Commits · c3803bcf6bc7f1e5e39db4f669624d40bb0b97aa · ensembl-gh-mirror / ensembl

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Oct 29, 2008
- modified to include new_fast method to allow fast creation of objects within the adaptors · c3803bcf
  Daniel Rios authored 16 years ago
  
  c3803bcf
- modified method get_species_and_object_type to retrieve ExonAdaptor as well... · ab2369b9
  Daniel Rios authored 16 years ago
```
modified method get_species_and_object_type to retrieve ExonAdaptor as well and changed implementation to make it easier to maintain
```
  ab2369b9
- added new_fast method to retrieve features within fetch_all methods · d0f581f3
  Daniel Rios authored 16 years ago
  
  d0f581f3
- added more informative error · 8d3d32de
  Daniel Rios authored 16 years ago
  
  8d3d32de
- changes introduced in release 52: new column description in external_db and... · 22756a9e
  Daniel Rios authored 16 years ago
```
changes introduced in release 52: new column description in external_db and new column in dna_align_feature
```
  22756a9e
- changes in schema for 52 · 1168f464
  Daniel Rios authored 16 years ago
  
  1168f464
- added a couple of tests to check new column: pair_dna_align_feature_id · 9fd360ae
  Daniel Rios authored 16 years ago
  
  9fd360ae
- added some information on how to dump the tables · 2e1ee73e
  Daniel Rios authored 16 years ago
  
  2e1ee73e
Oct 27, 2008
- Commited before branch · 5c449459
  Glenn Proctor authored 16 years ago
  
  5c449459
- Reverted to 51 schema, patch not in yet · 9681d2b4
  Glenn Proctor authored 16 years ago
  
  9681d2b4
- Reverted to 51 - branch not in yet. · 081cbca8
  Glenn Proctor authored 16 years ago
  
  081cbca8
- typo in patch b (meta) fixed · aae86c7b
  Stefan Graef authored 16 years ago
  
  aae86c7b
- Add a description column to external_db · c13a676e
  Glenn Proctor authored 16 years ago
  
  c13a676e
- Add a pair_dna_align_feature_id to allow support for paired reads · 12b2b38b
  Glenn Proctor authored 16 years ago
  
  12b2b38b
- typo with patch version · ee4c9ca8
  Daniel Rios authored 16 years ago
  
  ee4c9ca8
- modified method call · 6a82ae73
  Daniel Rios authored 16 years ago
  
  6a82ae73
- Incorporate patches for release 52. · 16f28749
  Glenn Proctor authored 16 years ago
  
  16f28749
- Change analysis.parameters to text, xref.description to text, coord_system.version to varchar(255). · a3eeb95a
  Glenn Proctor authored 16 years ago
  
  a3eeb95a
- Change versions in meta table. · c4763d64
  Glenn Proctor authored 16 years ago
  
  c4763d64
- Updated for 52. · 1699ae2e
  Glenn Proctor authored 16 years ago
  
  1699ae2e
- Changed version to 52. · 40dedd78
  Glenn Proctor authored 16 years ago
  
  40dedd78
Oct 24, 2008
- updated translation_attribs to calculate peptide stats in vega and otherfeatures databases · c6db8b19
  Daniel Rios authored 16 years ago
  
  c6db8b19
Oct 21, 2008
- Added $cs->species. · 416308b2
  Andrew Jenkinson authored 16 years ago
```
Modified $cs->equals to cope with DAS::CoordSystem
```
  416308b2
Oct 20, 2008

In the store() method: · 26a038a1

Andreas Kusalananda Kähäri authored 16 years ago

  When testing for existance of an object xref entry with
  linkage_annotation, treat NULLs as equals.

+ some formatting.

26a038a1

Oct 17, 2008
- Fix a couple of examples (there is no "fetch_by_Slice()" method). · cabfb8b7
  Andreas Kusalananda Kähäri authored 16 years ago
  
  cabfb8b7
- added hack to not return AlleleFeatures if StrainSlice is the fake reference one · 4b2426ad
  Daniel Rios authored 16 years ago
  
  4b2426ad
Oct 16, 2008
- Allow for single species core database names that contain an optional · 1e4772ec
  Andreas Kusalananda Kähäri authored 16 years ago
```
extra number (used by Ensembl Genomes) after the word "core", as in
"schizzosachromyces_pombe_core_0_51_1a".

Passes unit tests.
```
  1e4772ec
Oct 15, 2008
- ignore_release arg added to gene store . It was set to 1 before but can now be... · e42a3777
  Ian Longden authored 16 years ago
```
ignore_release arg added to gene store . It was set to 1 before but can now be passed, default is still set to 1
```
  e42a3777
- The entry for 'probe2Transcript' was not tab-delimited properly. · 39b2b361
  Andreas Kusalananda Kähäri authored 16 years ago
```
Removed empty line.

Removed trailing spaces.
```
  39b2b361
Oct 13, 2008
- added description for probe2Transcript · da3b7eb0
  Nathan Johnson authored 16 years ago
```
tweaked AffyAlign
removed AlignAffyProbe & AlignAffy
```
  da3b7eb0
- fixed errors · 034ccb06
  Beth Yates authored 16 years ago
  
  034ccb06
Oct 10, 2008
- update to add consequence_type of within_mature_miRNA · 9affb7d3
  Yuan Chen authored 16 years ago
  
  9affb7d3
- · 10054d1e
  Jan-hinnerk Vogel authored 16 years ago
```
firstEF added
```
  10054d1e
- · 57a092f5
  Jan-hinnerk Vogel authored 16 years ago
```
description added for Uniprot_non_vertebrate
```
  57a092f5
- added some xenopus descriptions · e5c86aa3
  Simon White authored 16 years ago
  
  e5c86aa3
Oct 09, 2008
- added some new extra descriptions · ea455116
  Julio Fernandez Banet authored 16 years ago
  
  ea455116
- added some new extra descriptions · 0ac70c61
  Julio Fernandez Banet authored 16 years ago
  
  0ac70c61
Oct 07, 2008
- Zebra finch pre-site analyses added (chicken_RepeatMask and zebra finch cDNA, EST and proteins). · e7f20e5d
  Susan Fairley authored 16 years ago
  
  e7f20e5d
Oct 06, 2008
- do not die if databases connection fails just give error and carry on · 423d64e3
  Ian Longden authored 16 years ago
  
  423d64e3
Oct 02, 2008
- Removed random disconnect/reconnect code as this was breaking mirror blast · 35d55e93
  Will Spooner authored 16 years ago
  
  35d55e93