Commits · bfa51d99f8f8a52a4d96913605edf189f93d0b07 · ensembl-gh-mirror / ensembl

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Dec 20, 2002
- *** empty log message *** · bfa51d99
  Graham McVicker authored 22 years ago
  
  bfa51d99
- snp alleles can use '|' or '/' as seperator, apparently · e9b8f306
  Graham McVicker authored 22 years ago
  
  e9b8f306
Dec 19, 2002
- removed no longer needed EMBLLOAD modules · 16d76946
  Graham McVicker authored 22 years ago
  
  16d76946
Dec 18, 2002
- Changes to coincide with relevant_xref_id -> display_xref_id · 32e75270
  Alistair Rust authored 22 years ago
  
  32e75270
- relevant_xref -> display_xref · 738ec456
  Alistair Rust authored 22 years ago
  
  738ec456
- relevant_xref_id -> display_xref_id · 5986c48c
  Alistair Rust authored 22 years ago
  
  5986c48c
- BaseAlignFeature split on contig boundary now looses split codon alignment · ddf36962
  Arne Stabenau authored 22 years ago
  
  ddf36962
- relevant_xref_id -> display_xref_id · e7fec65c
  Alistair Rust authored 22 years ago
```
Dropped the priority column from external_db table.
```
  e7fec65c
- deprecated several unused methods in Exon and incorrect implementation of... · 551995be
  Graham McVicker authored 22 years ago
```
deprecated several unused methods in Exon and incorrect implementation of translate method - added replacement peptide method
```
  551995be
- Transcript now sets alphabet and id of Bio::Seq returned from translate method · 32291943
  Graham McVicker authored 22 years ago
  
  32291943
- Updated tests for relevant_xref_id stuff. · 32cb1138
  Alistair Rust authored 22 years ago
  
  32cb1138
- Getter/setter for relevant_xref_id. · e0a3a53b
  Alistair Rust authored 22 years ago
  
  e0a3a53b
- get_relevant_xref_id method. · 66e8009b
  Alistair Rust authored 22 years ago
  
  66e8009b
- Set the relevant_xref_id to 0 in store. This will need to be updated during · f245514f
  Alistair Rust authored 22 years ago
```
the protein pipeline run.  The actual implementation of the update to the
table will be best discussed with Manu.
```
  f245514f
Dec 17, 2002
- More tests. · 107176ff
  Alistair Rust authored 22 years ago
  
  107176ff
- Access to relevant_xref_id stuff. · 9a49aa06
  Alistair Rust authored 22 years ago
  
  9a49aa06
- Updated tests for external_name and external_db. · 3e54e077
  Alistair Rust authored 22 years ago
  
  3e54e077
- Updated tests for external_name and external_db. · 151c35c2
  Alistair Rust authored 22 years ago
  
  151c35c2
- Refactored versions of external name and external db which now uses the · 4756ddf3
  Alistair Rust authored 22 years ago
```
relevant_xref_id columns.
```
  4756ddf3
- Refactored versions of external name and external db which now uses the · 2f75e83f
  Alistair Rust authored 22 years ago
```
relevant_xref_id columns.
```
  2f75e83f
- genomic2pep should take optional contig arg · 8c54544e
  Graham McVicker authored 22 years ago
  
  8c54544e
- podded and fixed Transcript::genomic2pep, added test cases · 26745356
  Graham McVicker authored 22 years ago
  
  26745356
- Removed tests for external name and external db. · 3be9d8bc
  Alistair Rust authored 22 years ago
  
  3be9d8bc
Dec 16, 2002
- added genomic2pep method to Transcript - not tested · 674c2c28
  Graham McVicker authored 22 years ago
  
  674c2c28
- Updated test db with new relevant_xref_id populated columns in the · 743aed0c
  Alistair Rust authored 22 years ago
```
gene and transcript tables.
```
  743aed0c
- Removed external_db and external_name method tests. · 1309dd72
  Alistair Rust authored 22 years ago
  
  1309dd72
Dec 13, 2002
- cleaned up RepeatFeature · ae99a40d
  Graham McVicker authored 22 years ago
  
  ae99a40d
Dec 12, 2002
- fix to transcripts generated from lite (some sanger transcripts don't have proper translations) · ba81c423
  Graham McVicker authored 22 years ago
  
  ba81c423
Dec 11, 2002
- Lite GeneAdaptor now sets more Translation information on gene retrieval · 1c194e4c
  Graham McVicker authored 22 years ago
  
  1c194e4c
- Transcript coding_start and coding_end should be flushed after transformation · ec94db48
  Graham McVicker authored 22 years ago
  
  ec94db48
- Added relevant_xref_id columns to gene and transcript tables for makeover · 1705ec4a
  Alistair Rust authored 22 years ago
```
of external_db / name stuff.
```
  1705ec4a
- finally removed StaticGoldenPathAdaptor · d51b415d
  Graham McVicker authored 22 years ago
  
  d51b415d
- 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