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Celine Mercier
2017-02-20 14:56:04 +01:00
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60
python/obitools3/dms/view.pxd
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#cython: language_level=3
from .capi.obiview cimport Obiview_p
from .capi.obitypes cimport index_t, \
obitype_t
from .dms cimport DMS
from .column cimport Column
cdef class View:
cdef DMS _dms
cdef Obiview_p _pointer
cpdef View clone(self,
object view_name,
object comments=*)
@staticmethod
cdef View _new(DMS dms,
bytes view_name,
bytes comments=*)
@staticmethod
cdef View _open(DMS dms,
bytes view_name)
cpdef close(self)
cpdef get_column(self,
object column_name)
cpdef delete_column(self,
object column_name)
cpdef rename_column(self,
object current_name,
object new_name)
cpdef View_line_selection new_selection(self,
list lines=*)
cdef class View_line_selection(list):
cdef View _view
cdef index_t* __build_binary_list__(self)
cpdef View materialize(self,
object view_name,
object comments=*)
cdef class View_line :
cdef index_t _index
cdef View _view

417
python/obitools3/dms/view.pyx
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#cython: language_level=3
from libc.stdlib cimport malloc
from .capi.obiview cimport obi_new_view, \
obi_open_view, \
obi_save_and_close_view, \
obi_view_get_pointer_on_column_in_view, \
obi_view_delete_column, \
obi_view_create_column_alias
from .capi.obidmscolumn cimport OBIDMS_column_p
from obitools3.utils cimport tobytes, \
bytes2str
cdef class View :
def __init__(self,dms,int __internalCall__):
if __internalCall__!=987654:
raise RuntimeError('OBIView constructor cannot be called directly')
self._dms = dms
self._pointer = NULL
cpdef View clone(self,
object view_name,
object comments=None):
cdef bytes view_name_b = tobytes(view_name)
cdef bytes comments_b
cdef View view = View(self._dms,
987654)
if comments is not None:
comments_b = tobytes(comments)
else:
comments_b = b''
view._pointer = obi_new_view(self._pointer.dms,
view_name_b,
self._pointer,
NULL,
comments_b)
if view._pointer == NULL :
raise RuntimeError("Error : Cannot clone view %s into view %s"
% (str(self.name),
bytes2str(view_name_b))
)
return view
@staticmethod
cdef View _new(DMS dms,
bytes view_name,
bytes comments=b""):
cdef View view = View(dms,
987654) # @DuplicatedSignature
view._pointer = obi_new_view(dms._pointer,
view_name,
NULL,
NULL,
comments)
if view._pointer == NULL :
raise RuntimeError("Error : Cannot create view %s" % view_name)
return view
@staticmethod
def new(DMS dms,
object view_name,
object comments=None):
cdef bytes view_name_b = tobytes(view_name)
cdef bytes comments_b
if comments is not None:
comments_b = tobytes(comments)
else:
comments_b = b''
return View._new(dms,
view_name_b,
comments_b)
@staticmethod
cdef View _open(DMS dms,
bytes view_name):
cdef View view = View(dms,
987654) # @DuplicatedSignature
view._pointer = obi_open_view(dms._pointer,
view_name)
if view._pointer == NULL :
raise RuntimeError("Error : Cannot open view %s" % bytes2str(view_name))
return view
@staticmethod
def open(DMS dms, # @ReservedAssignment
object view_name):
cdef bytes view_name_b = tobytes(view_name)
return View._open(dms,view_name_b)
cpdef close(self):
if (obi_save_and_close_view(self._pointer) < 0) :
raise Exception("Problem closing view %s" %
bytes2str(self.name))
def __dealloc__(self):
self.close()
def __repr__(self) :
cdef str s = "{name:s}\n{comments:s}\n{line_count:d} lines\n".format(name = str(self.name),
comments = str(self.comments),
line_count = self.line_count)
#for column_name in self._columns :
# s = s + repr(self._columns[column_name]) + '\n'
return s
cpdef get_column(self,
object column_name):
cdef bytes column_name_b = tobytes(column_name)
cdef OBIDMS_column_p* column_pp
cdef OBIDMS_column_p column_p
cdef Column column
cdef obitype_t column_type
column_pp = obi_view_get_pointer_on_column_in_view(self._pointer,
column_name_b)
if column_pp == NULL:
raise KeyError("Cannot access to column %s in view %s" % (
bytes2str(column_name_b),
bytes2str(self.name)
))
column_p = column_pp[0]
column_type = column_p.header.returned_data_type
column = DMS.get_column_class(column_type)(self)
column._pointer = column_pp
return column
cpdef delete_column(self,
object column_name) :
cdef bytes column_name_b = tobytes(column_name)
if obi_view_delete_column(self._pointer, column_name_b) < 0 :
raise Exception("Problem deleting column %s from a view",
bytes2str(column_name_b))
cpdef rename_column(self,
object current_name,
object new_name):
cdef Column column
cdef bytes current_name_b = tobytes(current_name)
cdef bytes new_name_b = tobytes(new_name)
if (obi_view_create_column_alias(self._pointer,
tobytes(current_name_b),
tobytes(new_name_b)) < 0) :
raise Exception("Problem in renaming column %s to %s" % (
bytes2str(current_name_b),
bytes2str(new_name_b)))
cpdef View_line_selection new_selection(self,list lines=None):
return View_line_selection(self,lines)
def __iter__(self):
# Iteration on each line of all columns
# Declarations
cdef index_t line_nb
cdef View_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 View_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 View_line line
cdef str to_print
to_print = ""
for line in self :
to_print = to_print + str(line) + "\n"
return to_print
@property
def dms(self):
return self._dms
# line_count property getter
@property
def line_count(self):
return self._pointer.infos.line_count
# name property getter
@property
def name(self):
return <bytes> self._pointer.infos.name
# view type property getter
@property
def type(self): # @ReservedAssignment
return bytes2str(self._pointer.infos.view_type)
# comments property getter
@property
def comments(self):
return <bytes> self._pointer.infos.comments
# TODO setter that concatenates new comments?
cdef class View_line_selection(list):
def __init__(self, View 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 IndexError("Error: trying to select line %d beyond the line count %d of view %s" %
(idx,
self._view.line_count,
bytes2str(self.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] = self[i]
line_selection_p[l_selection] = -1 # flagging the end of the array
return line_selection_p
cpdef View materialize(self,
object view_name,
object comments=""):
cdef View view = View(987654)
cdef bytes view_name_b=tobytes(view_name)
view._pointer = obi_new_view(self._view._pointer.dms,
view_name_b,
self._view._pointer,
self.__build_binary_list__(),
tobytes(comments))
if view._pointer == NULL :
raise RuntimeError("Error : Cannot clone view %s into view %s"
% (str(self.name),
view_name)
)
return view
cdef class View_line :
def __init__(self, View 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
# cdef bytes value_b
#
# 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 or value_type == bytes :
# if value_type == str :
# value_b = str2bytes(value)
# else :
# value_b = value
# if only_ATGC(value_b) : # 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 __iter__(self):
# for column_name in ((self._view)._columns) :
# yield column_name
#
# def __contains__(self, str column_name):
# return (column_name in self._view._columns)
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)
# cpdef dict get_view_infos(self, str view_name) :
#
# cdef Obiview_infos_p view_infos_p
# cdef dict view_infos_d
# cdef Alias_column_pair_p column_refs
# cdef int i, j
# cdef str column_name
#
# view_infos_p = obi_view_map_file(self._pointer,
# tobytes(view_name))
# view_infos_d = {}
# view_infos_d["name"] = bytes2str(view_infos_p.name)
# view_infos_d["comments"] = bytes2str(view_infos_p.comments)
# view_infos_d["view_type"] = bytes2str(view_infos_p.view_type)
# view_infos_d["column_count"] = <int> view_infos_p.column_count
# view_infos_d["line_count"] = <int> view_infos_p.line_count
# view_infos_d["created_from"] = bytes2str(view_infos_p.created_from)
# view_infos_d["creation_date"] = bytes2str(obi_format_date(view_infos_p.creation_date))
# if (view_infos_p.all_lines) :
# view_infos_d["line_selection"] = None
# else :
# view_infos_d["line_selection"] = {}
# view_infos_d["line_selection"]["column_name"] = bytes2str((view_infos_p.line_selection).column_name)
# view_infos_d["line_selection"]["version"] = <int> (view_infos_p.line_selection).version
# view_infos_d["column_references"] = {}
# column_references = view_infos_p.column_references
# for j in range(view_infos_d["column_count"]) :
# column_name = bytes2str((column_references[j]).alias)
# view_infos_d["column_references"][column_name] = {}
# view_infos_d["column_references"][column_name]["original_name"] = bytes2str((column_references[j]).column_refs.column_name)
# view_infos_d["column_references"][column_name]["version"] = (column_references[j]).column_refs.version
#
# obi_view_unmap_file(self._pointer, view_infos_p)
#
# return view_infos_d

0
python/obitools3/obidms/__init__.py
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65
python/obitools3/obidms/_obidms.cfiles
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../../../src/bloom.h
../../../src/bloom.c
../../../src/char_str_indexer.h
../../../src/char_str_indexer.c
../../../src/crc64.h
../../../src/crc64.c
../../../src/dna_seq_indexer.h
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
../../../src/obiblob_indexer.c
../../../src/obiblob.h
../../../src/obiblob.c
../../../src/obidebug.h
../../../src/obidms_taxonomy.h
../../../src/obidms_taxonomy.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/obidmscolumn_blob.c
../../../src/obidmscolumn_blob.h
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn_qual.h
../../../src/obidmscolumn_qual.c
../../../src/obidmscolumn_seq.c
../../../src/obidmscolumn_seq.h
../../../src/obidmscolumn_str.c
../../../src/obidmscolumn_str.h
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/obilittlebigman.h
../../../src/obilittlebigman.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/obiview.h
../../../src/obiview.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/uint8_indexer.h
../../../src/uint8_indexer.c
../../../src/upperband.h
../../../src/upperband.c
../../../src/utils.h
../../../src/utils.c

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python/obitools3/obidms/_obidms.pxd
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#cython: language_level=3
from .capi.obidms cimport OBIDMS_p
from .capi.obidmscolumn cimport OBIDMS_column_p
from .capi.obitypes cimport index_t
from ._obitaxo cimport OBI_Taxonomy
from ._obiview cimport OBIView, OBIView_line_selection
cdef class OBIDMS_column:
cdef str _alias # associated property: alias
cdef OBIDMS_column_p* _pointer
cdef OBIView _view
cpdef close(self)
@staticmethod
cdef object get_subclass_type(OBIDMS_column_p column_p)
cdef class OBIDMS_column_multi_elts(OBIDMS_column):
cpdef set_line(self, index_t line_nb, dict values)
cdef class OBIDMS_column_line:
cdef OBIDMS_column _column
cdef index_t _index
cdef class OBIDMS:
cdef OBIDMS_p _pointer
cpdef close(self)
cpdef OBI_Taxonomy open_taxonomy(self, str taxo_name)

