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b3c47809da
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First version of alignment functions (imported from suma* programs)
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2016-05-11 16:36:23 +02:00 |
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f961621f5d
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Minor improvements in _obidms Cython layer
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2016-05-04 13:43:26 +02:00 |
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bc12360490
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Reworked and commented a bit the cython layer for dms, columns and views
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2016-05-02 15:16:06 +02:00 |
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872071b104
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Removed a list of column pointers kept in the OBIView class that was not
really needed
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2016-05-02 14:23:42 +02:00 |
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baba2d742e
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commenting _obidms.pyx
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2016-04-29 16:07:03 +02:00 |
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87935c6678
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Fixed all compilation problems with new function names, locations etc
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2016-04-25 18:35:02 +02:00 |
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2aafecc3b5
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Changed sequence 'description' to 'definition' everywhere
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2016-04-15 16:31:43 +02:00 |
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02d67c257f
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The default name of an AVL is now the column name + '_indexer', and when
an AVL is opened (as opposed to created), it is read-only
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2016-04-15 12:55:26 +02:00 |
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4cb52e1632
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Made the truncating of columns automatic when closing them (note:
already the case for AVLs)
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2016-04-14 15:13:30 +02:00 |
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d8107533d8
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Obiblob_indexer API
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2016-04-12 14:53:33 +02:00 |
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21d1b2ed3e
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First implementation of taxonomy reading
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2016-03-11 13:56:38 +01:00 |
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a08def47e6
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It is now impossible to create a view with a name identical to one of an
existing written view
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2016-03-01 13:36:54 +01:00 |
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fc5a12bad7
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Closes #34
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2016-02-29 17:56:55 +01:00 |
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e323d8e702
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Cython classes for nucleotide sequences (outside or in the context of a
view)
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2016-02-29 16:33:30 +01:00 |
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4df313c54a
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Added Obiviews specialized for the handling of nucleotide sequences
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2016-02-25 09:43:27 +01:00 |
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ffc68d448f
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Deleted a forgotten print statement
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2016-02-18 15:15:42 +01:00 |
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a8f03248a8
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Major update : views
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2016-02-18 10:38:51 +01:00 |
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c139367555
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DNA sequences and character strings are now handled using AVL trees.
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2015-12-11 17:24:44 +01:00 |
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1586956d57
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Added the lists of opened columns and arrays in the OBIDMS structure,
and a counter in the OBIDMS column structure; fixed some bugs and
created tests for referring columns that are bound to disappear anyway.
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2015-12-02 17:32:07 +01:00 |
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b45b496b0e
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Major update: new type of columns containing indices referring to lines
in other columns
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2015-11-29 11:57:07 +01:00 |
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2cf10cb6f0
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Column type is now passed as a character string when creating the column
(either 'OBI_INT', 'OBI_FLOAT', 'OBI_BOOL', 'OBI_CHAR', 'OBI_STR' or
'OBI_SEQ')
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2015-11-23 15:48:27 +01:00 |
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6ab1c83302
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New column type for DNA sequences. Only for those coded on 2 bits (only
'ATGCatgc') for now.
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2015-11-19 18:12:48 +01:00 |
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e8417b4f6f
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The endianness of an OBIDMS is now stored in an informations file that
is read when opening the OBIDMS.
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2015-11-16 14:37:51 +01:00 |
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6579566c6e
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Minor changes in code to improve readability and fix C compilation
warnings
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2015-11-10 14:37:58 +01:00 |
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410e2e02a0
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When retrieving the header of a column, the version number of the column
wanted can now be provided.
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2015-11-10 13:30:10 +01:00 |
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c4b7e579cf
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Comments in column headers are now working.
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2015-11-10 10:56:45 +01:00 |
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0e3d6ed2d7
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Methods __len__ (number of lines used) and __sizeof__ (total size in
bytes) implemented for columns.
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2015-11-09 15:56:20 +01:00 |
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9b066f4327
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Major update: obiarrays with columns containing indices referring to
character strings.
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2015-11-06 17:55:15 +01:00 |
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456551ffeb
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obi arrays that don't work because of cython bug passing wrong pointers
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2015-11-03 14:22:00 +01:00 |
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ecb9d97adb
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Reorganized the code to have less functions, and the functions to get
and format the creation date of a column are now working.
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2015-10-15 15:12:45 +02:00 |
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0eaa5aa784
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Major changes : new cython subclasses to handle columns with multiple
elements per line in a more efficient way + now elements_names are
passed as a list + new function to recover only the header of a column
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2015-10-14 18:05:34 +02:00 |
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b553eef781
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Method to close a DMS is uncommented but not complete yet (columns have
to be closed separately)
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2015-10-08 10:44:13 +02:00 |
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392f110c8d
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new functions in the OBIDMS_column class to raise NotImplementedError
exceptions and to get the creation date of a column
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2015-10-02 13:51:26 +02:00 |
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72155c3b73
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entirely reworked cython wrapper
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2015-09-28 13:51:35 +02:00 |
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0951934f77
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test
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2015-09-25 11:28:23 +02:00 |
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