Merged master fixed conflict.
This commit is contained in:
Celine Mercier
65
python/obitools3/commands/lcs.cfiles
Normal file
65
python/obitools3/commands/lcs.cfiles
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@ -0,0 +1,65 @@
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../../../src/bloom.h
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../../../src/bloom.c
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../../../src/char_str_indexer.h
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../../../src/char_str_indexer.c
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../../../src/crc64.h
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../../../src/crc64.c
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../../../src/dna_seq_indexer.h
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../../../src/dna_seq_indexer.c
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../../../src/encode.h
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../../../src/encode.c
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../../../src/hashtable.h
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../../../src/hashtable.c
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../../../src/murmurhash2.h
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../../../src/murmurhash2.c
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../../../src/obi_align.h
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../../../src/obi_align.c
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../../../src/obiavl.h
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../../../src/obiavl.c
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../../../src/obiblob_indexer.h
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../../../src/obiblob_indexer.c
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../../../src/obiblob.h
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../../../src/obiblob.c
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../../../src/obidebug.h
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../../../src/obidms_taxonomy.h
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../../../src/obidms_taxonomy.c
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../../../src/obidms.h
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../../../src/obidms.c
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../../../src/obidmscolumn_blob.c
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../../../src/obidmscolumn_blob.h
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../../../src/obidmscolumn_bool.c
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../../../src/obidmscolumn_bool.h
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../../../src/obidmscolumn_char.c
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../../../src/obidmscolumn_char.h
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../../../src/obidmscolumn_float.c
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../../../src/obidmscolumn_float.h
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../../../src/obidmscolumn_idx.h
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../../../src/obidmscolumn_idx.c
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../../../src/obidmscolumn_int.c
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../../../src/obidmscolumn_int.h
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../../../src/obidmscolumn_qual.h
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../../../src/obidmscolumn_qual.c
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../../../src/obidmscolumn_seq.c
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../../../src/obidmscolumn_seq.h
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../../../src/obidmscolumn_str.c
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../../../src/obidmscolumn_str.h
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../../../src/obidmscolumn.h
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../../../src/obidmscolumn.c
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../../../src/obidmscolumndir.h
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../../../src/obidmscolumndir.c
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../../../src/obierrno.h
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../../../src/obierrno.c
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../../../src/obilittlebigman.h
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../../../src/obilittlebigman.c
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../../../src/obitypes.h
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../../../src/obitypes.c
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../../../src/obiview.h
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../../../src/obiview.c
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../../../src/sse_banded_LCS_alignment.h
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../../../src/sse_banded_LCS_alignment.c
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../../../src/uint8_indexer.h
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../../../src/uint8_indexer.c
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../../../src/upperband.h
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../../../src/upperband.c
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../../../src/utils.h
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../../../src/utils.c
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@ -4,7 +4,8 @@ from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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from obitools3.obidms._obidms cimport OBIDMS # TODO cimport doesn't work
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from obitools3.utils cimport str2bytes
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from obitools3.obidms.capi.obialign cimport obi_lcs_align_one_column
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from obitools3.obidms.capi.obialign cimport obi_lcs_align_one_column, \
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obi_lcs_align_two_columns
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import time
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@ -146,6 +147,13 @@ def addOptions(parser):
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default=False,
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help="Sequence counts are written in the output view. Default: they are not written.")
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group.add_argument('--thread-count','-p', # TODO should probably be in a specific option group
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action="store", dest="align:threadcount",
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metavar='<THREAD COUNT>',
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default=1,
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type=int,
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help="Number of threads to use for the computation. Default: one.")
