70e056a2aa
It is now impossible to open or clone a view that is not finished (= has
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been closed at least once)
2016-11-24 11:19:07 +01:00
8abbfa203a
Good file for commit 6fa9a8bd: When a view is cloned, a comment is added
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to the new view specifying the name of the cloned view
2016-11-23 11:32:39 +01:00
6fa9a8bd76
When a view is cloned, a comment is added to the new view specifying the
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name of the cloned view
2016-11-23 11:29:21 +01:00
0ab9e6c05a
When adding an existing column to a view, it is checked that the
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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
70c49e214a
Added the kmer filter to LCS alignments, and now obiblobs containing
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encoded sequences are directly put in int16_t arrays for the alignment
2016-11-18 16:29:28 +01:00
08e67a090f
Changed the inline functions syntax, which should make it compatible
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with more compilers
2016-11-18 16:21:26 +01:00
621b4972db
Functions to get obiblobs through views
2016-11-18 15:59:50 +01:00
7d022c1a52
If the indexer name is NULL when creating a column, it now becomes the
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column name
2016-11-18 15:56:51 +01:00
1c71c195fc
Goes with a0ebc2d8
2016-11-10 15:01:29 +01:00
54cfeffd85
Goes with 8f724f4f, forgotten file
2016-11-10 14:48:31 +01:00
a0ebc2d871
Functions to directly retrieve Obiblobs from indexers
2016-11-10 14:45:28 +01:00
8f724f4f8e
Some code refactoring
2016-11-09 16:48:00 +01:00
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
