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Author SHA1 Message Date
Celine Mercier d159b921eb Fixed obi import trying to print all lines at the end (source of 
segfault?)
 2016-04-27 13:14:19 +02:00
Celine Mercier 4e4cf46b16 Added all C files as source files for all cython files to stop having 
that kind of problem with linux systems
 2016-04-27 10:44:24 +02:00
Celine Mercier 6b61533650 Added more C source files for _obiseq 2016-04-27 10:41:00 +02:00
Celine Mercier 419885485b Added files in _obitaxo C sources for cython 2016-04-27 10:30:16 +02:00
Celine Mercier 0c8504b6db Commented #ifdef directive for detect_bucket_size function because it 
causes errors
 2016-04-27 10:24:40 +02:00
Celine Mercier a6c8d35491 import command a bit modified for tests 2016-04-26 14:29:54 +02:00
Celine Mercier 366264828e Renamed MurmurHash2.c file to murmurhash2.c as it could be a problem 2016-04-26 14:29:17 +02:00
Celine Mercier d3a6ff6043 Removed deprecated code 2016-04-26 14:27:16 +02:00
Celine Mercier 5ca84b91dc Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2016-04-25 18:35:57 +02:00
Celine Mercier 87935c6678 Fixed all compilation problems with new function names, locations etc 2016-04-25 18:35:02 +02:00
Celine Mercier 92980508c0 Made the function to clone a column in the context of a view private 2016-04-25 18:15:25 +02:00
Celine Mercier 65880db422 Made function to update the line count of a view private 2016-04-25 18:11:37 +02:00
Celine Mercier 767d9c7804 Reordered view functions for better coherence 2016-04-25 18:07:58 +02:00
Celine Mercier 2566377e2a Updated the documentation for utils functions 2016-04-25 18:02:58 +02:00
Celine Mercier 1fbbdd43f9 Updated obiversion_t declaration 2016-04-25 17:58:37 +02:00
Celine Mercier 8cdfbb379e Documentation for views and reworked the code a little 2016-04-25 17:58:12 +02:00
Celine Mercier 0a55e26520 Reworked obiview code and added more comments 2016-04-25 11:37:53 +02:00
Celine Mercier 68a8509c12 Updated documentation in obitypes.h 2016-04-25 10:33:01 +02:00
Celine Mercier 5f98d2ed5c Fixed the calculation of the size of data for OBI_STR and OBI_SEQ 
columns
 2016-04-25 10:26:51 +02:00
Celine Mercier 5d08da46a2 Updated the documentation in obidmscolumn.h 2016-04-22 17:55:53 +02:00
Celine Mercier 66045acf1d Creating a column now uses the function to create the indexer name if 
one was not provided
 2016-04-22 17:47:00 +02:00
Celine Mercier 6977c4315c Improved function to build an indexer name 2016-04-22 17:38:23 +02:00
Celine Mercier 839b3000a8 Added a function to build indexer names 2016-04-22 17:08:23 +02:00
Celine Mercier ffa4557928 changed MAP_PRIVATE flags to MAP_SHARED when opening a column because it 
seems a lot more efficient
 2016-04-22 16:26:24 +02:00
Celine Mercier 003cd11362 Fixed initialization of NA values for OBI_STR and OBI_SEQ columns 2016-04-22 16:14:23 +02:00
Celine Mercier c87227b65a Uncommented an error message that doesn't need to be commented anymore 2016-04-22 16:11:56 +02:00
Celine Mercier c07e75f2ac Updated the documentation for OBI_STR columns 2016-04-22 15:59:32 +02:00
Celine Mercier 6b394a5cf7 Updated the documentation for OBI_SEQ columns 2016-04-22 15:58:20 +02:00
Celine Mercier 2416b8ccd8 Deleted more unused inclusions in OBI_STR and OBI_SEQ column types code 2016-04-22 15:56:09 +02:00
Celine Mercier b9921e111d Removed unused inclusions and definitions in all column types code 2016-04-22 15:50:19 +02:00
Celine Mercier 8f5aa8841d Removed unused definition in OBI_IDX columns code 2016-04-22 15:44:30 +02:00
Celine Mercier 900d67de87 Updated the documentation for columns with the type OBI_IDX 2016-04-22 15:43:39 +02:00
Celine Mercier 22e3c3eeed Updated the documentation for obidms functions 2016-04-22 11:28:09 +02:00
Celine Mercier 4ead37ee48 Finished moving obiblob functions to obiblob files and documentation for 
obiblob functions
 2016-04-21 15:18:14 +02:00
Celine Mercier bce360bbd5 Documentation for obiblob indexer API 2016-04-21 15:08:40 +02:00
Celine Mercier 2a68cb26f8 Improved AVL tree documentation 2016-04-21 15:07:27 +02:00
Celine Mercier 043e70ff49 Updated AVL documentation 2016-04-21 14:39:03 +02:00
Celine Mercier 66021367f6 Moved some blob functions to obiblob.c 2016-04-21 14:20:26 +02:00
Celine Mercier e69f44ae3d Little annotations for the murmur hash function. 2016-04-21 13:53:29 +02:00