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cpdef align(str dms_n,
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str input_view_1_n, str output_view_n,
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@ -156,24 +164,42 @@ cpdef align(str dms_n,
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double threshold=0.0, bint normalize=True,
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int reference=0, bint similarity_mode=True,
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bint print_seq=False, bint print_count=False,
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comments="") :
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comments="",
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int thread_count=1) :
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cdef OBIDMS d
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d = OBIDMS(dms_n)
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# Align 1 column (2 columns not implemented yet)
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if obi_lcs_align_one_column(d._pointer, \
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str2bytes(input_view_1_n), \
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str2bytes(input_column_1_n), \
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str2bytes(input_elt_1_n), \
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str2bytes(id_column_1_n), \
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str2bytes(output_view_n), \
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str2bytes(comments), \
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print_seq, \
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print_count, \
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threshold, normalize, reference, similarity_mode) < 0 :
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raise Exception("Error aligning sequences")
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if input_view_2_n == "" and input_column_2_n == "" :
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if obi_lcs_align_one_column(d._pointer, \
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str2bytes(input_view_1_n), \
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str2bytes(input_column_1_n), \
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str2bytes(input_elt_1_n), \
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str2bytes(id_column_1_n), \
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str2bytes(output_view_n), \
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str2bytes(comments), \
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print_seq, \
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print_count, \
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threshold, normalize, reference, similarity_mode,
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thread_count) < 0 :
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raise Exception("Error aligning sequences")
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else :
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if obi_lcs_align_two_columns(d._pointer, \
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str2bytes(input_view_1_n), \
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str2bytes(input_view_2_n), \
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str2bytes(input_column_1_n), \
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str2bytes(input_column_2_n), \
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str2bytes(input_elt_1_n), \
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str2bytes(input_elt_2_n), \
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str2bytes(id_column_1_n), \
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str2bytes(id_column_2_n), \
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str2bytes(output_view_n), \
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str2bytes(comments), \
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print_seq, \
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print_count, \
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threshold, normalize, reference, similarity_mode) < 0 :
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raise Exception("Error aligning sequences")
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d.close()
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@ -199,8 +225,9 @@ def run(config):
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similarity_mode = config['align']['similarity'], \
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print_seq = config['align']['printseq'], \
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print_count = config['align']['printcount'], \
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comments = comments)
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comments = comments, \
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thread_count = config['align']['threadcount'])
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print("Done.")
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@ -97,8 +97,7 @@ def test_set_and_get(config, infos):
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return
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idx = random_int(config)
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value = infos['random_generator'][data_type](config)
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if len(element_names) > 1 :
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if col.nb_elements_per_line > 1 :
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elt = random.choice(element_names)
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col[idx][elt] = value
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assert col[idx][elt] == value, "Set value != gotten value "+str(col[idx][elt])+" != "+str(value)
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@ -187,6 +186,7 @@ def create_random_column(config, infos) :
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elements_names = []
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for i in range(nb_elements_per_line) :
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elements_names.append(random_unique_element_name(config, infos))
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elements_names = random.choice([None, elements_names])
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name = random_unique_name(infos)
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infos['view'].add_column(name,
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alias=alias,
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@ -358,7 +358,9 @@ def run(config):
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config['test']['elt_name_max_len'] = int((COL_COMMENTS_MAX_LEN - config['test']['maxelts']) / config['test']['maxelts'])
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print("Initializing the DMS and the first view...")
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shutil.rmtree(config['obi']['defaultdms']+'.obidms', ignore_errors=True)
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ini_dms_and_first_view(config, infos)
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print_test(config, repr(infos['view']))
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@ -7,7 +7,8 @@ from .capi.obidms cimport obi_dms, \
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from .capi.obidmscolumn cimport obi_close_column, \
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OBIDMS_column_p, \
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OBIDMS_column_header_p
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OBIDMS_column_header_p, \
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obi_get_elements_names
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from .capi.obiutils cimport obi_format_date
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@ -73,7 +74,7 @@ from .capi.obiview cimport Obiview_p, \
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DEFINITION_COLUMN, \
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QUALITY_COLUMN
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from libc.stdlib cimport malloc
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from libc.stdlib cimport malloc, free
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@ -100,17 +101,17 @@ cdef class OBIDMS_column :
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def __getitem__(self, index_t line_nb):
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return self.get_line(line_nb)
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def __len__(self):
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return self.lines_used
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def __len__(self): # TODO discuss
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return self._view.line_count
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def __sizeof__(self):
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return ((self._pointer)[0].header.header_size + (self._pointer)[0].header.data_size)
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def __iter__(self):
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def __iter__(self): # TODO discuss
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# Declarations
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cdef index_t line_nb
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# Yield each line
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for line_nb in range(self.lines_used):
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for line_nb in range(self._view.line_count):
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yield self.get_line(line_nb)
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def __str__(self) :
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@ -138,7 +139,12 @@ cdef class OBIDMS_column :
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# elements_names property getter
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@property
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def elements_names(self):
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return (bytes2str(((self._pointer)[0].header).elements_names)).split(';')
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cdef char* elts_names_b
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cdef str elts_names
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elts_names_b = obi_get_elements_names((self._pointer)[0])
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elts_names = bytes2str(elts_names_b)
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free(<char*>elts_names_b)
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return elts_names.split(';')
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# nb_elements_per_line property getter
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@property
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@ -160,11 +166,6 @@ cdef class OBIDMS_column :
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def version(self):
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return ((self._pointer)[0].header).version
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# lines_used property getter
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@property
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def lines_used(self):
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return (self._pointer)[0].header.lines_used
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# comments property getter
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@property
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def comments(self):
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@ -268,15 +269,6 @@ cdef class OBIDMS_column_line :
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######################################################################################################
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######################################################################################################
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######################################################################################################
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cdef class OBIView_line :
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def __init__(self, OBIView view, index_t line_nb) :
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@ -424,7 +416,7 @@ cdef class OBIDMS :
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cdef int i, j
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cdef str column_name
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view_infos_p = obi_view_map_file(self._pointer, str2bytes(view_name))
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view_infos_p = obi_view_map_file(self._pointer, str2bytes(view_name), True)
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view_infos_d = {}
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view_infos_d["name"] = bytes2str(view_infos_p.name)
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view_infos_d["comments"] = bytes2str(view_infos_p.comments)
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@ -22,7 +22,7 @@ cdef class OBIDMS_column_str(OBIDMS_column):
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result = None
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else :
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result = bytes2str(value)
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# NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
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# NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file.