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python/obitools3/obidms/_obidms.pyx
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#cython: language_level=3
from obitools3.utils cimport bytes2str, str2bytes
from .capi.obidms cimport obi_dms, \
obi_close_dms
from .capi.obidmscolumn cimport obi_close_column, \
OBIDMS_column_header_p, \
obi_get_elements_names
from .capi.obiutils cimport obi_format_date
from .capi.obitypes cimport const_char_p, \
OBIType_t, \
OBI_INT, \
OBI_FLOAT, \
OBI_BOOL, \
OBI_CHAR, \
OBI_QUAL, \
OBI_STR, \
OBI_SEQ, \
name_data_type
from .capi.obiview cimport Obiview_p, \
obi_view_get_pointer_on_column_in_view
from ._obidmscolumn_int cimport OBIDMS_column_int, \
OBIDMS_column_multi_elts_int
from ._obidmscolumn_float cimport OBIDMS_column_float, \
OBIDMS_column_multi_elts_float
from ._obidmscolumn_bool cimport OBIDMS_column_bool, \
OBIDMS_column_multi_elts_bool
from ._obidmscolumn_char cimport OBIDMS_column_char, \
OBIDMS_column_multi_elts_char
from ._obidmscolumn_qual cimport OBIDMS_column_qual, \
OBIDMS_column_multi_elts_qual
from ._obidmscolumn_str cimport OBIDMS_column_str, \
OBIDMS_column_multi_elts_str
from ._obidmscolumn_seq cimport OBIDMS_column_seq, \
OBIDMS_column_multi_elts_seq
from libc.stdlib cimport free
cdef class OBIDMS_column :
# Note: should only be initialized through a subclass
def __init__(self, OBIView view, str column_alias):
cdef OBIDMS_column_p column_p
cdef OBIDMS_column_p* column_pp
column_pp = obi_view_get_pointer_on_column_in_view(view._pointer, str2bytes(column_alias))
column_p = column_pp[0] # TODO ugly cython dereferencing but can't find better
# Fill structure
self._alias = column_alias
self._pointer = column_pp
self._view = view
def __setitem__(self, index_t line_nb, object value):
self.set_line(line_nb, value)
def __getitem__(self, index_t line_nb):
return self.get_line(line_nb)
def __len__(self): # TODO discuss
return self._view.line_count
def __sizeof__(self):
return ((self._pointer)[0].header.header_size + (self._pointer)[0].header.data_size)
def __iter__(self): # TODO discuss
# Declarations
cdef index_t line_nb
# Yield each line
for line_nb in range(self._view.line_count):
yield self.get_line(line_nb)
def __str__(self) :
cdef str to_print
to_print = ''
for line in self :
to_print = to_print + str(line) + "\n"
return to_print
def __repr__(self) :
return (self._alias + ", original name: " + self.original_name + ", version " + str(self.version) + ", data type: " + self.data_type)
cpdef close(self):
if obi_close_column((self._pointer)[0]) < 0 :
raise Exception("Problem closing a column")
# Column alias property getter and setter
@property
def alias(self):
return self._alias
@alias.setter
def alias(self, new_alias): # @DuplicatedSignature
self._view.change_column_alias(self._alias, new_alias)
# elements_names property getter
@property
def elements_names(self):
cdef char* elts_names_b
cdef str elts_names
elts_names_b = obi_get_elements_names((self._pointer)[0])
elts_names = bytes2str(elts_names_b)
free(<char*>elts_names_b)
return elts_names.split(';')
# nb_elements_per_line property getter
@property
def nb_elements_per_line(self):
return ((self._pointer)[0].header).nb_elements_per_line
# data_type property getter
@property
def data_type(self):
return bytes2str(name_data_type(((self._pointer)[0].header).returned_data_type))
# original_name property getter
@property
def original_name(self):
return bytes2str(((self._pointer)[0].header).name)
# version property getter
@property
def version(self):
return ((self._pointer)[0].header).version
# comments property getter
@property
def comments(self):
return bytes2str((self._pointer)[0].header.comments)
# creation_date property getter
@property
def creation_date(self):
return bytes2str(obi_format_date((self._pointer)[0].header.creation_date))
@staticmethod
cdef object get_subclass_type(OBIDMS_column_p column_p) :
cdef object subclass
cdef OBIDMS_column_header_p header
cdef OBIType_t col_type
cdef bint col_writable
cdef bint col_one_element_per_line
header = column_p.header
col_type = header.returned_data_type
col_writable = column_p.writable
col_one_element_per_line = ((header.nb_elements_per_line) == 1)
if col_type == OBI_INT :
if col_one_element_per_line :
subclass = OBIDMS_column_int
else :
subclass = OBIDMS_column_multi_elts_int
elif col_type == OBI_FLOAT :
if col_one_element_per_line :
subclass = OBIDMS_column_float
else :
subclass = OBIDMS_column_multi_elts_float
elif col_type == OBI_BOOL :
if col_one_element_per_line :
subclass = OBIDMS_column_bool
else :
subclass = OBIDMS_column_multi_elts_bool
elif col_type == OBI_CHAR :
if col_one_element_per_line :
subclass = OBIDMS_column_char
else :
subclass = OBIDMS_column_multi_elts_char
elif col_type == OBI_QUAL :
if col_one_element_per_line :
subclass = OBIDMS_column_qual
else :
subclass = OBIDMS_column_multi_elts_qual
elif col_type == OBI_STR :
if col_one_element_per_line :
subclass = OBIDMS_column_str
else :
subclass = OBIDMS_column_multi_elts_str
elif col_type == OBI_SEQ :
if col_one_element_per_line :
subclass = OBIDMS_column_seq
else :
subclass = OBIDMS_column_multi_elts_seq
else :
raise Exception("Problem with the data type")
return subclass
######################################################################################################
cdef class OBIDMS_column_multi_elts(OBIDMS_column) :
def __getitem__(self, index_t line_nb):
return OBIDMS_column_line(self, line_nb)
cpdef set_line(self, index_t line_nb, dict values):
for element_name in values :
self.set_item(line_nb, element_name, values[element_name])
######################################################################################################
cdef class OBIDMS_column_line :
def __init__(self, OBIDMS_column column, index_t line_nb) :
self._index = line_nb
self._column = column
def __getitem__(self, str element_name) :
return self._column.get_item(self._index, element_name)
def __setitem__(self, str element_name, object value):
self._column.set_item(self._index, element_name, value)
def __contains__(self, str element_name):
return (element_name in self._column.elements_names)
def __repr__(self) :
return str(self._column.get_line(self._index))
######################################################################################################
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._pointer = obi_dms(<const_char_p> dms_name_b)
if self._pointer == NULL :
raise Exception("Failed opening or creating an OBIDMS")
# name property getter
@property
def name(self):
return bytes2str(self._pointer.dms_name)
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)

65
python/obitools3/obidms/_obidmscolumn_bool.cfiles
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@ -1,65 +0,0 @@
../../../src/bloom.h
../../../src/bloom.c
../../../src/char_str_indexer.h
../../../src/char_str_indexer.c
../../../src/crc64.h
../../../src/crc64.c
../../../src/dna_seq_indexer.h
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
../../../src/obiblob_indexer.c
../../../src/obiblob.h
../../../src/obiblob.c
../../../src/obidebug.h
../../../src/obidms_taxonomy.h
../../../src/obidms_taxonomy.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/obidmscolumn_blob.c
../../../src/obidmscolumn_blob.h
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn_qual.h
../../../src/obidmscolumn_qual.c
../../../src/obidmscolumn_seq.c
../../../src/obidmscolumn_seq.h
../../../src/obidmscolumn_str.c
../../../src/obidmscolumn_str.h
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/obilittlebigman.h
../../../src/obilittlebigman.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/obiview.h
../../../src/obiview.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/uint8_indexer.h
../../../src/uint8_indexer.c
../../../src/upperband.h
../../../src/upperband.c
../../../src/utils.h
../../../src/utils.c

14
python/obitools3/obidms/_obidmscolumn_bool.pxd
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@ -1,14 +0,0 @@
#cython: language_level=3
from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts
cdef class OBIDMS_column_bool(OBIDMS_column):
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name)
cpdef object get_line(self, index_t line_nb)
cpdef set_item(self, index_t line_nb, str element_name, object value)

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python/obitools3/obidms/_obidmscolumn_bool.pyx
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@ -1,78 +0,0 @@
#cython: language_level=3
from .capi.obiview cimport obi_get_bool_with_elt_name_and_col_p_in_view, \
obi_get_bool_with_elt_idx_and_col_p_in_view, \
obi_set_bool_with_elt_name_and_col_p_in_view, \
obi_set_bool_with_elt_idx_and_col_p_in_view
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIBool_NA, obibool_t
from obitools3.utils cimport str2bytes
from cpython.bool cimport PyBool_FromLong
cdef class OBIDMS_column_bool(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef obibool_t value
cdef object result
value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIBool_NA :
result = None
else :
result = PyBool_FromLong(value)
return result
cpdef set_line(self, index_t line_nb, object value):
if value is None :
value = OBIBool_NA
if obi_set_bool_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, <obibool_t> value) < 0:
raise Exception("Problem setting a value in a column")
cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef obibool_t value
cdef object result
value = obi_get_bool_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIBool_NA :
result = None
else :
result = PyBool_FromLong(value)
return result
cpdef object get_line(self, index_t line_nb) :
cdef obibool_t value
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIBool_NA :
value_in_result = None
else :
value_in_result = PyBool_FromLong(value)
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, str element_name, object value):
if value is None :
value = OBIBool_NA
if obi_set_bool_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), <obibool_t> value) < 0:
raise Exception("Problem setting a value in a column")

65
python/obitools3/obidms/_obidmscolumn_char.cfiles
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@ -1,65 +0,0 @@
../../../src/bloom.h
../../../src/bloom.c
../../../src/char_str_indexer.h
../../../src/char_str_indexer.c
../../../src/crc64.h
../../../src/crc64.c
../../../src/dna_seq_indexer.h
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
../../../src/obiblob_indexer.c
../../../src/obiblob.h
../../../src/obiblob.c
../../../src/obidebug.h
../../../src/obidms_taxonomy.h
../../../src/obidms_taxonomy.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/obidmscolumn_blob.c
../../../src/obidmscolumn_blob.h
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn_qual.h
../../../src/obidmscolumn_qual.c
../../../src/obidmscolumn_seq.c
../../../src/obidmscolumn_seq.h
../../../src/obidmscolumn_str.c
../../../src/obidmscolumn_str.h
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/obilittlebigman.h
../../../src/obilittlebigman.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/obiview.h
../../../src/obiview.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/uint8_indexer.h
../../../src/uint8_indexer.c
../../../src/upperband.h
../../../src/upperband.c
../../../src/utils.h
../../../src/utils.c

14
python/obitools3/obidms/_obidmscolumn_char.pxd
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@ -1,14 +0,0 @@
#cython: language_level=3
from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts
cdef class OBIDMS_column_char(OBIDMS_column):
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name)
cpdef object get_line(self, index_t line_nb)
cpdef set_item(self, index_t line_nb, str element_name, object value)

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python/obitools3/obidms/_obidmscolumn_char.pyx
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@ -1,76 +0,0 @@
#cython: language_level=3
from .capi.obiview cimport obi_get_char_with_elt_name_and_col_p_in_view, \
obi_get_char_with_elt_idx_and_col_p_in_view, \
obi_set_char_with_elt_name_and_col_p_in_view, \
obi_set_char_with_elt_idx_and_col_p_in_view
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIChar_NA, obichar_t
from obitools3.utils cimport str2bytes, bytes2str
cdef class OBIDMS_column_char(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef obichar_t value
cdef object result
value = obi_get_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIChar_NA :
result = None
else :
result = bytes2str(value)
return result
cpdef set_line(self, index_t line_nb, object value):
if value is None :
value = OBIChar_NA
if obi_set_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, str2bytes(value)[0]) < 0:
raise Exception("Problem setting a value in a column")
cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef obichar_t value
cdef object result
value = obi_get_char_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIChar_NA :
result = None
else :
result = bytes2str(value)
return result
cpdef object get_line(self, index_t line_nb) :
cdef obichar_t value
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIChar_NA :
value_in_result = None
else :
value_in_result = bytes2str(value)
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, str element_name, object value):
if value is None :
value = OBIChar_NA
if obi_set_char_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)[0]) < 0:
raise Exception("Problem setting a value in a column")

