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408 Commits 18 Branches 66 Tags
b5b889c4a28c0db3cdf27ab50bc1f568c4379a64
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Author SHA1 Message Date
Celine Mercier
b5b889c4a2 Fixed the OBI_Nuc_Seq_Stored cython class not being up to date with the 
new properties of its parent class
 2016-11-08 11:26:37 +01:00
Celine Mercier
36ac315125 Fixed bugs with python view type when creating a new view, and a bug 
when trying to guess the obi type of a nucleotide sequence when its type
was bytes
 2016-11-08 11:23:54 +01:00
Celine Mercier
8291693309 obi grep: updated to work with the new line selection class and within 
the local sequence environment, and progress bar functioning
 2016-11-08 11:19:12 +01:00
Celine Mercier
4bc19c3e49 obi export: view type is now checked and progress bar functioning 2016-11-08 11:17:20 +01:00
Celine Mercier
2d2fe5279d Added functions to add new taxa to a taxonomy with handling of 
associated *.ldx files
 2016-11-03 17:59:21 +01:00
Celine Mercier
2504bf0fa9 Added an iterator to the OBI_Taxonomy cython class 2016-11-02 11:08:18 +01:00
Celine Mercier
d8a257e711 Taxonomy handling functions in C. Features: read taxdump, read binary 
files, write binary files. Not fully handled yet: *.adx, *.pdx, *.ldx,
merged.dmp and delnodes.dmp files.
 2016-10-27 18:56:11 +02:00
Celine Mercier
b63d0fb9fb Added C functions to write .rdx, .tdx, .ndx binary taxonomy files from a 
taxonomy C structure
 2016-10-14 17:03:10 +02:00
Celine Mercier
0dfd67ec89 The endianness of binary taxonomy files is now correctly checked 2016-10-10 17:04:29 +02:00
Celine Mercier
0faaac49cf The taxonomy directory of the DMS is now automatically created with the 
DMS
 2016-10-10 17:02:51 +02:00
Celine Mercier
1b07109e51 Removed deprecated code 2016-10-10 17:01:51 +02:00
Celine Mercier
60ab503a14 Added properties in the OBI_Taxonomy class 2016-10-10 17:01:17 +02:00
Celine Mercier
2dcfdc59fc When a new view is created with a line selection, the view to clone is 
automatically found + compacted redundant code + fixed potential bug
when cloning a NUC_SEQS view by name
 2016-10-06 17:55:18 +02:00
Celine Mercier
399fc2c051 Removed deprecated source files previously used for tests 2016-09-30 17:49:37 +02:00
Celine Mercier
9cd57deca9 Added OBIView_line_selection class to make new line selections 
associated with the view to clone, and improved and renamed method
closing a view
 2016-09-30 17:48:53 +02:00
Celine Mercier
d88811ed7d Added a seed option to the obi test command for reproducible tests 2016-09-29 17:34:48 +02:00
Celine Mercier
8c402101e4 Renamed private attributes as _* and removed some deprecated code 2016-09-28 16:56:44 +02:00
Celine Mercier
1a7b42018e Added some error checking when opening or creating a view 2016-09-28 14:28:34 +02:00
Celine Mercier
b717e8bb8b Added properties for the OBIView class and cleaned up deprecated code 2016-09-28 14:26:23 +02:00
Celine Mercier
03a2c8ef7c Finished restructuring the OBIDMS_column class properties 2016-09-27 14:16:30 +02:00
Celine Mercier
a7f891d1c9 Added a lines_used property to the OBIDS_column class 2016-09-26 18:04:28 +02:00
Celine Mercier
bd50b3f972 Added version property to OBIDMS_column class 2016-09-26 17:45:10 +02:00
Celine Mercier
81380363b7 Added original_name property to OBIDMS_column class 2016-09-26 17:31:32 +02:00
Celine Mercier
a4b8349274 Added data_type property to OBIDMS_column class 2016-09-26 17:12:20 +02:00
Celine Mercier
a474391b27 Added nb_elements_per_line property to OBIDMS_column class 2016-09-26 17:01:13 +02:00
Celine Mercier
a0bc45cc92 Added elements_names property to OBIDMS_column class 2016-09-26 16:53:16 +02:00
Celine Mercier
76f89717fe Added alias property to OBIDMS_column cython class 2016-09-26 16:12:48 +02:00
Celine Mercier
b408a4f6eb Changed file name limits to adapt to system limits + minor changes 2016-09-22 18:05:07 +02:00
Celine Mercier
b083745f56 Deleted the "new line selection while editing a view" system 2016-09-22 11:19:29 +02:00
Celine Mercier
43f3c69a40 Fixed bug when cloning column with line selection 2016-09-21 17:50:21 +02:00
Celine Mercier
e79507b629 Fixed bugs in the process ensuring that all the columns of a view have 
the same line count, fixed a bug when trying to set a value in a view
when a line selection exists, fixed a bug when adding a new column to a
view where line counts would be wrong
 2016-09-21 17:42:17 +02:00
Celine Mercier
bb25723d99 Improved documentation of a function 2016-09-21 17:30:39 +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
802bae110b Removed deprecated function 2016-09-21 17:09:59 +02:00
Celine Mercier
dd55aef3e5 Added column class method to get the unique references (name and 
version) of a column
 2016-09-21 17:08:44 +02:00
Celine Mercier
9ac522fde1 Better obi test command 2016-09-21 17:06:35 +02:00
Eric Coissac
6adb9eb623 Should solde issue #56 2016-09-19 21:40:40 +02:00
Celine Mercier
8f49553d5a First version of the obi test command, testing that the OBITools3 work 
correctly
 2016-09-15 12:26:07 +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
a240ec0169 Added error checking when closing file descriptors 2016-09-15 11:58:56 +02:00
Celine Mercier
0a3c23d9d0 Added a missing closedir 2016-09-15 11:58:34 +02:00
Celine Mercier
8724445fa1 Added error checking when closing files 2016-09-15 11:50:30 +02:00
Celine Mercier
de189fd7e0 Fixed major bug when cloning an AVL where the bloom filter was not 
copied properly (because the sutructure copy via assignation does not
work for structures with a variable size)
 2016-09-15 11:47:02 +02:00
Celine Mercier
9a97f1f633 View predicates are now carried over when cloning a view 2016-09-06 16:22:24 +02:00
Celine Mercier
00014eb023 View files now have the *.obiview extension 2016-09-06 14:19:13 +02:00
Celine Mercier
acc0da2d0b Readjusted some limits for file names and file numbers to be under OS 
limits
 2016-09-05 12:39:04 +02:00
Celine Mercier
668696fc5a Fixed major bug: when setting all the columns of a view to the same 
number of lines, columns are now cloned before being enlarged if needed
+ predicate functions now print error messages if the predicates are not
respected
 2016-09-05 12:37:36 +02:00
Celine Mercier
ba84ef4847 Fixed typo 2016-09-05 12:31:06 +02:00
Celine Mercier
c9dce03295 Fixed major bug when cloning an AVL group (last AVL of new group was not 
correctly enlarged before copying the data) + minor improvements
 2016-09-05 12:29:52 +02:00
Celine Mercier
eb82d088cb Added some view class methods 2016-09-05 12:20:00 +02:00