Commits · b4a3034cc3e9f01191d292ebeb6b71cc15b92c46 · ensembl-gh-mirror / ensembl

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

28 Oct, 2002 14 commits
- Avoid warning in BaseFeatureAdaptor · b4a3034c
  Graham McVicker authored Oct 28, 2002
  
  b4a3034c
- slight change to desc string of Slice and RawContig & avoid warning in... · a1987d52
  Graham McVicker authored Oct 28, 2002
```
slight change to desc string of Slice and RawContig & avoid warning in Slice::get_all_SimilarityFeatures
```
  a1987d52
- renamed Protein::all_SeqFeature to get_all_ProteinFeatures · ae60c4b7
  Graham McVicker authored Oct 28, 2002
  
  ae60c4b7
- removed some very outdated documents (and docs which were moved to tutorial subdir) · 84458e7d
  Graham McVicker authored Oct 28, 2002
  
  84458e7d
- Updated tutorial docs. Moved tutorial docs to new tutorial subdirectory · 97b72bd2
  Graham McVicker authored Oct 28, 2002
  
  97b72bd2
- similarity features made slightly more efficient · e2774759
  Web Admin authored Oct 28, 2002
  
  e2774759
- changes to mapfrag adaptor pulled back from branch · a0402a27
  Web Admin authored Oct 28, 2002
  
  a0402a27
- added Slice and type call · 61567fd1
  Web Admin authored Oct 28, 2002
  
  61567fd1
- Lite GeneAdaptor::fetch_by_stable_id and fetch_by_transcript_stable_id now... · e862ebba
  Graham McVicker authored Oct 28, 2002
```
Lite GeneAdaptor::fetch_by_stable_id and fetch_by_transcript_stable_id now return genes in RawContig coords
```
  e862ebba
- use Bio::PrimarySeqI -> use Bio::PrimarySeq · f9ad04a8
  Simon Potter authored Oct 28, 2002
  
  f9ad04a8
- updated some PODs · d5c4b388
  Graham McVicker authored Oct 28, 2002
```
renamed Slice::get_landmark_MarkerFeatures to get_all_landmark_MarkerFeatures
```
  d5c4b388
- removed align modules from core which are now in compara · bc72fa7d
  Graham McVicker authored Oct 28, 2002
  
  bc72fa7d
- removed Pep_SeqFeature module · 2a06b3d6
  Graham McVicker authored Oct 28, 2002
  
  2a06b3d6
- removed implements pragma · d4e4fcb3
  Graham McVicker authored Oct 28, 2002
  
  d4e4fcb3
25 Oct, 2002 11 commits
- Removed calls to deprecated each_DBLink : now get_all_DBLinks. · 298576a8
  Alistair Rust authored Oct 25, 2002
  
  298576a8
- removed potential memory leak problems with external feature adaptors · 5311ca65
  Graham McVicker authored Oct 25, 2002
  
  5311ca65
- ExternalFeatureAdaptor now integrated into API · d36d1cd9
  Graham McVicker authored Oct 25, 2002
```
old ExternalFeatureFactoryI now magically behaves as an ExternalFeatureAdaptor for backwards compatibility
```
  d36d1cd9
- chromosome_id tinyint-->int, exon index on exon_transcript · 6c556588
  Arne Stabenau authored Oct 25, 2002
  
  6c556588
- end phases are computed when transformig to a slice · 2be5c428
  Eduardo Eyras authored Oct 25, 2002
  
  2be5c428
- improved POD · 1b625294
  Eduardo Eyras authored Oct 25, 2002
  
  1b625294
- removed duplicated POD · a87e5803
  Eduardo Eyras authored Oct 25, 2002
  
  a87e5803
- transcript->type gets set to the gene type it belongs to · 3a90f126
  Eduardo Eyras authored Oct 25, 2002
  
  3a90f126
- gffstring returns an end_phase if it exists · 45e2543e
  Eduardo Eyras authored Oct 25, 2002
  
  45e2543e
- maybe I didnt understand BioPerl enough, sigh · 35591355
  Arne Stabenau authored Oct 25, 2002
  
  35591355
- moltype of protein now set by ProteinAdaptor · 0d8300a5
  Graham McVicker authored Oct 25, 2002
  
  0d8300a5
24 Oct, 2002 7 commits
- Slightly changed syntax of a sanity check in add_supporting_features such that... · 7c8f4221
  Dan T Andrews authored Oct 24, 2002
```
Slightly changed syntax of a sanity check in add_supporting_features such that test wont fail when a slice/contig is not defined for the self or feature exon.
```
  7c8f4221
- fetch_all functions that return array refs now have the arrayrefs initialised to [] · e65bef2b
  Web Admin authored Oct 24, 2002
  
  e65bef2b
- Added leniency in five_prime_utr and three_prime_utr methods for exons that... · 4ab59f2a
  Dan T Andrews authored Oct 24, 2002
```
Added leniency in five_prime_utr and three_prime_utr methods for exons that dont have a stable_id defined.
```
  4ab59f2a
- _transform_to_RawSlice was not aware of reverse slices, but it is now thanks... · be458dd9
  Dan T Andrews authored Oct 24, 2002
```
_transform_to_RawSlice was not aware of reverse slices, but it is now thanks to Graham.  Cleaned up a few other things.
```
  be458dd9
- Fixed typo for->foreach in transform method · 9ee91706
  Dan T Andrews authored Oct 24, 2002
  
  9ee91706
- Added new ExternalFeatureAdaptor as replacement/alternative to old ExternalFeatureFactoryI · 16fc9fa7
  Graham McVicker authored Oct 24, 2002
  
  16fc9fa7
- defined a phase values to start at 0 to avoid a warning · 85f16fe2
  Laura Clarke authored Oct 24, 2002
  
  85f16fe2
23 Oct, 2002 4 commits
- Nice explanation of phase from Ewan added to Exon.pm · 9c5f351b
  James Gilbert authored Oct 23, 2002
  
  9c5f351b
- sanger gene fix ..? · da7ffde1
  Arne Stabenau authored Oct 23, 2002
  
  da7ffde1
- in get_all_translateable_Exons(), phase of the truncated start exon should set to zero · ae605072
  Eduardo Eyras authored Oct 23, 2002
  
  ae605072
- more POD · f3a5aa75
  Eduardo Eyras authored Oct 23, 2002
  
  f3a5aa75
22 Oct, 2002 4 commits
- Fix to the fix - makes raw contig fetches work again. I was wondering · 8ca20aa6
  Michele Clamp authored Oct 22, 2002
```
where all my transcripts were disappearing to.

I'm assuming it still works for slices.  I don't have slice tests yet.
```
  8ca20aa6
- a bit more info added · 32a4fc07
  Eduardo Eyras authored Oct 22, 2002
  
  32a4fc07
- POD, POD, POD, everybody wants to POD · b49a8aa2
  Eduardo Eyras authored Oct 22, 2002
  
  b49a8aa2
- fixed typo in method call · 63bbe2bf
  Eduardo Eyras authored Oct 22, 2002
  
  63bbe2bf