65
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@ -1,65 +0,0 @@
../../../src/bloom.h
../../../src/bloom.c
../../../src/char_str_indexer.h
../../../src/char_str_indexer.c
../../../src/crc64.h
../../../src/crc64.c
../../../src/dna_seq_indexer.h
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
../../../src/obiblob_indexer.c
../../../src/obiblob.h
../../../src/obiblob.c
../../../src/obidebug.h
../../../src/obidms_taxonomy.h
../../../src/obidms_taxonomy.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/obidmscolumn_blob.c
../../../src/obidmscolumn_blob.h
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn_qual.h
../../../src/obidmscolumn_qual.c
../../../src/obidmscolumn_seq.c
../../../src/obidmscolumn_seq.h
../../../src/obidmscolumn_str.c
../../../src/obidmscolumn_str.h
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/obilittlebigman.h
../../../src/obilittlebigman.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/obiview.h
../../../src/obiview.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/uint8_indexer.h
../../../src/uint8_indexer.c
../../../src/upperband.h
../../../src/upperband.c
../../../src/utils.h
../../../src/utils.c

14
python/obitools3/obidms/_obidmscolumn_float.pxd
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@ -1,14 +0,0 @@
#cython: language_level=3
from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts
cdef class OBIDMS_column_float(OBIDMS_column):
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name)
cpdef object get_line(self, index_t line_nb)
cpdef set_item(self, index_t line_nb, str element_name, object value)

76
python/obitools3/obidms/_obidmscolumn_float.pyx
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@ -1,76 +0,0 @@
#cython: language_level=3
from .capi.obiview cimport obi_get_float_with_elt_name_and_col_p_in_view, \
obi_get_float_with_elt_idx_and_col_p_in_view, \
obi_set_float_with_elt_name_and_col_p_in_view, \
obi_set_float_with_elt_idx_and_col_p_in_view
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIFloat_NA, obifloat_t
from obitools3.utils cimport str2bytes
cdef class OBIDMS_column_float(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef obifloat_t value
cdef object result
value = obi_get_float_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIFloat_NA :
result = None
else :
result = <double> value
return result
cpdef set_line(self, index_t line_nb, object value):
if value is None :
value = OBIFloat_NA
if obi_set_float_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, <obifloat_t> value) < 0:
raise Exception("Problem setting a value in a column")
cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef obifloat_t value
cdef object result
value = obi_get_float_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIFloat_NA :
result = None
else :
result = <double> value
return result
cpdef object get_line(self, index_t line_nb) :
cdef obifloat_t value
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_float_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIFloat_NA :
value_in_result = None
else :
value_in_result = <double> value
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, str element_name, object value):
if value is None :
value = OBIFloat_NA
if obi_set_float_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), <obifloat_t> value) < 0:
raise Exception("Problem setting a value in a column")

65
python/obitools3/obidms/_obidmscolumn_int.cfiles
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@ -1,65 +0,0 @@
../../../src/bloom.h
../../../src/bloom.c
../../../src/char_str_indexer.h
../../../src/char_str_indexer.c
../../../src/crc64.h
../../../src/crc64.c
../../../src/dna_seq_indexer.h
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
../../../src/obiblob_indexer.c
../../../src/obiblob.h
../../../src/obiblob.c
../../../src/obidebug.h
../../../src/obidms_taxonomy.h
../../../src/obidms_taxonomy.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/obidmscolumn_blob.c
../../../src/obidmscolumn_blob.h
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn_qual.h
../../../src/obidmscolumn_qual.c
../../../src/obidmscolumn_seq.c
../../../src/obidmscolumn_seq.h
../../../src/obidmscolumn_str.c
../../../src/obidmscolumn_str.h
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/obilittlebigman.h
../../../src/obilittlebigman.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/obiview.h
../../../src/obiview.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/uint8_indexer.h
../../../src/uint8_indexer.c
../../../src/upperband.h
../../../src/upperband.c
../../../src/utils.h
../../../src/utils.c

14
python/obitools3/obidms/_obidmscolumn_int.pxd
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@ -1,14 +0,0 @@
#cython: language_level=3
from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts
cdef class OBIDMS_column_int(OBIDMS_column):
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name)
cpdef object get_line(self, index_t line_nb)
cpdef set_item(self, index_t line_nb, str element_name, object value)

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python/obitools3/obidms/_obidmscolumn_int.pyx
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@ -1,78 +0,0 @@
#cython: language_level=3
from .capi.obiview cimport obi_get_int_with_elt_name_and_col_p_in_view, \
obi_get_int_with_elt_idx_and_col_p_in_view, \
obi_set_int_with_elt_name_and_col_p_in_view, \
obi_set_int_with_elt_idx_and_col_p_in_view
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIInt_NA, obiint_t
from obitools3.utils cimport str2bytes
from cpython.int cimport PyInt_FromLong
cdef class OBIDMS_column_int(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef obiint_t value
cdef object result
value = obi_get_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIInt_NA :
result = None
else :
result = PyInt_FromLong(value)
return result
cpdef set_line(self, index_t line_nb, object value):
if value is None :
value = OBIInt_NA
if obi_set_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, <obiint_t> value) < 0:
raise Exception("Problem setting a value in a column")
cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef obiint_t value
cdef object result
value = obi_get_int_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIInt_NA :
result = None
else :
result = PyInt_FromLong(value)
return result
cpdef object get_line(self, index_t line_nb) :
cdef obiint_t value
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIInt_NA :
value_in_result = None
else :
value_in_result = PyInt_FromLong(value)
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None # TODO discuss
return result
cpdef set_item(self, index_t line_nb, str element_name, object value):
if value is None :
value = OBIInt_NA
if obi_set_int_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), <obiint_t> value) < 0:
raise Exception("Problem setting a value in a column")

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python/obitools3/obidms/_obidmscolumn_qual.cfiles
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@ -1,65 +0,0 @@
../../../src/bloom.h
../../../src/bloom.c
../../../src/char_str_indexer.h
../../../src/char_str_indexer.c
../../../src/crc64.h
../../../src/crc64.c
../../../src/dna_seq_indexer.h
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
../../../src/obiblob_indexer.c
../../../src/obiblob.h
../../../src/obiblob.c
../../../src/obidebug.h
../../../src/obidms_taxonomy.h
../../../src/obidms_taxonomy.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/obidmscolumn_blob.c
../../../src/obidmscolumn_blob.h
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn_qual.h
../../../src/obidmscolumn_qual.c
../../../src/obidmscolumn_seq.c
../../../src/obidmscolumn_seq.h
../../../src/obidmscolumn_str.c
../../../src/obidmscolumn_str.h
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/obilittlebigman.h
../../../src/obilittlebigman.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/obiview.h
../../../src/obiview.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/uint8_indexer.h
../../../src/uint8_indexer.c
../../../src/upperband.h
../../../src/upperband.c
../../../src/utils.h
../../../src/utils.c

20
python/obitools3/obidms/_obidmscolumn_qual.pxd
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@ -1,20 +0,0 @@
#cython: language_level=3
from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS_column , OBIDMS_column_multi_elts
cdef class OBIDMS_column_qual(OBIDMS_column):
cpdef object get_line(self, index_t line_nb)
cpdef object get_str_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cpdef set_str_line(self, index_t line_nb, object value)
cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name)
cpdef object get_str_item(self, index_t line_nb, str element_name)
cpdef object get_line(self, index_t line_nb)
cpdef object get_str_line(self, index_t line_nb)
cpdef set_item(self, index_t line_nb, str element_name, object value)
cpdef set_str_item(self, index_t line_nb, str element_name, object value)

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python/obitools3/obidms/_obidmscolumn_qual.pyx
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@ -1,189 +0,0 @@
#cython: language_level=3
from .capi.obiview cimport obi_get_qual_char_with_elt_name_and_col_p_in_view, \
obi_get_qual_char_with_elt_idx_and_col_p_in_view, \
obi_set_qual_char_with_elt_name_and_col_p_in_view, \
obi_set_qual_char_with_elt_idx_and_col_p_in_view, \
obi_get_qual_int_with_elt_name_and_col_p_in_view, \
obi_get_qual_int_with_elt_idx_and_col_p_in_view, \
obi_set_qual_int_with_elt_name_and_col_p_in_view, \
obi_set_qual_int_with_elt_idx_and_col_p_in_view
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIQual_char_NA, OBIQual_int_NA, const_char_p
from ._obidms cimport OBIView
from obitools3.utils cimport str2bytes, bytes2str
from libc.stdlib cimport free
from libc.string cimport strcmp
from libc.stdint cimport uint8_t
from libc.stdlib cimport malloc
cdef class OBIDMS_column_qual(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef const uint8_t* value
cdef int value_length
cdef object result
cdef int i
value = obi_get_qual_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, &value_length)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIQual_int_NA :
result = None
else :
result = []
for i in range(value_length) :
result.append(<int>value[i])
return result
cpdef object get_str_line(self, index_t line_nb):
cdef char* value
cdef object result
cdef int i
value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIQual_char_NA :
result = None
else :
result = bytes2str(value)
free(value)
return result
cpdef set_line(self, index_t line_nb, object value):
cdef uint8_t* value_b
cdef int value_length
if value is None :
if obi_set_qual_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, OBIQual_int_NA, 0) < 0:
raise Exception("Problem setting a value in a column")
else :
value_length = len(value)
value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t))
for i in range(value_length) :
value_b[i] = <uint8_t>value[i]
if obi_set_qual_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, value_b, value_length) < 0:
raise Exception("Problem setting a value in a column")
free(value_b)
cpdef set_str_line(self, index_t line_nb, object value):
cdef bytes value_b
if value is None :
if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, OBIQual_char_NA) < 0:
raise Exception("Problem setting a value in a column")
else :
if type(value) == str:
value_b = str2bytes(value)
else :
value_b = value
if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, value_b) < 0:
raise Exception("Problem setting a value in a column")
cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef const uint8_t* value
cdef int value_length
cdef object result
cdef int i
value = obi_get_qual_int_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), &value_length)
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIQual_int_NA :
result = None
else :
result = []
for i in range(value_length) :
result.append(<int>value[i])
return result
cpdef object get_str_item(self, index_t line_nb, str element_name):
cdef char* value
cdef object result
value = obi_get_qual_char_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIQual_char_NA :
result = None
else :
result = bytes2str(value)
free(value)
return result
cpdef object get_line(self, index_t line_nb) :
cdef const uint8_t* value
cdef int value_length
cdef object value_in_result
cdef dict result
cdef index_t i
cdef int j
cdef bint all_NA
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_qual_int_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i, &value_length)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIQual_int_NA :
value_in_result = None
else :
value_in_result = []
for j in range(value_length) :
value_in_result.append(<int>value[j])
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef object get_str_line(self, index_t line_nb) :
cdef char* value
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIQual_char_NA :
value_in_result = None
else :
value_in_result = bytes2str(value)
free(value)
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, str element_name, object value):
cdef uint8_t* value_b
cdef int value_length
if value is None :
if obi_set_qual_int_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), OBIQual_int_NA, 0) < 0:
raise Exception("Problem setting a value in a column")
else :
value_length = len(value)
value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t))
for i in range(value_length) :
value_b[i] = <uint8_t>value[i]
if obi_set_qual_int_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), value_b, value_length) < 0:
raise Exception("Problem setting a value in a column")
free(value_b)
cpdef set_str_item(self, index_t line_nb, str element_name, object value):
if value is None :
if obi_set_qual_char_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), OBIQual_char_NA) < 0:
raise Exception("Problem setting a value in a column")
else :
if obi_set_qual_char_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)) < 0:
raise Exception("Problem setting a value in a column")