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return result
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cpdef set_line(self, index_t line_nb, object value):
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@ -46,7 +46,7 @@ cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
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result = None
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else :
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result = bytes2str(value)
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# NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
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# NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file.
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return result
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cpdef object get_line(self, index_t line_nb) :
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@ -65,7 +65,7 @@ cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
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value_in_result = None
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else :
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value_in_result = bytes2str(value)
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# NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
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# NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file.
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result[self.elements_names[i]] = value_in_result
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if all_NA and (value_in_result is not None) :
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all_NA = False
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@ -17,4 +17,5 @@ cdef class OBI_Taxonomy :
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cdef class OBI_Taxon :
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cdef ecotx_t* _pointer
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cdef ecotx_t* _pointer
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cdef OBI_Taxonomy _tax
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@ -7,10 +7,10 @@ from .capi.obitaxonomy cimport obi_read_taxonomy, \
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obi_write_taxonomy, \
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obi_close_taxonomy, \
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obi_taxo_get_taxon_with_taxid, \
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obi_taxonomy_add_local_taxon, \
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obi_taxo_add_local_taxon, \
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obi_taxo_add_preferred_name_with_taxon, \
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ecotx_t
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|
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from ._obidms cimport OBIDMS
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from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
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@ -42,11 +42,11 @@ cdef class OBI_Taxonomy :
|
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if taxon_p == NULL :
|
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raise Exception("Taxon not found")
|
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taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
|
||||
return OBI_Taxon(taxon_capsule)
|
||||
return OBI_Taxon(taxon_capsule, self)
|
||||
else :
|
||||
raise Exception("Not implemented")
|
||||
|
||||
|
||||
|
||||
|
||||
def __iter__(self):
|
||||
|
||||
cdef ecotx_t* taxa
|
||||
@ -60,7 +60,7 @@ cdef class OBI_Taxonomy :
|
||||
for t in range(self._pointer.taxa.count):
|
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taxon_p = <ecotx_t*> (taxa+t)
|
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taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
|
||||
yield OBI_Taxon(taxon_capsule)
|
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yield OBI_Taxon(taxon_capsule, self)
|
||||
|
||||
|
||||
cpdef write(self, str prefix) :
|
||||
@ -70,7 +70,7 @@ cdef class OBI_Taxonomy :
|
||||
|
||||
cpdef int add_taxon(self, str name, str rank_name, int parent_taxid, int min_taxid=10000000) :
|
||||
cdef int taxid
|
||||
taxid = obi_taxonomy_add_local_taxon(self._pointer, str2bytes(name), str2bytes(rank_name), parent_taxid, min_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 :
|
||||
@ -85,10 +85,11 @@ cdef class OBI_Taxonomy :
|
||||
|
||||
cdef class OBI_Taxon : # TODO dict subclass?
|
||||
|
||||
def __init__(self, object taxon_capsule) :
|
||||
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 the taxonomy")
|
||||
raise Exception("Error reading a taxon (NULL pointer)")
|
||||
self._tax = tax
|
||||
|
||||
# name property getter
|
||||
@property
|
||||
@ -115,14 +116,25 @@ cdef class OBI_Taxon : # TODO dict subclass?
