Commits · f4a59f50568f28fd1e7511e176aeee744b17ef39 · ensembl-gh-mirror / ensembl

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Aug 20, 2010
- panda added · f4a59f50
  Jorge Zamora authored 14 years ago
  
  f4a59f50
Aug 19, 2010
- format slightly changed and use new exception types · aafc4a62
  Ian Longden authored 14 years ago
  
  aafc4a62
Aug 18, 2010
- Do not assume that canonical_transcript() returns a useful value. · affb3aef
  Andreas Kusalananda Kähäri authored 14 years ago
```
Thanks Bronwen for the heads up.
```
  affb3aef
- Modify previous patch to store() so that it actually might work. · cdacc4ef
  Andreas Kusalananda Kähäri authored 14 years ago
  
  cdacc4ef
- In store(): When first storing the gene, set canonical_transcript_id · dfc58ff8
  Andreas Kusalananda Kähäri authored 14 years ago
```
to zero and then update it when we know what the new internal ID of the
transcript is.
```
  dfc58ff8
- Use assert_ref() in canonical_transcript() to clean it up a bit. · e1e3fc04
  Andreas Kusalananda Kähäri authored 14 years ago
```
In load(): also load the canonical transcript.
```
  e1e3fc04
- 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