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b5b7995411
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new Cython DMS API
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2017-04-06 14:41:26 +02:00 |
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0dfb1eb3e6
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Cython typed columns
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2017-04-06 14:40:44 +02:00 |
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381194194c
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Cython API: compiling but not working
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2017-03-06 16:07:02 +01:00 |
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778acc48cd
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Added linked lists to handle lists of column pointers in views (not
tested)
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2017-03-06 16:06:17 +01:00 |
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fc20b83ad1
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Merging
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2017-02-20 14:56:04 +01:00 |
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431c1c8c6a
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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
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2017-02-20 14:55:36 +01:00 |
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f23315e26f
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New Cython API: compile but doesn't work
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2017-02-17 15:14:06 +01:00 |
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071a3b61ab
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Merged master fixed conflict.
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2017-02-14 10:58:43 +01:00 |
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e524041013
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Views: Files for unfinished views now have the extension
'.obiview_unfinished', renamed to '.obiview' when the view is finished.
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2017-02-07 17:16:09 +01:00 |
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7e9932f488
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Fixed a C function declaration
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2017-02-07 17:12:56 +01:00 |
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e50da64ea1
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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
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2017-01-31 16:48:06 +01:00 |
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c065c1914a
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Taxonomy: adding, writing and reading preferred names, changed some
function names, and fixed a bug with taxa indices not being properly
initialized
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2017-01-16 17:28:20 +01:00 |
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cf7f2de016
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Modify __init__ and close method to deal with registration process
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2017-01-10 14:26:16 +01:00 |
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4b02ba73ac
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Add the OBIObject concept
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2017-01-10 14:07:10 +01:00 |
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4a1d3167a7
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Last change on my branch
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2017-01-02 16:46:52 +01:00 |
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2139bfc748
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refactoring...
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2017-01-02 13:05:22 +01:00 |
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65f3b16e6d
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Refactoring ...
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2016-12-29 18:22:05 +01:00 |
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0526386337
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first working DMS class
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2016-12-27 06:17:45 +01:00 |
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62caf1346e
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temporary remove some files
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2016-12-26 15:03:24 +01:00 |
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3ac6e85fb3
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Big refactoring 4
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2016-12-26 14:58:03 +01:00 |
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5156f6bb9e
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Big refactoring 3
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2016-12-26 14:18:01 +01:00 |
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e6db2086d5
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Big refactoring 2
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2016-12-26 13:56:31 +01:00 |
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daacd0df76
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Strong refactoring 1
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2016-12-26 13:35:31 +01:00 |
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5c50e5b378
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Embryo of code for openMP parallelization of LCS alignment but
deactivated for now because can't make it compile with cython/clang
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2016-12-20 11:46:58 +01:00 |
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3cedd00d7f
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Add register function for column type
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2016-12-20 11:13:57 +01:00 |
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82fbe43980
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transfert method to obiviews
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2016-12-20 08:18:47 +01:00 |
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d1a972dfcb
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patch import
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2016-12-20 08:15:42 +01:00 |
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f43dc3e3ab
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separate the obicolumn classes in new files
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2016-12-20 08:15:08 +01:00 |
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9c71b06117
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Removed deprecated TODOs
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2016-12-19 14:36:40 +01:00 |
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3bf5260174
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Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
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2016-12-19 10:31:18 +01:00 |
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857a5198e4
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Updated `obi lcs` for the LCS alignment of two columns
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2016-12-16 19:40:36 +01:00 |
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490f5fe6b9
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Updated deprecated code in cython API for columns (using line count of
view instead of column)
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2016-12-16 19:04:21 +01:00 |
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191c83aafc
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Added missing *.cfiles
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2016-12-15 15:28:34 +01:00 |
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04d39c62ab
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Try for a new API
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2016-12-14 08:44:44 +01:00 |
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06cb7a9a58
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Some change in the way to manage access to special items of the
dictionary like sequence or quality
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2016-12-13 12:49:34 +01:00 |
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fc55fc117d
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Some cosmetic on the code
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2016-12-13 12:48:13 +01:00 |
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4ef5cb0d87
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Move the OBIView_NUC_SEQS class to files _obiview_nuc_seq.pxd and
_obiview_nuc_seq.pyx to avoid circular inclusion
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2016-12-13 12:46:49 +01:00 |
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fc805e5443
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Remove some warnings in the editor
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2016-12-13 08:29:22 +01:00 |
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8afb1644e9
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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.
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2016-12-12 11:58:59 +01:00 |
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fa4e4ffaff
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Changed the cython API to create new views so as to have different
functions for the different cases
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2016-12-07 14:17:57 +01:00 |
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936be64c34
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Goes with 5e0c9f87 (missing ';' and fixed compilation warnings)
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2016-12-05 11:18:29 +01:00 |
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852e5488c8
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The default element names for columns with multiple elements per line
are now "O;1;2;...;n"
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2016-12-02 17:54:51 +01:00 |
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98d0849653
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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)
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2016-11-29 16:15:02 +01:00 |
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76a4c6b14e
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Fixed a bug when cloning a view and checking its type
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2016-11-23 11:28:17 +01:00 |
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70c49e214a
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Added the kmer filter to LCS alignments, and now obiblobs containing
encoded sequences are directly put in int16_t arrays for the alignment
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2016-11-18 16:29:28 +01:00 |
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1c71c195fc
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Goes with a0ebc2d8
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2016-11-10 15:01:29 +01:00 |
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359578814b
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Added view type property to OBIView cython class and updated obi export
to use it
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2016-11-08 17:49:59 +01:00 |
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51b23915ca
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Added properties for Nuc_Seq cython classes (and updated commands using
them)
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2016-11-08 16:59:32 +01:00 |
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b5b889c4a2
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Fixed the OBI_Nuc_Seq_Stored cython class not being up to date with the
new properties of its parent class
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2016-11-08 11:26:37 +01:00 |
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36ac315125
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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
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2016-11-08 11:23:54 +01:00 |
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