|
||||
def parent(self):
|
||||
cdef object parent_capsule
|
||||
parent_capsule = PyCapsule_New(self._pointer.parent, NULL, NULL)
|
||||
return OBI_Taxon(parent_capsule)
|
||||
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['parent'] = self.parent.taxid
|
||||
d['farest'] = self.farest
|
||||
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)
|
||||
|
||||
|
||||
|
||||
65
python/obitools3/obidms/capi/obialign.cfiles
Normal file
65
python/obitools3/obidms/capi/obialign.cfiles
Normal file
@ -0,0 +1,65 @@
|
||||
../../../../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
|
||||
@ -18,5 +18,24 @@ cdef extern from "obi_align.h" nogil:
|
||||
double threshold,
|
||||
bint normalize,
|
||||
int reference,
|
||||
bint similarity_mode)
|
||||
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
Normal file
65
python/obitools3/obidms/capi/obidms.cfiles
Normal file
@ -0,0 +1,65 @@
|
||||
../../../../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/obidmscolumn.cfiles
Normal file
65
python/obitools3/obidms/capi/obidmscolumn.cfiles
Normal file
@ -0,0 +1,65 @@
|
||||
../../../../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
|
||||
@ -47,31 +47,8 @@ cdef extern from "obidmscolumn.h" nogil:
|
||||
bint writable
|
||||
|
||||
ctypedef OBIDMS_column_t* OBIDMS_column_p
|
||||
|
||||
OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
const_char_p column_name,
|
||||
OBIType_t type,
|
||||
index_t nb_lines,
|
||||
index_t nb_elements_per_line,
|
||||
const_char_p elements_names,
|
||||
const_char_p indexer_name,
|
||||
const_char_p associated_colum_name,
|
||||
obiversion_t associated_colum_version,
|
||||
const_char_p comments)
|
||||
|
||||
OBIDMS_column_p obi_open_column(OBIDMS_p dms,
|
||||
const_char_p column_name,
|
||||
obiversion_t version_number)
|
||||
|
||||
int obi_close_column(OBIDMS_column_p column)
|
||||
|
||||
OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
|
||||
OBIDMS_column_p line_selection,
|
||||
const_char_p column_name,
|
||||
obiversion_t version_number,
|
||||
bint clone_data)
|
||||
|
||||
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)
|
||||
@ -81,9 +58,9 @@ cdef extern from "obidmscolumn.h" nogil:
|
||||
obiversion_t version_number)
|
||||
|
||||
int obi_close_header(OBIDMS_column_header_p header)
|
||||
|
||||
int obi_select(OBIDMS_column_p line_selection_column, index_t line_to_grep)
|
||||
|
||||
|
||||
char* obi_get_elements_names(OBIDMS_column_p column)
|
||||
|
||||
|
||||
cdef extern from "obidmscolumn_int.h" nogil:
|
||||
|
||||
|
||||
65
python/obitools3/obidms/capi/obierrno.cfiles
Normal file
65
python/obitools3/obidms/capi/obierrno.cfiles
Normal file
@ -0,0 +1,65 @@
|
||||
../../../../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.cfiles
Normal file
65
python/obitools3/obidms/capi/obitaxonomy.cfiles
Normal file
@ -0,0 +1,65 @@
|
||||
../../../../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
|
||||
@ -13,7 +13,8 @@ cdef extern from "obidms_taxonomy.h" nogil:
|
||||
int32_t farest
|
||||
ecotxnode* parent
|
||||
char* name
|
||||
|
||||
char* preferred_name
|
||||
|
||||
ctypedef ecotxnode ecotx_t
|
||||
|
||||
|
||||
@ -56,4 +57,9 @@ cdef extern from "obidms_taxonomy.h" nogil:
|
||||
|
||||
ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
|
||||
|
||||
int obi_taxonomy_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_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)
|
||||
|
||||
|
||||
65
python/obitools3/obidms/capi/obitypes.cfiles
Normal file
65
python/obitools3/obidms/capi/obitypes.cfiles
Normal file
@ -0,0 +1,65 @@
|
||||
../../../../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/obiutils.cfiles
Normal file
65
python/obitools3/obidms/capi/obiutils.cfiles
Normal file
@ -0,0 +1,65 @@
|
||||
../../../../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/obiview.cfiles
Normal file
65
python/obitools3/obidms/capi/obiview.cfiles
Normal file
@ -0,0 +1,65 @@
|
||||
../../../../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
|
||||
@ -68,7 +68,7 @@ cdef extern from "obiview.h" nogil:
|
||||
|
||||
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)
|
||||
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)
|
||||
|
||||
@ -94,11 +94,7 @@ cdef extern from "obiview.h" nogil:
|
||||
|
||||
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_view(Obiview_p view)
|
||||
|
||||
int obi_close_view(Obiview_p view)
|
||||
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)
|
||||
|
||||
|
||||
Reference in New Issue
Block a user