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@ -1,65 +0,0 @@
../../../src/bloom.h
../../../src/bloom.c
../../../src/char_str_indexer.h
../../../src/char_str_indexer.c
../../../src/crc64.h
../../../src/crc64.c
../../../src/dna_seq_indexer.h
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
../../../src/obiblob_indexer.c
../../../src/obiblob.h
../../../src/obiblob.c
../../../src/obidebug.h
../../../src/obidms_taxonomy.h
../../../src/obidms_taxonomy.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/obidmscolumn_blob.c
../../../src/obidmscolumn_blob.h
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn_qual.h
../../../src/obidmscolumn_qual.c
../../../src/obidmscolumn_seq.c
../../../src/obidmscolumn_seq.h
../../../src/obidmscolumn_str.c
../../../src/obidmscolumn_str.h
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/obilittlebigman.h
../../../src/obilittlebigman.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/obiview.h
../../../src/obiview.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/uint8_indexer.h
../../../src/uint8_indexer.c
../../../src/upperband.h
../../../src/upperband.c
../../../src/utils.h
../../../src/utils.c

15
python/obitools3/obidms/_obidmscolumn_seq.pxd
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@ -1,15 +0,0 @@
#cython: language_level=3
from .capi.obitypes cimport index_t
from ._obidms cimport OBIView, OBIDMS_column, OBIDMS_column_multi_elts
cdef class OBIDMS_column_seq(OBIDMS_column):
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name)
cpdef object get_line(self, index_t line_nb)
cpdef set_item(self, index_t line_nb, str element_name, object value)

108
python/obitools3/obidms/_obidmscolumn_seq.pyx
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@ -1,108 +0,0 @@
#cython: language_level=3
from .capi.obiview cimport obi_get_seq_with_elt_name_and_col_p_in_view, \
obi_get_seq_with_elt_idx_and_col_p_in_view, \
obi_set_seq_with_elt_name_and_col_p_in_view, \
obi_set_seq_with_elt_idx_and_col_p_in_view
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBISeq_NA, const_char_p
from ._obidms cimport OBIView
from obitools3.utils cimport str2bytes, bytes2str
from libc.stdlib cimport free
cdef class OBIDMS_column_seq(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef char* value
cdef object result
value = obi_get_seq_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBISeq_NA :
result = None
else :
try:
result = <bytes> value
finally:
free(value)
return result
cpdef set_line(self, index_t line_nb, object value):
cdef bytes value_b
if value is None :
value_b = OBISeq_NA
elif isinstance(value, bytes) :
value_b = value
elif isinstance(value, str) :
value_b = str2bytes(value)
else:
raise TypeError('Sequence value must be of type Bytes, Str or None')
if obi_set_seq_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, value_b) < 0:
raise Exception("Problem setting a value in a column")
cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef char* value
cdef object result
value = obi_get_seq_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBISeq_NA :
result = None
else :
try:
result = <bytes> value
finally:
free(value)
return result
cpdef object get_line(self, index_t line_nb) :
cdef char* value
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_seq_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBISeq_NA :
value_in_result = None
else :
try:
value_in_result = <bytes> value
finally:
free(value)
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, str element_name, object value):
cdef bytes value_b
if value is None :
value_b = OBISeq_NA
elif isinstance(value, bytes) :
value_b = value
elif isinstance(value, str) :
value_b = str2bytes(value)
else:
raise TypeError('Sequence value must be of type Bytes, Str or None')
if obi_set_seq_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
raise Exception("Problem setting a value in a column")

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@ -1,65 +0,0 @@
../../../src/bloom.h
../../../src/bloom.c
../../../src/char_str_indexer.h
../../../src/char_str_indexer.c
../../../src/crc64.h
../../../src/crc64.c
../../../src/dna_seq_indexer.h
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
../../../src/obiblob_indexer.c
../../../src/obiblob.h
../../../src/obiblob.c
../../../src/obidebug.h
../../../src/obidms_taxonomy.h
../../../src/obidms_taxonomy.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/obidmscolumn_blob.c
../../../src/obidmscolumn_blob.h
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn_qual.h
../../../src/obidmscolumn_qual.c
../../../src/obidmscolumn_seq.c
../../../src/obidmscolumn_seq.h
../../../src/obidmscolumn_str.c
../../../src/obidmscolumn_str.h
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/obilittlebigman.h
../../../src/obilittlebigman.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/obiview.h
../../../src/obiview.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/uint8_indexer.h
../../../src/uint8_indexer.c
../../../src/upperband.h
../../../src/upperband.c
../../../src/utils.h
../../../src/utils.c

14
python/obitools3/obidms/_obidmscolumn_str.pxd
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@ -1,14 +0,0 @@
#cython: language_level=3
from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts
cdef class OBIDMS_column_str(OBIDMS_column):
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name)
cpdef object get_line(self, index_t line_nb)
cpdef set_item(self, index_t line_nb, str element_name, object value)

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python/obitools3/obidms/_obidmscolumn_str.pyx
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@ -1,84 +0,0 @@
#cython: language_level=3
from .capi.obiview cimport obi_get_str_with_elt_name_and_col_p_in_view, \
obi_get_str_with_elt_idx_and_col_p_in_view, \
obi_set_str_with_elt_name_and_col_p_in_view, \
obi_set_str_with_elt_idx_and_col_p_in_view
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIStr_NA, const_char_p
from obitools3.utils cimport str2bytes, bytes2str
cdef class OBIDMS_column_str(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef const_char_p value
cdef object result
value = obi_get_str_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIStr_NA :
result = None
else :
result = bytes2str(value)
# NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file.
return result
cpdef set_line(self, index_t line_nb, object value):
if value is None :
if obi_set_str_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, OBIStr_NA) < 0:
raise Exception("Problem setting a value in a column")
else :
if obi_set_str_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, str2bytes(value)) < 0:
raise Exception("Problem setting a value in a column")
cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef const_char_p value
cdef object result
value = obi_get_str_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIStr_NA :
result = None
else :
result = bytes2str(value)
# NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file.
return result
cpdef object get_line(self, index_t line_nb) :
cdef const_char_p value # @DuplicatedSignature
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_get_str_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIStr_NA :
value_in_result = None
else :
value_in_result = bytes2str(value)
# NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file.
result[self.elements_names[i]] = value_in_result
if all_NA and (value_in_result is not None) :
all_NA = False
if all_NA :
result = None
return result
cpdef set_item(self, index_t line_nb, str element_name, object value):
cdef bytes value_b
if value is None :
value_b = OBIStr_NA
else :
value_b = str2bytes(value)
if obi_set_str_with_elt_name_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
raise Exception("Problem setting a value in a column")

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@ -1,65 +0,0 @@
../../../src/bloom.h
../../../src/bloom.c
../../../src/char_str_indexer.h
../../../src/char_str_indexer.c
../../../src/crc64.h
../../../src/crc64.c
../../../src/dna_seq_indexer.h
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
../../../src/obiblob_indexer.c
../../../src/obiblob.h
../../../src/obiblob.c
../../../src/obidebug.h
../../../src/obidms_taxonomy.h
../../../src/obidms_taxonomy.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/obidmscolumn_blob.c
../../../src/obidmscolumn_blob.h
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn_qual.h
../../../src/obidmscolumn_qual.c
../../../src/obidmscolumn_seq.c
../../../src/obidmscolumn_seq.h
../../../src/obidmscolumn_str.c
../../../src/obidmscolumn_str.h
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/obilittlebigman.h
../../../src/obilittlebigman.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/obiview.h
../../../src/obiview.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/uint8_indexer.h
../../../src/uint8_indexer.c
../../../src/upperband.h
../../../src/upperband.c
../../../src/utils.h
../../../src/utils.c

21
python/obitools3/obidms/_obiseq.pxd
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@ -1,21 +0,0 @@
#cython: language_level=3
from ._obiview cimport OBIView_line
cdef class OBI_Seq(dict) :
cdef str _id
cdef object _seq
cdef str _definition
cdef class OBI_Nuc_Seq(OBI_Seq) :
cdef object _quality
cpdef object get_str_quality(self)
#cpdef object reverse_complement(self)
cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
cpdef object get_str_quality(self)
#cpdef object reverse_complement(self)

187
python/obitools3/obidms/_obiseq.pyx
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@ -1,187 +0,0 @@
#cython: language_level=3
from obitools3.utils cimport bytes2str, str2bytes
from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
ID_COLUMN, \
DEFINITION_COLUMN, \
QUALITY_COLUMN
cdef str __str__ID_COLUMN__ = bytes2str(ID_COLUMN)
cdef str __str__DEFINITION_COLUMN__ = bytes2str(DEFINITION_COLUMN)
cdef str __str__QUALITY_COLUMN__ = bytes2str(QUALITY_COLUMN)
cdef str __str__NUC_SEQUENCE_COLUMN__ = bytes2str(NUC_SEQUENCE_COLUMN)
cdef class OBI_Seq(dict) :
def __init__(self, str id,
object seq,
str definition=None,
dict tags=None) :
if tags is not None:
self.update(tags)
self._id = id
self._seq = seq
if definition is not None :
self._definition = definition
else:
self._definition = None
def __getitem__(self,str key):
if key == __str__ID_COLUMN__:
return self._id
elif key == __str__DEFINITION_COLUMN__:
return self._definition
else:
return dict.__getitem__(self,key)
def __setitem__(self,str key,object value):
if key == __str__ID_COLUMN__:
self._id=value
elif key == __str__DEFINITION_COLUMN__:
self._definition=value
else:
dict.__setitem__(self,key,value)
# sequence id property getter and setter
@property
def id(self): # @ReservedAssignment
return self._id
@id.setter
def id(self, str new_id): # @ReservedAssignment @DuplicatedSignature
self._id = new_id
# sequence property getter and setter
@property
def seq(self):
return self._seq
@seq.setter
def seq(self, object new_seq): # @DuplicatedSignature
self._seq = new_seq
# self["SEQ"] = new_seq # TODO discuss
# sequence definition property getter and setter
@property
def definition(self):
return self._definition
@definition.setter
def definition(self, object new_definition): # @DuplicatedSignature
self._definition = new_definition
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):
if key == __str__NUC_SEQUENCE_COLUMN__:
return self._seq
elif key == __str__QUALITY_COLUMN__:
return self._quality
else:
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
return self._quality
# nuc sequence property getter and setter
@property
def seq(self):
return self._seq
@seq.setter
def seq(self, object new_seq): # @DuplicatedSignature
self._seq = new_seq
# self[bytes2str(NUC_SEQUENCE_COLUMN)] = new_seq
# sequence quality property getter and setter
@property
def quality(self):
return self._quality
@quality.setter
def quality(self, object new_quality): # @DuplicatedSignature
self._quality = new_quality
# self[bytes2str(QUALITY_COLUMN)] = new_quality
# cpdef str reverse_complement(self) : TODO in C ?
# pass
cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
# TODO store the str version of column name macros?
# sequence id property getter and setter
@property
def id(self): # @ReservedAssignment @DuplicatedSignature
return self[__str__ID_COLUMN__]
@id.setter
def id(self, str new_id): # @ReservedAssignment @DuplicatedSignature
self[__str__ID_COLUMN__] = new_id
# sequence definition property getter and setter
@property
def definition(self):
return self[__str__DEFINITION_COLUMN__]
@definition.setter
def definition(self, str new_def): # @DuplicatedSignature
self[__str__DEFINITION_COLUMN__] = new_def
# nuc_seq property getter and setter
@property
def nuc_seq(self):
return self[__str__NUC_SEQUENCE_COLUMN__]
@nuc_seq.setter
def nuc_seq(self, object new_seq): # @DuplicatedSignature
self[__str__NUC_SEQUENCE_COLUMN__] = new_seq
# quality property getter and setter
@property
def quality(self):
return self[__str__QUALITY_COLUMN__]
@quality.setter
def quality(self, object new_qual): # @DuplicatedSignature
if (type(new_qual) == list) or (new_qual is None) : # TODO check that quality column exists
self[__str__QUALITY_COLUMN__] = new_qual
else : # Quality is in str form
(((self._view).columns)[__str__QUALITY_COLUMN__]).set_str_line(self._index, new_qual)
cpdef object get_str_quality(self) : # TODO not ideal. Make quality_int and quality_str properties
return ((self._view).columns)[__str__QUALITY_COLUMN__].get_str_line(self._index)
# cpdef str reverse_complement(self) : TODO in C ?
# pass
# TODO static method to import OBI_Nuc_Seq to OBI_Nuc_Seq_Stored ?

