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dfd51939a03a13b6b81beaa34668f3967dd76cbe
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307 Commits

Author SHA1 Message Date
Celine Mercier
dfd51939a0 Views are now rollbacked if an error occurs, and unfinished views and 
columns are deleted when an OBIDMS is opened.
 2017-10-26 18:58:48 +02:00
Celine Mercier
04e065094a All DMS opened by a program are now listed and closed with atexit system 2017-10-16 10:35:07 +02:00
Celine Mercier
9fc6868341 Increased maximum length for elements names 2017-10-04 16:10:53 +02:00
Celine Mercier
535692b020 Taxonomy: new functions and improvements 2017-10-04 15:55:13 +02:00
Celine Mercier
5ed6835e0e Fixed a bug where the new line count when truncating a column would not 
be computed correctly when dealing with high numbers (bad automatic type
for intermediate result)
 2017-09-25 10:52:19 +02:00
Celine Mercier
7c57bd33e5 Added check to prevent views from having the name 'taxonomy' (used for 
URIs)
 2017-09-15 14:54:55 +02:00
Celine Mercier
38029b1f77 Forgot a ; 2017-08-20 17:56:18 +02:00
Celine Mercier
c559ddf487 BUG FIX: creation of a new column would fail because of a case not 
handled when a high number of elements per line would imply less than
one line per memory page
 2017-08-20 17:30:23 +02:00
Celine Mercier
93cff94e7f Fixed some compilation warnings 2017-08-20 17:25:58 +02:00
Celine Mercier
9744a48a67 BUG FIX: seemingly identical obiblobs would have different hash values 
because of the padding added by the compiler. Fixed by using calloc
instead of malloc for obiblob memory allocation.
 2017-08-20 17:25:15 +02:00
Celine Mercier
6afdc9fb5f AVLs: Added an error check 2017-08-20 17:21:06 +02:00
Celine Mercier
6f202363f4 Fixed a typo in doc 2017-08-20 17:20:13 +02:00
Celine Mercier
4b86aa67a8 New C functions to import a column and a view from a DMS to another DMS 2017-08-03 16:33:12 +02:00
Celine Mercier
a3e81930c2 Views: finished handling and documenting the conditions for an existing 
column to be added to a view
 2017-08-03 16:32:22 +02:00
Celine Mercier
644b55b49f Fixed doc typo 2017-08-03 16:29:25 +02:00
Celine Mercier
927c684fc2 Utils: new function to copy the content of a file into another file 2017-08-03 16:28:54 +02:00
Celine Mercier
344566d9e9 AVLs: made some functions public and changed some rights to be able to 
import AVLs from a DMS to another
 2017-08-03 16:27:43 +02:00
Eric Coissac
7c0d882bc9 Patch a bug when creating a DMS not in the current directory. Use the 
basename function to locate the DMS name instead of the loop...
 2017-07-28 15:56:21 +02:00
Celine Mercier
9482c663c0 minor comments and changes 2017-07-27 19:46:34 +02:00
Celine Mercier
c5f3fdc295 Increased maximum element names length in columns 2017-07-27 19:44:49 +02:00
Celine Mercier
15d383fa8b Added possibility to specify the offset for encoding and decoding 
sequence quality character strings
 2017-07-27 19:24:41 +02:00
Celine Mercier
59dd0a8a8c Standardized and improved the API to create new columns, updated the doc 2017-07-18 17:34:32 +02:00
Celine Mercier
c88df2e12c First version of automatic ID and COUNT columns, to discuss (for now, 
columns created when NUC_SEQ views are closed if the columns don't
already exist)
 2017-07-17 17:31:09 +02:00
Celine Mercier
1e57bfacb4 Fixed some C documentation 2017-07-17 16:45:08 +02:00
Celine Mercier
3e6aecc635 Added a C function to add a COUNT column to a view with all lines set to 
1
 2017-07-11 16:44:23 +02:00
Celine Mercier
f03928c679 Committing minor comments before merging branch with master 2017-07-06 10:56:39 +02:00
Celine Mercier
d10192ab0e C functions to detect IUPAC sequences 2017-07-05 17:26:03 +02:00
Celine Mercier
cb5ad2ed2d Added functions to try to open a DMS if it exists 2017-07-05 15:38:22 +02:00
Celine Mercier
f5e992abbf Added a check on the element when setting a value in a column 2017-07-05 14:49:20 +02:00
Celine Mercier
1d2996c6c0 Better handling and tracing of Index Errors between C and Cython 2017-07-05 14:45:43 +02:00
Celine Mercier
71b1a43df8 Added functions to clone views with a simpler API 2017-04-21 11:58:15 +02:00
Celine Mercier
2f0c4b90d7 Fixed a problem where a view would have a wrong line count after adding 
a first column to it if there was already a Line selection associated
(happening when cloning), and fixed a bad error check.
