Commits · 9dacbe881d8137efcd07bd8448a9576c2d9a6937 · ensembl-gh-mirror / ensembl

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Jun 09, 2011
- Remain Pod tweaks. Majority of errors removed ready for Doxygen · 9dacbe88
  Kieron Taylor authored 13 years ago
  
  9dacbe88
- Guess what? Pod messed up · 2c9685da
  Kieron Taylor authored 13 years ago
  
  2c9685da
- Pod corrections. Sometimes I even surprise myself · 24e56a8b
  Kieron Taylor authored 13 years ago
  
  24e56a8b
- pod me do · 029ef7b2
  Kieron Taylor authored 13 years ago
  
  029ef7b2
- Pod section moved closer to method it refers to · 1944f890
  Kieron Taylor authored 13 years ago
  
  1944f890
- Wish I knew who had combined method documentation for so many methods. Very inconvenient. · 7d6992d3
  Kieron Taylor authored 13 years ago
  
  7d6992d3
- Guess what? Pod split to cover methods independently · 42e27976
  Kieron Taylor authored 13 years ago
  
  42e27976
- Pod fix. Sloppy update of Pod after renaming of get_all_DAS_Features? · 1d7ea1b1
  Kieron Taylor authored 13 years ago
  
  1d7ea1b1
- Pod fix. Method documentation was nowhere near the method · 872dbad5
  Kieron Taylor authored 13 years ago
  
  872dbad5
Jun 08, 2011
- Major POD update, removal of reference to Ensembl::Lite · 474eb0d1
  Kieron Taylor authored 13 years ago
  
  474eb0d1
- Added new method: cds2genomic. · c996feea
  Monika Komorowska authored 13 years ago
  
  c996feea
- POD fix for method get_all_DAS_Features · 5f0644b0
  Kieron Taylor authored 13 years ago
  
  5f0644b0
- Updated descriptions for pep2genomic · d87acfea
  Monika Komorowska authored 13 years ago
  
  d87acfea
- Amended description for method pep2genomic · 4c98cd1f
  Monika Komorowska authored 13 years ago
  
  4c98cd1f
Jun 06, 2011
- Updated comments. · d3c979f5
  Monika Komorowska authored 13 years ago
  
  d3c979f5
- Updated methods store_on_ and remove_from_ to undefine Slice->{'circular'}... · 56342d8f
  Monika Komorowska authored 13 years ago
```
Updated methods store_on_ and remove_from_ to undefine Slice->{'circular'} SliceAdaptor->{'is_circular'} and SliceAdaptor->{'circular_sr_id_cache'} when the attribute code is 'circular_seq' and object is a slice
```
  56342d8f
- removed some comments · c0513e94
  Nathan Johnson authored 13 years ago
  
  c0513e94
- corrected local vs sr check for overlap splice on fetch_Iterator_by_Slice · 5da89472
  Nathan Johnson authored 13 years ago
  
  5da89472
- corrected 0 start on slice · 317f7fe8
  Nathan Johnson authored 13 years ago
  
  317f7fe8
Jun 05, 2011
- Added update to avoid recreating analysis snpdensity · d620e795
  Daniel Sobral authored 13 years ago
  
  d620e795
- Added constraint to avoid fetching transcript variations on LRG transcripts · 1713447b
  Pontus Larsson authored 13 years ago
  
  1713447b
Jun 03, 2011
- added BaseFeatureAdaptor fetch_Iterator tests · 607efca2
  Nathan Johnson authored 13 years ago
  
  607efca2
- overlapping exon check bug fix · c2f4a16a
  Ian Longden authored 13 years ago
  
  c2f4a16a
Jun 02, 2011
- Added extra biotype · a1e0f0f1
  Daniel Sobral authored 13 years ago
  
  a1e0f0f1
- for multiple gene numbers the zebrafish naming need to use the original name... · d70bcb8c
  Ian Longden authored 13 years ago
```
for multiple gene numbers the zebrafish naming need to use the original name and not the modified one in future gene numbers.
```
  d70bcb8c
- Update the get_all_StructuralVariations and get_all_CopyNumberVariantProbes methods · cbd2209e
  Laurent Gil authored 13 years ago
  
  cbd2209e
Jun 01, 2011
- Fixed small bug concerning the name of the tables · 7d445fa5
  Laurent Gil authored 13 years ago
  
  7d445fa5
- Ian modified code to deal with name change for Corf genes when there are one to many. · 600f9d5a
  Rhoda Kinsella authored 13 years ago
  
  600f9d5a
- Changed regular expression for Corf gene names. Now using \w · 011c6b50
  Rhoda Kinsella authored 13 years ago
  
  011c6b50
- Linked xrefs to genes for 3 more external dbs. · 11a550ad
  Monika Komorowska authored 13 years ago
  
  11a550ad
- Fix bug that was causing no names to be projected in species other than zebrafish. · 8b50f7e8
  Glenn Proctor authored 13 years ago
  
  8b50f7e8
- *** empty log message *** · e59b6a8a
  Rhoda Kinsella authored 13 years ago
  
  e59b6a8a
- Added change to ZFIN regular expression for Corf gene names · 712e4b09
  Rhoda Kinsella authored 13 years ago
  
  712e4b09
May 26, 2011

CCDS -> Ensembl transcript is not a one to one mapping so cannot use a key... · b9458db0

Ian Longden authored 13 years ago

CCDS -> Ensembl transcript is not a one to one mapping so cannot use a key value pairs in hash. Hence now the hash uses a anonymous array to stire multiple values

b9458db0

May 25, 2011
- Some redundant Lite references removed from commented out tests. · 52e726a1
  Kieron Taylor authored 13 years ago
  
  52e726a1
- Additional references to Ensembl::Lite removed · 15c55521
  Kieron Taylor authored 13 years ago
  
  15c55521
- Removing ancient Ensembl::Lite package that is neither used nor functional · bb9171f3
  Kieron Taylor authored 13 years ago
  
  bb9171f3
- added / to uniprot search to make sure we do not link to uniprot_genename · 400b9e14
  Ian Longden authored 13 years ago
  
  400b9e14
May 24, 2011
- add the synonyms · 454cac5d
  Ian Longden authored 13 years ago
  
  454cac5d
- return the xref_id of the newly created xref · 82a2218d
  Ian Longden authored 13 years ago
  
  82a2218d