[Bio] / FigKernelPackages / FIGO.pm Repository:
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revision 1.10, Mon Feb 26 22:03:12 2007 UTC revision 1.11, Mon Feb 26 22:21:38 2007 UTC
# Line 542  Line 542 
542    
543  =item USAGE:  =item USAGE:
544    
545      C<< my $tax_id = $contig->genome(); >>      C<< my $tax_id = $contig->genome->id(); >>
546    
547  =item RETURNS:  =item RETURNS:
548    
# Line 581  Line 581 
581      my($self) = @_;      my($self) = @_;
582    
583      my $fig = $self->{_figO}->{_fig};      my $fig = $self->{_figO}->{_fig};
584      my $contig_lengths = $fig->contig_lengths($self->genome);      my $contig_lengths = $fig->contig_lengths($self->genome->id);
585      return $contig_lengths->{$self->id};      return $contig_lengths->{$self->id};
586  }  }
587    
# Line 619  Line 619 
619      if (($beg && (&FIG::between(1,$beg,$max))) &&      if (($beg && (&FIG::between(1,$beg,$max))) &&
620          ($end && (&FIG::between(1,$end,$max))))          ($end && (&FIG::between(1,$end,$max))))
621      {      {
622          return $fig->dna_seq($self->genome,join("_",($self->id,$beg,$end)));          return $fig->dna_seq($self->genome->id,join("_",($self->id,$beg,$end)));
623      }      }
624      else      else
625      {      {
# Line 651  Line 651 
651  sub display {  sub display {
652      my($self) = @_;      my($self) = @_;
653    
654      print join("ContigO",$self->genome,$self->id,$self->contig_length),"\n";      print join("ContigO",$self->genome->id,$self->id,$self->contig_length),"\n";
655  }  }
656    
657  sub features_in_region {  sub features_in_region {
# Line 874  Line 874 
874                      my $contig = $1;                      my $contig = $1;
875                      my $beg    = $2;                      my $beg    = $2;
876                      my $end = $3;                      my $end = $3;
877                      my $contigO = new ContigO($figO,$self->genome,$contig);                      my $contigO = new ContigO($figO,$self->genome->id,$contig);
878                      my $begA = &max(1,$beg - $adjL);                      my $begA = &max(1,$beg - $adjL);
879                      my $endA = &min($end+$adjR,$contigO->contig_length);                      my $endA = &min($end+$adjR,$contigO->contig_length);
880                      my $dna  = $contigO->dna_seq($begA,$endA);                      my $dna  = $contigO->dna_seq($begA,$endA);

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