column_pp
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column_pp = obi_view_get_pointer_on_column_in_view(view.pointer, str2bytes(column_name))
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column_p = column_pp[0] # TODO ugly cython dereferencing but can't find better
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# Fill structure
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self.pointer = column_pp
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self.dms = view.dms
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self.view = view
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self.data_type = bytes2str(name_data_type((column_p.header).returned_data_type))
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self.column_name = bytes2str((column_p.header).name)
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self.nb_elements_per_line = (column_p.header).nb_elements_per_line
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self.elements_names = (bytes2str((column_p.header).elements_names)).split(';')
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def __setitem__(self, index_t line_nb, object value):
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self.set_line(line_nb, value)
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def __getitem__(self, index_t line_nb):
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return self.get_line(line_nb)
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def __len__(self):
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return (self.pointer)[0].header.lines_used
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def __sizeof__(self):
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return ((self.pointer)[0].header.header_size + (self.pointer)[0].header.data_size)
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def __iter__(self):
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# Declarations
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cdef index_t lines_used
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cdef index_t line_nb
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# Yield each line
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lines_used = (self.pointer)[0].header.lines_used
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for line_nb in range(lines_used):
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yield self.get_line(line_nb)
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cpdef update_pointer(self):
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self.pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self.view.pointer, str2bytes(self.column_name))
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cpdef list get_elements_names(self):
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return self.elements_names
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cpdef str get_data_type(self):
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return self.data_type
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cpdef index_t get_nb_lines_used(self):
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return (self.pointer)[0].header.lines_used
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cpdef str get_creation_date(self):
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return bytes2str(obi_format_date((self.pointer)[0].header.creation_date))
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cpdef str get_comments(self):
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return bytes2str((self.pointer)[0].header.comments)
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def __str__(self) :
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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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def __repr__(self) :
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return (self.column_name + ", version " + str((self.pointer)[0].header.version) + ", data type: " + self.data_type)
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cpdef close(self):
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if obi_close_column((self.pointer)[0]) < 0 :
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raise Exception("Problem closing a column")
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@staticmethod
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cdef object get_subclass_type(OBIDMS_column_p column_p) :
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cdef object subclass
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cdef OBIDMS_column_header_p header
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cdef OBIType_t col_type
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cdef bint col_writable
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cdef bint col_one_element_per_line
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header = column_p.header
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col_type = header.returned_data_type
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col_writable = column_p.writable
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col_one_element_per_line = ((header.nb_elements_per_line) == 1)
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if col_type == OBI_INT :
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if col_one_element_per_line :
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subclass = OBIDMS_column_int
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else :
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subclass = OBIDMS_column_multi_elts_int
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elif col_type == OBI_FLOAT :
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if col_one_element_per_line :
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subclass = OBIDMS_column_float
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else :
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subclass = OBIDMS_column_multi_elts_float
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elif col_type == OBI_BOOL :
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if col_one_element_per_line :
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subclass = OBIDMS_column_bool
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else :
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subclass = OBIDMS_column_multi_elts_bool
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elif col_type == OBI_CHAR :
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if col_one_element_per_line :
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subclass = OBIDMS_column_char
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else :
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subclass = OBIDMS_column_multi_elts_char
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elif col_type == OBI_QUAL :
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if col_one_element_per_line :
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subclass = OBIDMS_column_qual
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else :
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subclass = OBIDMS_column_multi_elts_qual
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elif col_type == OBI_STR :
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if col_one_element_per_line :
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subclass = OBIDMS_column_str
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else :
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subclass = OBIDMS_column_multi_elts_str
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elif col_type == OBI_SEQ :
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if col_one_element_per_line :
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subclass = OBIDMS_column_seq
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else :
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subclass = OBIDMS_column_multi_elts_seq
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else :
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raise Exception("Problem with the data type")
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return subclass
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######################################################################################################
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cdef class OBIDMS_column_multi_elts(OBIDMS_column) :
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def __getitem__(self, index_t line_nb):
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return OBIDMS_column_line(self, line_nb)
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cpdef set_line(self, index_t line_nb, dict values):
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for element_name in values :
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self.set_item(line_nb, element_name, values[element_name])
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######################################################################################################
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cdef class OBIDMS_column_line :
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def __init__(self, OBIDMS_column column, index_t line_nb) :
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self.index = line_nb
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self.column = column
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def __getitem__(self, str element_name) :
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return self.column.get_item(self.index, element_name)
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def __setitem__(self, str element_name, object value):
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self.column.set_item(self.index, element_name, value)
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def __contains__(self, str element_name):
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return (element_name in self.column.elements_names)
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def __repr__(self) :
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return str(self.column.get_line(self.index))
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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, list line_selection=None, str comments=""):
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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_header_p header
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cdef index_t* line_selection_p
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self.dms = dms
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# Create the C array for the line selection if needed
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if line_selection is not None :
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line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))
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for i in range(len(line_selection)) :
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line_selection_p[i] = line_selection[i]
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line_selection_p[len(line_selection)] = -1
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else :
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line_selection_p = NULL
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# Create the view if needed
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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_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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elif view_to_clone is None :
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view = obi_new_view(dms.pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments))
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# Else, open the existing view
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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) # TODO discuss
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if view == NULL :
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raise Exception("Error creating/opening a view")
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self.pointer = view
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self.name = bytes2str(view.name)
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# Go through columns to build list of corresponding python instances
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self.columns = {}
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for i in range(view.column_count) :
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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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subclass = OBIDMS_column.get_subclass_type(column_p)
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self.columns[col_name] = subclass(self, col_name)
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def __repr__(self) :
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cdef str s
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s = str(self.name) + ", " + str(self.comments) + ", " + str(self.pointer.line_count) + " lines\n"
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for column_name in self.columns :
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s = s + self.columns[column_name].__repr__() + '\n'
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return s
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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_p
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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_header_p header
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cdef str column_n
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view = self.pointer
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if obi_view_delete_column(view_p, 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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for column_n in self.columns :
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(self.columns[column_n]).update_pointer()
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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 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 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 nb_elements_per_line > 1 :
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elements_names_b = str2bytes(';'.join(elements_names))
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elif nb_elements_per_line == 1 :
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elements_names_b = column_name_b
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if type :
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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, # TODO should return pointer on column?
