Commits · b18a5c628e34223eb874ff604badce2716aa420a · ensembl-gh-mirror / ensembl

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Apr 18, 2000
- 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
- added clone stats to get out coding potential for clones · 708ed6b6
  Ewan Birney authored 24 years ago
  
  708ed6b6
- hmm... haven't done anything in Obj... I hope · fc363f74
  Elia Stupka authored 24 years ago
```
Gene2flat now has -webdump option which creates a directory for the dump files
and also when printing out errors writes the clone in which the gene is
```
  fc363f74
- hmm... haven't done anything in Obj... I hope · 39e31cb0
  Elia Stupka authored 24 years ago
  
  39e31cb0
- Added $vc->extend_maximally(_left/right) to virtual contig code · e4e2fa36
  Tony Cox authored 24 years ago
```
Not the prettiest way to do it but it works.
```
  e4e2fa36
Apr 15, 2000
- updated test suite to test vcs - cant see a problem! · 1c22f3b3
  Ewan Birney authored 24 years ago
  
  1c22f3b3
- got clone2flat to work with new vc based stuff · 25ed2157
  Ewan Birney authored 24 years ago
  
  25ed2157
- made documentation more contig based · 3e9adeac
  Ewan Birney authored 24 years ago
  
  3e9adeac
- added ExternalFeature support, in DB interfaces and DBSQL Obj and RawContig.... · a578038e
  Ewan Birney authored 24 years ago
```
added ExternalFeature support, in DB interfaces and DBSQL Obj and RawContig. Compiles ok, but I have not tested the ExternalFeature code itself
```
  a578038e
- *** empty log message *** · 3c7353a5
  Michele Clamp authored 24 years ago
  
  3c7353a5
Apr 14, 2000
- Removed stupid bug in found_right_end. · 190b8239
  Michele Clamp authored 24 years ago
```
When converting feature coordinates converts sub_SeqFeature coordinates as well.
```
  190b8239
- re-applied lost changed to extend() (sigh) · ed144ab1
  Tony Cox authored 24 years ago
  
  ed144ab1
- fixed typo in found_left/right_end · ef7b9bdc
  Tony Cox authored 24 years ago
  
  ef7b9bdc
- debug code · c3a5aa9b
  Tony Cox authored 24 years ago
  
  c3a5aa9b
- Set embl_offset and order in Timdb · 3da334b0
  Michele Clamp authored 24 years ago
  
  3da334b0
- Reformatted some sql queries in Obj · 38635c0e
  Michele Clamp authored 24 years ago
  
  38635c0e
- Added found_left_end,found_right_end,is_truncated to VirtualContig · 74d10011
  Michele Clamp authored 24 years ago
  
  74d10011
- Fixed the virtual contig 'off by 3' bug. Cahnges to _initialize and length · 6c966c7e
  Tony Cox authored 24 years ago
```
methods
```
  6c966c7e
- Refactored so Contig doesn't need all its data in its · e55c2d0c
  Michele Clamp authored 24 years ago
```
constructor and Clone has subroutines and no nasty hashes.
```
  e55c2d0c
- Hmm. Did I edit these? · 86f4e744
  Michele Clamp authored 24 years ago
  
  86f4e744
Apr 13, 2000
- chr, species, embl_offset, embl_order in TimDB · b1470920
  humpub authored 24 years ago
  
  b1470920
Apr 12, 2000
- added debug code · 34f7df9d
  Tony Cox authored 24 years ago
  
  34f7df9d
- Changed my temporary changes · 65a85003
  Michele Clamp authored 24 years ago
  
  65a85003
- Whoops. These shouldn't be here · 6fb61d39
  Michele Clamp authored 24 years ago
  
  6fb61d39
- Added the new schema changes in the contigoverlap table to Obj and RawContig · bf33ba00
  Michele Clamp authored 24 years ago
  
  bf33ba00
- Changed virtual contig to use the new ContigOverlap object. · f753effa
  Michele Clamp authored 24 years ago
  
  f753effa
- Started changes to pairAlign · ee15958d
  Michele Clamp authored 24 years ago
  
  ee15958d
- New object that is symmetrical in contig space · 8091a043
  Michele Clamp authored 24 years ago
  
  8091a043
- added debugging code · 7cf06d18
  Tony Cox authored 24 years ago
  
  7cf06d18