view release on metacpan or  search on metacpan

gbrowse_plugins/BS_CodonJuggler.pm  view on Meta::CPAN

  }
  if ($cwarning)
  {
    my $cwarn  = "$cwarning already exists; if you increment the chromosome ";
       $cwarn .= "version it will be overwritten.";
    $scalewarns .= p("<strong style=\"color:#FF0000;\">$cwarn.</strong><br> ");
  }
 
  my $CODON_TABLE = $chromosome->GD->codontable;
  my @codons      = sort keys %{$CODON_TABLE};
 
  my @choices;
  
  push @choices, TR(
    {-class => 'searchtitle'},
    th("Codon Juggler Configuration<br>")
  );
     
  push @choices, TR(
    {-class => 'searchtitle'},
    th("Editor Name"),
    td(
      textfield(
        -name       => $self->config_name('EDITOR'),
        -default    => $ENV{REMOTE_USER},
        -size       => 25,
        -maxlength  => 20
      )
    )
  );
           
  push @choices, TR(
    {-class => 'searchtitle'},
    th("Notes"),
    td(
      textfield(
        -name => $self->config_name('MEMO'),
        -size => 50
      )
    )
  );
           
  push @choices, TR(
    {-class => 'searchtitle'},
    th("Increment genome version or chromosome version?$scalewarns"),
    td(
      radio_group(
        -name     => $self->config_name('SCALE'),
        -values   => ['genome', 'chrom'],
        -labels   => {'chrom' => 'chromosome', 'genome' => 'genome'},
        -default  => 'genome'
      )
    )
  );
           
  push @choices, TR(
    {-class => 'searchbody'},
    th("Codon replacement"),
    td(
      "replace all ",
      popup_menu(
        -name   => $self->config_name('FROM'),
        -values => \@codons
      ),
      " codons with ",
      popup_menu(
        -name   => $self->config_name('TO'),
        -values => \@codons
      ),
      " codons"
    )
  );

  my $dlabel  = "allow non synonymous changes to dubious ORFs";
     $dlabel .= " on behalf of non-dubious ORFs";
  my $vlabel = "allow non synonymous changes to verified ORFs";
     $vlabel .= " on behalf of non-dubious ORFs";
  my $alabel = "allow even nonsynonymous changes to all ORFs";
  push @choices, TR(
    {-class => 'searchbody'},
    th("Overlapping ORF priority"),
    td(
      checkbox(
        -name     => $self->config_name('DUBWHACK'),
        -checked  => "checked",
        -value    => "1",
        -label    => $dlabel
      ),
      "<br>",
      checkbox(
        -name     => $self->config_name('VERWHACK'),
        -value    => "1",
        -label    => $vlabel
      ),
      "<br>",
      checkbox(
        -name     => $self->config_name('ALLWHACK'),
        -value    => "1",
        -label    => $alabel
      )
    )
  );
           
  push @choices, TR(
    {-class => 'searchbody'},
    th('Scope of edit'),
    td(
      radio_group(
        -name     => $self->config_name('SCOPE'),
        -values   => ['chrom', 'seg'],
        -default  => 'chrom',
        -labels   => {
          'chrom' => 'whole chromosome',
          'seg'   => 'the genes contained in the current view'
        },
      )
    )
  );
         
  my $html = table(@choices);
  return $html;
}

=head2 dump

Call BS_ChromosomeCutter and pass the parameters