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Author SHA1 Message Date
Celine Mercier
d40d2d0c76 Fixed error in documentation 2016-11-28 10:55:23 +01:00
Celine Mercier
f897e87600 When closing a view, it is now automatically checked that all OBI_QUAL 
columns correspond to their associated OBI_SEQ column
 2016-11-25 12:04:57 +01:00
Celine Mercier
70e056a2aa It is now impossible to open or clone a view that is not finished (= has 
been closed at least once)
 2016-11-24 11:19:07 +01:00
Celine Mercier
8abbfa203a Good file for commit 6fa9a8bd: When a view is cloned, a comment is added 
to the new view specifying the name of the cloned view
 2016-11-23 11:32:39 +01:00
Celine Mercier
6fa9a8bd76 When a view is cloned, a comment is added to the new view specifying the 
name of the cloned view
 2016-11-23 11:29:21 +01:00
Celine Mercier
76a4c6b14e Fixed a bug when cloning a view and checking its type 2016-11-23 11:28:17 +01:00
Celine Mercier
0ab9e6c05a When adding an existing column to a view, it is checked that the 
column's line count is at least the view's line count. This can't be
more stringent for reasons that need to be rediscussed
 2016-11-23 11:04:53 +01:00
Celine Mercier
70c49e214a Added the kmer filter to LCS alignments, and now obiblobs containing 
encoded sequences are directly put in int16_t arrays for the alignment
 2016-11-18 16:29:28 +01:00
Celine Mercier
08e67a090f Changed the inline functions syntax, which should make it compatible 
with more compilers
 2016-11-18 16:21:26 +01:00
Celine Mercier
621b4972db Functions to get obiblobs through views 2016-11-18 15:59:50 +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
1c71c195fc Goes with a0ebc2d8 2016-11-10 15:01:29 +01:00
Celine Mercier
54cfeffd85 Goes with 8f724f4f, forgotten file 2016-11-10 14:48:31 +01:00
Celine Mercier
a0ebc2d871 Functions to directly retrieve Obiblobs from indexers 2016-11-10 14:45:28 +01:00
Celine Mercier
8f724f4f8e Some code refactoring 2016-11-09 16:48:00 +01:00
Celine Mercier
359578814b Added view type property to OBIView cython class and updated obi export 
to use it
 2016-11-08 17:49:59 +01:00
Celine Mercier
51b23915ca Added properties for Nuc_Seq cython classes (and updated commands using 
them)
 2016-11-08 16:59:32 +01:00
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