[Bioperl-guts-l] bioperl-live/Bio/Graphics Feature.pm, 1.39, 1.40 Glyph.pm, 1.84, 1.85 Panel.pm, 1.99, 1.100

[Lincoln Stein]

Update of /home/repository/bioperl/bioperl-live/Bio/Graphics
In directory pub.open-bio.org:/tmp/cvs-serv11483/Bio/Graphics

Modified Files:
	Feature.pm Glyph.pm Panel.pm 
Log Message:
fixed problem in which portions of tracks would randomly disappear


Index: Feature.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Feature.pm,v
retrieving revision 1.39
retrieving revision 1.40
diff -C2 -d -r1.39 -r1.40
*** Feature.pm	7 Dec 2004 13:03:43 -0000	1.39
--- Feature.pm	29 Jul 2005 19:16:50 -0000	1.40
***************
*** 268,273 ****
      $self->{segments} = [ sort {$a->start <=> $b->start } @segments ];
      $self->{ref}    ||= $self->{segments}[0]->seq_id;
!     $self->{start}    = $self->{segments}[0]->start;
!     ($self->{stop})   = sort { $b <=> $a } map { $_->end } @segments;
    }
  }
--- 268,278 ----
      $self->{segments} = [ sort {$a->start <=> $b->start } @segments ];
      $self->{ref}    ||= $self->{segments}[0]->seq_id;
!     my $seg_start     = $self->{segments}[0]->start;
!     my $seg_stop;
!     foreach (@segments) {
!       $seg_stop = $_->end if !defined $seg_stop or $_->end > $seg_stop;
!     }
!     $self->{start}    = $seg_start if !defined $self->{start} || $self->{start} > $seg_start;
!     $self->{stop}     = $seg_stop  if !defined $self->{stop}  || $self->{end}   < $seg_stop;
    }
  }

Index: Panel.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Panel.pm,v
retrieving revision 1.99
retrieving revision 1.100
diff -C2 -d -r1.99 -r1.100
*** Panel.pm	24 Jul 2005 16:27:41 -0000	1.99
--- Panel.pm	29 Jul 2005 19:16:50 -0000	1.100
***************
*** 367,373 ****
    my $feature = Bio::Graphics::Feature->new(
  					    -segments=>$features,
! 					    -start => $self->offset+1,
! 					    -stop  => $self->offset+$self->length,
! 					    -type => 'track'
  					   );
  
--- 367,373 ----
    my $feature = Bio::Graphics::Feature->new(
  					    -segments=>$features,
! 					    -start   => $self->offset+1,
! 					    -stop    => $self->offset+$self->length,
! 					    -type    => 'track'
  					   );
  

Index: Glyph.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph.pm,v
retrieving revision 1.84
retrieving revision 1.85
diff -C2 -d -r1.84 -r1.85
*** Glyph.pm	20 Jul 2005 14:51:33 -0000	1.84
--- Glyph.pm	29 Jul 2005 19:16:50 -0000	1.85
***************
*** 78,81 ****
--- 78,82 ----
      $self->{width}   = $right - $left + 1;
    }
+ 
    if (@subglyphs) {
        my $l            = $subglyphs[0]->left;