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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(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, column_name_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)[column_name] = subclass(self, column_name)
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cpdef save_and_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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def __iter__(self):
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# iter on each line of all columns
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# Declarations
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cdef index_t lines_used
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cdef index_t line_nb
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cdef OBIView_line line # TODO Check that this works for NUC SEQ views
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# Yield each line
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lines_used = (self.pointer).line_count
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for line_nb in range(lines_used) :
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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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cpdef select_line(self, index_t line_nb) :
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if obi_select_line(self.pointer, line_nb) < 0 :
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raise Exception("Problem selecting a line")
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cpdef select_lines(self, list line_selection) :
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cdef index_t* line_selection_p
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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]
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line_selection_p[len(line_selection)] = -1
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if obi_select_lines(self.pointer, line_selection_p) < 0 :
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raise Exception("Problem selecting a list of lines")
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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 __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.__iter__() :
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to_print = to_print + str(line) + "\n"
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return to_print
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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, str comments=""):
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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_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]
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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, str2bytes(comments))
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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))
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elif view_to_clone is None :
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view = obi_new_view_nuc_seqs(dms.pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments))
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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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self.comments = bytes2str(view.comments)
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# Go through columns to build list of corresponding python instances
|
|
self.columns = {}
|
|
for i in range(view.column_count) :
|
|
column_p = <OBIDMS_column_p> (view.columns)[i]
|
|
header = (column_p).header
|
|
col_name = bytes2str(header.name)
|
|
subclass = OBIDMS_column.get_subclass_type(column_p)
|
|
self.columns[col_name] = subclass(self, col_name)
|
|
|
|
self.ids = self.columns[bytes2str(ID_COLUMN)]
|
|
self.sequences = self.columns[bytes2str(NUC_SEQUENCE_COLUMN)]
|
|
self.definitions = self.columns[bytes2str(DEFINITION_COLUMN)]
|
|
self.qualities = self.columns[bytes2str(QUALITY_COLUMN)]
|
|
|
|
def __getitem__(self, object item) :
|
|
if type(item) == str :
|
|
return (self.columns)[item]
|
|
elif type(item) == int :
|
|
return OBI_Nuc_Seq_Stored(self, item)
|
|
|
|
def __setitem__(self, index_t line_idx, OBI_Nuc_Seq sequence_obj) :
|
|
for key in sequence_obj :
|
|
self[line_idx][key] = sequence_obj[key]
|
|
|
|
|
|
#############################################
|
|
|
|
cdef class OBIView_line :
|
|
|
|
def __init__(self, OBIView view, index_t line_nb) :
|
|
self.index = line_nb
|
|
self.view = view
|
|
|
|
def __getitem__(self, str column_name) :
|
|
return ((self.view).columns)[column_name][self.index]
|
|
|
|
def __setitem__(self, str column_name, object value):
|
|
# TODO detect multiple elements (dict type)? put somewhere else? but more risky (in get)
|
|
# TODO OBI_QUAL ?
|
|
cdef type value_type
|
|
cdef str value_obitype
|
|
if column_name not in self.view :
|
|
if value == None :
|
|
raise Exception("Trying to create a column from a None value (can't guess type)")
|
|
value_type = type(value)
|
|
if value_type == int :
|
|
value_obitype = 'OBI_INT'
|
|
elif value_type == float :
|
|
value_obitype = 'OBI_FLOAT'
|
|
elif value_type == bool :
|
|
value_obitype = 'OBI_BOOL'
|
|
elif value_type == str :
|
|
if only_ATGC(str2bytes(value)) : # TODO detect IUPAC?
