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DNA sequences and character strings are now handled using AVL trees.

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This commit is contained in:
Celine Mercier
2015-12-11 17:24:44 +01:00
parent 1586956d57
commit c139367555
26 changed files with 2178 additions and 1711 deletions
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4
python/obitools3/obidms/_obidms.cfiles
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@ -12,7 +12,7 @@
../../../src/obitypes.c
../../../src/private_at_functions.h
../../../src/private_at_functions.c
../../../src/obiarray.h
../../../src/obiarray.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/encode.h
../../../src/encode.c

2
python/obitools3/obidms/_obidms.pxd
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@ -25,7 +25,7 @@ cdef class OBIDMS:
index_t nb_lines=*,
index_t nb_elements_per_line=*,
list elements_names=*,
str array_name=*,
str avl_name=*,
str comments=*)

12
python/obitools3/obidms/_obidms.pyx
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@ -133,7 +133,7 @@ cdef class OBIDMS :
index_t nb_lines=0,
index_t nb_elements_per_line=0,
list elements_names=None,
str array_name="default_obiarray",
str avl_name="default_AVL_tree",
str comments=""):
# Declarations
@ -263,7 +263,7 @@ cdef class OBIDMS :
referring,
version_number, data_type,
nb_lines, nb_elements_per_line,
elements_names, array_name,
elements_names, avl_name,
comments)
return column
@ -284,13 +284,13 @@ cdef class OBIDMS_column :
index_t nb_lines,
index_t nb_elements_per_line,
list elements_names,
str array_name,
str avl_name,
str comments):
# Declarations
cdef bytes column_name_b
cdef bytes dms_name_b
cdef bytes array_name_b
cdef bytes avl_name_b
cdef bytes elements_names_b
cdef bytes comments_b
@ -304,7 +304,7 @@ cdef class OBIDMS_column :
# Format the character strings to send them to C functions
column_name_b = str2bytes(column_name)
dms_name_b = str2bytes(self.dms.dms_name)
array_name_b = str2bytes(array_name)
avl_name_b = str2bytes(avl_name)
comments_b = str2bytes(comments)
# Create, clone or open column
@ -315,7 +315,7 @@ cdef class OBIDMS_column :
elements_names_b = str2bytes(";".join(elements_names))
self.pointer = obi_create_column(self.dms.pointer, column_name_b, type,
nb_lines, nb_elements_per_line,
elements_names_b, array_name_b, comments_b,
elements_names_b, avl_name_b, comments_b,
referring)
else :
if clone :

4
python/obitools3/obidms/_obidmscolumn_bool.cfiles
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@ -14,5 +14,5 @@
../../../src/obitypes.c
../../../src/private_at_functions.h
../../../src/private_at_functions.c
../../../src/obiarray.h
../../../src/obiarray.c
../../../src/obiavl.h
../../../src/obiavl.c

4
python/obitools3/obidms/_obidmscolumn_char.cfiles
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@ -14,5 +14,5 @@
../../../src/obitypes.c
../../../src/private_at_functions.h
../../../src/private_at_functions.c
../../../src/obiarray.h
../../../src/obiarray.c
../../../src/obiavl.h
../../../src/obiavl.c

4
python/obitools3/obidms/_obidmscolumn_float.cfiles
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@ -14,5 +14,5 @@
../../../src/obitypes.c
../../../src/private_at_functions.h
../../../src/private_at_functions.c
../../../src/obiarray.h
../../../src/obiarray.c
../../../src/obiavl.h
../../../src/obiavl.c

4
python/obitools3/obidms/_obidmscolumn_int.cfiles
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@ -14,5 +14,5 @@
../../../src/obitypes.c
../../../src/private_at_functions.h
../../../src/private_at_functions.c
../../../src/obiarray.h
../../../src/obiarray.c
../../../src/obiavl.h
../../../src/obiavl.c

4
python/obitools3/obidms/_obidmscolumn_seq.cfiles
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@ -14,5 +14,5 @@
../../../src/obitypes.c
../../../src/private_at_functions.h
../../../src/private_at_functions.c
../../../src/obiarray.h
../../../src/obiarray.c
../../../src/obiavl.h
../../../src/obiavl.c

4
python/obitools3/obidms/_obidmscolumn_str.cfiles
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@ -14,5 +14,5 @@
../../../src/obitypes.c
../../../src/private_at_functions.h
../../../src/private_at_functions.c
../../../src/obiarray.h
../../../src/obiarray.c
../../../src/obiavl.h
../../../src/obiavl.c

4
python/obitools3/obidms/capi/obidmscolumn.pxd
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@ -30,7 +30,7 @@ cdef extern from "obidmscolumn.h" nogil:
bint referring
obiversion_t referred_column_version
const_char_p name
const_char_p array_name
const_char_p avl_name
const_char_p comments
ctypedef OBIDMS_column_header_t* OBIDMS_column_header_p
@ -47,7 +47,7 @@ cdef extern from "obidmscolumn.h" nogil:
index_t nb_lines,
index_t nb_elements_per_line,
const_char_p elements_names,
const_char_p array_name,
const_char_p avl_name,
const_char_p comments,
bint referring)