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  • a3fad27190 Cython API: automatic importing of column classes now works Celine Mercier 2017-04-06 15:45:02 +02:00
  • f351540b0b Merge branch 'Eric_new_Python_API' of git@git.metabarcoding.org:obitools/obitools3.git into Eric_new_Python_API Celine Mercier 2017-04-06 15:39:52 +02:00
  • 6dccaa0213 Patch the registering function : register_all_column_classes Eric Coissac 2017-04-06 15:37:51 +02:00
  • 5de9e0de51 Cython API: now using const char* instead of char* for the type of values read from OBI_STR columns Celine Mercier 2017-04-06 15:15:20 +02:00
  • ad8de80353 Views: better checks when adding an existing column to a view Celine Mercier 2017-04-06 14:44:07 +02:00
  • 8cd3e3604f Cython Column API Celine Mercier 2017-04-06 14:42:11 +02:00
  • 255f3c92ae Cython View API Celine Mercier 2017-04-06 14:41:58 +02:00
  • 08be4e231d Cython Object API Celine Mercier 2017-04-06 14:41:43 +02:00
  • b5b7995411 new Cython DMS API Celine Mercier 2017-04-06 14:41:26 +02:00
  • 0dfb1eb3e6 Cython typed columns Celine Mercier 2017-04-06 14:40:44 +02:00
  • 381194194c Cython API: compiling but not working Celine Mercier 2017-03-06 16:07:02 +01:00
  • 778acc48cd Added linked lists to handle lists of column pointers in views (not tested) Celine Mercier 2017-03-06 16:06:17 +01:00
  • 3319ede837 Views: Column dictionaries now store and return pointers on column pointers instead of column pointers. Celine Mercier 2017-02-22 13:49:50 +01:00
  • fc20b83ad1 Merging Celine Mercier 2017-02-20 14:56:04 +01:00
  • 431c1c8c6a Merge branch 'Eric_new_Python_API' of git@git.metabarcoding.org:obitools/obitools3.git into Eric_new_Python_API Celine Mercier 2017-02-20 14:55:36 +01:00
  • f23315e26f New Cython API: compile but doesn't work Celine Mercier 2017-02-17 15:14:06 +01:00
  • 071a3b61ab Merged master fixed conflict. Celine Mercier 2017-02-14 10:58:43 +01:00
  • e524041013 Views: Files for unfinished views now have the extension '.obiview_unfinished', renamed to '.obiview' when the view is finished. Celine Mercier 2017-02-07 17:16:09 +01:00
  • a9102620f5 Fixed missing email address Celine Mercier 2017-02-07 17:14:10 +01:00
  • 7e9932f488 Fixed a C function declaration Celine Mercier 2017-02-07 17:12:56 +01:00
  • 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 Celine Mercier 2017-01-31 16:48:06 +01:00
  • 651c1d7845 utilities: bsearch and qsort with additional user_data pointer argument Celine Mercier 2017-01-31 16:45:47 +01:00
  • 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) Celine Mercier 2017-01-18 18:22:49 +01:00
  • c065c1914a Taxonomy: adding, writing and reading preferred names, changed some function names, and fixed a bug with taxa indices not being properly initialized Celine Mercier 2017-01-16 17:28:20 +01:00
  • 0385a92e02 Taxonomy: Refactored the taxdump reading, and little fixes Celine Mercier 2017-01-11 16:36:08 +01:00
  • cf7f2de016 Modify __init__ and close method to deal with registration process Eric Coissac 2017-01-10 14:26:16 +01:00
  • 5122ad52a7 Merge branch 'Eric_new_Python_API' of git@git.metabarcoding.org:obitools/obitools3.git into Eric_new_Python_API Eric Coissac 2017-01-10 14:07:50 +01:00
  • 4b02ba73ac Add the OBIObject concept Eric Coissac 2017-01-10 14:07:10 +01:00
  • 41ad3deec0 Taxonomy: informations about deleted taxids is now read from delnodes.dmp file and added to *.adx file Celine Mercier 2017-01-09 17:28:49 +01:00
  • 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. Celine Mercier 2017-01-06 15:52:21 +01:00
  • f396625f98 Taxonomy: function to write *.adx files Celine Mercier 2017-01-05 15:37:13 +01:00
  • 897032387f Taxonomy: reading merged.dmp file in taxdump Celine Mercier 2017-01-05 14:28:36 +01:00
  • 4a1d3167a7 Last change on my branch Eric Coissac 2017-01-02 16:46:17 +01:00
  • 153c22257f Last change on my branch Eric Coissac 2017-01-02 16:46:17 +01:00
  • 2139bfc748 refactoring... Eric Coissac 2017-01-02 13:05:22 +01:00
  • 65f3b16e6d Refactoring ... Eric Coissac 2016-12-29 18:22:05 +01:00
