Commits · c1393675553846113a26e20b18af1304ffbba496 · OBITools / OBITools3

11 Dec, 2015 1 commit
- DNA sequences and character strings are now handled using AVL trees. · c1393675
  Celine Mercier authored Dec 11, 2015
  
  c1393675
02 Dec, 2015 1 commit

Added the lists of opened columns and arrays in the OBIDMS structure, · 1586956d

Celine Mercier authored Dec 02, 2015

and a counter in the OBIDMS column structure; fixed some bugs and
created tests for referring columns that are bound to disappear anyway.

1586956d

29 Nov, 2015 1 commit
- Major update: new type of columns containing indices referring to lines · b45b496b
  Celine Mercier authored Nov 29, 2015
```
in other columns
```
  b45b496b
23 Nov, 2015 4 commits
- Column type is now passed as a character string when creating the column · 2cf10cb6
  Celine Mercier authored Nov 23, 2015
```
(either 'OBI_INT', 'OBI_FLOAT', 'OBI_BOOL', 'OBI_CHAR', 'OBI_STR' or
'OBI_SEQ')
```
  2cf10cb6
- deleting useless .pyc files · 5a551630
  Celine Mercier authored Nov 23, 2015
  
  5a551630
- Fixed a major bug with the versioning of columns that was introduced in · d6a99baf
  Celine Mercier authored Nov 23, 2015
```
f6ec8ba9
```
  d6a99baf
- Increased maximum line count of columns to 1^9 · 08f2657e
  Celine Mercier authored Nov 23, 2015
  
  08f2657e
20 Nov, 2015 2 commits
- DNA sequences are now encoded on 4 bits when they are in IUPAC · 6aa2f929
  Celine Mercier authored Nov 20, 2015
  
  6aa2f929
- modified the encoding function on 2 bits a little · 87044b41
  Celine Mercier authored Nov 20, 2015
  
  87044b41
19 Nov, 2015 2 commits
- New column type for DNA sequences. Only for those coded on 2 bits (only · 6ab1c833
  Celine Mercier authored Nov 19, 2015
```
'ATGCatgc') for now.
```
  6ab1c833
- changed version to 0.0.0 · e3712485
  Celine Mercier authored Nov 19, 2015
  
  e3712485
18 Nov, 2015 1 commit
- The endianness of a DMS is now stored in the OBIDMS structure · dbf94632
  Celine Mercier authored Nov 18, 2015
  
  dbf94632
16 Nov, 2015 2 commits
- Fixed minor error in the documentation of a function. · eb12af4d
  Celine Mercier authored Nov 16, 2015
  
  eb12af4d
- The endianness of an OBIDMS is now stored in an informations file that · e8417b4f
  Celine Mercier authored Nov 16, 2015
```
is read when opening the OBIDMS.
```
  e8417b4f
10 Nov, 2015 6 commits
- Minor changes in code to improve readability and fix C compilation · 6579566c
  Celine Mercier authored Nov 10, 2015
```
warnings
```
  6579566c
- When retrieving the header of a column, the version number of the column · 410e2e02
  Celine Mercier authored Nov 10, 2015
```
wanted can now be provided.
```
  410e2e02
- When enlarging a column, the function doesn't try anymore to keep the · 8ce4f264
  Celine Mercier authored Nov 10, 2015
```
mapped region at the same pointer (never works), and unmap/remap
instead.
```
  8ce4f264
- The header size when creating a column is now calculated according to · d885eb48
  Celine Mercier authored Nov 10, 2015
```
the size of the header structure and the page size of the platform.
```
  d885eb48
- In OBI_CHAR columns, characters are now given and retrieved as decoded · 661fe360
  Celine Mercier authored Nov 10, 2015
```
(unicode) characters.
```
  661fe360
- Comments in column headers are now working. · c4b7e579
  Celine Mercier authored Nov 10, 2015
  
  c4b7e579
09 Nov, 2015 6 commits
- The header size is now directly read in the file when a column or an · f6ec8ba9
  Celine Mercier authored Nov 09, 2015
```
array is opened.
```
  f6ec8ba9
- Methods __len__ (number of lines used) and __sizeof__ (total size in · 0e3d6ed2
  Celine Mercier authored Nov 09, 2015
```
bytes) implemented for columns.
```
  0e3d6ed2
- The data size in bytes is now stored in the header of a column. · 01bfc145
  Celine Mercier authored Nov 09, 2015
  
  01bfc145
- Minor changes to make the creation of files and directories cleaner · 65c1b1e8
  Celine Mercier authored Nov 09, 2015
  
  65c1b1e8
- File descriptors for dms, column and array directories are now stored in · b37bd8f2
  Celine Mercier authored Nov 09, 2015
```
structures.
```
  b37bd8f2
- Minor changes in code to improve readability (freeing some character · 05e3956a
  Celine Mercier authored Nov 09, 2015
```
strings earlier)
```
  05e3956a
06 Nov, 2015 1 commit
- Major update: obiarrays with columns containing indices referring to · 9b066f43
  Celine Mercier authored Nov 06, 2015
```
character strings.
```
  9b066f43
03 Nov, 2015 1 commit
- obi arrays that don't work because of cython bug passing wrong pointers · 456551ff
  Celine Mercier authored Nov 03, 2015
  
  456551ff
15 Oct, 2015 1 commit
- Reorganized the code to have less functions, and the functions to get · ecb9d97a
  Celine Mercier authored Oct 15, 2015
```
and format the creation date of a column are now working.
```
  ecb9d97a
14 Oct, 2015 1 commit

Major changes : new cython subclasses to handle columns with multiple · 0eaa5aa7

Celine Mercier authored Oct 14, 2015

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

0eaa5aa7

12 Oct, 2015 2 commits
- The unit tests now test for None values · 21923e21
  Celine Mercier authored Oct 12, 2015
  
  21923e21
- Fixed a critical bug where values were initialized to NA at the wrong · 6877fc48
  Celine Mercier authored Oct 12, 2015
```
location when there was multiple elements per line
```
  6877fc48
09 Oct, 2015 3 commits
- New module for unit testing with PyUnit · dbed3d9d
  Celine Mercier authored Oct 09, 2015
  
  dbed3d9d
- Fixed a critical bug in the computation of the new number of lines of a · fc8bf167
  Celine Mercier authored Oct 09, 2015
```
column when truncating
```
  fc8bf167
- fixed a critical bug where data size was not calculated correctly and · e114a3c9
  Celine Mercier authored Oct 09, 2015
```
column directory is now closed when column is closed
```
  e114a3c9
08 Oct, 2015 5 commits
- fixed a bug where Cython was casting doubles in floats · ebc9f6f5
  Celine Mercier authored Oct 08, 2015
  
  ebc9f6f5
- Removed deprecated script · 2b3f03ec
  Celine Mercier authored Oct 08, 2015
  
  2b3f03ec
- Fixed missing file for documentation compilation · 8fd9c06b
  Celine Mercier authored Oct 08, 2015
  
  8fd9c06b
- Method to close a DMS is uncommented but not complete yet (columns have · b553eef7
  Celine Mercier authored Oct 08, 2015
```
to be closed separately)
```
  b553eef7
- Fixed a bug where cloning a column would fail if the data was empty · ee4c513f
  Celine Mercier authored Oct 08, 2015
  
  ee4c513f