[Bio] / FigKernelPackages / FIGO.pm Repository:
ViewVC logotype

Diff of /FigKernelPackages/FIGO.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.17, Tue Mar 13 02:05:51 2007 UTC revision 1.20, Sun Mar 25 14:21:41 2007 UTC
# Line 1377  Line 1377 
1377      my $all    = $args{-all}    ? $args{-all}    : "fig";      my $all    = $args{-all}    ? $args{-all}    : "fig";
1378      my $max    = $args{-max}    ? $args{-max}    : 10000;      my $max    = $args{-max}    ? $args{-max}    : 10000;
1379    
1380      return $fig->sims($self->id,$max,$cutoff,$all);      my @sims = $fig->sims($self->id,$max,$cutoff,$all);
1381    
1382        if (@sims) {
1383            my $peg1 = FeatureO->new($figO, $sims[0]->[0]);
1384    
1385            foreach my $sim (@sims) {
1386                $sim->[0] = $peg1;
1387                $sim->[1] = FeatureO->new($figO, $sim->[1]);
1388            }
1389        }
1390    
1391        return @sims;
1392  }  }
1393    
1394    
# Line 1747  Line 1758 
1758      my $figO = $self->{_figO};      my $figO = $self->{_figO};
1759      my $fig  = $figO->{_fig};      my $fig  = $figO->{_fig};
1760      my @ev = ();      my @ev = ();
1761      foreach my $tuple ($fig->coupling_evidence($self->peg1,$self->peg2))      foreach my $tuple ($fig->coupling_evidence($self->peg1->id,$self->peg2->id))
1762      {      {
1763          my($peg3,$peg4,$rep) = @$tuple;          my($peg3,$peg4,$rep) = @$tuple;
1764          push(@ev,[&FeatureO::new('FeatureO',$figO,$peg3),          push(@ev,[&FeatureO::new('FeatureO',$figO,$peg3),
# Line 2012  Line 2023 
2023      my $famO = $self->{_famO};      my $famO = $self->{_famO};
2024      if (! $famO) { $famO = $self->{_famO} = &FigFam::new('FigFam',$fig,$self->id) }      if (! $famO) { $famO = $self->{_famO} = &FigFam::new('FigFam',$fig,$self->id) }
2025    
2026      return map { &FigFamO::new('FigFamO',$figO,$_) } $famO->list_members;      return map { &FeatureO::new('FeatureO',$figO,$_) } $famO->list_members;
2027  }  }
2028    
   
   
2029  =head3 rep_seqs  =head3 rep_seqs
2030    
2031  =cut  =cut

Legend:
Removed from v.1.17  
changed lines
  Added in v.1.20

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3