Commits · e55c2d0c1adb41284ba0a934d420a35f78004f2f · ensembl-gh-mirror / ensembl

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Apr 14, 2000
- Refactored so Contig doesn't need all its data in its · e55c2d0c
  Michele Clamp authored 25 years ago
```
constructor and Clone has subroutines and no nasty hashes.
```
  e55c2d0c
- Hmm. Did I edit these? · 86f4e744
  Michele Clamp authored 25 years ago
  
  86f4e744
Apr 13, 2000
- chr, species, embl_offset, embl_order in TimDB · b1470920
  humpub authored 25 years ago
  
  b1470920
Apr 12, 2000
- added debug code · 34f7df9d
  Tony Cox authored 25 years ago
  
  34f7df9d
- Changed my temporary changes · 65a85003
  Michele Clamp authored 25 years ago
  
  65a85003
- Whoops. These shouldn't be here · 6fb61d39
  Michele Clamp authored 25 years ago
  
  6fb61d39
- Added the new schema changes in the contigoverlap table to Obj and RawContig · bf33ba00
  Michele Clamp authored 25 years ago
  
  bf33ba00
- Changed virtual contig to use the new ContigOverlap object. · f753effa
  Michele Clamp authored 25 years ago
  
  f753effa
- Started changes to pairAlign · ee15958d
  Michele Clamp authored 25 years ago
  
  ee15958d
- New object that is symmetrical in contig space · 8091a043
  Michele Clamp authored 25 years ago
  
  8091a043
- added debugging code · 7cf06d18
  Tony Cox authored 25 years ago
  
  7cf06d18
Apr 11, 2000
- added EMBL flat file dumping support · 520d7aac
  Ewan Birney authored 25 years ago
  
  520d7aac
- Added some calls for accessing Chromosomes from Contigs, storing them in DBSQL... · b823298e
  Arne Stabenau authored 25 years ago
```
Added some calls for accessing Chromosomes from Contigs, storing them in DBSQL and loading them from there.
UNTESTED! Please test for me :-)
Should compile.
```
  b823298e
- Fixes to extend method · f3201d56
  Tony Cox authored 25 years ago
  
  f3201d56
Apr 10, 2000
- fixed extend bug · f8d458f2
  Tony Cox authored 25 years ago
  
  f8d458f2
- implemented the $vc->extend(n,n) method · de3ef6d2
  Tony Cox authored 25 years ago
  
  de3ef6d2
- Changed argument name for v/c new() from focus to focuscontig for clarity - it · 4f00c022
  Tony Cox authored 25 years ago
```
was confusing how it differed from 'focusposition'
```
  4f00c022
- added throw on primary_seq to catch error in padding "N"'s (-ve number!) · ff415cc9
  Tony Cox authored 25 years ago
  
  ff415cc9
Apr 09, 2000
- Initial checkin for Species and Chromosome objects. All hardcoded, so no special · ded112bd
  Arne Stabenau authored 25 years ago
```
TimDB and DBSQL version.
```
  ded112bd
Apr 08, 2000
- Added random number generator for v/contig names. Previous integer · d90ea4d5
  Tony Cox authored 25 years ago
```
increment system would break badly if run under mod_perl
```
  d90ea4d5
- unique ID warning.... · 35f2058a
  Tony Cox authored 25 years ago
  
  35f2058a
Apr 07, 2000
- Added ContigOverlapHelper.pm · 7ae07e16
  Michele Clamp authored 25 years ago
  
  7ae07e16
- Added ContigOverlapHelper.pm · d3db2e59
  Michele Clamp authored 25 years ago
  
  d3db2e59
- got embl dumping for virtual contigs to work - hurray! - lots of extra fiddles to add to the system · 906719b0
  Ewan Birney authored 25 years ago
  
  906719b0
- Tracked down pesky feature naming but to FeaturePair->set_all_fields call · acf33a54
  Michele Clamp authored 25 years ago
  
  acf33a54
- *** empty log message *** · 62847625
  Michele Clamp authored 25 years ago
  
  62847625
- Exon->contig_id is the exon name but is switched over when · aabda0eb
  Michele Clamp authored 25 years ago
```
writing to the database.
```
  aabda0eb
- feature seqname fixed (I hope, fingers crossed) · f02ca9fa
  Michele Clamp authored 25 years ago
  
  f02ca9fa
Apr 06, 2000
- start of new embl dumping code. Alot of ripple effect from new vc on embl... · 968ba22c
  Ewan Birney authored 25 years ago
```
start of new embl dumping code. Alot of ripple effect from new vc on embl contigs. Stopped due to seqname bug
```
  968ba22c
- Added same paranoya to cloneid_to_geneid · 6838b10c
  Elia Stupka authored 25 years ago
  
  6838b10c
- Added paranoya to check in delete_Clone whether an object is passed rather · 92f61d48
  Elia Stupka authored 25 years ago
```
than a variable
```
  92f61d48
- fixed virtual contig sequence code to put in Ns · 59804f5b
  Ewan Birney authored 25 years ago
  
  59804f5b
- removed Contig.pm - passes tests, so shouldnt break code · f1ba49bb
  Ewan Birney authored 25 years ago
  
  f1ba49bb
- made some changes to transfer.t - now actually tests things ;). We need to... · 48aab3fe
  Ewan Birney authored 25 years ago
```
made some changes to transfer.t - now actually tests things ;). We need to have a smaller database in the donor.dump
```
  48aab3fe
- commented out and back in some lines, no change · ac928f0a
  Elia Stupka authored 25 years ago
  
  ac928f0a
- Fixed delete bug, UpdateManager was passing a clone object instead of an id · 6fe02d11
  Elia Stupka authored 25 years ago
```
to delete_Clone
Also fixed deleting of dna rows (no contig row in dna table anymore)
Transfer.t no change
```
  6fe02d11
- Fixed delete bug, UpdateManager was passing a clone object instead of an id · 2f90f5a9
  Elia Stupka authored 25 years ago
```
to delete_Clone
Also fixed deleting of dna rows (no contig row in dna table anymore)
```
  2f90f5a9
- Fixed delete bug, delete_Clone was passing an object instead of an id · 2eacc52a
  Elia Stupka authored 25 years ago
  
  2eacc52a
- Fixed write_Contig where internal id whas the same as the external id · b0b468bf
  Michele Clamp authored 25 years ago
  
  b0b468bf
- Fixed update with all the conf variables · f23941bc
  Elia Stupka authored 25 years ago
  
  f23941bc