Commits · 2073a424406d491c39f0aa6ff3101d296134af07 · ensembl-gh-mirror / ensembl

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Aug 18, 2010
- entry RefSeq_peptide::MULTI-complete in twice so removed one instance · 2073a424
  Ian Longden authored 14 years ago
  
  2073a424
- entry RefSeq_dna::MULTI-complete in twice so removed one instance · 18d7e316
  Ian Longden authored 14 years ago
  
  18d7e316
Aug 17, 2010
- Comment out buggy EG code (see "EG BUG: FIXME"). · 0b0760c9
  Andreas Kusalananda Kähäri authored 14 years ago
  
  0b0760c9
- Allow the slice() method to be used to undef the slice · 4850cb84
  Andreas Kusalananda Kähäri authored 14 years ago
```
("$f->slice(undef)").
```
  4850cb84
- In is_circular(): If there is no adaptor, assume it's not circular (and · aa73e977
  Andreas Kusalananda Kähäri authored 14 years ago
```
warn user).

Also, comment out buggy EG code in project() (see "EG BUG: FIXME").
```
  aa73e977
Aug 16, 2010
- Fix spelling mistake. · 9fa32045
  Andreas Kusalananda Kähäri authored 14 years ago
  
  9fa32045
- Make expand() aware of circular chromosomes. Patch from EG. · 364b8822
  Andreas Kusalananda Kähäri authored 14 years ago
  
  364b8822
- Make project() aware of circular chromosomes. Patch from EG. · 35563034
  Andreas Kusalananda Kähäri authored 14 years ago
  
  35563034
- Re-implement is_circular(). Patch from EG. · c7b996f0
  Andreas Kusalananda Kähäri authored 14 years ago
```
Also reformat is_toplevel() and is_reference().
```
  c7b996f0
- Deal with circular chromosome in length(). Patch from EG. · 174e40b8
  Andreas Kusalananda Kähäri authored 14 years ago
  
  174e40b8
- In new(): don't require start to be less than end. Patch from EG. · 3852e871
  Andreas Kusalananda Kähäri authored 14 years ago
  
  3852e871
- Change the Ensembl developers list email address in all modules from · 83e0894d
  Andreas Kusalananda Kähäri authored 14 years ago
```
<ensembl-dev@ebi.ac.uk> to <dev@ensembl.org>.
```
  83e0894d
- Allow start > end in RangeRegistry. Patch from EG. · 9d4834e4
  Andreas Kusalananda Kähäri authored 14 years ago
  
  9d4834e4
- Make seq_region_start() and seq_region_end() aware of circular · 2f4524e5
  Andreas Kusalananda Kähäri authored 14 years ago
```
chromosomes.  Patch from EG.
```
  2f4524e5
- Re-jig some of the simpler methods. · e7716d0e
  Andreas Kusalananda Kähäri authored 14 years ago
  
  e7716d0e
Aug 13, 2010
- Make seq() aware of circular chromosomes. Patch from EG. · fc6f3f7c
  Andreas Kusalananda Kähäri authored 14 years ago
  
  fc6f3f7c
- Make _objs_from_sth() aware of circular chromosomes. Patch from EG. · 824f9544
  Andreas Kusalananda Kähäri authored 14 years ago
  
  824f9544
- Remove deprecated modules scheduled for removal in release 60. · ecba7548
  Andreas Kusalananda Kähäri authored 14 years ago
  
  ecba7548
- Small POD mod. · 3bbeece2
  Andreas Kusalananda Kähäri authored 14 years ago
  
  3bbeece2
- Add CircularSlice.pm from the EG people. · 9fbddc17
  Andreas Kusalananda Kähäri authored 14 years ago
  
  9fbddc17
- Make fetch_by_region() aware of circular chromosomes. Patch from EG. · 474a9cce
  Andreas Kusalananda Kähäri authored 14 years ago
  
  474a9cce
- Remove one instance of double 'my' in · 65ce5d24
  Andreas Kusalananda Kähäri authored 14 years ago
```
_fetch_by_Slice_start_end_strand_circular().
```
  65ce5d24
- Get some of the logic right. · 04bb67f9
  Andreas Kusalananda Kähäri authored 14 years ago
  
  04bb67f9
- Make _objs_from_sth() know about circular chromosomes. Patch from EG. · 3ab0f398
  Andreas Kusalananda Kähäri authored 14 years ago
  
  3ab0f398
- Modified previous bugfix in seq(): If stable IDs are not available, and · 6dbed007
  Andreas Kusalananda Kähäri authored 14 years ago
```
dbIDs are not available, use genomic start/end coordinates to figure out
whether "this" translation is the same as the canonical translation or
not.
```
  6dbed007
- Slight modifications to yesterday's circular chromosome patch. · 5e05c09e
  Andreas Kusalananda Kähäri authored 14 years ago
  
  5e05c09e
- set up regexp filters for gene descriptions do not allow undefined or UNKNOWN · b6e8d70b
  Ian Longden authored 14 years ago
  
  b6e8d70b
- If the translations do not have stable IDs, use their dbIDs to compare · 81f06bd0
  Andreas Kusalananda Kähäri authored 14 years ago
```
them instead.  Bug fix for Amy.
```
  81f06bd0
- Fix for splice sites being called at transcript ends · a2c01565
  William McLaren authored 14 years ago
  
  a2c01565
- Added new direct Jamboree mappings · af19e37c
  Ian Longden authored 14 years ago
  
  af19e37c
Aug 12, 2010
- Modify comment that wasn't right anymore. · 63bbcd60
  Andreas Kusalananda Kähäri authored 14 years ago
  
  63bbcd60
- Handle cicular chromosomes in _objs_from_sth(). Patch from EG. · eacfb265
  Andreas Kusalananda Kähäri authored 14 years ago
  
  eacfb265
- Minor cleanup of package head. · 8e2369a8
  Andreas Kusalananda Kähäri authored 14 years ago
  
  8e2369a8
- Always display API version with exceptions, warnings, and deprecation · 554b6817
  Andreas Kusalananda Kähäri authored 14 years ago
```
messages.  Makes it easier to debug reported errors...
```
  554b6817
- Make the registry use the new ApiVersion module. · 79fb61a9
  Andreas Kusalananda Kähäri authored 14 years ago
  
  79fb61a9
- Put the API version into its own module: · 995e9733
  Andreas Kusalananda Kähäri authored 14 years ago
```
  DESCRIPTION
    The module exports the software_version() subroutine which
    returns the release version of the Ensembl Core API.
```
  995e9733
- Detect duplicated source sections in the configuration file. · 6affe06e
  Andreas Kusalananda Kähäri authored 14 years ago
  
  6affe06e
- Get rid of old commented-out code in _objs_from_sth(). · ff99106b
  Andreas Kusalananda Kähäri authored 14 years ago
  
  ff99106b
- In fetch_all_by_Transcript(): Handle cicular genomes. Patch from EG. · 35ecf251
  Andreas Kusalananda Kähäri authored 14 years ago
  
  35ecf251
- added dog_ensembl_proteins · 4c3fd99c
  Magali Ruffier authored 14 years ago
  
  4c3fd99c