Commits · 9fd360aea824badb827148d94d1f98520592834b · ensembl-gh-mirror / ensembl

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Oct 29, 2008
- 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
- Changed genes to transcripts for ensembl_havana_transcript · d2519c1a
  Glenn Proctor authored 16 years ago
  
  d2519c1a
Sep 29, 2008
- use external db display name rather than dbname for source in descriptions · 6ff0e047
  Ian Longden authored 16 years ago
  
  6ff0e047
- parse species, source and not source correctly · b6b2df80
  Ian Longden authored 16 years ago
  
  b6b2df80
- only report the sources available for a particular species not them all (too much data) · bbe479a0
  Ian Longden authored 16 years ago
  
  bbe479a0
- moved methods from private to public: fetch_all_by_attrib and fetch_by_attrib · 28e806fa
  Daniel Rios authored 16 years ago
  
  28e806fa
Sep 23, 2008

moved ENSEMBL_DB - > DATABASE_CORE and OTHER (non web user dbs) from... · f7a87683

James Smith authored 16 years ago

moved ENSEMBL_DB - > DATABASE_CORE and OTHER (non web user dbs) from ENSEMBL_{} -> DATABASE_, and changed the connection stuff to DATABASE_ as well

f7a87683