Commits · 0d94e16396998eb09d058ade5744420baeda45fd · ensembl-gh-mirror / ensembl

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Dec 11, 2002
- updated some comments · 0d94e163
  Graham McVicker authored 22 years ago
  
  0d94e163
- Minor update - no longer need to checkout ensembl-lite to use the Lite code. · 443f5d3f
  Dan T Andrews authored 22 years ago
  
  443f5d3f
- ProxyAdaptor should define DESTROY method (not DELETE) · 30914fd4
  Graham McVicker authored 22 years ago
  
  30914fd4
Dec 10, 2002
- fix to Transcript::get_all_peptide_variations (negative strand snps weren't correctly) · 09b32785
  Graham McVicker authored 22 years ago
  
  09b32785
- tidied constructor · 5f1436eb
  Graham McVicker authored 22 years ago
  
  5f1436eb
- Fix to load_genomic_mapper method in StickyExon · b2697d9c
  Graham McVicker authored 22 years ago
  
  b2697d9c
- Fix alternate peptide calculations in Transcript · aa520c87
  Graham McVicker authored 22 years ago
  
  aa520c87
- *** empty log message *** · 511f9231
  Emmanuel Mongin authored 22 years ago
  
  511f9231
- More ditching of external_db stuff. Not tested. · e6474621
  Alistair Rust authored 22 years ago
  
  e6474621
- Initial ditching of the much-maligned external_db stuff. · bfdecd90
  Alistair Rust authored 22 years ago
  
  bfdecd90
- added a script to load anopheles karyotype data · 17837d13
  Emmanuel Mongin authored 22 years ago
  
  17837d13
Dec 09, 2002
- For a second time unashamedly removing the html version of the tutorial from the head. · f8a4942c
  Dan T Andrews authored 22 years ago
  
  f8a4942c
- Updated cvsro host and code branch information. Fixed problem with reversed... · 388c4183
  Dan T Andrews authored 22 years ago
```
Updated cvsro host and code branch information.  Fixed problem with reversed gffstring order.  Made a gazillion different tutorial file formats.
```
  388c4183
- added method Transcript::get_all_peptide_variations - not tested · 73acc879
  Graham McVicker authored 22 years ago
  
  73acc879
Dec 06, 2002
- stole bioperl Bio::Root::RootI implementation, · 3586e2b9
  Graham McVicker authored 22 years ago
```
so switch to bioperl 1 will be less painful
```
  3586e2b9
- added method Transcript::get_all_cdna_SNPs, fixed error in Transcript::get_all_SNPs · 81efab59
  Graham McVicker authored 22 years ago
  
  81efab59
- fixes to Transcript::get_all_SNPs method · f1e4f3fa
  Graham McVicker authored 22 years ago
  
  f1e4f3fa
- AssemblyMapperAdaptor should come from dnadb (merge from manu's branch change) · 3f7fd6ad
  Graham McVicker authored 22 years ago
  
  3f7fd6ad
- adjusted incorrect POD · 9c0141d9
  Graham McVicker authored 22 years ago
  
  9c0141d9
- added get_all_SNPs to transcript - untested · 5a713fd0
  Graham McVicker authored 22 years ago
  
  5a713fd0
- compiles; should work; needs testing · 93103f63
  Ewan Birney authored 22 years ago
  
  93103f63
Dec 05, 2002
- added genomic2cdna method to Transcript and PredictionTranscript, refactored... · 3c6008d9
  Graham McVicker authored 22 years ago
```
added genomic2cdna method to Transcript and PredictionTranscript, refactored cdna2genomic & pep2genomic methods in PredictionTranscript
```
  3c6008d9
- Removed cdn2genomic method from Exon · adcd076d
  Graham McVicker authored 22 years ago
  
  adcd076d
- set up the adaptor when creating a slice in the method fetch_by_supercontig_name · d214fb8d
  Emmanuel Mongin authored 22 years ago
  
  d214fb8d
- fixed cdna_coding_start bug · 339630d7
  Graham McVicker authored 22 years ago
  
  339630d7
- added tests for new transcript methods · 486c732d
  Graham McVicker authored 22 years ago
  
  486c732d
Dec 04, 2002
- bugfixes in new cdna2genomic cdna_coding_start/end · 572200dc
  Arne Stabenau authored 22 years ago
  
  572200dc
- cdna_coding_xxxx methods added, others deprecated and refactored, not tested · 45c82f76
  Graham McVicker authored 22 years ago
  
  45c82f76
- took clone adaptor creation out of the loop where every DAS feature is created... · cd3dc7c5
  Web Admin authored 22 years ago
```
took clone adaptor creation out of the loop where every DAS feature is created and now only do it once!
```
  cd3dc7c5
- main trunkified · e9f3b354
  Simon Potter authored 22 years ago
  
  e9f3b354
- Change taken over from branch · e54cc8a8
  Arne Stabenau authored 22 years ago
  
  e54cc8a8
- moved Gene/Slice/Transcript wrapper fixes to head · e5ea05e7
  Web Admin authored 22 years ago
  
  e5ea05e7
- added extra calls · 5442e289
  Web Admin authored 22 years ago
  
  5442e289
- density plot stuff · f067f683
  Web Admin authored 22 years ago
  
  f067f683
- moving from branch · a94df20c
  Web Admin authored 22 years ago
  
  a94df20c
Nov 29, 2002
- New schema update · 19c2f5dc
  Emmanuel Mongin authored 22 years ago
  
  19c2f5dc
- If the polyA has any Ns in it, they will be treated as potential As. Likewise for the polyT · e26b2055
  Eduardo Eyras authored 22 years ago
  
  e26b2055
- new module. The clipping code is centralised, so that it can be used anywhere... · dcb1c1be
  Eduardo Eyras authored 22 years ago
```
new module. The clipping code is centralised, so that it can be used anywhere without duplication. It can clip, mask or softmask the polyA and the polyT if any.
```
  dcb1c1be
- specific anopheles scripts · b02845e6
  Emmanuel Mongin authored 22 years ago
  
  b02845e6
Nov 28, 2002
- PGA now returns true · 2cc687bc
  Web Admin authored 22 years ago
  
  2cc687bc