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9d042f7bd011a6a59fd0b23df1a2c820695411bf
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Author SHA1 Message Date
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
Eric Coissac
6157633137 prototype for the obi unix command and the count sub command 2016-03-08 16:06:00 +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
Celine Mercier
e371248567 changed version to 0.0.0 2015-11-19 18:11:21 +01:00
Celine Mercier
dbf9463238 The endianness of a DMS is now stored in the OBIDMS structure 2015-11-18 15:35:09 +01:00
Celine Mercier
eb12af4da4 Fixed minor error in the documentation of a function. 2015-11-16 15:38:01 +01:00
Celine Mercier
e8417b4f6f The endianness of an OBIDMS is now stored in an informations file that 
is read when opening the OBIDMS.
 2015-11-16 14:37:51 +01:00
Celine Mercier
6579566c6e Minor changes in code to improve readability and fix C compilation 
warnings
 2015-11-10 14:37:58 +01:00