  • 0526386337 first working DMS class Eric Coissac 2016-12-27 06:17:45 +01:00
  • 62caf1346e temporary remove some files Eric Coissac 2016-12-26 15:03:24 +01:00
  • 3ac6e85fb3 Big refactoring 4 Eric Coissac 2016-12-26 14:58:03 +01:00
  • 5156f6bb9e Big refactoring 3 Eric Coissac 2016-12-26 14:18:01 +01:00
  • e6db2086d5 Big refactoring 2 Eric Coissac 2016-12-26 13:56:31 +01:00
  • daacd0df76 Strong refactoring 1 Eric Coissac 2016-12-26 13:35:31 +01:00
  • 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) Celine Mercier 2016-12-22 17:06:23 +01:00
  • 30e4359c85 LCS alignment: documentation for all the lowest level functions Celine Mercier 2016-12-22 17:03:51 +01:00
  • 5c50e5b378 Embryo of code for openMP parallelization of LCS alignment but deactivated for now because can't make it compile with cython/clang Celine Mercier 2016-12-20 11:46:58 +01:00
  • 3cedd00d7f Add register function for column type Eric Coissac 2016-12-20 11:13:57 +01:00
  • 82fbe43980 transfert method to obiviews Eric Coissac 2016-12-20 08:18:47 +01:00
  • d1a972dfcb patch import Eric Coissac 2016-12-20 08:15:42 +01:00
  • f43dc3e3ab separate the obicolumn classes in new files Eric Coissac 2016-12-20 08:14:24 +01:00
  • 9c71b06117 Removed deprecated TODOs Celine Mercier 2016-12-19 14:36:40 +01:00
  • 3bf5260174 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git Celine Mercier 2016-12-19 10:31:18 +01:00
  • 857a5198e4 Updated `obi lcs` for the LCS alignment of two columns Celine Mercier 2016-12-16 19:40:36 +01:00
  • d99447c12b C function for LCS alignment of two columns, and optimized and fixed line count bug in function to align one column Celine Mercier 2016-12-16 19:39:02 +01:00
  • 303bd6f445 Added function to build kmer table for 2 columns, and fixed bug (with line count) when building kmer table of one column Celine Mercier 2016-12-16 19:10:18 +01:00
  • 490f5fe6b9 Updated deprecated code in cython API for columns (using line count of view instead of column) Celine Mercier 2016-12-16 19:04:21 +01:00
  • 191c83aafc Added missing *.cfiles Celine Mercier 2016-12-15 15:28:34 +01:00
  • 04d39c62ab Try for a new API Eric Coissac 2016-12-14 08:44:44 +01:00
  • 9b24818fe2 Refactored alignment code for minimum redundancy between the function that aligns 1 column and the function that aligns 2 columns Celine Mercier 2016-12-13 17:18:12 +01:00
  • 06cb7a9a58 Some change in the way to manage access to special items of the dictionary like sequence or quality Eric Coissac 2016-12-13 12:49:34 +01:00
  • fc55fc117d Some cosmetic on the code Eric Coissac 2016-12-13 12:48:13 +01:00
  • 4ef5cb0d87 Move the OBIView_NUC_SEQS class to files _obiview_nuc_seq.pxd and _obiview_nuc_seq.pyx to avoid circular inclusion Eric Coissac 2016-12-13 12:46:49 +01:00
  • fc805e5443 Remove some warnings in the editor Eric Coissac 2016-12-13 08:29:22 +01:00
  • 8d7ef7d3d1 patch the distutils to add the C source directory in the include path. This should solve most of the compilation problems related to .h files located in this directory Eric Coissac 2016-12-13 08:02:09 +01:00
  • 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. Celine Mercier 2016-12-12 11:58:59 +01:00
  • fa4e4ffaff Changed the cython API to create new views so as to have different functions for the different cases Celine Mercier 2016-12-07 14:17:57 +01:00
  • 936be64c34 Goes with 5e0c9f87 (missing ';' and fixed compilation warnings) Celine Mercier 2016-12-05 11:18:29 +01:00
  • 5e0c9f878b Added the doc for the function building the element names, and a missing free Celine Mercier 2016-12-05 10:46:21 +01:00
  • 852e5488c8 The default element names for columns with multiple elements per line are now "O;1;2;...;n" Celine Mercier 2016-12-02 17:54:51 +01:00
  • e60497651c Updated the documentation for the functions to set and get in the context of a view Celine Mercier 2016-11-30 12:22:47 +01:00
  • 4ad8c16a73 Finished adding all the functions to directly set and get indices in columns containing indices referring to any type of data. Celine Mercier 2016-11-30 11:08:11 +01:00
