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Author SHA1 Message Date
Celine Mercier 89e2f80fd8 Goes with previous commit 2017-07-27 19:43:00 +02:00
Celine Mercier 7112f44fb7 Bug fixes for input handlers, openers, parsers etc. Compiling but not 
tested
 2017-07-27 19:42:44 +02:00
Celine Mercier b2fc1f4611 obi uniq: first version 2017-07-27 19:40:19 +02:00
Celine Mercier 75f691d55a Cython API: Seq classes reworked 2017-07-27 19:39:58 +02:00
Celine Mercier 0655063bb0 Cython API: view_NUC_SEQS changes to go with previous commits 2017-07-27 19:39:26 +02:00
Celine Mercier 9701b1230c Cython API: OBIWrapper.new method is now OBIWrapper.new_wrapper to avoid 
mismatching method definitions with subclasses
 2017-07-27 19:38:25 +02:00
Celine Mercier f8a4428674 Cython API: DMS test_open method doesn't raise an exception anymore 2017-07-27 19:36:28 +02:00
Celine Mercier 1a0f18a11a Cython API: added a __setitem__ method to the View class that can detect 
if the item is a Line and create the corresponding columns if needed +
minor changes
 2017-07-27 19:35:28 +02:00
Celine Mercier 3d7aa52c90 Cython API: Fixed a bug when setting NA values in Column_multi_elts, and 
added some properties
 2017-07-27 19:31:15 +02:00
Celine Mercier 69c50ff922 Cython API: added a Column subclass to allow direct access to indexes 
for columns that store indexes referring to other data
 2017-07-27 19:29:10 +02:00
Celine Mercier c91969126b Cython C API declarations to go with previous commit 2017-07-27 19:26:59 +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 99ceed5fff Cython API: renamed OBI_Taxonomy to Taxonomy and OBI_Taxon to Taxon 2017-07-27 19:21:45 +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 ced9a268a1 obi import: added an option to specify the NA value in the input file 
(default is 'NA', same as in R's read.table function)
 2017-07-11 12:10:33 +02:00
Celine Mercier df2ad41150 Cython APi: Added a width property to views, corresponding to their 
column count
 2017-07-11 11:46:32 +02:00
Celine Mercier f8895e879d Cython API: Added a function to get a column from its index in the view 2017-07-11 11:36:42 +02:00
Celine Mercier b729b8928f obi less: fixed bug when the length of a view would be less than the 
default number of lines printed
 2017-07-10 17:04:02 +02:00
Celine Mercier b6b95f26b6 obi import: Skipping sequences is now done through the iterators so that 
sequences are not uselessly parsed
 2017-07-10 17:02:30 +02:00
Celine Mercier b94ec9557f Cython API: None values aren't inclued anymore in the dictionary 
returned when getting a line from a column with multiple elements per
line, and reworked that function to be more optimized
 2017-07-07 17:28:53 +02:00
Celine Mercier 143bddf1d1 Cython API: Added an __iter__ method to the class Column_line (iterating 
on the elements names) (previously an iteration would work but with
unexpected results)
 2017-07-07 15:41:10 +02:00
Celine Mercier a718081ebd Bug with error handling: for now obi_errno needs to be passed to the 
function handling errors and exceptions, as it can't read the right
value of the global obi_errno (Cython configuration problem?)
 2017-07-07 15:36:11 +02:00
Celine Mercier 740d021276 obi import: fixed bugs when rewriting a column: a bug with new elements 
names ignoring previous elements names found, a bug with the global
obi_errno being reset too late, and a bug with the column dictionary
used by obi import not being updated after rewriting a column
 2017-07-07 15:33:43 +02:00
Celine Mercier 906343187b Fixed bug with view option in obi less and obi check 2017-07-06 16:42:27 +02:00
Celine Mercier c3cd57a9e3 Removed deprecated file 2017-07-06 10:57:14 +02:00
Celine Mercier f03928c679 Committing minor comments before merging branch with master 2017-07-06 10:56:39 +02:00
Celine Mercier 717ee46f08 Commented a loose print 2017-07-05 18:02:18 +02:00
Celine Mercier 313508cc94 Better *Seq* classes but still need work 2017-07-05 17:53:46 +02:00
Celine Mercier 535fc2af83 Column rewriter and optimized View getter 2017-07-05 17:49:05 +02:00
Celine Mercier 3bbc2ae469 More optimized Column item getter 2017-07-05 17:37:19 +02:00
Celine Mercier 5ee0b3989a Cython API: set_line of Column_multi_elts now accept as values argument 
any class where values are referenced by keys with an iterator
 2017-07-05 17:32:32 +02:00
Celine Mercier d10192ab0e C functions to detect IUPAC sequences 2017-07-05 17:26:03 +02:00
Celine Mercier 101f764cce New obi import with rewriting of columns when column type or line 
elements (keys) change
 2017-07-05 17:15:23 +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 f6631f3857 Removed deprecated declarations 2017-07-05 14:42:21 +02:00
Celine Mercier 3f5fef10b9 obi test: minor changes 2017-07-05 14:37:27 +02:00
Celine Mercier 20c72af697 Basic obi check command to check DMS and view informations 2017-07-05 13:54:19 +02:00