|
|
value_obitype = 'OBI_SEQ'
|
|
elif len(value) == 1 :
|
|
value_obitype = 'OBI_CHAR'
|
|
elif (len(value) > 1) :
|
|
value_obitype = 'OBI_STR'
|
|
else :
|
|
raise Exception("Could not guess the type of a value to create a new column")
|
|
self.view.add_column(column_name, type=value_obitype)
|
|
|
|
(((self.view).columns)[column_name]).set_line(self.index, value)
|
|
|
|
def __contains__(self, str column_name):
|
|
return (column_name in self.view)
|
|
|
|
def __repr__(self):
|
|
cdef dict line
|
|
cdef str column_name
|
|
line = {}
|
|
for column_name in self.view.columns :
|
|
line[column_name] = self[column_name]
|
|
return str(line)
|
|
|
|
##########################################
|
|
|
|
cdef class OBIDMS :
|
|
|
|
def __init__(self, str dms_name) :
|
|
|
|
# Declarations
|
|
cdef bytes dms_name_b
|
|
|
|
# Format the character string to send to C function
|
|
dms_name_b = str2bytes(dms_name)
|
|
|
|
# Fill structure and create or open the DMS
|
|
self.dms_name = dms_name
|
|
self.pointer = obi_dms(<const_char_p> dms_name_b)
|
|
if self.pointer == NULL :
|
|
raise Exception("Failed opening or creating an OBIDMS")
|
|
|
|
|
|
cpdef close(self) :
|
|
if (obi_close_dms(self.pointer)) < 0 :
|
|
raise Exception("Problem closing an OBIDMS")
|
|
|
|
|
|
cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name) :
|
|
return OBI_Taxonomy(self, taxo_name)
|
|
|
|
|
|
cpdef OBIView open_view(self, str view_name) :
|
|
|
|
cdef object view_class
|
|
cdef dict view_infos
|
|
|
|
view_infos = self.read_view_infos(view_name)
|
|
|
|
if view_infos["view_type"] == bytes2str(VIEW_TYPE_NUC_SEQS) :
|
|
view_class = OBIView_NUC_SEQS
|
|
else :
|
|
view_class = OBIView
|
|
|
|
return view_class(self, view_name)
|
|
|
|
|
|
cpdef OBIView new_view(self, str view_name, object view_to_clone=None, list line_selection=None, str view_type=None, str comments="") :
|
|
|
|
cdef object view_class
|
|
|
|
if view_type is not None :
|
|
if view_type == bytes2str(VIEW_TYPE_NUC_SEQS) :
|
|
view_class = OBIView_NUC_SEQS
|
|
else :
|
|
view_class = OBIView
|
|
|
|
return view_class(self, view_name, new=True, view_to_clone=view_to_clone, line_selection=line_selection, comments=comments)
|
|
|
|
|
|
cpdef dict read_view_infos(self, str view_name) :
|
|
all_views = self.read_views()
|
|
return all_views[view_name]
|
|
|
|
|
|
cpdef dict read_views(self) : # TODO function that prints the dic nicely and function that prints 1 view nicely. Add column type in col ref
|
|
|
|
cdef Obiviews_infos_all_p all_views_p
|
|
cdef Obiview_infos_p view_p
|
|
cdef Column_reference_p column_refs
|
|
cdef int nb_views
|
|
cdef int i, j
|
|
cdef str view_name
|
|
cdef str column_name
|
|
cdef dict views
|
|
cdef bytes name_b
|
|
|
|
views = {}
|
|
all_views_p = obi_read_view_infos(self.pointer)
|
|
if all_views_p == NULL :
|
|
raise Exception("No views to read")
|
|
nb_views = <int> (all_views_p.header).view_count
|
|
for i in range(nb_views) :
|
|
view_p = (<Obiview_infos_p> (all_views_p.view_infos)) + i
|
|
view_name = bytes2str(view_p.name)
|
|
views[view_name] = {}
|
|
views[view_name]["comments"] = bytes2str(view_p.comments)
|
|
views[view_name]["view_type"] = bytes2str(view_p.view_type)
|
|
views[view_name]["column_count"] = <int> view_p.column_count
|
|
views[view_name]["line_count"] = <int> view_p.line_count
|
|
views[view_name]["view_number"] = <int> view_p.view_number
|
|
views[view_name]["created_from"] = bytes2str(view_p.created_from)
|
|
views[view_name]["creation_date"] = bytes2str(obi_format_date(view_p.creation_date))
|
|
if (view_p.all_lines) :
|
|
views[view_name]["line_selection"] = None
|
|
else :
|
|
views[view_name]["line_selection"] = {}
|
|
views[view_name]["line_selection"]["column_name"] = bytes2str((view_p.line_selection).column_name)
|
|
views[view_name]["line_selection"]["version"] = <int> (view_p.line_selection).version
|
|
views[view_name]["column_references"] = {}
|
|
column_refs = view_p.column_references
|
|
for j in range(views[view_name]["column_count"]) :
|
|
column_name = bytes2str((column_refs[j]).column_name)
|
|
views[view_name]["column_references"][column_name] = {}
|
|
views[view_name]["column_references"][column_name]["version"] = column_refs[j].version
|
|
|
|
obi_close_view_infos(all_views_p);
|
|
|
|
return views
|
|
|
|
|
|
|
|
|