Celine Mercier 1941a3785e Updated encode functions documentation 2016-04-21 13:46:02 +02:00
Celine Mercier c7b8db6a2e Replaced malloc+memset with calloc 2016-04-21 13:45:39 +02:00
Celine Mercier 1dc4a3be49 Documentation for DNA sequence indexing functions 2016-04-21 13:36:51 +02:00
Celine Mercier 09597016fd Short doc for crc function 2016-04-21 13:23:52 +02:00
Celine Mercier 1a2fa0923c Documented the functions indexing and retrieving character strings 2016-04-21 11:35:21 +02:00
Celine Mercier 00f2f2cc51 Documented changes made in bloom functions 2016-04-21 11:22:31 +02:00
Celine Mercier 7a88ca619a First obi import (doesn't import tags yet because NA values aren't 
handled)
 2016-04-15 17:00:08 +02:00
Celine Mercier eddd19a245 Changes in obi commands 2016-04-15 16:59:21 +02:00
Celine Mercier 2aafecc3b5 Changed sequence 'description' to 'definition' everywhere 2016-04-15 16:31:43 +02:00
Celine Mercier 094b2371e9 Deleted obsolete directory 2016-04-15 14:44:31 +02:00
Celine Mercier c1034d300d merging and fixed git conflict with obiavl.h 2016-04-15 13:23:29 +02:00
Celine Mercier 02d67c257f The default name of an AVL is now the column name + '_indexer', and when 
an AVL is opened (as opposed to created), it is read-only
 2016-04-15 12:55:26 +02:00
Celine Mercier e04ea85d1e Fixed problematic __str__ method and useless declarations in the 
OBI_Nuc_Seq_Stored class
 2016-04-15 11:22:05 +02:00
Celine Mercier 527d3555f0 Moved the functions getting full paths for files and directories to 
obidms.c/.h files
 2016-04-15 11:11:13 +02:00
Celine Mercier 71492ad229 Made the handling of listing and unlisting opened columns and indexers 
functions in the obidms files.
 2016-04-15 10:49:12 +02:00
Celine Mercier 73d64e5aff Renamed 'unmap_header' function to 'close_header' 2016-04-14 15:19:27 +02:00
Celine Mercier 4cb52e1632 Made the truncating of columns automatic when closing them (note: 
already the case for AVLs)
 2016-04-14 15:13:30 +02:00
Celine Mercier 9d042f7bd0 Refactored and relocated the set and get functions of all column types, 
both within and out of the context of a view
 2016-04-13 15:10:24 +02:00
Celine Mercier 5ec2d8842e Character string indexer API 2016-04-12 17:21:01 +02:00
Celine Mercier 04c9470f7d Fixed and cleaned DNA_seq_indexer API 2016-04-12 17:20:24 +02:00
Celine Mercier be05c889e2 DNA_seq_indexer API 2016-04-12 16:38:47 +02:00
Celine Mercier 04e3a7b5a9 Added more references in cython .cfiles files because it seems necessary 
for linux distributions
 2016-04-12 15:10:54 +02:00
Celine Mercier d8107533d8 Obiblob_indexer API 2016-04-12 14:53:33 +02:00
Celine Mercier cd4e65e190 Fixed typo and includes in obiblob files 2016-04-12 14:52:27 +02:00
Celine Mercier 375bfcce8a Renamed "Obi_byte_arrays" to "Obiblobs" and moved Obiblob functions to 
separate obiblob.c and obiblob.h files
 2016-04-12 11:21:14 +02:00
Celine Mercier c225cfd8b6 Fixed bug with retrieval of values from AVLs (bad cast in byte array 
structure)
 2016-04-11 17:07:22 +02:00
Celine Mercier 966b1325ed Deleted declaration of obsolete public function 2016-04-11 11:14:20 +02:00
Celine Mercier 019dfc01b4 Branch to refactor and debug (AVLs bugged) 2016-04-08 15:38:57 +02:00
Celine Mercier edc4fd7b3e Fixed minor warning 2016-03-25 16:11:52 +01:00
Celine Mercier ff6c27acf2 Implemented the retrieval of values with groups of AVLs 2016-03-25 15:35:16 +01:00
Celine Mercier 69856f18dd untested (and no possible retrieval) of CRC used to represent data in 
AVL trees
 2016-03-24 16:38:11 +01:00
Celine Mercier 58ac860cc7 Added macro for the bloom filter parameters and deleted old unused 
macros for crc
 2016-03-23 13:33:40 +01:00
Celine Mercier d44117d625 obiimport function for testing purposes 2016-03-23 13:00:02 +01:00
Celine Mercier 6bd42132c4 Minor fixes to silence warnings and replaced two asprintf uses 2016-03-23 12:58:53 +01:00
Celine Mercier 4085904362 Merge branch 'multiple_avls_bloom' 2016-03-22 14:14:10 +01:00
Celine Mercier b04b4b5902 made POSIX compliant 2016-03-21 11:33:06 +01:00
Celine Mercier 383e738ab7 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2016-03-18 15:49:53 +01:00
Celine Mercier 3681cecb4d Multiple AVLs with bloom filters (very raw test version) 2016-03-18 11:06:02 +01:00
Celine Mercier 545ed8111a Code for tests storing data in multiple AVLs. 
