Bio-Align-Graphics

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lib/Bio/Align/Graphics.pm  view on Meta::CPAN

#
#Produces:  An image file
#
#Revision History: 
#09/01/2006 - WDM - Introduction of "wrap" flag, allowing alignment to be
#                   wrapped at a set base and stacked vertically
#                   Addition of internal members y_num and y_size for tracking
#                   of number of vertical panels and size of panels,
#                   respectively
#
#09/06/2006 - WDM - Introduction of "p_legend" flag, for printing of an optional
#                   colored legend when protein coloring is selected
#
#09/24/2008 - WDM - Test file created for the module
#
#03/01/2009 - YH -  Introduction of "show_nonsynonymous" flag which enables
#                   highlighting of nonsynonymous mutations in nucleotide
#                   alignments. Addition of internal members codon_table and
#                   missense_pos for translating codons -> amino acids and for
#                   keeping track of missense mutation positions respectively.
#
#03/05/2009 - YH  - Swapped names of subroutines x_label and y_label to match

lib/Bio/Align/Graphics.pm  view on Meta::CPAN

	font => defined($options{font}) ? $FONT_TABLE{$options{font}} : $FONT_TABLE{2},
	x_label => defined($options{x_label}) ? $options{x_label} : 1,
	y_label => defined($options{y_label}) ? $options{y_label} : 1,
	
	#Colors
	bg_color => $options{bg_color} || 'white',
	fg_color => $options{font_color} || 'black',
	x_label_color => $options{x_label_color} || 'blue',
	y_label_color => $options{y_label_color} || 'red',
	p_color => $options{p_color} || undef,
	p_legend => $options{p_legend} || undef,
	p_color_table => undef,
			
	#Sequence Defaults
	reference => $options{reference} || undef,
	reference_id => $options{reference_id} || undef,
	match_char => $options{match_char} || ".",
	block_size => defined($options{block_size}) ? $options{block_size} : 10,
	block_space => defined ($options{block_space}) ? ($options{block_space} * ($options{font} ? $FONT_TABLE{$options{font}}->width : $FONT_TABLE{2}->width)) : ( ($options{font} ? ($FONT_TABLE{$options{font}}->width * 2 ) : ($FONT_TABLE{2}->width * 2)) )...
	wrap => $options{wrap} || 80,
	show_nonsynonymous => $options{show_nonsynonymous} || undef, # If turned on, will highlight nonsynonymous (missense) mutations. Valid only for nucleotide alignments

lib/Bio/Align/Graphics.pm  view on Meta::CPAN

	$self->{seq_start_y} = ($self->{pad_top} + length($self->{seq_length_aa}) + $self->{y_label_space}) * $self->{y_char_size};
	$self->{width} = $self->{seq_start_x} + ((( $self->{wrap} / $self->{block_size}) + 1) * $self->{block_space}) + ( ($self->{wrap} + $self->{pad_right}) * ($self->{x_char_size} + 1.2) ) + ( ($self->{seq_length} / 3) * 2); # Needed to add this for widt...
}else
{
	$self->{seq_start_y} = ($self->{pad_top} + length($self->{seq_length}) + $self->{y_label_space}) * $self->{y_char_size};
	$self->{width} = $self->{seq_start_x} + ((( $self->{wrap} / $self->{block_size}) + 1) * $self->{block_space}) + ($self->{wrap} + $self->{pad_right}) * $self->{x_char_size};
}