65
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@ -1,65 +0,0 @@
../../../src/bloom.h
../../../src/bloom.c
../../../src/char_str_indexer.h
../../../src/char_str_indexer.c
../../../src/crc64.h
../../../src/crc64.c
../../../src/dna_seq_indexer.h
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
../../../src/obiblob_indexer.c
../../../src/obiblob.h
../../../src/obiblob.c
../../../src/obidebug.h
../../../src/obidms_taxonomy.h
../../../src/obidms_taxonomy.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/obidmscolumn_blob.c
../../../src/obidmscolumn_blob.h
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn_qual.h
../../../src/obidmscolumn_qual.c
../../../src/obidmscolumn_seq.c
../../../src/obidmscolumn_seq.h
../../../src/obidmscolumn_str.c
../../../src/obidmscolumn_str.h
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/obilittlebigman.h
../../../src/obilittlebigman.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/obiview.h
../../../src/obiview.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/uint8_indexer.h
../../../src/uint8_indexer.c
../../../src/upperband.h
../../../src/upperband.c
../../../src/utils.h
../../../src/utils.c

21
python/obitools3/obidms/_obitaxo.pxd
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@ -1,21 +0,0 @@
#cython: language_level=3
from .capi.obitaxonomy cimport ecotx_t, OBIDMS_taxonomy_p
from ._obidms cimport OBIDMS
cdef class OBI_Taxonomy :
cdef str _name
cdef OBIDMS_taxonomy_p _pointer
cdef OBIDMS _dms
cpdef write(self, str prefix)
cpdef int add_taxon(self, str name, str rank_name, int parent_taxid, int min_taxid=*)
cpdef close(self)
cdef class OBI_Taxon :
cdef ecotx_t* _pointer
cdef OBI_Taxonomy _tax

141
python/obitools3/obidms/_obitaxo.pyx
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@ -1,141 +0,0 @@
#cython: language_level=3
from obitools3.utils cimport bytes2str, str2bytes
from .capi.obitaxonomy cimport obi_read_taxonomy, \
obi_read_taxdump, \
obi_write_taxonomy, \
obi_close_taxonomy, \
obi_taxo_get_taxon_with_taxid, \
obi_taxo_add_local_taxon, \
obi_taxo_add_preferred_name_with_taxon, \
ecotx_t
from ._obidms cimport OBIDMS
from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
from logging import raiseExceptions
cdef class OBI_Taxonomy :
# TODO function to import taxonomy?
def __init__(self, OBIDMS dms, str name, bint taxdump=False) :
self._dms = dms
self._name = name
if taxdump :
self._pointer = obi_read_taxdump(str2bytes(name))
else :
self._pointer = obi_read_taxonomy(dms._pointer, str2bytes(name), True) # TODO discuss
# TODO if not found in DMS, try to import?
def __getitem__(self, object ref):
cdef ecotx_t* taxon_p
cdef object taxon_capsule
if type(ref) == int :
taxon_p = obi_taxo_get_taxon_with_taxid(self._pointer, ref)
if taxon_p == NULL :
raise Exception("Taxon not found")
taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
return OBI_Taxon(taxon_capsule, self)
else :
raise Exception("Not implemented")
def __iter__(self):
cdef ecotx_t* taxa
cdef ecotx_t* taxon_p
cdef object taxon_capsule
cdef int t
taxa = self._pointer.taxa.taxon
# Yield each taxid
for t in range(self._pointer.taxa.count):
taxon_p = <ecotx_t*> (taxa+t)
taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
yield OBI_Taxon(taxon_capsule, self)
cpdef write(self, str prefix) :
if obi_write_taxonomy(self._dms._pointer, self._pointer, str2bytes(prefix)) < 0 :
raise Exception("Error writing the taxonomy to binary files")
cpdef int add_taxon(self, str name, str rank_name, int parent_taxid, int min_taxid=10000000) :
cdef int taxid
taxid = obi_taxo_add_local_taxon(self._pointer, str2bytes(name), str2bytes(rank_name), parent_taxid, min_taxid)
if taxid < 0 :
raise Exception("Error adding a new taxon to the taxonomy")
else :
return taxid
cpdef close(self) :
if (obi_close_taxonomy(self._pointer) < 0) :
raise Exception("Error closing the taxonomy")
cdef class OBI_Taxon : # TODO dict subclass?
def __init__(self, object taxon_capsule, OBI_Taxonomy tax) :
self._pointer = <ecotx_t*> PyCapsule_GetPointer(taxon_capsule, NULL)
if self._pointer == NULL :
raise Exception("Error reading a taxon (NULL pointer)")
self._tax = tax
# name property getter
@property
def name(self):
return bytes2str(self._pointer.name)
# taxid property getter
@property
def taxid(self):
return self._pointer.taxid
# rank property getter
@property
def rank(self):
return self._pointer.rank
# farest property getter
@property
def farest(self):
return self._pointer.farest
# parent property getter
@property
def parent(self):
cdef object parent_capsule
parent_capsule = PyCapsule_New(self._pointer.parent, NULL, NULL)
return OBI_Taxon(parent_capsule, self._tax)
# preferred name property getter and setter
@property
def preferred_name(self):
if self._pointer.preferred_name != NULL :
return bytes2str(self._pointer.preferred_name)
@preferred_name.setter
def preferred_name(self, str new_preferred_name) : # @DuplicatedSignature
if (obi_taxo_add_preferred_name_with_taxon(self._tax._pointer, self._pointer, str2bytes(new_preferred_name)) < 0) :
raise Exception("Error adding a new preferred name to a taxon")
def __repr__(self):
d = {}
d['taxid'] = self.taxid
d['name'] = self.name
d['preferred name'] = self.preferred_name
d['parent'] = self.parent.taxid
d['farest'] = self.farest
return str(d)

70
python/obitools3/obidms/_obiview.pxd
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@ -1,70 +0,0 @@
#cython: language_level=3
from ._obidms cimport OBIDMS
from .capi.obiview cimport Obiview_p
from .capi.obitypes cimport obiversion_t, index_t
cdef class OBIView:
cdef Obiview_p _pointer
cdef dict _columns
cdef __init_columns__(self)
cpdef OBIView clone(self,
str view_name,
str comments=*)
@staticmethod
cdef OBIView new(OBIDMS dms,
str view_name,
str comments=*)
@staticmethod
cdef 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 :
cdef index_t _index
cdef OBIView _view
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=*)

426
python/obitools3/obidms/_obiview.pyx
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@ -1,426 +0,0 @@
#cython: language_level=3
from obitools3.utils cimport bytes2str, str2bytes
from .capi.obitypes cimport OBI_INT, \
OBI_FLOAT, \
OBI_BOOL, \
OBI_CHAR, \
OBI_QUAL, \
OBI_STR, \
OBI_SEQ, \
only_ATGC
from .capi.obiview cimport Obiview_p, \
obi_new_view, \
obi_open_view, \
obi_view_delete_column, \
obi_view_add_column, \
obi_view_create_column_alias, \
obi_view_get_column, \
obi_view_get_pointer_on_column_in_view, \
obi_save_and_close_view
from .capi.obidmscolumn cimport OBIDMS_column_p
from ._obidms cimport OBIDMS, \
OBIDMS_column
from libc.stdlib cimport malloc
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__()
return view
@staticmethod
cdef 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__()
return view
@staticmethod
cdef 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__()
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 :
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
cdef bytes value_b
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 or value_type == bytes :
if value_type == str :
value_b = str2bytes(value)
else :
value_b = value
if only_ATGC(value_b) : # 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 __iter__(self):
for column_name in ((self._view)._columns) :
yield column_name
def __contains__(self, str column_name):
return (column_name in self._view._columns)
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 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" %
(idx,
self._view.line_count,
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 len_selection = len(self)
line_selection_p = <index_t*> malloc((len_selection + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array
for i in range(len_selection) :
line_selection_p[i] = self[i]
line_selection_p[len_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__()
return view

29
python/obitools3/obidms/_obiview_nuc_seq.pxd
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@ -1,29 +0,0 @@
#cython: language_level=3
from ._obidms cimport OBIDMS
from ._obiview cimport OBIView, OBIView_line_selection
cdef class OBIView_NUC_SEQS(OBIView):
cpdef OBIView clone(self,
str new_view_name,
str comments=*)
cpdef OBIView_line_selection new_selection(self, list lines=*)
@staticmethod
cdef OBIView new(OBIDMS dms,
str view_name,
str comments=*)
@staticmethod
cdef 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=*)

113
python/obitools3/obidms/_obiview_nuc_seq.pyx
View File

@ -1,113 +0,0 @@
#cython: language_level=3
from .capi.obitypes cimport index_t
from ._obiseq cimport OBI_Nuc_Seq, OBI_Nuc_Seq_Stored
from .capi.obiview cimport obi_new_view_nuc_seqs, \
obi_open_view
from obitools3.utils cimport str2bytes
cdef class OBIView_NUC_SEQS(OBIView):
cpdef OBIView clone(self,
str new_view_name,
str comments=""):
cdef OBIView view = OBIView_NUC_SEQS(987654)
view._pointer = obi_new_view_nuc_seqs(self._pointer.dms,
str2bytes(new_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), new_view_name))
view.__init_columns__()
return view
@staticmethod
cdef 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__()
return view
@staticmethod
cdef 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__()
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) :
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_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_nuc_seqs(self._view._pointer.dms,
str2bytes(view_name),
self._view._pointer,
self.__build_binary_list__(),
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__()
return view

