Bio::Graphics::Glyph Factory
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Summary
Bio::Graphics::Glyph::Factory - Factory for Bio::Graphics::Glyph objects
Package variables
Privates (from "my" definitions)
%LOADED_GLYPHS = ()
%GENERIC_OPTIONS = ( bgcolor => 'turquoise', fgcolor => 'black', fontcolor => 'black', font2color => 'turquoise', height => 8, font => gdSmallFont, bump => +1, )
Included modules
Carp qw ( :DEFAULT cluck )
GD
Synopsis
See Bio::Graphics::Panel.
Description
This class is used internally by Bio::Graphics to generate new Glyph
objects by combining a list of features with the user's desired
configuration. It is intended to be used internally by Bio::Graphics.
Methods
cloneDescriptionCode
feature_to_glyphDescriptionCode
fontDescriptionCode
global_optsDescriptionCode
glyph_mapDescriptionCode
make_glyph
No description
Code
map_no_truncDescriptionCode
map_ptDescriptionCode
newDescriptionCode
option
No description
Code
option_mapDescriptionCode
optionsDescriptionCode
panelDescriptionCode
scaleDescriptionCode
set_optionDescriptionCode
stylesheetDescriptionCode
translate_colorDescriptionCode
Methods description
clonecode    nextTop
  Title    : clone
Usage : $f2 = $f->clone
Function : Deep copy of a factory object
Returns : a deep copy of the factory object
Args : None
Status : Internal to Bio::Graphics
feature_to_glyphcodeprevnextTop
  Title    : feature_to_glyph
Usage : $glyph_name = $f->feature_to_glyph($feature)
Function : choose the glyph name given a feature
Returns : a glyph name
Args : a Bio::Seq::FeatureI object
Status : Internal to Bio::Graphics
fontcodeprevnextTop
  Title    : font
Usage : $font = $f->font
Function : accessor for the font
Returns : a font name
Args : None
Status : Internal to Bio::Graphics
This returns a GD font name.
global_optscodeprevnextTop
  Title    : global_opts
Usage : $map = $f->global_opts
Function : accessor for global options
Returns : a hash mapping option names to values
Args : None
Status : Internal to Bio::Graphics
This returns a set of defaults for option values.
glyph_mapcodeprevnextTop
  Title    : glyph_map
Usage : $map = $f->glyph_map
Function : accessor for the glyph map
Returns : a hash mapping primary tags to glyphs
Args : None
Status : Internal to Bio::Graphics
map_no_trunccodeprevnextTop
  Title    : map_no_trunc
Usage : @pixel_positions = $f->map_no_trunc(@bp_positions)
Function : map bp positions to pixel positions
Returns : a list of pixel positions
Args : a list of bp positions
Status : Internal to Bio::Graphics
Same as map_pt(), but it will NOT clip pixel positions to be within
the drawing frame.
map_ptcodeprevnextTop
  Title    : map_pt
Usage : @pixel_positions = $f->map_pt(@bp_positions)
Function : map bp positions to pixel positions
Returns : a list of pixel positions
Args : a list of bp positions
Status : Internal to Bio::Graphics
The real work is done by the panel, but factory subclasses can
override if desired.
newcodeprevnextTop
  Title   : new
Usage : $f = Bio::Graphics::Glyph::Factory->new(
-stylesheet => $stylesheet,
-glyph_map => $glyph_map,
-options => $options);
Function : create a new Bio::Graphics::Glyph::Factory object
Returns : the new object
Args : $stylesheet is a Bio::Das::Stylesheet object that can
convert Bio::Das feature objects into glyph names and
associated options.
$glyph_map is a hash that maps primary tags to glyph names.
$options is a hash that maps option names to their values.
Status : Internal to Bio::Graphics
option_mapcodeprevnextTop
  Title    : option_map
Usage : $map = $f->option_map
Function : accessor for the option map
Returns : a hash mapping option names to values
Args : None
Status : Internal to Bio::Graphics
optionscodeprevnextTop
  Title    : options
Usage : @option_names = $f->options
Function : return all configured option names
Returns : a list of option names
Args : none
Status : Internal to Bio::Graphics
panelcodeprevnextTop
  Title    : panel
Usage : $panel = $f->panel
Function : accessor for Bio::Graphics::Panel
Returns : a Bio::Graphics::Panel
Args : None
Status : Internal to Bio::Graphics
This returns the panel with which the factory is associated.
scalecodeprevnextTop
  Title    : scale
Usage : $scale = $f->scale
Function : accessor for the scale
Returns : a floating point number
Args : None
Status : Internal to Bio::Graphics
This returns the scale, in pixels/bp for glyphs constructed by this
factory.
set_optioncodeprevnextTop
  Title    : set_option
Usage : $f->set_option($option_name=>$option_value)
Function : set or change an option
Returns : nothing
Args : a name/value pair
Status : Internal to Bio::Graphics
stylesheetcodeprevnextTop
  Title    : stylesheet
Usage : $stylesheet = $f->stylesheet
Function : accessor for stylesheet
Returns : a Bio::Das::Stylesheet object
Args : None
Status : Internal to Bio::Graphics
translate_colorcodeprevnextTop
  Title    : translate_color
Usage : $index = $f->translate_color($color_name)
Function : translate symbolic color names into GD indexes
Returns : an integer
Args : a color name in format "green" or "#00FF00"
Status : Internal to Bio::Graphics
The real work is done by the panel, but factory subclasses can
override if desired.
Methods code
clonedescriptionprevnextTop
sub clone {
  my $self = shift;
  my %new = %$self;
  my $new = bless\% new,ref($self);
  $new;
}
feature_to_glyphdescriptionprevnextTop
sub feature_to_glyph {
  my $self    = shift;
  my $feature = shift;