$self->{footer_start} = $self->{seq_start_y} + $self->{y_size} * $self->{y_num};

if(defined($self->{p_color}) && defined($self->{p_legend}) && $self->{p_legend}){
$self->{height} = $self->{seq_start_y} + $self->{footer_size} + $self->{y_size} * $self->{y_num};
}else{
 $self->{height} = $self->{seq_start_y} + $self->{y_size} * $self->{y_num};
}
$self->{image} = GD::Simple->new($self->{width},$self->{height});
$self->{image}->alphaBlending(1);
$self->{image}->saveAlpha(1);
$self->{image}->bgcolor($self->{bg_color});
$self->{image}->fgcolor($self->{fg_color});
$self->{image}->rectangle(0,0,$self->{width}-1, $self->{height} - 1);

lib/Bio/Align/Graphics.pm  view on Meta::CPAN

}elsif  ( defined($self->{show_nonsynonymous}) )
 {
 	$self->{codon_table} = Bio::Tools::CodonTable->new();
 	$self->{missense_pos} = {};
# 	print STDERR "You are using option show_nonsynonymous. Option works best if wrap value is a multiple of 4.\n"
 }

if(defined($self->{p_color}) && $self->{seq_format} eq "protein")
{
$self->_draw_colored_sequences();
	if(defined($self->{p_legend}) && $self->{p_legend})
	{
	 $self->_draw_legend();
	}
}elsif(defined($self->{p_color}) && ($self->{seq_format} ne "protein"))
 {
  die "draw:Option p_color only works with Protein alignments!\n";
 }else
  {
   $self->_draw_sequences();
  }

if(defined($self->{dm_label_start}))

lib/Bio/Align/Graphics.pm  view on Meta::CPAN

	 }
	 
	 
	 $block_total += $block_num; 
	}
$block_total = 0;
	}
}
}

sub _draw_legend{

my $self = shift;
my $title_font = $FONT_TABLE{3};
my @l_order = ("Negatively Charged", "Positively Charged", "Hydrophobic", "Aromatic", "Found in Loops", "Large Polar Acids");
my %legend = ("Negatively Charged" => ["D" , "E"] , "Positively Charged" => ["K", "R"] , "Hydrophobic" => ["A","F","I","L","M","V","W","Y"] ,
		"Aromatic" => ["F", "H", "W", "Y"] , "Found in Loops" => ["D", "G", "P", "S", "T"] , "Large Polar Acids" => ["H", "K", "N", "Q", "R"]);

my $x1 = 2;
my $x2 = 42;

my $colors = $self->{p_color_table};

my $y_start = $self->{footer_start};
my $label = "Protein Color Legend";
$self->{image}->bgcolor($self->{bg_color});

lib/Bio/Align/Graphics.pm  view on Meta::CPAN

foreach my $c_label (@l_order)
{

if( ($count % 2) == 0)
{

$self->{image}->moveTo( $x2 *  $self->{x_char_size}, $y_start + ( ($count - 1) * $self->{y_char_size}));
$self->{image}->font($self->{font});
$self->{image}->string($c_label);
	my $i = 0;
	foreach my $chars(@{$legend{$c_label}})
	{
	 $self->{image}->bgcolor($$colors{$chars});
	 $self->{image}->fgcolor($$colors{$chars});
	 $self->{image}->rectangle( ($x2 + 20 + $i) * $self->{x_char_size}, $y_start + ( ($count - 2) * $self->{y_char_size}), ($x2 + 20 + $i + 1) * $self->{x_char_size}, $y_start + ( ($count -1) * $self->{y_char_size}));
	 $self->{image}->bgcolor($self->{bg_color});
	 $self->{image}->fgcolor($self->{fg_color});
	 $i++;
	}

}else
 {
  $self->{image}->moveTo($x1 * $self->{x_char_size} , $y_start + ($count * $self->{y_char_size}));
  $self->{image}->font($self->{font});
  $self->{image}->string($c_label);
	my $i = 0;
	foreach my $chars(@{$legend{$c_label}})
	{
	 $self->{image}->bgcolor($$colors{$chars});
	 $self->{image}->fgcolor($$colors{$chars});
	 $self->{image}->rectangle( ($x1 + 20 + $i) * $self->{x_char_size}, $y_start + ( ($count - 1) * $self->{y_char_size}), ($x1 + 20 + $i + 1) * $self->{x_char_size}, $y_start + ( ($count) * $self->{y_char_size}));
	 $self->{image}->bgcolor($self->{bg_color});
	 $self->{image}->fgcolor($self->{fg_color});
	 $i++;
	}
 }