28
python/obitools3/obidms/_obiview_nuc_seq_qual.pxd
View File

@ -1,28 +0,0 @@
#cython: language_level=3
from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS
from ._obiview cimport OBIView
from ._obiview_nuc_seq cimport OBIView_NUC_SEQS, OBIView_NUC_SEQS_line_selection
cdef class OBIView_NUC_SEQS_QUAL(OBIView_NUC_SEQS):
cpdef OBIView clone(self,
str view_name,
str comments=*)
@staticmethod
cdef OBIView new(OBIDMS dms,
str view_name,
str comments=*)
@staticmethod
cdef 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=*)

97
python/obitools3/obidms/_obiview_nuc_seq_qual.pyx
View File

@ -1,97 +0,0 @@
#cython: language_level=3
from .capi.obitypes cimport index_t
from .capi.obiview cimport obi_new_view_nuc_seqs, \
obi_open_view
from obitools3.utils cimport bytes2str, str2bytes
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__()
return view
@staticmethod
cdef 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__()
return view
@staticmethod
cdef 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__()
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_nuc_seqs(self._view._pointer.dms,
str2bytes(view_name),
self._view._pointer,
self.__build_binary_list__(),
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__()
return view

0
python/obitools3/obidms/capi/__init__.py
View File

65
python/obitools3/obidms/capi/obialign.cfiles
View File

@ -1,65 +0,0 @@
../../../../src/bloom.h
../../../../src/bloom.c
../../../../src/char_str_indexer.h
../../../../src/char_str_indexer.c
../../../../src/crc64.h
../../../../src/crc64.c
../../../../src/dna_seq_indexer.h
../../../../src/dna_seq_indexer.c
../../../../src/encode.h
../../../../src/encode.c
../../../../src/hashtable.h
../../../../src/hashtable.c
../../../../src/murmurhash2.h
../../../../src/murmurhash2.c
../../../../src/obi_align.h
../../../../src/obi_align.c
../../../../src/obiavl.h
../../../../src/obiavl.c
../../../../src/obiblob_indexer.h
../../../../src/obiblob_indexer.c
../../../../src/obiblob.h
../../../../src/obiblob.c
../../../../src/obidebug.h
../../../../src/obidms_taxonomy.h
../../../../src/obidms_taxonomy.c
../../../../src/obidms.h
../../../../src/obidms.c
../../../../src/obidmscolumn_blob.c
../../../../src/obidmscolumn_blob.h
../../../../src/obidmscolumn_bool.c
../../../../src/obidmscolumn_bool.h
../../../../src/obidmscolumn_char.c
../../../../src/obidmscolumn_char.h
../../../../src/obidmscolumn_float.c
../../../../src/obidmscolumn_float.h
../../../../src/obidmscolumn_idx.h
../../../../src/obidmscolumn_idx.c
../../../../src/obidmscolumn_int.c
../../../../src/obidmscolumn_int.h
../../../../src/obidmscolumn_qual.h
../../../../src/obidmscolumn_qual.c
../../../../src/obidmscolumn_seq.c
../../../../src/obidmscolumn_seq.h
../../../../src/obidmscolumn_str.c
../../../../src/obidmscolumn_str.h
../../../../src/obidmscolumn.h
../../../../src/obidmscolumn.c
../../../../src/obidmscolumndir.h
../../../../src/obidmscolumndir.c
../../../../src/obierrno.h
../../../../src/obierrno.c
../../../../src/obilittlebigman.h
../../../../src/obilittlebigman.c
../../../../src/obitypes.h
../../../../src/obitypes.c
../../../../src/obiview.h
../../../../src/obiview.c
../../../../src/sse_banded_LCS_alignment.h
../../../../src/sse_banded_LCS_alignment.c
../../../../src/uint8_indexer.h
../../../../src/uint8_indexer.c
../../../../src/upperband.h
../../../../src/upperband.c
../../../../src/utils.h
../../../../src/utils.c

41
python/obitools3/obidms/capi/obialign.pxd
View File

@ -1,41 +0,0 @@
#cython: language_level=3
from obitools3.obidms.capi.obidms cimport OBIDMS_p
from obitools3.obidms.capi.obitypes cimport const_char_p
cdef extern from "obi_align.h" nogil:
int obi_lcs_align_one_column(OBIDMS_p dms,
const_char_p seq_view_name,
const_char_p seq_column_name,
const_char_p seq_elt_name,
const_char_p id_column_name,
const_char_p output_view_name,
const_char_p output_view_comments,
bint print_seq,
bint print_count,
double threshold,
bint normalize,
int reference,
bint similarity_mode,
int thread_count)
int obi_lcs_align_two_columns(OBIDMS_p dms,
const_char_p seq1_view_name,
const_char_p seq2_view_name,
const_char_p seq1_column_name,
const_char_p seq2_column_name,
const_char_p seq1_elt_name,
const_char_p seq2_elt_name,
const_char_p id1_column_name,
const_char_p id2_column_name,
const_char_p output_view_name,
const_char_p output_view_comments,
bint print_seq,
bint print_count,
double threshold,
bint normalize,
int reference,
bint similarity_mode);

65
python/obitools3/obidms/capi/obidms.cfiles
View File

@ -1,65 +0,0 @@
../../../../src/bloom.h
../../../../src/bloom.c
../../../../src/char_str_indexer.h
../../../../src/char_str_indexer.c
../../../../src/crc64.h
../../../../src/crc64.c
../../../../src/dna_seq_indexer.h
../../../../src/dna_seq_indexer.c
../../../../src/encode.h
../../../../src/encode.c
../../../../src/hashtable.h
../../../../src/hashtable.c
../../../../src/murmurhash2.h
../../../../src/murmurhash2.c
../../../../src/obi_align.h
../../../../src/obi_align.c
../../../../src/obiavl.h
../../../../src/obiavl.c
../../../../src/obiblob_indexer.h
../../../../src/obiblob_indexer.c
../../../../src/obiblob.h
../../../../src/obiblob.c
../../../../src/obidebug.h
../../../../src/obidms_taxonomy.h
../../../../src/obidms_taxonomy.c
../../../../src/obidms.h
../../../../src/obidms.c
../../../../src/obidmscolumn_blob.c
../../../../src/obidmscolumn_blob.h
../../../../src/obidmscolumn_bool.c
../../../../src/obidmscolumn_bool.h
../../../../src/obidmscolumn_char.c
../../../../src/obidmscolumn_char.h
../../../../src/obidmscolumn_float.c
../../../../src/obidmscolumn_float.h
../../../../src/obidmscolumn_idx.h
../../../../src/obidmscolumn_idx.c
../../../../src/obidmscolumn_int.c
../../../../src/obidmscolumn_int.h
../../../../src/obidmscolumn_qual.h
../../../../src/obidmscolumn_qual.c
../../../../src/obidmscolumn_seq.c
../../../../src/obidmscolumn_seq.h
../../../../src/obidmscolumn_str.c
../../../../src/obidmscolumn_str.h
../../../../src/obidmscolumn.h
../../../../src/obidmscolumn.c
../../../../src/obidmscolumndir.h
../../../../src/obidmscolumndir.c
../../../../src/obierrno.h
../../../../src/obierrno.c
../../../../src/obilittlebigman.h
../../../../src/obilittlebigman.c
../../../../src/obitypes.h
../../../../src/obitypes.c
../../../../src/obiview.h
../../../../src/obiview.c
../../../../src/sse_banded_LCS_alignment.h
../../../../src/sse_banded_LCS_alignment.c
../../../../src/uint8_indexer.h
../../../../src/uint8_indexer.c
../../../../src/upperband.h
../../../../src/upperband.c
../../../../src/utils.h
../../../../src/utils.c

12
python/obitools3/obidms/capi/obidms.pxd
View File

@ -1,12 +0,0 @@
#cython: language_level=3
from .obitypes cimport const_char_p
cdef extern from "obidms.h" nogil:
struct OBIDMS_t:
const_char_p dms_name
ctypedef OBIDMS_t* OBIDMS_p
OBIDMS_p obi_dms(const_char_p dms_name)
int obi_close_dms(OBIDMS_p dms)

65
python/obitools3/obidms/capi/obidmscolumn.cfiles
View File

@ -1,65 +0,0 @@
../../../../src/bloom.h
../../../../src/bloom.c
../../../../src/char_str_indexer.h
../../../../src/char_str_indexer.c
../../../../src/crc64.h
../../../../src/crc64.c
../../../../src/dna_seq_indexer.h
../../../../src/dna_seq_indexer.c
../../../../src/encode.h
../../../../src/encode.c
../../../../src/hashtable.h
../../../../src/hashtable.c
../../../../src/murmurhash2.h
../../../../src/murmurhash2.c
../../../../src/obi_align.h
../../../../src/obi_align.c
../../../../src/obiavl.h
../../../../src/obiavl.c
../../../../src/obiblob_indexer.h
../../../../src/obiblob_indexer.c
../../../../src/obiblob.h
../../../../src/obiblob.c
../../../../src/obidebug.h
../../../../src/obidms_taxonomy.h
../../../../src/obidms_taxonomy.c
../../../../src/obidms.h
../../../../src/obidms.c
../../../../src/obidmscolumn_blob.c
../../../../src/obidmscolumn_blob.h
../../../../src/obidmscolumn_bool.c
../../../../src/obidmscolumn_bool.h
../../../../src/obidmscolumn_char.c
../../../../src/obidmscolumn_char.h
../../../../src/obidmscolumn_float.c
../../../../src/obidmscolumn_float.h
../../../../src/obidmscolumn_idx.h
../../../../src/obidmscolumn_idx.c
../../../../src/obidmscolumn_int.c
../../../../src/obidmscolumn_int.h
../../../../src/obidmscolumn_qual.h
../../../../src/obidmscolumn_qual.c
../../../../src/obidmscolumn_seq.c
../../../../src/obidmscolumn_seq.h
../../../../src/obidmscolumn_str.c
../../../../src/obidmscolumn_str.h
../../../../src/obidmscolumn.h
../../../../src/obidmscolumn.c
../../../../src/obidmscolumndir.h
../../../../src/obidmscolumndir.c
../../../../src/obierrno.h
../../../../src/obierrno.c
../../../../src/obilittlebigman.h
../../../../src/obilittlebigman.c
../../../../src/obitypes.h
../../../../src/obitypes.c
../../../../src/obiview.h
../../../../src/obiview.c
../../../../src/sse_banded_LCS_alignment.h
../../../../src/sse_banded_LCS_alignment.c
../../../../src/uint8_indexer.h
../../../../src/uint8_indexer.c
../../../../src/upperband.h
../../../../src/upperband.c
../../../../src/utils.h
../../../../src/utils.c

