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Author SHA1 Message Date
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
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
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 661fe3606a In OBI_CHAR columns, characters are now given and retrieved as decoded 
(unicode) characters.
 2015-11-10 11:24:08 +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 0e3d6ed2d7 Methods __len__ (number of lines used) and __sizeof__ (total size in 
bytes) implemented for columns.
 2015-11-09 15:56:20 +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
Celine Mercier 9b066f4327 Major update: obiarrays with columns containing indices referring to 
character strings.
 2015-11-06 17:55:15 +01:00
Celine Mercier 456551ffeb obi arrays that don't work because of cython bug passing wrong pointers 2015-11-03 14:22:00 +01:00
Celine Mercier ecb9d97adb Reorganized the code to have less functions, and the functions to get 
and format the creation date of a column are now working.
 2015-10-15 15:12:45 +02:00
Celine Mercier 0eaa5aa784 Major changes : new cython subclasses to handle columns with multiple 
elements per line in a more efficient way + now elements_names are
passed as a list + new function to recover only the header of a column
 2015-10-14 18:05:34 +02:00
Celine Mercier 21923e213d The unit tests now test for None values 2015-10-12 18:02:40 +02:00
Celine Mercier 6877fc4892 Fixed a critical bug where values were initialized to NA at the wrong 
location when there was multiple elements per line
 2015-10-12 17:54:36 +02:00
Celine Mercier dbed3d9d1d New module for unit testing with PyUnit 2015-10-09 15:42:57 +02:00
Celine Mercier fc8bf16769 Fixed a critical bug in the computation of the new number of lines of a 
column when truncating
 2015-10-09 13:49:48 +02:00
Celine Mercier e114a3c9cb fixed a critical bug where data size was not calculated correctly and 
column directory is now closed when column is closed
 2015-10-09 10:25:40 +02:00
Celine Mercier ebc9f6f512 fixed a bug where Cython was casting doubles in floats 2015-10-08 15:28:30 +02:00
Celine Mercier 2b3f03ec28 Removed deprecated script 2015-10-08 10:46:46 +02:00
Celine Mercier 8fd9c06be2 Fixed missing file for documentation compilation 2015-10-08 10:45:54 +02:00
Celine Mercier b553eef781 Method to close a DMS is uncommented but not complete yet (columns have 
to be closed separately)
 2015-10-08 10:44:13 +02:00
Celine Mercier ee4c513fd4 Fixed a bug where cloning a column would fail if the data was empty 2015-10-08 10:36:02 +02:00
Celine Mercier c013e6ad33 fixed typo in doxygen doc 2015-10-08 10:33:19 +02:00
Celine Mercier c98d567e2f Updated the documentation and restructured a bit because it wasn't 
compiling (note: Breathe not working)
 2015-10-06 11:09:01 +02:00
Celine Mercier 392f110c8d new functions in the OBIDMS_column class to raise NotImplementedError 
exceptions and to get the creation date of a column
 2015-10-02 13:51:26 +02:00
Celine Mercier 6ced3c4896 new functions to get the creation date of a column 2015-10-02 13:47:53 +02:00
Celine Mercier 4b8bf41a71 closes #13, obi_errno is initialized to 0 2015-10-02 13:46:34 +02:00
Celine Mercier c59a244e9d Fixed little typo 2015-09-30 12:07:13 +02:00
Celine Mercier 4b7f2d268b Doxygen documentation corrected and completed. 2015-09-30 12:03:46 +02:00
Celine Mercier 45af8396b8 minor change in variable name for better coherence 2015-09-28 13:52:41 +02:00
Celine Mercier eeebbc77c3 missing __init__ file in previous commit 2015-09-28 13:52:13 +02:00
Celine Mercier 72155c3b73 entirely reworked cython wrapper 2015-09-28 13:51:35 +02:00