Commits · cvs/attic/branch-ensembl-07 · ensembl-gh-mirror / ensembl

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May 15, 2000
- Fixed delete_Gene bug! · b2c6392d
  Elia Stupka authored 24 years ago
  
  cvs/attic/branch-ensembl-07
  
  b2c6392d
May 14, 2000
- added mouse disk to ensConf · 26be537b
  humpub authored 24 years ago
  
  26be537b
May 12, 2000
- corrected the method names in the documentation from · 3ecd6a47
  heikki authored 24 years ago
```
get_External_SeqFeatures_* to get_Ensembl_SeqFeatures_
```
  3ecd6a47
Apr 28, 2000
- added exon clipping code · ac8baf81
  Ewan Birney authored 24 years ago
  
  ac8baf81
Apr 27, 2000
- Bug fix, now transfer transfers ePCR features. · 1eb321f6
  Arne Stabenau authored 24 years ago
  
  1eb321f6
- Added extras into overlap test · edce2ef7
  Michele Clamp authored 24 years ago
  
  edce2ef7
- Should have said in previous commit - left_overhang bug fixed · 772d014d
  Michele Clamp authored 24 years ago
  
  772d014d
- changed default min size of NNNs to 1 · ee898078
  Michele Clamp authored 24 years ago
  
  ee898078
- Added comment · 82650e79
  Michele Clamp authored 24 years ago
  
  82650e79
- Some pod changes · 0b4aa45a
  Michele Clamp authored 24 years ago
  
  0b4aa45a
- Changed default overlap size from 0 to 1 · 1360f4d3
  Michele Clamp authored 24 years ago
  
  1360f4d3
- Put the right number of tests in overlap.t · 7a579c63
  Michele Clamp authored 24 years ago
  
  7a579c63
- Added test script for virtual contig · 62092f59
  Michele Clamp authored 24 years ago
  
  62092f59
Apr 26, 2000
- Modified for MarkerFeatures, not yet tested, but should compile. · 8c9fd6a8
  Arne Stabenau authored 24 years ago
  
  8c9fd6a8
Apr 25, 2000
- fixed typo in package definition · 426a981d
  Tony Cox authored 24 years ago
  
  426a981d
- delt with left and right overhang possibilities. · f3625fc9
  Ewan Birney authored 24 years ago
```
checked lengths. Look good.
```
  f3625fc9
Apr 22, 2000
- added some fixes to vc. Will it be enough? · cadda367
  Ewan Birney authored 24 years ago
  
  cadda367
Apr 20, 2000
- fixed bug in windowed VC, start/end/ori_in contig · fd9ba289
  Tony Cox authored 24 years ago
  
  fd9ba289
Apr 19, 2000
- Modified table.sql (removed some columns and the mapbin table) · 1305b5b4
  Michele Clamp authored 24 years ago
```
Added database scripts drop_ensembl and get_tables
```
  1305b5b4
- Added test_genes which just fetches genes from the database · b0d31954
  Michele Clamp authored 24 years ago
```
Added overlap_test which tests VirtualContig and ContigOverlap
```
  b0d31954
- Generated a new donor.dump for testing · ea88f30f
  Michele Clamp authored 24 years ago
```
Change the contig used in DB.t for testing overlaps
```
  ea88f30f
- Prototype Obj object for the new rdb based TimDB · 12a089ec
  Michele Clamp authored 24 years ago
  
  12a089ec
- TimDB/Clone is rewritten to use the new ContigOverlap object and · fbb12cac
  Michele Clamp authored 24 years ago
```
to get rid of those nasty hashes.
```
  fbb12cac
- Changed how DBSQL/Clone fetches ContigOverlaps · 6d6fd156
  Michele Clamp authored 24 years ago
```
Obj deletes ContigOverlaps when clone is deleted.
Obj also writes ContigOverlaps using the new object/schema
RawContig loads Overlaps using the new schema
```
  6d6fd156
- Changed how VirtualContig builds contig maps · f274b01d
  Michele Clamp authored 24 years ago
  
  f274b01d
- Added file ExonPair and Programs · 8a72bb86
  Michele Clamp authored 24 years ago
  
  8a72bb86
- *** empty log message *** · c79b016b
  Michele Clamp authored 24 years ago
  
  c79b016b
Apr 18, 2000
- Made VirtualContig.pm compile again (changed postion to position), replaced... · c81e4b2a
  Arek Icrapzych authored 24 years ago
```
Made VirtualContig.pm compile again (changed postion to position), replaced $exon->contig_id with $exon->seqname in SeqContigDraw.pm
```
  c81e4b2a
- added virtual contigs · b18a5c62
  Ewan Birney authored 24 years ago
  
  b18a5c62
- Stupid bug in get_all_ContigOverlaps · 7f406ef8
  Michele Clamp authored 24 years ago
  
  7f406ef8
- ContigOverlap distance put in Obj · 844d8f38
  Michele Clamp authored 24 years ago
```
get_all_ContigOverlaps put in clone
```
  844d8f38
- *** empty log message *** · 827ae0f0
  Michele Clamp authored 24 years ago
  
  827ae0f0
- ContigOverlap->source set when creating object · 8ec43c59
  Michele Clamp authored 24 years ago
  
  8ec43c59
- write_ContigOverlap now uses the $overlap->source method · 7cc0df8b
  Michele Clamp authored 24 years ago
```
instead of taking a type string
```
  7cc0df8b
- AceDB/Contig inherits from RawContig now. · c6061e33
  Michele Clamp authored 24 years ago
```
VirtualContig had stupid bug in is_truncated
```
  c6061e33
- Added source method to ContigOverlap · 09ed96be
  Michele Clamp authored 24 years ago
  
  09ed96be
Apr 17, 2000
- added contig map functions · 069be779
  Ewan Birney authored 24 years ago
  
  069be779
- Wrote in a new donor.dump file with a 1 clone mini-db and · b836a3a7
  Elia Stupka authored 24 years ago
```
altered defaults in transfer.t All tested and working
```
  b836a3a7
- Added ContigOverlap into TimDB · 6fc7fcc9
  Michele Clamp authored 24 years ago
  
  6fc7fcc9
- added $vc->_clear_vc_cache · 01636d71
  Tony Cox authored 24 years ago
  
  01636d71