227
python/obitools3/obidms/capi/obidmscolumn.pxd
View File

@ -1,227 +0,0 @@
#cython: language_level=3
from ..capi.obidms cimport OBIDMS_p
from ..capi.obitypes cimport const_char_p, \
OBIType_t, \
obiversion_t, \
obiint_t, \
obibool_t, \
obichar_t, \
obifloat_t, \
index_t, \
time_t
from libc.stdint cimport uint8_t
cdef extern from "obidmscolumn.h" nogil:
struct Column_reference_t :
const_char_p column_name
obiversion_t version
ctypedef Column_reference_t* Column_reference_p
struct OBIDMS_column_header_t:
size_t header_size
size_t data_size
index_t line_count
index_t lines_used
index_t nb_elements_per_line
const_char_p elements_names
OBIType_t returned_data_type
OBIType_t stored_data_type
time_t creation_date
obiversion_t version
obiversion_t cloned_from
const_char_p name
const_char_p indexer_name
Column_reference_t associated_column
const_char_p comments
ctypedef OBIDMS_column_header_t* OBIDMS_column_header_p
struct OBIDMS_column_t:
OBIDMS_p dms
OBIDMS_column_header_p header
bint writable
ctypedef OBIDMS_column_t* OBIDMS_column_p
int obi_close_column(OBIDMS_column_p column)
obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms,
const_char_p column_name)
OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms,
const_char_p column_name,
obiversion_t version_number)
int obi_close_header(OBIDMS_column_header_p header)
char* obi_get_elements_names(OBIDMS_column_p column)
cdef extern from "obidmscolumn_int.h" nogil:
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
obiint_t value)
int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
obiint_t value)
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
cdef extern from "obidmscolumn_bool.h" nogil:
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
obibool_t value)
int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
obibool_t value)
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
cdef extern from "obidmscolumn_char.h" nogil:
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
obichar_t value)
int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
obichar_t value)
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
cdef extern from "obidmscolumn_float.h" nogil:
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
obifloat_t value)
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
obifloat_t value)
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
cdef extern from "obidmscolumn_str.h" nogil:
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
const_char_p value)
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
const_char_p value)
const_char_p obi_column_get_obistr_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
const_char_p obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
cdef extern from "obidmscolumn_seq.h" nogil:
int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
const_char_p value)
int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
const_char_p value)
char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
cdef extern from "obidmscolumn_qual.h" nogil:
int obi_column_set_obiqual_char_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
const_char_p value)
int obi_column_set_obiqual_char_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
const_char_p value)
int obi_column_set_obiqual_int_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
const uint8_t* value,
int value_length)
int obi_column_set_obiqual_int_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
const uint8_t* value,
int value_length)
char* obi_column_get_obiqual_char_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
char* obi_column_get_obiqual_char_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
const uint8_t* obi_column_get_obiqual_int_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
int* value_length)
const uint8_t* obi_column_get_obiqual_int_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
int* value_length)

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python/obitools3/obidms/capi/obierrno.cfiles
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@ -1,65 +0,0 @@
../../../../src/bloom.h
../../../../src/bloom.c
../../../../src/char_str_indexer.h
../../../../src/char_str_indexer.c
../../../../src/crc64.h
../../../../src/crc64.c
../../../../src/dna_seq_indexer.h
../../../../src/dna_seq_indexer.c
../../../../src/encode.h
../../../../src/encode.c
../../../../src/hashtable.h
../../../../src/hashtable.c
../../../../src/murmurhash2.h
../../../../src/murmurhash2.c
../../../../src/obi_align.h
../../../../src/obi_align.c
../../../../src/obiavl.h
../../../../src/obiavl.c
../../../../src/obiblob_indexer.h
../../../../src/obiblob_indexer.c
../../../../src/obiblob.h
../../../../src/obiblob.c
../../../../src/obidebug.h
../../../../src/obidms_taxonomy.h
../../../../src/obidms_taxonomy.c
../../../../src/obidms.h
../../../../src/obidms.c
../../../../src/obidmscolumn_blob.c
../../../../src/obidmscolumn_blob.h
../../../../src/obidmscolumn_bool.c
../../../../src/obidmscolumn_bool.h
../../../../src/obidmscolumn_char.c
../../../../src/obidmscolumn_char.h
../../../../src/obidmscolumn_float.c
../../../../src/obidmscolumn_float.h
../../../../src/obidmscolumn_idx.h
../../../../src/obidmscolumn_idx.c
../../../../src/obidmscolumn_int.c
../../../../src/obidmscolumn_int.h
../../../../src/obidmscolumn_qual.h
../../../../src/obidmscolumn_qual.c
../../../../src/obidmscolumn_seq.c
../../../../src/obidmscolumn_seq.h
../../../../src/obidmscolumn_str.c
../../../../src/obidmscolumn_str.h
../../../../src/obidmscolumn.h
../../../../src/obidmscolumn.c
../../../../src/obidmscolumndir.h
../../../../src/obidmscolumndir.c
../../../../src/obierrno.h
../../../../src/obierrno.c
../../../../src/obilittlebigman.h
../../../../src/obilittlebigman.c
../../../../src/obitypes.h
../../../../src/obitypes.c
../../../../src/obiview.h
../../../../src/obiview.c
../../../../src/sse_banded_LCS_alignment.h
../../../../src/sse_banded_LCS_alignment.c
../../../../src/uint8_indexer.h
../../../../src/uint8_indexer.c
../../../../src/upperband.h
../../../../src/upperband.c
../../../../src/utils.h
../../../../src/utils.c

5
python/obitools3/obidms/capi/obierrno.pxd
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@ -1,5 +0,0 @@
#cython: language_level=3
cdef extern from "obierrno.h" nogil:
extern int obi_errno

65
python/obitools3/obidms/capi/obitaxonomy.cfiles
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@ -1,65 +0,0 @@
../../../../src/bloom.h
../../../../src/bloom.c
../../../../src/char_str_indexer.h
../../../../src/char_str_indexer.c
../../../../src/crc64.h
../../../../src/crc64.c
../../../../src/dna_seq_indexer.h
../../../../src/dna_seq_indexer.c
../../../../src/encode.h
../../../../src/encode.c
../../../../src/hashtable.h
../../../../src/hashtable.c
../../../../src/murmurhash2.h
../../../../src/murmurhash2.c
../../../../src/obi_align.h
../../../../src/obi_align.c
../../../../src/obiavl.h
../../../../src/obiavl.c
../../../../src/obiblob_indexer.h
../../../../src/obiblob_indexer.c
../../../../src/obiblob.h
../../../../src/obiblob.c
../../../../src/obidebug.h
../../../../src/obidms_taxonomy.h
../../../../src/obidms_taxonomy.c
../../../../src/obidms.h
../../../../src/obidms.c
../../../../src/obidmscolumn_blob.c
../../../../src/obidmscolumn_blob.h
../../../../src/obidmscolumn_bool.c
../../../../src/obidmscolumn_bool.h
../../../../src/obidmscolumn_char.c
../../../../src/obidmscolumn_char.h
../../../../src/obidmscolumn_float.c
../../../../src/obidmscolumn_float.h
../../../../src/obidmscolumn_idx.h
../../../../src/obidmscolumn_idx.c
../../../../src/obidmscolumn_int.c
../../../../src/obidmscolumn_int.h
../../../../src/obidmscolumn_qual.h
../../../../src/obidmscolumn_qual.c
../../../../src/obidmscolumn_seq.c
../../../../src/obidmscolumn_seq.h
../../../../src/obidmscolumn_str.c
../../../../src/obidmscolumn_str.h
../../../../src/obidmscolumn.h
../../../../src/obidmscolumn.c
../../../../src/obidmscolumndir.h
../../../../src/obidmscolumndir.c
../../../../src/obierrno.h
../../../../src/obierrno.c
../../../../src/obilittlebigman.h
../../../../src/obilittlebigman.c
../../../../src/obitypes.h
../../../../src/obitypes.c
../../../../src/obiview.h
../../../../src/obiview.c
../../../../src/sse_banded_LCS_alignment.h
../../../../src/sse_banded_LCS_alignment.c
../../../../src/uint8_indexer.h
../../../../src/uint8_indexer.c
../../../../src/upperband.h
../../../../src/upperband.c
../../../../src/utils.h
../../../../src/utils.c

65
python/obitools3/obidms/capi/obitaxonomy.pxd
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@ -1,65 +0,0 @@
#cython: language_level=3
from .obitypes cimport const_char_p
from .obidms cimport OBIDMS_p
from libc.stdint cimport int32_t
cdef extern from "obidms_taxonomy.h" nogil:
struct ecotxnode :
int32_t taxid
int32_t rank
int32_t farest
ecotxnode* parent
char* name
char* preferred_name
ctypedef ecotxnode ecotx_t
struct ecotxidx_t :
int32_t count
int32_t max_taxid
int32_t buffer_size
ecotx_t* taxon
struct OBIDMS_taxonomy_t :
# ecorankidx_t* ranks
# econameidx_t* names
ecotxidx_t* taxa
ctypedef OBIDMS_taxonomy_t* OBIDMS_taxonomy_p
OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const_char_p taxonomy_name, bint read_alternative_names)
OBIDMS_taxonomy_p obi_read_taxdump(const_char_p taxdump)
int obi_write_taxonomy(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const_char_p tax_name)
int obi_close_taxonomy(OBIDMS_taxonomy_p taxonomy)
ecotx_t* obi_taxo_get_parent_at_rank(ecotx_t* taxon, int32_t rankidx)
ecotx_t* obi_taxo_get_taxon_with_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid)
bint obi_taxo_is_taxon_under_taxid(ecotx_t* taxon, int32_t other_taxid)
ecotx_t* obi_taxo_get_species(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
ecotx_t* obi_taxo_get_genus(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
ecotx_t* obi_taxo_get_family(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
ecotx_t* obi_taxo_get_kingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
int obi_taxo_add_local_taxon(OBIDMS_taxonomy_p tax, const char* name, const char* rank_name, int32_t parent_taxid, int32_t min_taxid)
int obi_taxo_add_preferred_name_with_taxid(OBIDMS_taxonomy_p tax, int32_t taxid, const char* preferred_name)
int obi_taxo_add_preferred_name_with_taxon(OBIDMS_taxonomy_p tax, ecotx_t* taxon, const char* preferred_name)

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@ -1,65 +0,0 @@
../../../../src/bloom.h
../../../../src/bloom.c
../../../../src/char_str_indexer.h
../../../../src/char_str_indexer.c
../../../../src/crc64.h
../../../../src/crc64.c
../../../../src/dna_seq_indexer.h
../../../../src/dna_seq_indexer.c
../../../../src/encode.h
../../../../src/encode.c
../../../../src/hashtable.h
../../../../src/hashtable.c
../../../../src/murmurhash2.h
../../../../src/murmurhash2.c
../../../../src/obi_align.h
../../../../src/obi_align.c
../../../../src/obiavl.h
../../../../src/obiavl.c
../../../../src/obiblob_indexer.h
../../../../src/obiblob_indexer.c
../../../../src/obiblob.h
../../../../src/obiblob.c
../../../../src/obidebug.h
../../../../src/obidms_taxonomy.h
../../../../src/obidms_taxonomy.c
../../../../src/obidms.h
../../../../src/obidms.c
../../../../src/obidmscolumn_blob.c
../../../../src/obidmscolumn_blob.h
../../../../src/obidmscolumn_bool.c
../../../../src/obidmscolumn_bool.h
../../../../src/obidmscolumn_char.c
../../../../src/obidmscolumn_char.h
../../../../src/obidmscolumn_float.c
../../../../src/obidmscolumn_float.h
../../../../src/obidmscolumn_idx.h
../../../../src/obidmscolumn_idx.c
../../../../src/obidmscolumn_int.c
../../../../src/obidmscolumn_int.h
../../../../src/obidmscolumn_qual.h
../../../../src/obidmscolumn_qual.c
../../../../src/obidmscolumn_seq.c
../../../../src/obidmscolumn_seq.h
../../../../src/obidmscolumn_str.c
../../../../src/obidmscolumn_str.h
../../../../src/obidmscolumn.h
../../../../src/obidmscolumn.c
../../../../src/obidmscolumndir.h
../../../../src/obidmscolumndir.c
../../../../src/obierrno.h
../../../../src/obierrno.c
../../../../src/obilittlebigman.h
../../../../src/obilittlebigman.c
../../../../src/obitypes.h
../../../../src/obitypes.c
../../../../src/obiview.h
../../../../src/obiview.c
../../../../src/sse_banded_LCS_alignment.h
../../../../src/sse_banded_LCS_alignment.c
../../../../src/uint8_indexer.h
../../../../src/uint8_indexer.c
../../../../src/upperband.h
../../../../src/upperband.c
../../../../src/utils.h
../../../../src/utils.c

