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459 Commits 18 Branches 66 Tags
5122ad52a719dd72df0ce52732645427cb535934
Commit Graph

89 Commits

Author SHA1 Message Date
Eric Coissac
daacd0df76 Strong refactoring 1 2016-12-26 13:35:31 +01:00
Celine Mercier
936be64c34 Goes with 5e0c9f87 (missing ';' and fixed compilation warnings) 2016-12-05 11:18:29 +01:00
Celine Mercier
5e0c9f878b Added the doc for the function building the element names, and a missing 
free
 2016-12-05 10:46:21 +01:00
Celine Mercier
852e5488c8 The default element names for columns with multiple elements per line 
are now "O;1;2;...;n"
 2016-12-02 17:54:51 +01:00
Celine Mercier
7d022c1a52 If the indexer name is NULL when creating a column, it now becomes the 
column name
 2016-11-18 15:56:51 +01:00
Celine Mercier
8f724f4f8e Some code refactoring 2016-11-09 16:48:00 +01:00
Celine Mercier
43f3c69a40 Fixed bug when cloning column with line selection 2016-09-21 17:50:21 +02:00
Celine Mercier
a0da984003 Fixed bug where columns would not get truncated to the right size, and 
fixed bug where column directories would be open and not closed in some
instances
 2016-09-21 17:28:52 +02:00
Celine Mercier
986f90c59e Fixed bug where column directories weren't closed correctly, leading to 
too many file descriptors open, and added error checking when closing
file descriptors
 2016-09-15 12:18:40 +02:00
Celine Mercier
2d8ac2b035 Fixed bug when creating an OBI_IDX column 2016-08-11 17:30:32 +02:00
Celine Mercier
38718320f9 First version for the association of one column to another. Closes #55 2016-07-15 15:38:49 +02:00
Celine Mercier
799b942017 Deleted old debugging print 2016-06-03 18:57:32 +02:00
Celine Mercier
e681ca646d Fixed a problem with some columns being shorter in views and triggering 
errors when trying to get values. Temporary fix that needs discussion
 2016-05-20 18:45:29 +02:00
Celine Mercier
8ae7644945 First version of quality handling (not working yet) and now it is 
checked that a column is writable before enlarging it
 2016-05-11 16:38:14 +02:00
Celine Mercier
f3b20b809d Fixed bug with indexer names being defined and generating seg fault if 
creating a column not using indexers
 2016-04-27 14:01:36 +02:00
Celine Mercier
66045acf1d Creating a column now uses the function to create the indexer name if 
one was not provided
 2016-04-22 17:47:00 +02:00
Celine Mercier
ffa4557928 changed MAP_PRIVATE flags to MAP_SHARED when opening a column because it 
seems a lot more efficient
 2016-04-22 16:26:24 +02:00
Celine Mercier
003cd11362 Fixed initialization of NA values for OBI_STR and OBI_SEQ columns 2016-04-22 16:14:23 +02:00
Celine Mercier
c87227b65a Uncommented an error message that doesn't need to be commented anymore 2016-04-22 16:11:56 +02:00
Celine Mercier
2aafecc3b5 Changed sequence 'description' to 'definition' everywhere 2016-04-15 16:31:43 +02:00
Celine Mercier
02d67c257f 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
 2016-04-15 12:55:26 +02:00
Celine Mercier
71492ad229 Made the handling of listing and unlisting opened columns and indexers 
functions in the obidms files.
 2016-04-15 10:49:12 +02:00
Celine Mercier
73d64e5aff Renamed 'unmap_header' function to 'close_header' 2016-04-14 15:19:27 +02:00
Celine Mercier
4cb52e1632 Made the truncating of columns automatic when closing them (note: 
already the case for AVLs)
 2016-04-14 15:13:30 +02:00
Celine Mercier
9d042f7bd0 Refactored and relocated the set and get functions of all column types, 
both within and out of the context of a view
 2016-04-13 15:10:24 +02:00
Celine Mercier
d8107533d8 Obiblob_indexer API 2016-04-12 14:53:33 +02:00
Celine Mercier
019dfc01b4 Branch to refactor and debug (AVLs bugged) 2016-04-08 15:38:57 +02:00
Celine Mercier
4085904362 Merge branch 'multiple_avls_bloom' 2016-03-22 14:14:10 +01:00
Celine Mercier
b04b4b5902 made POSIX compliant 2016-03-21 11:33:06 +01:00
Celine Mercier
3681cecb4d Multiple AVLs with bloom filters (very raw test version) 2016-03-18 11:06:02 +01:00
Celine Mercier
545ed8111a Code for tests storing data in multiple AVLs. 
(note: unretrievable data as implemented)
 2016-03-11 15:34:55 +01:00
Celine Mercier
a8f03248a8 Major update : views 2016-02-18 10:38:51 +01:00
Celine Mercier
c139367555 DNA sequences and character strings are now handled using AVL trees. 2015-12-11 17:24:44 +01:00
Celine Mercier
1586956d57 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.
 2015-12-02 17:32:07 +01:00
Celine Mercier
b45b496b0e Major update: new type of columns containing indices referring to lines 
in other columns
 2015-11-29 11:57:07 +01:00
Celine Mercier
d6a99bafea Fixed a major bug with the versioning of columns that was introduced in 
f6ec8ba9
 2015-11-23 13:34:51 +01:00
Celine Mercier
6ab1c83302 New column type for DNA sequences. Only for those coded on 2 bits (only 
'ATGCatgc') for now.
 2015-11-19 18:12:48 +01:00
Celine Mercier
e8417b4f6f The endianness of an OBIDMS is now stored in an informations file that 
is read when opening the OBIDMS.
 2015-11-16 14:37:51 +01:00
Celine Mercier
6579566c6e Minor changes in code to improve readability and fix C compilation 
warnings
 2015-11-10 14:37:58 +01:00
Celine Mercier
410e2e02a0 When retrieving the header of a column, the version number of the column 
wanted can now be provided.
 2015-11-10 13:30:10 +01:00
Celine Mercier
8ce4f264aa When enlarging a column, the function doesn't try anymore to keep the 
mapped region at the same pointer (never works), and unmap/remap
instead.
 2015-11-10 13:18:36 +01:00
Celine Mercier
d885eb48ff The header size when creating a column is now calculated according to 
the size of the header structure and the page size of the platform.
 2015-11-10 13:09:30 +01:00
Celine Mercier
c4b7e579cf Comments in column headers are now working. 2015-11-10 10:56:45 +01:00
Celine Mercier
f6ec8ba963 The header size is now directly read in the file when a column or an 
array is opened.
 2015-11-09 17:50:32 +01:00
Celine Mercier
01bfc14503 The data size in bytes is now stored in the header of a column. 2015-11-09 15:55:00 +01:00
Celine Mercier
65c1b1e8b2 Minor changes to make the creation of files and directories cleaner 2015-11-09 15:22:01 +01:00
Celine Mercier
b37bd8f21c File descriptors for dms, column and array directories are now stored in 
structures.
 2015-11-09 15:06:02 +01:00
Celine Mercier
05e3956a0c Minor changes in code to improve readability (freeing some character 
strings earlier)
 2015-11-09 11:22:51 +01:00
Celine Mercier
9b066f4327 Major update: obiarrays with columns containing indices referring to 
character strings.
 2015-11-06 17:55:15 +01:00
Celine Mercier
456551ffeb obi arrays that don't work because of cython bug passing wrong pointers 2015-11-03 14:22:00 +01:00