Commits · 03dc7d286cc70ffeb116e529f9adafdc1141ba02 · ensembl-gh-mirror / ensembl

This project is mirrored from https://:*****@github.com/Ensembl/ensembl.git. Pull mirroring updated Jan 31, 2023.

21 Jan, 2004 1 commit

· 03dc7d28

Laura Clarke authored Jan 21, 2004

made sure seqname was maintained in alignfeatures and corrected an error message in SliceAdaptor

03dc7d28

16 Jan, 2004 1 commit
- corrected arithmetic error in fetch_all pointed out by vivek · fdb511c8
  Graham McVicker authored Jan 16, 2004
  
  fdb511c8
14 Jan, 2004 2 commits
- perform fuzzy matching of seq_region versions if no exact matching seq_region is found · 47ff4b54
  Graham McVicker authored Jan 14, 2004
  
  47ff4b54
- made some caches larger, and made caching in fetch_all more intelligent · a6b0996d
  Graham McVicker authored Jan 14, 2004
  
  a6b0996d
13 Jan, 2004 2 commits
- Changes so seq_region_length is set when creating slices · 71d0bfd5
  Graham McVicker authored Jan 13, 2004
  
  71d0bfd5
- add some calc stuff · 9d3d3eaa
  Web Admin authored Jan 13, 2004
  
  9d3d3eaa
09 Jan, 2004 1 commit
- Merged in the new-seqstore into HEAD version · fc6ced68
  Arne Stabenau authored Jan 09, 2004
  
  fc6ced68
15 Dec, 2003 1 commit
- Added %age context on Gene based slices, tweaks to stable id fetches, and white space removal · 893438b2
  Web Admin authored Dec 15, 2003
  
  893438b2
24 Sep, 2003 1 commit
- formatting of SQL · 9a1dceca
  Web Admin authored Sep 24, 2003
  
  9a1dceca
14 Apr, 2003 1 commit
- whitespace change · 9acb2f1e
  Colin Kingswood authored Apr 14, 2003
  
  9acb2f1e
08 Apr, 2003 1 commit
- made error message more useful · 02dbdff3
  Ewan Birney authored Apr 08, 2003
  
  02dbdff3
24 Mar, 2003 1 commit
- fix cache and DBentry problems · 4b728760
  Web Admin authored Mar 24, 2003
  
  4b728760
30 Jan, 2003 1 commit
- removed deprecated methods · 809f1d70
  Graham McVicker authored Jan 30, 2003
  
  809f1d70
28 Jan, 2003 1 commit
- fixing busted calls · fff326c5
  Web Admin authored Jan 28, 2003
  
  fff326c5
16 Jan, 2003 1 commit
- Fixed code to return slice only if valid · a41846a9
  Web Admin authored Jan 16, 2003
  
  a41846a9
06 Dec, 2002 1 commit
- adjusted incorrect POD · 9c0141d9
  Graham McVicker authored Dec 06, 2002
  
  9c0141d9
05 Dec, 2002 1 commit
- set up the adaptor when creating a slice in the method fetch_by_supercontig_name · d214fb8d
  Emmanuel Mongin authored Dec 05, 2002
  
  d214fb8d
04 Dec, 2002 1 commit
- moving from branch · a94df20c
  Web Admin authored Dec 04, 2002
  
  a94df20c
22 Nov, 2002 1 commit
- added 1; at the end of module · 7d3e8ccd
  Abel Ureta-Vidal authored Nov 22, 2002
  
  7d3e8ccd
21 Nov, 2002 1 commit
- nt_contigs as slices supported · 506a9249
  Arne Stabenau authored Nov 21, 2002
  
  506a9249
19 Nov, 2002 1 commit
- Updated PODs · a2f48ed7
  Graham McVicker authored Nov 19, 2002
  
  a2f48ed7
13 Nov, 2002 1 commit
- variable renamed to avoid perl complain. Hope I didn't break anything · d13f9c73
  Eduardo Eyras authored Nov 13, 2002
  
  d13f9c73
08 Nov, 2002 1 commit
- added back fetch_by_mapfrag so mouse works · 4f3123af
  Web Admin authored Nov 08, 2002
  
