2d2fe5279d
Added functions to add new taxa to a taxonomy with handling of
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associated *.ldx files
2016-11-03 17:59:21 +01:00
d8a257e711
Taxonomy handling functions in C. Features: read taxdump, read binary
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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
b63d0fb9fb
Added C functions to write .rdx, .tdx, .ndx binary taxonomy files from a
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taxonomy C structure
2016-10-14 17:03:10 +02:00
0dfd67ec89
The endianness of binary taxonomy files is now correctly checked
2016-10-10 17:04:29 +02:00
0faaac49cf
The taxonomy directory of the DMS is now automatically created with the
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DMS
2016-10-10 17:02:51 +02:00
9cd57deca9
Added OBIView_line_selection class to make new line selections
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associated with the view to clone, and improved and renamed method
closing a view
2016-09-30 17:48:53 +02:00
1a7b42018e
Added some error checking when opening or creating a view
2016-09-28 14:28:34 +02:00
b408a4f6eb
Changed file name limits to adapt to system limits + minor changes
2016-09-22 18:05:07 +02:00
b083745f56
Deleted the "new line selection while editing a view" system
2016-09-22 11:19:29 +02:00
43f3c69a40
Fixed bug when cloning column with line selection
2016-09-21 17:50:21 +02:00
e79507b629
Fixed bugs in the process ensuring that all the columns of a view have
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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
bb25723d99
Improved documentation of a function
2016-09-21 17:30:39 +02:00
a0da984003
Fixed bug where columns would not get truncated to the right size, and
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fixed bug where column directories would be open and not closed in some
instances
2016-09-21 17:28:52 +02:00
802bae110b
Removed deprecated function
2016-09-21 17:09:59 +02:00
986f90c59e
Fixed bug where column directories weren't closed correctly, leading to
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too many file descriptors open, and added error checking when closing
file descriptors
2016-09-15 12:18:40 +02:00
a240ec0169
Added error checking when closing file descriptors
2016-09-15 11:58:56 +02:00
0a3c23d9d0
Added a missing closedir
2016-09-15 11:58:34 +02:00
8724445fa1
Added error checking when closing files
2016-09-15 11:50:30 +02:00
de189fd7e0
Fixed major bug when cloning an AVL where the bloom filter was not
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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
9a97f1f633
View predicates are now carried over when cloning a view
2016-09-06 16:22:24 +02:00
00014eb023
View files now have the *.obiview extension
2016-09-06 14:19:13 +02:00
acc0da2d0b
Readjusted some limits for file names and file numbers to be under OS
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limits
2016-09-05 12:39:04 +02:00
668696fc5a
Fixed major bug: when setting all the columns of a view to the same
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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
ba84ef4847
Fixed typo
2016-09-05 12:31:06 +02:00
c9dce03295
Fixed major bug when cloning an AVL group (last AVL of new group was not
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correctly enlarged before copying the data) + minor improvements
2016-09-05 12:29:52 +02:00
f46ea0b988
Finished fixing issues with DMS paths
2016-08-30 11:09:45 +02:00
5b2e370ffb
Fixed a bug when using an absolute path for a DMS
2016-08-29 17:30:31 +02:00
7b780ffb28
View files now have a dynamic size to allow unlimited comments size
2016-08-18 17:57:03 +02:00
e4129610cf
Quality columns are now optional in NUC_SEQS views + minor fixes
2016-08-16 15:17:26 +02:00
92cad61417
Fixed bug when closing views with no associated predicate
2016-08-12 15:52:38 +02:00
2d8ac2b035
Fixed bug when creating an OBI_IDX column
2016-08-11 17:30:32 +02:00
5b7917bb5a
Fixed bug when writing predicates in view file
2016-08-11 17:30:09 +02:00
2aaa87edcc
1st version of obi align command and reworked functions that handle
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column alignment
2016-08-10 14:51:02 +02:00
26b8e1f215
Modified C API to set and get in columns: added functions to set and get
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using column names instead of pointers, and changed function names
2016-08-02 16:33:19 +02:00
312f50ff0f
Major update: Column aliases. Columns are now identified in the context
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of a view by an alias that can be modified.
2016-08-01 18:25:30 +02:00
3843485a04
Deleted deprecated function declaration that would make compilation
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impossible and fixed error in documentation
2016-07-22 16:21:02 +02:00
20425a5d2b
Deleted deprecated structure declarations
2016-07-19 15:48:56 +02:00
56e4848ebd
The predicates associated with a view are now described in its comments
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field
2016-07-19 15:31:21 +02:00
38718320f9
First version for the association of one column to another. Closes #55
2016-07-15 15:38:49 +02:00
8ee85c3005
A first version of predicate functions that are checked when a new view
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is saved and closed
2016-07-12 14:54:11 +02:00
0869b9ba3f
Closes issue #47 by storing each view in a separate file named with the
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view's name and created upon view creation.
2016-06-30 11:41:30 +02:00
ad2af0b512
Some comments updated
2016-06-16 11:26:54 +02:00
2a1ea3ba3f
Setting NA values is now handled properly for OBI_SEQ, OBI_STR and
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OBI_QUAL columns
2016-06-09 14:22:36 +02:00
fc3641d7ff
Read-only AVLs are now hard-linked instead of copied when cloning an AVL
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group to make it writable. Also fixed several bugs when handling AVL
groups.
2016-06-03 19:02:46 +02:00
799b942017
Deleted old debugging print
2016-06-03 18:57:32 +02:00
6e3f5b230e
Fixed typo in doc
2016-06-03 18:56:45 +02:00
2f57f80c63
Fixed a bug where an unmapped variable would be read
2016-06-03 18:55:58 +02:00
2962c4d250
Goes with previous commit
2016-06-03 18:54:25 +02:00
e681ca646d
Fixed a problem with some columns being shorter in views and triggering
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errors when trying to get values. Temporary fix that needs discussion
2016-05-20 18:45:29 +02:00
3b59043ea8
Major update: New column type to store sequence qualities. Closes #41
2016-05-20 16:45:22 +02:00
Celine Mercier