 2017-04-14 16:25:55 +02:00
Celine Mercier
537b9847da Minor C doc clarification 2017-04-14 16:23:17 +02:00
Celine Mercier
ad8de80353 Views: better checks when adding an existing column to a view 2017-04-06 14:44:07 +02:00
Celine Mercier
778acc48cd Added linked lists to handle lists of column pointers in views (not 
tested)
 2017-03-06 16:06:17 +01:00
Celine Mercier
3319ede837 Views: Column dictionaries now store and return pointers on column 
pointers instead of column pointers.
 2017-02-22 13:49:50 +01:00
Celine Mercier
431c1c8c6a Merge branch 'Eric_new_Python_API' of 
git@git.metabarcoding.org:obitools/obitools3.git into
Eric_new_Python_API

Conflicts:
	python/obitools3/obidms/_obidms.pxd
	python/obitools3/obidms/_obidms.pyx
	python/obitools3/obidms/_obidmscolumn_bool.pyx
	python/obitools3/obidms/_obidmscolumn_str.pyx
	python/obitools3/obidms/_obiseq.pxd
	python/obitools3/obidms/_obiseq.pyx
	python/obitools3/obidms/_obitaxo.pxd
	python/obitools3/obidms/_obitaxo.pyx
	python/obitools3/obidms/_obiview.pxd
	python/obitools3/obidms/_obiview.pyx
	python/obitools3/obidms/_obiview_nuc_seq.pxd
	python/obitools3/obidms/_obiview_nuc_seq.pyx
	python/obitools3/obidms/_obiview_nuc_seq_qual.pxd
	python/obitools3/obidms/_obiview_nuc_seq_qual.pyx
	python/obitools3/obidms/capi/obialign.pxd
	python/obitools3/obidms/capi/obidmscolumn.pxd
	python/obitools3/obidms/capi/obitaxonomy.pxd
	python/obitools3/obidms/capi/obiview.pxd
 2017-02-20 14:55:36 +01:00
Celine Mercier
e524041013 Views: Files for unfinished views now have the extension 
'.obiview_unfinished', renamed to '.obiview' when the view is finished.
 2017-02-07 17:16:09 +01:00
Celine Mercier
a9102620f5 Fixed missing email address 2017-02-07 17:14:10 +01:00
Celine Mercier
e50da64ea1 The elements names when a column contains several elements per line are 
now formatted with '\0' as separator and handled in a more optimized way
 2017-01-31 16:48:06 +01:00
Celine Mercier
651c1d7845 utilities: bsearch and qsort with additional user_data pointer argument 2017-01-31 16:45:47 +01:00
Celine Mercier
c0bcdce724 Taxonomy: documentation for all the functions, and fixed bugs when 
closing the taxonomy (overwriting of .pdx files, missing freeing, and
re-placed a misplaced condition)
 2017-01-18 18:22:49 +01:00
Celine Mercier
c065c1914a Taxonomy: adding, writing and reading preferred names, changed some 
function names, and fixed a bug with taxa indices not being properly
initialized
 2017-01-16 17:28:20 +01:00
Celine Mercier
0385a92e02 Taxonomy: Refactored the taxdump reading, and little fixes 2017-01-11 16:36:08 +01:00
Celine Mercier
41ad3deec0 Taxonomy: informations about deleted taxids is now read from 
delnodes.dmp file and added to *.adx file
 2017-01-09 17:28:49 +01:00
Celine Mercier
d68374018b Taxonomy: functions to read the *.adx file (containing the deprecated 
and current taxids and their corresponding indices in the taxa
structure) and to find the taxa using the merged index.
 2017-01-06 15:52:21 +01:00
Celine Mercier
f396625f98 Taxonomy: function to write *.adx files 2017-01-05 15:37:13 +01:00
Celine Mercier
897032387f Taxonomy: reading merged.dmp file in taxdump 2017-01-05 14:28:36 +01:00
Eric Coissac
daacd0df76 Strong refactoring 1 2016-12-26 13:35:31 +01:00
Celine Mercier
8e92bf6dac LCS alignment: it is now checked that sequences are not longer than what 
a 16 bits integer can code for (as the LCS and alignment lengths are
kept in 16 bits registers)
 2016-12-22 17:06:23 +01:00