  4f3123af
06 Nov, 2002 1 commit
- some clarification about fetch_by_chr_name · a7c86c29
  Eduardo Eyras authored Nov 06, 2002
  
  a7c86c29
30 Oct, 2002 1 commit
- slices from chromosomes, chromosome adaptor caches on name, tests in a second · 75130c9f
  Arne Stabenau authored Oct 30, 2002
  
  75130c9f
17 Oct, 2002 1 commit
- Add missing fetch_all_by_RawContig_and_score to BaseFeatureAdaptor · 9440d0ed
  Graham McVicker authored Oct 17, 2002
```
Updates so slices can handle negative strand, not finished yet, and not tested
```
  9440d0ed
16 Oct, 2002 1 commit
- lists -> listrefs · cb9c682b
  Graham McVicker authored Oct 16, 2002
  
  cb9c682b
24 Sep, 2002 1 commit
- Container now updates its symbol table on the fly when AUTOLOAD is called (as... · b5826b66
  Graham McVicker authored Sep 24, 2002
```
Container now updates its symbol table on the fly when AUTOLOAD is called (as suggested by Jim Stalker)
```
  b5826b66
23 Aug, 2002 2 commits
- Added some sanity checks to ChromosomeAdaptor, Fixed some more bugs in... · 863868eb
  Graham McVicker authored Aug 23, 2002
```
Added some sanity checks to ChromosomeAdaptor, Fixed some more bugs in SliceAdaptor in which chromosome id was being used as chromosome name
```
  863868eb
- Fixed bug in SliceAdaptor::fetch_by_gene_stable_id method in which slice... · a32ce4bb
  Graham McVicker authored Aug 23, 2002
```
Fixed bug in SliceAdaptor::fetch_by_gene_stable_id method in which slice chromosome was sometimes incorrectly set
```
  a32ce4bb
16 Aug, 2002 1 commit
- s/chrname/chr_name/g in an attempt to be consistent · aa363adf
  Graham McVicker authored Aug 16, 2002
  
  aa363adf
15 Aug, 2002 1 commit
- Small bug fix, and checking to ensure that slice->start > 1 · 416b9bff
  Graham McVicker authored Aug 15, 2002
  
  416b9bff
14 Aug, 2002 3 commits

Typo fix. · cdc455d5
David Barnwell authored Aug 14, 2002

cdc455d5
-Corrected sql syntax in AssemblyMapperAdaptor · 66a8062a
Graham McVicker authored Aug 14, 2002
```
-fixed and renamed fetch_by_clone_name in SliceAdaptor
```
66a8062a

-Restructured SliceAdaptor · a2e8fcab

Graham McVicker authored Aug 14, 2002

-Deprecated SliceAdaptor related methods in StaticGoldenPathAdaptor
-Updated RepeatFeatureAdaptorI interface
-Updated ProxyRepeatFeatureAdaptor to implement interface changes
-Deprecated is_golden method of Clone

a2e8fcab

08 Aug, 2002 2 commits
- fetch_Slice_by_transcript method added. Takes a trnascript stable ID. · 3c516185
  David Barnwell authored Aug 08, 2002
  
  3c516185
- fetch_Slice_by_transcript_dbID method added. · 02544e5f
  David Barnwell authored Aug 08, 2002
  
  02544e5f
07 Aug, 2002 1 commit
- Change static_golden_path_type to assembly_type (so as to work with · 7873b631
  David Barnwell authored Aug 07, 2002
```
rev. 1.79 DBAdaptor.pm).
```
  7873b631
26 Jul, 2002 1 commit
- Genscan Transcripts now draw using new main trunk · 3c26c675
  Graham McVicker authored Jul 26, 2002
  
  3c26c675
04 Jul, 2002 1 commit

Added some functionality from StaticGoldenPathAdaptor. Added methods... · 6112e049

Dan T Andrews authored Jul 04, 2002

Added some functionality from StaticGoldenPathAdaptor.  Added methods fetch_Slice_by_contig, fetch_Slice_by_clone, fetch_Slice_by_gene, and three attendant methods get_chr_start_end_of_contig, fetch_Slice_by_chr_start_end and get_Gene_chr_bp.  Checked generally that these are returning what is expected sequence-wise.

6112e049