Commits · 838c24fabdd2ea819cc5983725b5c7504d019b20 · ensembl-gh-mirror / ensembl

This project is mirrored from https://:*****@github.com/Ensembl/ensembl.git. Pull mirroring updated Jan 29, 2023.

08 Dec, 2004 14 commits
- Updated to use exonerate 0.9 · 838c24fa
  Glenn Proctor authored Dec 08, 2004
  
  838c24fa
- change source_id -> linkage_source_id · 2239b76c
  Ian Longden authored Dec 08, 2004
  
  2239b76c
- set_list to use all primary xrefs for humans as default · 64b9b0e1
  Ian Longden authored Dec 08, 2004
  
  64b9b0e1
- source_id removed from synonym,dependent_xref and primary_xref this... · b0b66b4d
  Ian Longden authored Dec 08, 2004
```
source_id removed from synonym,dependent_xref and primary_xref this information is available via the xref. linkage_source_id added to dependent xref. create_xrefs now also returns a hashref
```
  b0b66b4d
- Re-factored gene display xref calculation to make it clearer. · 620200c3
  Glenn Proctor authored Dec 08, 2004
  
  620200c3
- not quite sure this is the full patch 21 to 22 (Dont even remember generating it). · 84115d1a
  Arne Stabenau authored Dec 08, 2004
  
  84115d1a
- implemented register all chained for the chimp building (which is still not working). · 57d8589b
  Arne Stabenau authored Dec 08, 2004
  
  57d8589b
- essentially rewritten, should be useless soon thanks to Vivek and Craig · e40c7ca0
  Arne Stabenau authored Dec 08, 2004
  
  e40c7ca0
- removed double coord recaculation on Transcript add · ee34ddf3
  Arne Stabenau authored Dec 08, 2004
  
  ee34ddf3
- snp_lite_density replaced by variation_density.pl · ea6c2f37
  Arne Stabenau authored Dec 08, 2004
  
  ea6c2f37
- new run parameters. shouldnt really be in cvs I guess · 19497b97
  Arne Stabenau authored Dec 08, 2004
  
  19497b97
- small changes. Got Coord system and assembly mapper now from chimp db instead... · 85ea4ef8
  Arne Stabenau authored Dec 08, 2004
```
small changes. Got Coord system and assembly mapper now from chimp db instead of human. Made bigger mapper cache and did preload.
```
  85ea4ef8
- changed for the right assembly name, needs refactoring · fc290b5c
  Arne Stabenau authored Dec 08, 2004
  
  fc290b5c
- Added gene display_xref calculation (not fully tested yet). · c58e700e
  Glenn Proctor authored Dec 08, 2004
  
  c58e700e
07 Dec, 2004 5 commits
- removed end check in get_all_translateable exons · 3d3d6858
  Arne Stabenau authored Dec 07, 2004
  
  3d3d6858
- make get_valid_codes - return hashref · 5004b72c
  Ian Longden authored Dec 07, 2004
  
  5004b72c
- Renamed upload_xrefs to more descriptive upload_xref_object_graphs · a32280aa
  Glenn Proctor authored Dec 07, 2004
  
  a32280aa
- moved to the superclass BaseMetaContainer the common methods for all meta containers · 5c556ed4
  Daniel Rios authored Dec 07, 2004
  
  5c556ed4
- Generic Meta Container · 107ec434
  Daniel Rios authored Dec 07, 2004
  
  107ec434
06 Dec, 2004 8 commits
- preliminary checkin for fetch_by_display_label · d743620e
  Arne Stabenau authored Dec 06, 2004
  
  d743620e
- updated test db to new schema, was quite out of date · d6013c2a
  Arne Stabenau authored Dec 06, 2004
  
  d6013c2a
- utility function get_ranges to read the internals of the rangeRegistry · 4cf79e9f
  Arne Stabenau authored Dec 06, 2004
  
  4cf79e9f
- Updated regexp · e52ce5ec
  Abel Ureta-Vidal authored Dec 06, 2004
  
  e52ce5ec
- *** empty log message *** · 35314ae9
  Abel Ureta-Vidal authored Dec 06, 2004
  
  35314ae9
- Updated to new dbc calls, added few comments related to buggy refseq xrefs · c4abcff9
  Abel Ureta-Vidal authored Dec 06, 2004
  
  c4abcff9
- Added new nodes to copy from and to · f7f9aa64
  Abel Ureta-Vidal authored Dec 06, 2004
  
  f7f9aa64
- Added monodelphis domestica and xenopus tropicalis. · e952912d
  Glenn Proctor authored Dec 06, 2004
  
  e952912d
05 Dec, 2004 1 commit
- someone forgot to put "" with an update sql statement making it non-compiling · 95b9c728
  Arek Icrapzych authored Dec 05, 2004
```
naughty, naughty man! ;-)
```
  95b9c728
03 Dec, 2004 5 commits
- corrected. Only structural patches in here · 7482015b
  Arne Stabenau authored Dec 03, 2004
  
  7482015b
- · 3d1f60f4
  Laura Clarke authored Dec 03, 2004
```
another addition to make arnes sql to avoid race conditions work, apparently NULL is not less than 1 in mysql
```
  3d1f60f4
- Update the meta_coord table in core databases · 84533467
  Abel Ureta-Vidal authored Dec 03, 2004
  
  84533467
- · 2330bf3e
  Laura Clarke authored Dec 03, 2004
```
changes to make the filling out the meta_coord.max_length column on the fly work
```
  2330bf3e
- sources added etc · 1a7d9645
  Ian Longden authored Dec 03, 2004
  
  1a7d9645
02 Dec, 2004 1 commit
- unique restriction on interpro, longer probesets · f8fbef43
  Arne Stabenau authored Dec 02, 2004
  
  f8fbef43
30 Nov, 2004 3 commits
- SQL to bring a v26 database to v27. · 29d0bb87
  Glenn Proctor authored Nov 30, 2004
  
  29d0bb87
- Fixed typo AFYY->AFFY for ID 3116 · e9dcce1e
  Glenn Proctor authored Nov 30, 2004
  
  e9dcce1e
- type fix. · ab18e771
  Ian Longden authored Nov 30, 2004
  
  ab18e771
29 Nov, 2004 2 commits
- · 7f6b5acc
  Jan-hinnerk Vogel authored Nov 29, 2004
```
external db's for flybase added
```
  7f6b5acc
- changes method names in AnalysisAdaptor · 58ba593c
  Will Spooner authored Nov 29, 2004
  
  58ba593c
26 Nov, 2004 1 commit
- Spelling & typos · 20b98632
  Glenn Proctor authored Nov 26, 2004
  
  20b98632