Commits · 33903f2109596356393e4e2894c2802da450d724 · ensembl-gh-mirror / ensembl

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Oct 28, 2005
- made get_all_DAS_Features the same as for Translation and Transcript · 33903f21
  Eugene Kulesha authored 19 years ago
  
  33903f21
- Add ZFIN to list of sources for display_xref · 3afee541
  Glenn Proctor authored 19 years ago
  
  3afee541
Oct 27, 2005
- Minor change to prevent crash if a go_xref has a blank linkage_type. · 80fe881b
  Glenn Proctor authored 19 years ago
  
  80fe881b
Oct 26, 2005
- drosophila bits and improved human hgnc data · 4b1cf1a7
  Ian Longden authored 19 years ago
  
  4b1cf1a7
- try download 5 times then die if failed to wget file · ccaeb5e7
  Ian Longden authored 19 years ago
  
  ccaeb5e7
- added use Bio::EnsEMBL::Utils::Exception; · 2d87447b
  Abel Ureta-Vidal authored 19 years ago
  
  2d87447b
- Updated to use warning instead of $self->warn · 09b171a6
  Abel Ureta-Vidal authored 19 years ago
  
  09b171a6
Oct 25, 2005
- *** empty log message *** · ffa1d636
  Glenn Proctor authored 19 years ago
  
  ffa1d636
- Updated to deal with new way of handling cisred factors. Parsing now simpler,... · 9e52cf5e
  Glenn Proctor authored 19 years ago
```
Updated to deal with new way of handling cisred factors. Parsing now simpler, has support for features which don't have an associated factor.
```
  9e52cf5e
- fix for no version check · 12b8551c
  Ian Longden authored 19 years ago
  
  12b8551c
- use metacoordcontainer to get gene level coorsystems rather than long sql query · 8d37f7b1
  Ian Longden authored 19 years ago
  
  8d37f7b1
- use not defined rather then == undef in test · 3835609c
  Ian Longden authored 19 years ago
  
  3835609c
Oct 24, 2005
- fix for register_all_chained where mid_cs is undef. i.e. mouse/rat etc · 98a1c0b5
  Ian Longden authored 19 years ago
  
  98a1c0b5
Oct 21, 2005
- populate hashes if empty. This could be due to species specific routines not filling these · 3bf48cde
  Ian Longden authored 19 years ago
  
  3bf48cde
- new column aliases added · 055b53f5
  Ian Longden authored 19 years ago
  
  055b53f5
- added test for types · edb0c1c0
  Ian Longden authored 19 years ago
  
  edb0c1c0
- Changed display_label_linkable to 1 for MarkerSymbol · 485d8612
  Glenn Proctor authored 19 years ago
  
  485d8612
- removed debug print statement · 67ec33ee
  Ian Longden authored 19 years ago
  
  67ec33ee
- now works and parses the data sensibly · 8dec6bc3
  Ian Longden authored 19 years ago
  
  8dec6bc3
- remove direct xrefs aswell · 92a14d79
  Ian Longden authored 19 years ago
  
  92a14d79
- use FlyBaseName_x not flaybase_name for descriptions · e379559d
  Ian Longden authored 19 years ago
  
  e379559d
Oct 20, 2005
- docfix · 0602d621
  Jan-hinnerk Vogel authored 19 years ago
  
  0602d621
- cached DAS features by SOURCE_URL/MAPPING_TYPE rather than by NAME · d4785cb8
  Eugene Kulesha authored 19 years ago
  
  d4785cb8
- create log dir if not exists · 3e4d08ba
  Patrick Meidl authored 19 years ago
  
  3e4d08ba
Oct 19, 2005
- Changed display name for ID 3114 to Affymx Microarray Rat230 to match db name. · 214bbcae
  Glenn Proctor authored 19 years ago
  
  214bbcae
Oct 18, 2005
- Switched enum and status for transcript status · 941cf757
  Sarah Dyer authored 19 years ago
  
  941cf757
- fix for Registry using wrong dnadb by default · 2d68e138
  Patrick Meidl authored 19 years ago
  
  2d68e138
Oct 17, 2005
- Only store the correct types as direct xref. · b6c411f9
  Ian Longden authored 19 years ago
  
  b6c411f9
- update · 3f29d109
  Yuan Chen authored 19 years ago
  
  3f29d109
- changed confidence to status (again?) I thought I did that already ... · 6eb79f33
  Arne Stabenau authored 19 years ago
  
  6eb79f33
- Typo · 34770f47
  Glenn Proctor authored 19 years ago
  
  34770f47
Oct 15, 2005
- do triage on all primary data sources. Plus dump dependent xrefs for the non mapped primarys aswell · 6efd2525
  Ian Longden authored 19 years ago
  
  6efd2525
Oct 14, 2005
- Add ;mysql_local_infile=1 to DBI initialisation call to work around MySQL... · 16e1b696
  Glenn Proctor authored 19 years ago
```
Add ;mysql_local_infile=1 to DBI initialisation call to work around MySQL change that causes errors such as

	DBD::mysql::db do failed: The used command is not allowed with this MySQL version
	at /nfs/acari/gp1/work/ensembl-test/modules/Bio/EnsEMBL/Test/MultiTestDB.pm line 313.

when using LOAD DATA INFILE.
```
  16e1b696
- Bug fix: rename fetch_by_AffyArray to fetch_all_by_AffyArray; the later is used in AffyArray. · 4d3020ff
  Glenn Proctor authored 19 years ago
```
Retain deprecated fetch_by_AffyArray for backwards compatibility.
```
  4d3020ff
- Typo in pdoc · 13f32820
  Glenn Proctor authored 19 years ago
  
  13f32820
- clear registry properly on clear · dfc12409
  Ian Longden authored 19 years ago
  
  dfc12409
Oct 13, 2005
- Updated to v35 · 74157b18
  Glenn Proctor authored 19 years ago
  
  74157b18
- Fix for subseq of sequence on small seq_regions (< 250k) which was · bcec7c4f
  Stephen Searle authored 19 years ago
```
failing because it was requesting a sub slice which was longer than
the seq_region in the new caching code
```
  bcec7c4f
- Added monodelphis · 60eaf459
  Stephen Searle authored 19 years ago
  
  60eaf459
Oct 12, 2005
- ENV{HOME} may not be defined · 3d4affbb
  Leo Gordon authored 19 years ago
  
  3d4affbb