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Author SHA1 Message Date
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
Celine Mercier 5e0c9f878b Added the doc for the function building the element names, and a missing 
free
 2016-12-05 10:46:21 +01:00
Celine Mercier 852e5488c8 The default element names for columns with multiple elements per line 
are now "O;1;2;...;n"
 2016-12-02 17:54:51 +01:00
Celine Mercier e60497651c Updated the documentation for the functions to set and get in the 
context of a view
 2016-11-30 12:22:47 +01:00
Celine Mercier 4ad8c16a73 Finished adding all the functions to directly set and get indices in 
columns containing indices referring to any type of data.
 2016-11-30 11:08:11 +01:00
Celine Mercier 6f6099687d Sequence alignment: if no sequence column is given and the view has the 
type NUC_SEQS_VIEW, the default sequence column is aligned
 2016-11-29 16:52:41 +01:00
Celine Mercier 98d0849653 Sequence alignment: added the possibility to specify the index of the 
sequences to align in a column containing multiple sequences per line (C
level for now)
 2016-11-29 16:15:02 +01:00
Celine Mercier 5fb025f310 When aligning, it is now quickly checked whether the sequences are 
identical using their indexes
 2016-11-28 11:39:29 +01:00
Celine Mercier 8ce6f6c80b Added an argument to specify whether the two sequences can be identical 
when applying filters before aligning
 2016-11-28 11:38:02 +01:00
Celine Mercier 3e53f9418b Added functions to recover the indexes themselves from any column 
referring to indexed values
 2016-11-28 11:35:19 +01:00
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