(note: unretrievable data as implemented)
 2016-03-11 15:34:55 +01:00
Celine Mercier 86071d30c9 Minor improvement in AVL initial size calculation 2016-03-11 14:07:40 +01:00
Celine Mercier 21d1b2ed3e First implementation of taxonomy reading 2016-03-11 13:56:38 +01:00
Celine Mercier a08def47e6 It is now impossible to create a view with a name identical to one of an 
existing written view
 2016-03-01 13:36:54 +01:00
Celine Mercier fc5a12bad7 Closes #34 2016-02-29 17:56:55 +01:00
Celine Mercier e323d8e702 Cython classes for nucleotide sequences (outside or in the context of a 
view)
 2016-02-29 16:33:30 +01:00
Celine Mercier b350ea0393 Fixed minor error 2016-02-29 16:28:34 +01:00
Celine Mercier 8e9e21a02e Increased the maximum depth of AVL trees 2016-02-29 16:27:23 +01:00
Celine Mercier 4df313c54a Added Obiviews specialized for the handling of nucleotide sequences 2016-02-25 09:43:27 +01:00
Celine Mercier ffc68d448f Deleted a forgotten print statement 2016-02-18 15:15:42 +01:00
Celine Mercier a8f03248a8 Major update : views 2016-02-18 10:38:51 +01:00
Celine Mercier cfaf069095 Fixed more typos and formatting imperfections. 2015-12-11 17:37:25 +01:00
Celine Mercier a6144eabe2 Fixed typos 2015-12-11 17:26:20 +01:00
Celine Mercier c139367555 DNA sequences and character strings are now handled using AVL trees. 2015-12-11 17:24:44 +01:00
Celine Mercier 1586956d57 Added the lists of opened columns and arrays in the OBIDMS structure, 
and a counter in the OBIDMS column structure; fixed some bugs and
created tests for referring columns that are bound to disappear anyway.
 2015-12-02 17:32:07 +01:00
Celine Mercier b45b496b0e Major update: new type of columns containing indices referring to lines 
in other columns
 2015-11-29 11:57:07 +01:00
Celine Mercier 2cf10cb6f0 Column type is now passed as a character string when creating the column 
(either 'OBI_INT', 'OBI_FLOAT', 'OBI_BOOL', 'OBI_CHAR', 'OBI_STR' or
'OBI_SEQ')
 2015-11-23 15:48:27 +01:00
Celine Mercier 5a5516303d deleting useless .pyc files 2015-11-23 14:43:34 +01:00
Celine Mercier d6a99bafea Fixed a major bug with the versioning of columns that was introduced in 
f6ec8ba9
 2015-11-23 13:34:51 +01:00
Celine Mercier 08f2657e18 Increased maximum line count of columns to 1^9 2015-11-23 13:23:18 +01:00
Celine Mercier 6aa2f92930 DNA sequences are now encoded on 4 bits when they are in IUPAC 2015-11-20 15:32:09 +01:00
Celine Mercier 87044b41d8 modified the encoding function on 2 bits a little 2015-11-20 11:32:47 +01:00
Celine Mercier 6ab1c83302 New column type for DNA sequences. Only for those coded on 2 bits (only 
'ATGCatgc') for now.
 2015-11-19 18:12:48 +01:00