obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity
487 Commits 18 Branches 66 Tags
fc20b83ad1c49d59d5950909609f907118175296
Commit Graph

271 Commits

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 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 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 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 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 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 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 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
Celine Mercier 410e2e02a0 When retrieving the header of a column, the version number of the column 
wanted can now be provided.
 2015-11-10 13:30:10 +01:00
Celine Mercier 8ce4f264aa When enlarging a column, the function doesn't try anymore to keep the 
mapped region at the same pointer (never works), and unmap/remap
instead.
 2015-11-10 13:18:36 +01:00
Celine Mercier d885eb48ff The header size when creating a column is now calculated according to 
the size of the header structure and the page size of the platform.
 2015-11-10 13:09:30 +01:00
Celine Mercier c4b7e579cf Comments in column headers are now working. 2015-11-10 10:56:45 +01:00
Celine Mercier f6ec8ba963 The header size is now directly read in the file when a column or an 
array is opened.
 2015-11-09 17:50:32 +01:00
Celine Mercier 01bfc14503 The data size in bytes is now stored in the header of a column. 2015-11-09 15:55:00 +01:00
Celine Mercier 65c1b1e8b2 Minor changes to make the creation of files and directories cleaner 2015-11-09 15:22:01 +01:00
Celine Mercier b37bd8f21c File descriptors for dms, column and array directories are now stored in 
structures.
 2015-11-09 15:06:02 +01:00
Celine Mercier 05e3956a0c Minor changes in code to improve readability (freeing some character 
strings earlier)
 2015-11-09 11:22:51 +01:00