Commits · 3586e2b9de0de06d58b6888398ad75bfc40b95e9 · ensembl-gh-mirror / ensembl

This project is mirrored from https://:*****@github.com/Ensembl/ensembl.git. Pull mirroring updated Feb 09, 2023.

06 Dec, 2002 7 commits
- stole bioperl Bio::Root::RootI implementation, · 3586e2b9
  Graham McVicker authored Dec 06, 2002
```
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 Dec 06, 2002
  
  81efab59
- fixes to Transcript::get_all_SNPs method · f1e4f3fa
  Graham McVicker authored Dec 06, 2002
  
  f1e4f3fa
- AssemblyMapperAdaptor should come from dnadb (merge from manu's branch change) · 3f7fd6ad
  Graham McVicker authored Dec 06, 2002
  
  3f7fd6ad
- adjusted incorrect POD · 9c0141d9
  Graham McVicker authored Dec 06, 2002
  
  9c0141d9
- added get_all_SNPs to transcript - untested · 5a713fd0
  Graham McVicker authored Dec 06, 2002
  
  5a713fd0
- compiles; should work; needs testing · 93103f63
  Ewan Birney authored Dec 06, 2002
  
  93103f63
05 Dec, 2002 5 commits
- added genomic2cdna method to Transcript and PredictionTranscript, refactored... · 3c6008d9
  Graham McVicker authored Dec 05, 2002
```
added genomic2cdna method to Transcript and PredictionTranscript, refactored cdna2genomic & pep2genomic methods in PredictionTranscript
```
  3c6008d9
- Removed cdn2genomic method from Exon · adcd076d
  Graham McVicker authored Dec 05, 2002
  
  adcd076d
- set up the adaptor when creating a slice in the method fetch_by_supercontig_name · d214fb8d
  Emmanuel Mongin authored Dec 05, 2002
  
  d214fb8d
- fixed cdna_coding_start bug · 339630d7
  Graham McVicker authored Dec 05, 2002
  
  339630d7
- added tests for new transcript methods · 486c732d
  Graham McVicker authored Dec 05, 2002
  
  486c732d
04 Dec, 2002 9 commits
- bugfixes in new cdna2genomic cdna_coding_start/end · 572200dc
  Arne Stabenau authored Dec 04, 2002
  
  572200dc
- cdna_coding_xxxx methods added, others deprecated and refactored, not tested · 45c82f76
  Graham McVicker authored Dec 04, 2002
  
  45c82f76
- took clone adaptor creation out of the loop where every DAS feature is created... · cd3dc7c5
  Web Admin authored Dec 04, 2002
```
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 Dec 04, 2002
  
  e9f3b354
- Change taken over from branch · e54cc8a8
  Arne Stabenau authored Dec 04, 2002
  
  e54cc8a8
- moved Gene/Slice/Transcript wrapper fixes to head · e5ea05e7
  Web Admin authored Dec 04, 2002
  
  e5ea05e7
- added extra calls · 5442e289
  Web Admin authored Dec 04, 2002
  
  5442e289
- density plot stuff · f067f683
  Web Admin authored Dec 04, 2002
  
  f067f683
- moving from branch · a94df20c
  Web Admin authored Dec 04, 2002
  
  a94df20c
29 Nov, 2002 4 commits
- New schema update · 19c2f5dc
  Emmanuel Mongin authored Nov 29, 2002
  
  19c2f5dc
- If the polyA has any Ns in it, they will be treated as potential As. Likewise for the polyT · e26b2055
  Eduardo Eyras authored Nov 29, 2002
  
  e26b2055
- new module. The clipping code is centralised, so that it can be used anywhere... · dcb1c1be
  Eduardo Eyras authored Nov 29, 2002
```
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 Nov 29, 2002
  
  b02845e6
28 Nov, 2002 1 commit
- PGA now returns true · 2cc687bc
  Web Admin authored Nov 28, 2002
  
  2cc687bc
27 Nov, 2002 7 commits
- fix slice invert problem · 5bcd277c
  Arne Stabenau authored Nov 27, 2002
  
  5bcd277c
- lite store tested, but only if lite schema in test_genome · 18fda5f2
  Arne Stabenau authored Nov 27, 2002
  
  18fda5f2
- first go on store · 5b875dd3
  Arne Stabenau authored Nov 27, 2002
  
  5b875dd3
- fixed supporting evidence lazy loading bug · c3a155c3
  Arne Stabenau authored Nov 27, 2002
  
  c3a155c3
- More tests - wip. · 16a52015
  Alistair Rust authored Nov 27, 2002
  
  16a52015
- removed duplicated method · 34b64d9b
  Eduardo Eyras authored Nov 27, 2002
  
  34b64d9b
- Tests. · f6773ae7
  Alistair Rust authored Nov 27, 2002
  
  f6773ae7
26 Nov, 2002 7 commits
- Re-jigging of external_db and external_name tests. · a1aec194
  Alistair Rust authored Nov 26, 2002
  
  a1aec194
- primary_id -> display_id · ac735220
  Alistair Rust authored Nov 26, 2002
  
  ac735220
- Wasn't quite right... · 0ebfc1bb
  Alistair Rust authored Nov 26, 2002
  
  0ebfc1bb
- rat assembly loader · ddc28a98
  Simon Potter authored Nov 26, 2002
  
  ddc28a98
- list_geneIds made consistent with list_gene_stable_ids and both rather return... · 4e3a467e
  Eduardo Eyras authored Nov 26, 2002
```
list_geneIds made consistent with list_gene_stable_ids and both rather return an arrayref, to be fashionable
```
  4e3a467e
- list_geneIds made consistent with list_gene_stable_ids and both return an array · bc716c86
  Eduardo Eyras authored Nov 26, 2002
  
  bc716c86
- Added EMBL into the priority list of dbs used by external_name and external_db · bc6d6f47
  Alistair Rust authored Nov 26, 2002
  
  bc6d6f47