Bio-BioStudio

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gbrowse_plugins/BS_ChromosomeAnalyzer.pm  view on Meta::CPAN

        -label    => q{ },
        -checked  => 0
      )
    )
  );
           
  push @choices, TR(
    {-class => 'searchbody'},
    th('Enzyme set'),
    td(
      popup_menu(
        -name     => $self->config_name('RESET'),
        -values   => \@enzlists,
        -default  => 'standard_and_IIB'
      )
    )
  );

  my $html = table(@choices);
  return $html;
}

gbrowse_plugins/BS_ChromosomeCutter.pm  view on Meta::CPAN

  unshift @featkeys, $featdefault;
 
  my $BS_FEATS = $BS->custom_features();
  my @BSKINDS = map {"<strong>" . $_->prototype . "</strong> " . $_->primary_tag  . "<br>"} values %{$BS_FEATS};
  @BSKINDS = sort {$a cmp $b} @BSKINDS;
  my @inskeys = sort {$a cmp $b} map {$_->prototype} values %{$BS_FEATS};
  unshift @inskeys, $featdefault;
 
  my %DELHASH;

  my $popupseqdelbsfeat = popup_menu(
    -name     => $self->config_name("seqdel.INSERT"),
    -values   => \@inskeys,
    -default  => $featdefault);
  $DELHASH{'seqdel'} = "delete this segment (and replace with a $popupseqdelbsfeat)<br>";
 
  $DELHASH{'seqdelprp'} = "propose this segment for deletion<br>";

  my $popupfeatdel = popup_menu(
    -name     => $self->config_name("featdel.TYPE"),
    -values   => \@featkeys,
    -default  => $featdefault);
  my $popupfeatdelbsfeat = popup_menu(
    -name     => $self->config_name("featdel.INSERT"),
    -values   => \@inskeys,
    -default  => $featdefault);
  $DELHASH{'featdel'} = "delete the $popupfeatdel features wholly contained within this segment (and replace with $popupfeatdelbsfeat)<br>";
 
  my $popupfeatdelprp = popup_menu(
    -name     => $self->config_name("featdelprp.TYPE"),
    -values   => \@featkeys,
    -default  => $featdefault);
  $DELHASH{'featdelprp'} = "propose the $popupfeatdelprp features wholly contained within this segment for deletion<br>";

  my $tfield = textfield(
    -name     => $self->config_name("listdel.FEATURES"),
    -value    => q{},
    -size     => 50);
  $DELHASH{'listdel'} = "delete the features with the following names: $tfield<br>";
  
  my @choices = ();
  
  push @choices, TR(

gbrowse_plugins/BS_ChromosomeDiff.pm  view on Meta::CPAN

    th(
      {-align=>'CENTER'},
      "Choose a \"variant\""
    )
  );
       
  push @choices, TR(
    {-class => 'searchtitle'},
    td(
      {-align => 'CENTER', -width => '50%'},
      popup_menu(
        -name     => $self->config_name('FIRST'),
        -values   => \@srcs,
        -default  => $sourcename
      ),
    ),
    td(
      {-align=>'CENTER'},
      popup_menu(
        -name     => $self->config_name('SECOND'),
        -values   => \@srcs,
        -default  => $sourcename
      )
    )
  );
       
  my $html= table(@choices);
  return $html;
}

gbrowse_plugins/BS_ChromosomeSegmenter.pm  view on Meta::CPAN

        -maxlength  => 2,
        -default    => 40
      )
    )
  );
           
  push @choices, TR(
    {-class => 'searchbody'},
    th("Original Chromosome for ISS substitution"),
    td(
      popup_menu(
        -name     => $self->config_name('WTCHR'),
        -values   => \@srcs,
        -default  => $srcs[0]
      )
    )
  );
         
  my $html = table(@choices);
  return $html;
}

gbrowse_plugins/BS_ChromosomeSplicer.pm  view on Meta::CPAN

  my $BS_FEATS = $BS->custom_features();
  my @BSKINDS = map {"<strong>" . $_->prototype . "</strong> " . $_->primary_tag . "<br>"} values %{$BS_FEATS};
  @BSKINDS = sort {$a cmp $b} @BSKINDS;
  my @inskeys = sort {$a cmp $b} map {$_->prototype} values %{$BS_FEATS};
  unshift @inskeys, $featdefault;
 
  #my %dirlabels = {"3'" => "W", "5'" => 5, "5' and 3'" => 35};
  my $dirlabels = {"3" => "3'", "5" => "5'", "35" => "5' and 3'"};
  my %BSFEATINSHASH;
 
  my $popupsegmflankbsfeat = popup_menu(
    -name     => $self->config_name("segmentflank.INSERT"),
    -values   => \@inskeys,
    -default  => $featdefault);
  $BSFEATINSHASH{"segmentflank"} = "flank this segment with $popupsegmflankbsfeat features (intrusive)<br>";
 
  my $popupfeatflank = popup_menu(
    -name     => $self->config_name("featflank.FEATURE"),
    -values   => \@featkeys,
    -default  => $featdefault);
  my $flankdist = textfield (
    -name       => $self->config_name("featflank.DISTANCE"),
    -default    =>'10',
    -size       => 4,
    -maxlength  => 3);
  my $flankdir = popup_menu(
    -name     => $self->config_name("featflank.DIRECTION"),
    -labels   => $dirlabels,
    -values   => [5, 3, 35],
    -default  => 35);
  my $popupfeatflankbsfeat = popup_menu(
    -name     => $self->config_name("featflank.INSERT"),
    -values   => \@inskeys,
    -default  => $featdefault);
  $BSFEATINSHASH{"featflank"} = "put $popupfeatflankbsfeat features $flankdist bases $flankdir of the $popupfeatflank features in this segment (non-intrusive)<br>";
 
  my $popupbsfeatins = popup_menu(
    -name     => $self->config_name("featins.INSERT"),
    -values   => \@inskeys,
    -default  => $featdefault);
  my $namebsfeatins = textfield (
    -name       => $self->config_name("featins.NAME"),
    -default    => "$sourcename:$start..$stop",
    -size       => 30,
    -maxlength  => 30);
  $BSFEATINSHASH{"featins"} = "insert a $popupbsfeatins feature here and name it $namebsfeatins (intrusive)<br>";
 
  my (@choices, @facts) = ((), ());
  
  push @choices, TR(
    {-class => 'searchtitle'},
    th("Editing Chromosome Features<br>")
  );
     
  push @choices, TR(
    {-class => 'searchtitle'},

gbrowse_plugins/BS_CodonJuggler.pm  view on Meta::CPAN

        -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";