Bio-Phylo

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lib/Bio/Phylo/Treedrawer/Abstract.pm  view on Meta::CPAN

            		my $tips = $self->_tree->get_root->get_terminals;
            		$self->_tree->set_meta_object( 'map:tree_size' => scalar(@$tips) );
            	}
            	$logger->debug("going to draw clade label");
            	$self->_draw_clade_label($node);
            }
        }
    );
    $logger->debug("going to draw node pie charts");
    $self->_draw_pies;
    $logger->debug("going to draw legend");
    $self->_draw_legend;
    return $self->_finish;
}

sub _draw_pies {
    my $self = shift;
    $logger->warn( ref($self) . " can't draw pies" );
}

sub _draw_legend {
    my $self = shift;
    $logger->warn( ref($self) . " can't draw a legend" );
}

sub _finish {
    my $self = shift;
    throw 'NotImplemented' => ref($self) . " won't complete its drawing";
}

sub _draw_text {
    my $self = shift;
    throw 'NotImplemented' => ref($self) . " can't draw text";

lib/Bio/Phylo/Treedrawer/Processing.pm  view on Meta::CPAN

                        $$api .=
                          "    drawArc($cx,$cy,$r,0,1,$color,$start,$stop);\n";
                        $start += $slice;
                    }
                }
            }
        }
    );
}

sub _draw_legend {
    my $self = shift;
    if (%colors) {
        my $api  = $self->_api;
        my $tree = $self->_tree;
        my $draw = $self->_drawer;
        my @keys = keys %colors;
        my $increment =
          ( $tree->get_tallest_tip->get_x - $tree->get_root->get_x ) /
          scalar @keys;
        my $x = sprintf( "%.3f", $tree->get_root->get_x + 5 );

lib/Bio/Phylo/Treedrawer/Processing.pm  view on Meta::CPAN

                '-y'    => int( $draw->get_height - 60 ),
                '-text' => $key || ' ',
            );
            $x += $increment;
        }
        $self->_draw_text(
            '-x' => int(
                $tree->get_tallest_tip->get_x + $draw->get_text_horiz_offset
            ),
            '-y'    => int( $draw->get_height - 80 ),
            '-text' => 'Node value legend',
        );
    }
}

sub _finish {
    my $self     = shift;
    my $commands = $self->_api;
    my $tmpl     = do { local $/; <DATA> };
    return sprintf( $tmpl,
        __PACKAGE__, my $time = localtime(),

lib/Bio/Phylo/Treedrawer/Svg.pm  view on Meta::CPAN

					}
                }
            }
        }
    );
}

=begin comment

 Type    : Internal method.
 Title   : _draw_legend
 Usage   : $svg->_draw_legend();
 Function: Draws likelihood pie legend
 Returns :
 Args    : None

=end comment

=cut

sub _draw_legend {
    my $self = shift;
    if (%colors) {
        my $svg  = $self->_api;
        my $tree = $self->_tree;
        my $draw = $self->_drawer;
        my @keys = keys %colors;
        my $increment =
          ( $tree->get_tallest_tip->get_x - $tree->get_root->get_x ) /
          scalar @keys;
        my $x = $tree->get_root->get_x + 5;
        foreach my $key (@keys) {
            $svg->rectangle(
                'x'      => $x,
                'y'      => ( $draw->get_height - 90 ),
                'width'  => ( $increment - 10 ),
                'height' => 10,
                'id'     => 'legend_' . $key,
                'style'  => {
                    'fill'         => $colors{$key},
                    'stroke'       => 'black',
                    'stroke-width' => '1',
                },
            );
            $self->_draw_text(
                '-x'    => $x,
                '-y'    => ( $draw->get_height - 60 ),
                '-text' => $key || ' ',
                'class' => 'legend_label'
            );
            $x += $increment;
        }
        $self->_draw_text(
            '-x' =>
              ( $tree->get_tallest_tip->get_x + $draw->get_text_horiz_offset ),
            '-y'    => ( $draw->get_height - 80 ),
            '-text' => 'Node value legend',
            'class' => 'legend_text',
        );
    }
}

=head1 SEE ALSO

There is a mailing list at L<https://groups.google.com/forum/#!forum/bio-phylo> 
for any user or developer questions and discussions.

=over