55
python/obitools3/obidms/capi/obitypes.pxd
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@ -1,55 +0,0 @@
#cython: language_level=3
from libc.stdint cimport int32_t, int64_t, uint8_t
from posix.types cimport time_t
cdef extern from *:
ctypedef char* const_char_p "const char*"
cdef extern from "encode.h" nogil:
bint only_ATGC(const_char_p seq)
cdef extern from "obitypes.h" nogil:
enum OBIType:
OBI_VOID,
OBI_INT,
OBI_FLOAT,
OBI_BOOL,
OBI_CHAR,
OBI_QUAL,
OBI_STR,
OBI_SEQ,
OBI_IDX
ctypedef OBIType OBIType_t
enum OBIBool:
pass
ctypedef OBIBool obibool_t
ctypedef int32_t obiint_t
ctypedef double obifloat_t
ctypedef char obichar_t
ctypedef int64_t index_t
ctypedef int32_t obiversion_t
extern obiint_t OBIInt_NA
extern index_t OBIIdx_NA
extern obifloat_t OBIFloat_NA
extern obichar_t OBIChar_NA
extern obibool_t OBIBool_NA
extern const_char_p OBISeq_NA
extern const_char_p OBIStr_NA
extern const_char_p OBIQual_char_NA
extern uint8_t* OBIQual_int_NA
const_char_p name_data_type(int data_type)

65
python/obitools3/obidms/capi/obiutils.cfiles
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@ -1,65 +0,0 @@
../../../../src/bloom.h
../../../../src/bloom.c
../../../../src/char_str_indexer.h
../../../../src/char_str_indexer.c
../../../../src/crc64.h
../../../../src/crc64.c
../../../../src/dna_seq_indexer.h
../../../../src/dna_seq_indexer.c
../../../../src/encode.h
../../../../src/encode.c
../../../../src/hashtable.h
../../../../src/hashtable.c
../../../../src/murmurhash2.h
../../../../src/murmurhash2.c
../../../../src/obi_align.h
../../../../src/obi_align.c
../../../../src/obiavl.h
../../../../src/obiavl.c
../../../../src/obiblob_indexer.h
../../../../src/obiblob_indexer.c
../../../../src/obiblob.h
../../../../src/obiblob.c
../../../../src/obidebug.h
../../../../src/obidms_taxonomy.h
../../../../src/obidms_taxonomy.c
../../../../src/obidms.h
../../../../src/obidms.c
../../../../src/obidmscolumn_blob.c
../../../../src/obidmscolumn_blob.h
../../../../src/obidmscolumn_bool.c
../../../../src/obidmscolumn_bool.h
../../../../src/obidmscolumn_char.c
../../../../src/obidmscolumn_char.h
../../../../src/obidmscolumn_float.c
../../../../src/obidmscolumn_float.h
../../../../src/obidmscolumn_idx.h
../../../../src/obidmscolumn_idx.c
../../../../src/obidmscolumn_int.c
../../../../src/obidmscolumn_int.h
../../../../src/obidmscolumn_qual.h
../../../../src/obidmscolumn_qual.c
../../../../src/obidmscolumn_seq.c
../../../../src/obidmscolumn_seq.h
../../../../src/obidmscolumn_str.c
../../../../src/obidmscolumn_str.h
../../../../src/obidmscolumn.h
../../../../src/obidmscolumn.c
../../../../src/obidmscolumndir.h
../../../../src/obidmscolumndir.c
../../../../src/obierrno.h
../../../../src/obierrno.c
../../../../src/obilittlebigman.h
../../../../src/obilittlebigman.c
../../../../src/obitypes.h
../../../../src/obitypes.c
../../../../src/obiview.h
../../../../src/obiview.c
../../../../src/sse_banded_LCS_alignment.h
../../../../src/sse_banded_LCS_alignment.c
../../../../src/uint8_indexer.h
../../../../src/uint8_indexer.c
../../../../src/upperband.h
../../../../src/upperband.c
../../../../src/utils.h
../../../../src/utils.c

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@ -1,12 +0,0 @@
#cython: language_level=3
from posix.types cimport time_t
from ..capi.obitypes cimport const_char_p
cdef extern from "utils.h" nogil:
const_char_p obi_format_date(time_t date)

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@ -1,65 +0,0 @@
../../../../src/bloom.h
../../../../src/bloom.c
../../../../src/char_str_indexer.h
../../../../src/char_str_indexer.c
../../../../src/crc64.h
../../../../src/crc64.c
../../../../src/dna_seq_indexer.h
../../../../src/dna_seq_indexer.c
../../../../src/encode.h
../../../../src/encode.c
../../../../src/hashtable.h
../../../../src/hashtable.c
../../../../src/murmurhash2.h
../../../../src/murmurhash2.c
../../../../src/obi_align.h
../../../../src/obi_align.c
../../../../src/obiavl.h
../../../../src/obiavl.c
../../../../src/obiblob_indexer.h
../../../../src/obiblob_indexer.c
../../../../src/obiblob.h
../../../../src/obiblob.c
../../../../src/obidebug.h
../../../../src/obidms_taxonomy.h
../../../../src/obidms_taxonomy.c
../../../../src/obidms.h
../../../../src/obidms.c
../../../../src/obidmscolumn_blob.c
../../../../src/obidmscolumn_blob.h
../../../../src/obidmscolumn_bool.c
../../../../src/obidmscolumn_bool.h
../../../../src/obidmscolumn_char.c
../../../../src/obidmscolumn_char.h
../../../../src/obidmscolumn_float.c
../../../../src/obidmscolumn_float.h
../../../../src/obidmscolumn_idx.h
../../../../src/obidmscolumn_idx.c
../../../../src/obidmscolumn_int.c
../../../../src/obidmscolumn_int.h
../../../../src/obidmscolumn_qual.h
../../../../src/obidmscolumn_qual.c
../../../../src/obidmscolumn_seq.c
../../../../src/obidmscolumn_seq.h
../../../../src/obidmscolumn_str.c
../../../../src/obidmscolumn_str.h
../../../../src/obidmscolumn.h
../../../../src/obidmscolumn.c
../../../../src/obidmscolumndir.h
../../../../src/obidmscolumndir.c
../../../../src/obierrno.h
../../../../src/obierrno.c
../../../../src/obilittlebigman.h
../../../../src/obilittlebigman.c
../../../../src/obitypes.h
../../../../src/obitypes.c
../../../../src/obiview.h
../../../../src/obiview.c
../../../../src/sse_banded_LCS_alignment.h
../../../../src/sse_banded_LCS_alignment.c
../../../../src/uint8_indexer.h
../../../../src/uint8_indexer.c
../../../../src/upperband.h
../../../../src/upperband.c
../../../../src/utils.h
../../../../src/utils.c

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python/obitools3/obidms/capi/obiview.pxd
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@ -1,294 +0,0 @@
#cython: language_level=3
from .obitypes cimport const_char_p, \
OBIType_t, \
obiversion_t, \
obiint_t, \
obibool_t, \
obichar_t, \
obifloat_t, \
index_t, \
time_t
from ..capi.obidms cimport OBIDMS_p
from ..capi.obidmscolumn cimport OBIDMS_column_p, \
Column_reference_t, \
Column_reference_p
from libc.stdint cimport uint8_t
cdef extern from "obiview.h" nogil:
extern const_char_p VIEW_TYPE_NUC_SEQS
extern const_char_p NUC_SEQUENCE_COLUMN
extern const_char_p ID_COLUMN
extern const_char_p DEFINITION_COLUMN
extern const_char_p QUALITY_COLUMN
struct Alias_column_pair_t :
Column_reference_t column_refs
const_char_p alias
ctypedef Alias_column_pair_t* Alias_column_pair_p
struct Obiview_infos_t :
time_t creation_date
const_char_p name
const_char_p created_from
const_char_p view_type
bint all_lines
Column_reference_t line_selection
index_t line_count
int column_count
Alias_column_pair_p column_references
const_char_p comments
ctypedef Obiview_infos_t* Obiview_infos_p
struct Obiview_t :
Obiview_infos_p infos
OBIDMS_p dms
bint read_only
OBIDMS_column_p line_selection
OBIDMS_column_p columns
int nb_predicates
# TODO declarations for column dictionary and predicate function array?
ctypedef Obiview_t* Obiview_p
Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection, const_char_p comments, bint quality_column)
Obiview_p obi_new_view(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection, const_char_p comments)
Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments)
Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments, bint quality_column)
Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name, bint finished)
int obi_view_unmap_file(OBIDMS_p dms, Obiview_infos_p view_infos)
Obiview_p obi_open_view(OBIDMS_p dms, const_char_p view_name)
int obi_view_add_column(Obiview_p view,
const_char_p column_name,
obiversion_t version_number,
const_char_p alias,
OBIType_t data_type,
index_t nb_lines,
index_t nb_elements_per_line,
char* elements_names,
const_char_p indexer_name,
const_char_p associated_column_name,
obiversion_t associated_column_version,
const_char_p comments,
bint create)
int obi_view_delete_column(Obiview_p view, const_char_p column_name)
OBIDMS_column_p obi_view_get_column(Obiview_p view, const_char_p column_name)
OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const_char_p column_name)
int obi_view_create_column_alias(Obiview_p view, const_char_p current_name, const_char_p alias)
int obi_save_and_close_view(Obiview_p view)
# OBI_INT
int obi_set_int_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name,
obiint_t value)
int obi_set_int_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx,
obiint_t value)
obiint_t obi_get_int_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name)
obiint_t obi_get_int_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx)
# OBI_BOOL
int obi_set_bool_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name,
obibool_t value)
int obi_set_bool_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx,
obibool_t value)
obibool_t obi_get_bool_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name)
obibool_t obi_get_bool_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx)
# OBI_CHAR
int obi_set_char_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name,
obichar_t value)
int obi_set_char_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx,
obichar_t value)
obichar_t obi_get_char_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name)
obichar_t obi_get_char_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx)
# OBI_FLOAT
int obi_set_float_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name,
obifloat_t value)
int obi_set_float_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx,
obifloat_t value)
obifloat_t obi_get_float_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name)
obifloat_t obi_get_float_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx)
# OBI_QUAL
int obi_set_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx,
const char* value)
int obi_set_qual_int_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx,
const uint8_t* value,
int value_length)
char* obi_get_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx)
const uint8_t* obi_get_qual_int_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx,
int* value_length)
int obi_set_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const char* element_name,
const char* value)
int obi_set_qual_int_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const char* element_name,
const uint8_t* value,
int value_length)
char* obi_get_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const char* element_name)
const uint8_t* obi_get_qual_int_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const char* element_name,
int* value_length)
# OBI_STR
int obi_set_str_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name,
const_char_p value)
int obi_set_str_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx,
const_char_p value)
const_char_p obi_get_str_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name)
const_char_p obi_get_str_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx)
# OBI_SEQ
int obi_set_seq_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name,
const_char_p value)
int obi_set_seq_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx,
const_char_p value)
char* obi_get_seq_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name)
char* obi_get_seq_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx)