Commits · 924d95595874048965456e1a19deaf797f929eb7 · ensembl-gh-mirror / ensembl

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Feb 16, 2010
- 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
- Patch from Any Yates to get multi-species database to be picked up properly. · 6af98df7
  Andreas Kusalananda Kähäri authored 15 years ago
  
  6af98df7
- Correct display label from "snpDensity" to "SNP Density". · 00c13edc
  Andreas Kusalananda Kähäri authored 15 years ago
  
  00c13edc
Feb 02, 2010
- Added imported ccds set (for otherfeatures) · c1ed3062
  Bronwen Aken authored 15 years ago
  
  c1ed3062
- Update year in Copyright notice. · 6b9a6526
  Andreas Kusalananda Kähäri authored 15 years ago
  
  6b9a6526
- Fetch all the transcript variant structure (in terms of exons) from a core · 37686359
  Gautier Koscielny authored 15 years ago
```
database in GFF format (STDOUT).
```
  37686359
- Added code to delete names/GO terms if the -delete_only option is specified.... · 4c7155ff
  Rhoda Kinsella authored 15 years ago
```
Added code to delete names/GO terms if the -delete_only option is specified. Added code to check whether
-registryconf is submitted as a string from the submit_projections.pl script or as a file on the command
line.
```
  4c7155ff
- Added code to delete names and GO projections before carrying out new projections. · fb4b1a79
  Rhoda Kinsella authored 15 years ago
  
  fb4b1a79
- Use "GC content" rather than "PercentGC" as display label. · 7f353cb9
  Andreas Kusalananda Kähäri authored 15 years ago
  
  7f353cb9