  return scalar $self->{stylesheet}->glyph($feature) if $self->{stylesheet};
  my $map = $self->glyph_map    or return 'generic';
  if (ref($map) eq 'CODE') {
    my $val = eval {$map->($feature)};
    warn $@ if $@;
    return $val || 'generic';
  }
  return $map->{$feature->primary_tag} || 'generic';
}
fontdescriptionprevnextTop
sub font {
  my $self = shift;
  my $glyph = shift;
  $self->option($glyph,'font') || $self->{font};
}
global_optsdescriptionprevnextTop
sub global_opts {
shift->{global_opts}
}
glyph_mapdescriptionprevnextTop
sub glyph_map {
 shift->{glyph_map}
}
make_glyphdescriptionprevnextTop
sub make_glyph {
  my $self  = shift;
  my $level = shift;
  my @result;
  my $panel = $self->panel;
  my ($leftmost,$rightmost) = ($panel->left,$panel->right);
  my $flip   = $panel->flip;

  for my $f (@_) {

    my $type = $self->feature_to_glyph($f);
    my $glyphclass = 'Bio::Graphics::Glyph';
    $type ||= 'generic';
    $glyphclass .= "\:\:\L$type";

    unless ($LOADED_GLYPHS{$glyphclass}++) {
      carp("the requested glyph class, ``$type'' is not available: $@")
	unless (eval "require $glyphclass");
    }
    my $glyph = $glyphclass->new(-feature  => $f,
				 -factory  => $self,
				 -flip     => $flip,
				 -level    => $level);

    # this is removing glyphs that are not onscreen at all.
# But never remove tracks!
push @result,$glyph if $type eq 'track' || ($glyph->{left} + $glyph->{width} > $leftmost && $glyph->{left} < $rightmost); } return wantarray ? @result : $result[0];
}
map_no_truncdescriptionprevnextTop
sub map_no_trunc {
  my $self = shift;
  my @result = $self->panel->map_no_trunc(@_);
  return wantarray ? @result : $result[0];
}
map_ptdescriptionprevnextTop
sub map_pt {
  my $self = shift;
  my @result = $self->panel->map_pt(@_);
  return wantarray ? @result : $result[0];
}
newdescriptionprevnextTop
sub new {
  my $class = shift;
  my $panel = shift;
  my %args = @_;
  my $stylesheet = $args{-stylesheet};   # optional, for Bio::Das compatibility
my $map = $args{-map}; # map type name to glyph name
my $options = $args{-options}; # map type name to glyph options
return bless { stylesheet => $stylesheet, glyph_map => $map, options => $options, panel => $panel, },$class;
}
optiondescriptionprevnextTop
sub option {
  my $self = shift;
  my ($glyph,$option_name,$partno,$total_parts) = @_;
  return unless defined $option_name;
  $option_name = lc $option_name;   # canonicalize
return $self->{overriding_options}{$option_name} if exists $self->{overriding_options} && exists $self->{overriding_options}{$option_name}; if (my $map = $self->option_map) { if (defined(my $value = $map->{$option_name})) { my $feature = $glyph->feature; return $value unless ref $value eq 'CODE'; return unless $feature->isa('Bio::SeqFeatureI'); my $val = eval { $value->($feature,$option_name,$partno,$total_parts,$glyph)}; warn $@ if $@; return defined $val && $val eq '*default*' ? $GENERIC_OPTIONS{$option_name} : $val; } } if (my $ss = $self->stylesheet) { my($glyph,%options) = $ss->glyph($glyph->feature); my $value = $options{$option_name}; return $value if defined $value; } return $GENERIC_OPTIONS{$option_name};
}
option_mapdescriptionprevnextTop
sub option_map {
 shift->{options}
}
optionsdescriptionprevnextTop
sub options {
  my $self = shift;
  my %options;
  if (my $map    = $self->option_map) {
    $options{lc($_)}++ foreach keys %$map;
  }
  $options{lc($_)}++ foreach keys %GENERIC_OPTIONS;
  return keys %options;
}

1;
}
paneldescriptionprevnextTop
sub panel {
 shift->{panel}
}
scaledescriptionprevnextTop
sub scale {
 shift->{panel}->scale
}
set_optiondescriptionprevnextTop
sub set_option {
  my $self = shift;
  my ($option_name,$option_value) = @_;
  $self->{overriding_options}{lc $option_name} = $option_value;
}

# options:
# the overriding_options hash has precedence
# ...followed by the option_map
# ...followed by the stylesheet
# ...followed by generic options
}
stylesheetdescriptionprevnextTop
sub stylesheet {
 shift->{stylesheet}
}
translate_colordescriptionprevnextTop
sub translate_color {
  my $self = shift;
  my $color_name = shift;
  $self->panel->translate_color($color_name);
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org             - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:
  bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
AUTHOR - Lincoln SteinTop
Email - lstein@cshl.org
SEE ALSOTop
Bio::Graphics::Panel
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with an "_"
(underscore).
glyphTop
  Title    : glyph
Usage : @glyphs = $f->glyph($level,$feature1,$feature2...)
Function : transform features into glyphs.
Returns : a list of Bio::Graphics::Glyph objects
Args : a feature "level", followed by a list of FeatureI objects.
Status : Internal to Bio::Graphics
The level is used to track the level of nesting of features that have
subfeatures.