Commits · 42c8c0353f331b04e4432118ee370792ef049f9c · ensembl-gh-mirror / ensembl

This project is mirrored from https://:*****@github.com/Ensembl/ensembl.git. Pull mirroring failed 2 months ago.
Repository mirroring has been paused due to too many failed attempts. It can be resumed by a project maintainer or owner.
Last successful update 6 months ago.

Feb 18, 2010
- Added aligned_seq method · 42c8c035
  William McLaren authored 15 years ago
  
  42c8c035
Feb 17, 2010
- New attribs from Ensembl Genomes (Uma). · 04a15da4
  Andreas Kusalananda Kähäri authored 15 years ago
```
Folded some older comments for readability.
```
  04a15da4
- make sure type is lower case · ce36d9db
  Ian Longden authored 15 years ago
  
  ce36d9db
- Adding dictyBase (id=20303) for Ensembl Genomes (from Uma). · 0bff5eb6
  Andreas Kusalananda Kähäri authored 15 years ago
  
  0bff5eb6
- bug fix for get_direct_xref · a19baf4e
  Ian Longden authored 15 years ago
  
  a19baf4e
Feb 16, 2010
- Added StrainSlice methods · c31e8a56
  William McLaren authored 15 years ago
  
  c31e8a56
- Added expanded_length method and changed seq method to use it · 420b66f6
  William McLaren authored 15 years ago
  
  420b66f6
- Initial check in · 9e8910b0
  William McLaren authored 15 years ago
  
  9e8910b0
- make sure there is a species set · 924d9559
  Ian Longden authored 15 years ago
  
  924d9559
Feb 12, 2010
- fixed the various methods routines. this was not working at all but no one... · 6923f410
  Ian Longden authored 15 years ago
```
fixed the various methods routines. this was not working at all but no one ever used it so was never noticed. Needed now for uniprot swissport having a different percentage cutoff
```
  6923f410
- just do the gene slice project rather than the gene transfer it is safer and quicker · 9aa197ea
  Ian Longden authored 15 years ago
  
  9aa197ea
- gapped alignment at 100 percent · e3734666
  Ian Longden authored 15 years ago
  
  e3734666
Feb 11, 2010
- updated amino acid sub text · 1094a4e9
  Bronwen Aken authored 15 years ago
  
  1094a4e9
- Drop a $sth->finish(). · df508b8d
  Andreas Kusalananda Kähäri authored 15 years ago
  
  df508b8d
- Make SQL nicer. · d66ab883
  Andreas Kusalananda Kähäri authored 15 years ago
  
  d66ab883
- Made amino_acid_sub more generic. · 8aedd2ef
  Amonida Zadissa authored 15 years ago
  
  8aedd2ef
Feb 10, 2010
- Update documentation slightly. · 317a2125
  Andreas Kusalananda Kähäri authored 15 years ago
  
  317a2125
Feb 09, 2010
- merge from branch-ensembl-dec09 · 6c9580d1
  Steve Trevanion authored 15 years ago
  
  6c9580d1
- new type for Vega · 31d97ee0
  Steve Trevanion authored 15 years ago
  
  31d97ee0
- Add "_synonym" to database name for cross reference lines that are generated... · 4adf5ffc
  Glenn Proctor authored 15 years ago
```
Add "_synonym" to database name for cross reference lines that are generated from external_synonyms (previously they were indistinguishable).

Note that Uniprot, EMBL etc are still "merged" so that Uniprot/SWISSPROT and Uniprot/TREMBL become Uniprot.

Also fixed bug that was causing EntrezGene to be changed to ENSEMBLGene
```
  4adf5ffc
- making sure this is on the head! · 5c6628cc
  Stephen Keenan authored 15 years ago
  
  5c6628cc
Feb 05, 2010
- Added masked_seq and supporting methods · 0a6cf7be
  William McLaren authored 15 years ago
  
  0a6cf7be
- added new methods to store/remove AssemblyExceptionFeature objects in the database · dfce65c7
  Daniel Rios authored 15 years ago
  
  dfce65c7
- added new test to store/remove AssemblyExceptionFeatures in the database · ef7bccad
  Daniel Rios authored 15 years ago
  
  ef7bccad
- Also write error reports. · e706cf5c
  Andreas Kusalananda Kähäri authored 15 years ago
  
  e706cf5c
- Readability fix in store(). · 9888a01d
  Andreas Kusalananda Kähäri authored 15 years ago
  
  9888a01d
Feb 04, 2010
- Add missing license boilerplate. · abdb6ad5
  Andreas Kusalananda Kähäri authored 15 years ago
  
  abdb6ad5
- Buglet fix: In sub_SeqFeature(): explicitly return empty list. · 8b9a245a
  Andreas Kusalananda Kähäri authored 15 years ago
  
  8b9a245a
- BUGFIX: In transform(): $self->project() returns a listref. · 6745900a
  Andreas Kusalananda Kähäri authored 15 years ago
  
  6745900a
- Correct documentation. · 54fb4327
  Andreas Kusalananda Kähäri authored 15 years ago
  
  54fb4327
- BUGFIX: In transform(): $self->project() returns a listref. · fbda1179
  Andreas Kusalananda Kähäri authored 15 years ago
  
  fbda1179
- BUGFIX: In transform(): $self->project() returns a listref. · d6f5c850
  Andreas Kusalananda Kähäri authored 15 years ago
  
  d6f5c850
- Get rid of call to get_all_Transcripts() (result not used). · 8ecf4f7d
  Andreas Kusalananda Kähäri authored 15 years ago
  
  8ecf4f7d
- Correct documentation. · 9901314d
  Andreas Kusalananda Kähäri authored 15 years ago
  
  9901314d
- Remove unimplemented methods from synopsis. · 73efbf7d
  Andreas Kusalananda Kähäri authored 15 years ago
  
  73efbf7d
- Correct documentation. · 560242fd
  Andreas Kusalananda Kähäri authored 15 years ago
  
  560242fd
- Correct some documentation. · af64970b
  Andreas Kusalananda Kähäri authored 15 years ago
  
  af64970b
- BUGFIX: · 7b79629c
  Andreas Kusalananda Kähäri authored 15 years ago
```
Always de-reference the value got from get_mapping_path().
Found by Magali.
```
  7b79629c
Feb 03, 2010
- Configure configuration file for the AltSplicingToolkit distribution. · 4501b68b
  Gautier Koscielny authored 15 years ago
  
  4501b68b
- First official release of the Alternative Splicing Toolkit as part of Ensembl · b60f6802
  Gautier Koscielny authored 15 years ago
```
distribution.
```
  b60f6802