Celine Mercier d252131950 Basic obi less command 2017-07-05 13:44:12 +02:00
Celine Mercier ca16ce0bb0 Basic obi grep with new Cython API 2017-07-05 11:58:10 +02:00
Celine Mercier ac94b35336 Removed unused import 2017-07-05 11:52:31 +02:00
Celine Mercier 2d65db4ebc Goes with c2af955b : forgotten files for NUC_SEQS views 2017-04-21 15:15:12 +02:00
Celine Mercier 4b037ae236 Updated obi test to test NUC_SEQS views and the taxonomy API 2017-04-21 12:09:04 +02:00
Celine Mercier c2af955b78 Cython view API: added NUC_SEQS views and sequence classes + changed 
cloning API
 2017-04-21 12:08:14 +02:00
Celine Mercier 71b1a43df8 Added functions to clone views with a simpler API 2017-04-21 11:58:15 +02:00
Celine Mercier 1725b8b80c Reworked taxonomy Cython API to be a subclass of OBIWrapper 2017-04-21 11:54:05 +02:00
Celine Mercier ab0d08293e Cython API: removed unnecessary imports 2017-04-21 11:51:05 +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 b998373be5 Cython API: updated the test command for the new API and deactivated the 
other commands for now
 2017-04-14 16:21:33 +02:00
Celine Mercier 6f780148e2 Cython API: added taxonomy API 2017-04-14 16:20:30 +02:00
Celine Mercier 0e08fc486a Cython API: fixed bug when deleting a column from a view where the 
Cython wrapper wasn't closed, and fixed the Line selection
materialization
 2017-04-14 16:19:18 +02:00
Celine Mercier 2bbee64e57 Cython API: fixed problems with Column class 2017-04-14 16:14:41 +02:00
Celine Mercier 693859eec2 Cython API: fixed conversion bugs when setting and getting values 
(especially NA values) in OBI_CHAR, OBI_STR and OBI_SEQ columns
 2017-04-14 16:07:23 +02:00
Celine Mercier a3fad27190 Cython API: automatic importing of column classes now works 2017-04-06 15:45:02 +02:00
Celine Mercier f351540b0b Merge branch 'Eric_new_Python_API' of git@git.metabarcoding.org:obitools/obitools3.git into Eric_new_Python_API 2017-04-06 15:39:52 +02:00
Celine Mercier 5de9e0de51 Cython API: now using const char* instead of char* for the type of 
values read from OBI_STR columns
 2017-04-06 15:15:20 +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 8cd3e3604f Cython Column API 2017-04-06 14:42:11 +02:00
Celine Mercier 255f3c92ae Cython View API 2017-04-06 14:41:58 +02:00
Celine Mercier 08be4e231d Cython Object API 2017-04-06 14:41:43 +02:00
Celine Mercier b5b7995411 new Cython DMS API 2017-04-06 14:41:26 +02:00
Celine Mercier 0dfb1eb3e6 Cython typed columns 2017-04-06 14:40:44 +02:00
Celine Mercier 381194194c Cython API: compiling but not working 2017-03-06 16:07:02 +01:00
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 fc20b83ad1 Merging 2017-02-20 14:56:04 +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 f23315e26f New Cython API: compile but doesn't work 2017-02-17 15:14:06 +01:00
Celine Mercier 071a3b61ab Merged master fixed conflict. 2017-02-14 10:58:43 +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 7e9932f488 Fixed a C function declaration 2017-02-07 17:12:56 +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
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
Celine Mercier 30e4359c85 LCS alignment: documentation for all the lowest level functions 2016-12-22 17:03:51 +01:00
Celine Mercier 5c50e5b378 Embryo of code for openMP parallelization of LCS alignment but 
deactivated for now because can't make it compile with cython/clang
 2016-12-20 11:46:58 +01:00
Celine Mercier 9c71b06117 Removed deprecated TODOs 2016-12-19 14:36:40 +01:00
Celine Mercier 3bf5260174 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2016-12-19 10:31:18 +01:00
Celine Mercier 857a5198e4 Updated `obi lcs` for the LCS alignment of two columns 2016-12-16 19:40:36 +01:00
Celine Mercier d99447c12b C function for LCS alignment of two columns, and optimized and fixed 
line count bug in function to align one column
 2016-12-16 19:39:02 +01:00
Celine Mercier 303bd6f445 Added function to build kmer table for 2 columns, and fixed bug (with 
line count) when building kmer table of one column
 2016-12-16 19:10:18 +01:00
Celine Mercier 490f5fe6b9 Updated deprecated code in cython API for columns (using line count of 
view instead of column)
 2016-12-16 19:04:21 +01:00
Celine Mercier 191c83aafc Added missing *.cfiles 2016-12-15 15:28:34 +01:00
Celine Mercier 9b24818fe2 Refactored alignment code for minimum redundancy between the function 
that aligns 1 column and the function that aligns 2 columns
 2016-12-13 17:18:12 +01:00
Celine Mercier 8afb1644e9 Alignment: API rework. 'obi align' is now 'obi lcs', and the results are 
now written to columns automatically created in the output view, all
optimally handled at the C level.
 2016-12-12 11:58:59 +01:00
Celine Mercier fa4e4ffaff Changed the cython API to create new views so as to have different 
functions for the different cases
 2016-12-07 14:17:57 +01:00
Celine Mercier 936be64c34 Goes with 5e0c9f87 (missing ';' and fixed compilation warnings) 2016-12-05 11:18:29 +01:00