  • 6f6099687d Sequence alignment: if no sequence column is given and the view has the type NUC_SEQS_VIEW, the default sequence column is aligned Celine Mercier 2016-11-29 16:52:41 +01:00
  • 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) Celine Mercier 2016-11-29 16:15:02 +01:00
  • 5fb025f310 When aligning, it is now quickly checked whether the sequences are identical using their indexes Celine Mercier 2016-11-28 11:39:29 +01:00
  • 8ce6f6c80b Added an argument to specify whether the two sequences can be identical when applying filters before aligning Celine Mercier 2016-11-28 11:38:02 +01:00
  • 3e53f9418b Added functions to recover the indexes themselves from any column referring to indexed values Celine Mercier 2016-11-28 11:35:19 +01:00
  • d40d2d0c76 Fixed error in documentation Celine Mercier 2016-11-28 10:55:23 +01:00
  • f897e87600 When closing a view, it is now automatically checked that all OBI_QUAL columns correspond to their associated OBI_SEQ column Celine Mercier 2016-11-25 12:04:57 +01:00
  • 70e056a2aa It is now impossible to open or clone a view that is not finished (= has been closed at least once) Celine Mercier 2016-11-24 11:19:07 +01:00
  • 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 Celine Mercier 2016-11-23 11:32:39 +01:00
  • 6fa9a8bd76 When a view is cloned, a comment is added to the new view specifying the name of the cloned view Celine Mercier 2016-11-23 11:29:21 +01:00
  • 76a4c6b14e Fixed a bug when cloning a view and checking its type Celine Mercier 2016-11-23 11:28:17 +01:00
  • 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 Celine Mercier 2016-11-23 11:04:53 +01:00
  • 70c49e214a Added the kmer filter to LCS alignments, and now obiblobs containing encoded sequences are directly put in int16_t arrays for the alignment Celine Mercier 2016-11-18 16:29:28 +01:00
  • 08e67a090f Changed the inline functions syntax, which should make it compatible with more compilers Celine Mercier 2016-11-18 16:21:26 +01:00
  • 621b4972db Functions to get obiblobs through views Celine Mercier 2016-11-18 15:59:50 +01:00
  • 7d022c1a52 If the indexer name is NULL when creating a column, it now becomes the column name Celine Mercier 2016-11-18 15:56:51 +01:00
  • 1c71c195fc Goes with a0ebc2d8 Celine Mercier 2016-11-10 15:01:29 +01:00
  • 54cfeffd85 Goes with 8f724f4f, forgotten file Celine Mercier 2016-11-10 14:48:31 +01:00
  • a0ebc2d871 Functions to directly retrieve Obiblobs from indexers Celine Mercier 2016-11-10 14:45:28 +01:00
  • 8f724f4f8e Some code refactoring Celine Mercier 2016-11-09 16:48:00 +01:00
  • 359578814b Added view type property to OBIView cython class and updated obi export to use it Celine Mercier 2016-11-08 17:49:59 +01:00
  • 51b23915ca Added properties for Nuc_Seq cython classes (and updated commands using them) Celine Mercier 2016-11-08 16:59:32 +01:00
  • b5b889c4a2 Fixed the OBI_Nuc_Seq_Stored cython class not being up to date with the new properties of its parent class Celine Mercier 2016-11-08 11:26:37 +01:00
  • 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 Celine Mercier 2016-11-08 11:23:54 +01:00
  • 8291693309 obi grep: updated to work with the new line selection class and within the local sequence environment, and progress bar functioning Celine Mercier 2016-11-08 11:19:12 +01:00
  • 4bc19c3e49 obi export: view type is now checked and progress bar functioning Celine Mercier 2016-11-08 11:17:20 +01:00
  • 2d2fe5279d Added functions to add new taxa to a taxonomy with handling of associated *.ldx files Celine Mercier 2016-11-03 17:59:21 +01:00
  • 2504bf0fa9 Added an iterator to the OBI_Taxonomy cython class Celine Mercier 2016-11-02 11:08:18 +01:00
  • 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. Celine Mercier 2016-10-27 18:56:11 +02:00
  • b63d0fb9fb Added C functions to write .rdx, .tdx, .ndx binary taxonomy files from a taxonomy C structure Celine Mercier 2016-10-14 17:03:10 +02:00