[Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph Factory.pm, 1.17, 1.18 arrow.pm, 1.23, 1.24 processed_transcript.pm, 1.8, 1.9

Lincoln Stein lstein at pub.open-bio.org
Sat Apr 16 14:44:38 EDT 2005


Update of /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph
In directory pub.open-bio.org:/tmp/cvs-serv22019/Bio/Graphics/Glyph

Modified Files:
	Factory.pm arrow.pm processed_transcript.pm 
Log Message:
fiddled with arrow glyph to fix off-by-one errors that appear at base pair scales


Index: arrow.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph/arrow.pm,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** arrow.pm	30 Jun 2004 21:57:27 -0000	1.23
--- arrow.pm	16 Apr 2005 18:44:36 -0000	1.24
***************
*** 161,165 ****
  	
      my $first_tick = $major_interval * int(0.5 + $start/$major_interval);
!     my $last_tick  = $major_interval * int(0.5 + $stop/$major_interval);
  
      for (my $i = $first_tick; $i <= $last_tick; $i += $major_interval) {
--- 161,165 ----
  	
      my $first_tick = $major_interval * int(0.5 + $start/$major_interval);
!     my $last_tick  = $major_interval * int(0.5 + ($stop+2)/$major_interval);
  
      for (my $i = $first_tick; $i <= $last_tick; $i += $major_interval) {
***************
*** 176,190 ****
        }
  
!       $abs = $end - $abs if $flipped;
  
        my $tickpos = $dx + $self->map_pt($abs);
!       next if $tickpos < $left or $tickpos > $right;
!       $gd->line($tickpos,$center-$a2,$tickpos,$center+$a2,$tickpen);
        my $label = $scale ? $i / $scale : $i;
        my $scaled = $label/$divisor;
        $label = sprintf($format,$scaled,$unit_label);
  
!       my $middle = $tickpos - (length($label) * $width)/2;
!       next if $middle < $left or $middle > $right;
  
        $gd->string($font,$middle,$center+$a2-1,$label,$font_color)
--- 176,196 ----
        }
  
!       $abs = $end - $abs + 1 if $flipped;
  
        my $tickpos = $dx + $self->map_pt($abs);
!       next if $tickpos < $x1 || $tickpos > $x2;
! 
!       $gd->line($tickpos,$center-$a2,$tickpos,$center+$a2,$tickpen)
! 	unless $tickpos < $left or $tickpos > $right;
! 
        my $label = $scale ? $i / $scale : $i;
        my $scaled = $label/$divisor;
        $label = sprintf($format,$scaled,$unit_label);
  
!       my $label_len = length($label) * $width;
! 
!       my $middle = $tickpos - $label_len/2;
!       $middle = $left if $middle < $left;
!       $middle = $x2 - $label_len if $middle+$label_len > $x2;
  
        $gd->string($font,$middle,$center+$a2-1,$label,$font_color)
***************
*** 195,199 ****
  
        $first_tick = $minor_interval * int(0.5 + $start/$minor_interval);
!       $last_tick  = $minor_interval * int(0.5 + $stop/$minor_interval);
  
        my $a4 = $self->height/4;
--- 201,205 ----
  
        $first_tick = $minor_interval * int(0.5 + $start/$minor_interval);
!       $last_tick  = $minor_interval * int(0.5 + ($stop+2)/$minor_interval);
  
        my $a4 = $self->height/4;

Index: processed_transcript.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph/processed_transcript.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** processed_transcript.pm	13 Apr 2005 21:16:23 -0000	1.8
--- processed_transcript.pm	16 Apr 2005 18:44:36 -0000	1.9
***************
*** 22,27 ****
    foreach ($self->parts) {
      $exons++ if $_->feature->type =~ /exon/i;
!     $utrs++  if $_->feature->type =~ /utr/i;
!     $cds++   if $_->feature->type =~ /cds/i;
      $self->configure(implied_utrs=>1) if $exons && $cds && !$utrs;
      $self->configure(adjust_exons=>1) if $exons && $utrs;
--- 22,27 ----
    foreach ($self->parts) {
      $exons++ if $_->feature->type =~ /exon/i;
!     $utrs++  if $_->feature->type =~ /utr$/i;
!     $cds++   if $_->feature->type =~ /^cds/i;
      $self->configure(implied_utrs=>1) if $exons && $cds && !$utrs;
      $self->configure(adjust_exons=>1) if $exons && $utrs;

Index: Factory.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph/Factory.pm,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** Factory.pm	18 Sep 2004 06:04:55 -0000	1.17
--- Factory.pm	16 Apr 2005 18:44:36 -0000	1.18
***************
*** 311,315 ****
  
      unless ($LOADED_GLYPHS{$glyphclass}++) {
!       carp("the requested glyph class, ``$type'' is not available: $@")
          unless (eval "require $glyphclass");
      }
--- 311,315 ----
  
      unless ($LOADED_GLYPHS{$glyphclass}++) {
!       carp("The requested glyph class, ``$type'' is not available: $@")
          unless (eval "require $glyphclass");
      }



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