ffebc6acfb
Cython API: better handling of default quality offset value
2018-05-17 15:01:25 +02:00
123fb9d7ba
Cython API: in taxonomy, added get_taxon_at_rank() function for Taxonomy
...
class and rank_idx property for Taxon class
2018-03-21 16:38:26 +01:00
ea58e254da
Cython API: repr function for DMS
2018-03-19 13:08:06 +01:00
dad21823ff
Cython API: trying to guess the type of a column when adding a None
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value does not generate an exception anymore, and RollbackException can
now rollback several views
2018-03-12 18:03:37 +01:00
96bf2daae8
Cython API: added slices in Seq classes and fixes
2018-03-12 17:51:41 +01:00
b2cfa4b52f
Cython Sequence classes: reworked improved etc
2018-02-12 14:54:47 +01:00
94a899de12
Cython View API: added small tools
2018-02-12 14:48:27 +01:00
156fb04e88
Implemented functions to build reverse complement sequences
2018-01-05 16:08:36 +01:00
1a5b499b5c
Cython API to add an OBI_QUAL column after creating a view
2017-12-19 11:06:24 +01:00
b7b8ba7e5a
Better handling of elements names in Cython
2017-12-13 23:12:14 +01:00
1fd3323372
Columns: elements names informations are now kept in a memory arena of
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adapted size in the header, and added a boolean in the header indicating
whether the values should be evaluated (typically character strings to
be evaluated in Python)
2017-12-13 22:46:50 +01:00
2df5932b67
Cython column API: fixed a memory leak, optimized the reading of
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elements names, added a __len__ method to Column_line, and the API for
columns with character strings to evaluate
2017-12-13 22:27:36 +01:00
9e3ac477eb
OBIDMS: Opened DMS now have a counter associated so that DMS are not
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actually opened several times by the same program, which triggers the
cleaning of unfinished views and columns (to discuss)
2017-11-24 17:58:47 +01:00
ee5d647d0d
Taxonomy: fixed a bug un parental tree iterator
2017-11-24 17:55:17 +01:00
9a50803c00
Added tuple columns containing immutable indexed data arrays of any type
2017-11-15 13:48:59 +01:00
dfd51939a0
Views are now rollbacked if an error occurs, and unfinished views and
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columns are deleted when an OBIDMS is opened.
2017-10-26 18:58:48 +02:00
04e065094a
All DMS opened by a program are now listed and closed with atexit system
2017-10-16 10:35:07 +02:00
09a5f89849
Column API: improvements to be more flexible when referring to elements
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in columns with several elements per line.
2017-10-04 15:59:23 +02:00
535692b020
Taxonomy: new functions and improvements
2017-10-04 15:55:13 +02:00
0e140df0fb
Cython API: added some imports in __init__ files
2017-09-14 18:30:04 +02:00
663a1a1091
Cython API: column elements: added possibility to check if an element
...
exists from its index, and a dict-like get() method
2017-08-20 17:44:05 +02:00
c6d5436a58
Cython API: fixed a bug where iteration on a NUC_SEQS view would not be
...
done correctly (bug appeared with optimization modifications done
lately)
2017-08-20 17:41:41 +02:00
47cad285d6
Cython API: fixed 2 little bugs in Seq API
2017-08-20 17:39:30 +02:00
7f1ff49aa2
Cython API to import a column and a view from a DMS to another DMS
2017-08-03 16:34:02 +02:00
35b0c55a8c
Cython API: various improvements and checks
2017-07-28 13:15:13 +02:00
84bb93096f
Cython API: fixes and improvements in Column API
2017-07-28 10:27:04 +02:00
01c69e7e25
Cython API: fixed a bug when printing a column
2017-07-28 10:01:56 +02:00
adf5cbef97
Added DMS method to create a DMS if it doesn't already exists, otherwise
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opens it
2017-07-28 09:55:43 +02:00
75f691d55a
Cython API: Seq classes reworked
2017-07-27 19:39:58 +02:00
0655063bb0
Cython API: view_NUC_SEQS changes to go with previous commits
2017-07-27 19:39:26 +02:00
9701b1230c
Cython API: OBIWrapper.new method is now OBIWrapper.new_wrapper to avoid
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mismatching method definitions with subclasses
2017-07-27 19:38:25 +02:00
f8a4428674
Cython API: DMS test_open method doesn't raise an exception anymore
2017-07-27 19:36:28 +02:00
1a0f18a11a
Cython API: added a __setitem__ method to the View class that can detect
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if the item is a Line and create the corresponding columns if needed +
minor changes
2017-07-27 19:35:28 +02:00
3d7aa52c90
Cython API: Fixed a bug when setting NA values in Column_multi_elts, and
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added some properties
2017-07-27 19:31:15 +02:00
69c50ff922
Cython API: added a Column subclass to allow direct access to indexes
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for columns that store indexes referring to other data
2017-07-27 19:29:10 +02:00
c91969126b
Cython C API declarations to go with previous commit
2017-07-27 19:26:59 +02:00
15d383fa8b
Added possibility to specify the offset for encoding and decoding
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sequence quality character strings
2017-07-27 19:24:41 +02:00
99ceed5fff
Cython API: renamed OBI_Taxonomy to Taxonomy and OBI_Taxon to Taxon
2017-07-27 19:21:45 +02:00
df2ad41150
Cython APi: Added a width property to views, corresponding to their
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column count
2017-07-11 11:46:32 +02:00
f8895e879d
Cython API: Added a function to get a column from its index in the view
2017-07-11 11:36:42 +02:00
b94ec9557f
Cython API: None values aren't inclued anymore in the dictionary
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returned when getting a line from a column with multiple elements per
line, and reworked that function to be more optimized
2017-07-07 17:28:53 +02:00
143bddf1d1
Cython API: Added an __iter__ method to the class Column_line (iterating
...
on the elements names) (previously an iteration would work but with
unexpected results)
2017-07-07 15:41:10 +02:00
a718081ebd
Bug with error handling: for now obi_errno needs to be passed to the
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function handling errors and exceptions, as it can't read the right
value of the global obi_errno (Cython configuration problem?)
2017-07-07 15:36:11 +02:00
717ee46f08
Commented a loose print
2017-07-05 18:02:18 +02:00
313508cc94
Better *Seq* classes but still need work
2017-07-05 17:53:46 +02:00
535fc2af83
Column rewriter and optimized View getter
2017-07-05 17:49:05 +02:00
3bbc2ae469
More optimized Column item getter
2017-07-05 17:37:19 +02:00
5ee0b3989a
Cython API: set_line of Column_multi_elts now accept as values argument
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any class where values are referenced by keys with an iterator
2017-07-05 17:32:32 +02:00
d10192ab0e
C functions to detect IUPAC sequences
2017-07-05 17:26:03 +02:00
cb5ad2ed2d
Added functions to try to open a DMS if it exists
2017-07-05 15:38:22 +02:00
