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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

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

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);

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}))

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});

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++;
	}
 }

Bio/Search/Tiling/MapTiling.pm view on Meta::CPAN

    if (!defined $self->{"coverage_map_${type}_${context}"}) {
	$self->warn("No HSPS present for type '$type' in context '$context' for this hit");
	return undef;
    }
    return @{$self->{"coverage_map_${type}_${context}"}};
}

=head2 coverage_map_as_text

 Title   : coverage_map_as_text
 Usage   : $tiling->coverage_map_as_text($type, $legend_flag)
 Function: Format a text-graphic representation of the
           coverage map
 Returns : an array of scalar strings, suitable for printing
 Args    : $type: one of 'query', 'hit', 'subject'
           $context: strand/frame context string
           $legend_flag: boolean; add a legend indicating
            the actual interval coordinates for each component
            interval and hsp (in the $type sequence context)
 Example : print $tiling->coverage_map_as_text('query',1);

=cut

sub coverage_map_as_text{
    my $self = shift;
    my ($type, $context, $legend_q) = @_;
    $self->_check_type_arg(\$type);
    $self->_check_context_arg($type, \$context);

    my @map = $self->coverage_map($type, $context);
    my @ret;
    my @hsps = $self->hit->hsps;
    my %hsps_i;
    require Tie::RefHash;
    tie %hsps_i, 'Tie::RefHash';
    @hsps_i{@hsps} = (0..$#hsps);

Bio/Search/Tiling/MapTiling.pm view on Meta::CPAN

	@hspx[@hsps_i{@these_hsps}] = ('*') x @these_hsps;
	$mx[$_] = \@hspx;
    }
    untie %hsps_i;

    push @ret, "\tIntvl\n";
    push @ret, "HSPS\t", join ("\t", (0..$#map)), "\n";
    foreach my $h (0..$#hsps) {
	push @ret, join("\t", $h, map { $mx[$_][$h] } (0..$#map)  ),"\n";
    }
    if ($legend_q) {
	push @ret, "Interval legend\n";
	foreach (0..$#map) {
	    push @ret, sprintf("%d\t[%d, %d]\n", $_, @{$map[$_][0]});
	}
	push @ret, "HSP legend\n";
	my @ints = get_intervals_from_hsps($type,@hsps);
	foreach (0..$#hsps) {
	    push @ret, sprintf("%d\t[%d, %d]\n", $_, @{$ints[$_]});
	}
    }
    return @ret;
}

=head2 hit

t/data/sv40_small.xml view on Meta::CPAN

               <fullName>predetermined participant</fullName>
             </names>
             <xref>
               <primaryRef db="psi-mi" id="MI:0396"/>
               <secondaryRef db="pubmed" id="7940758"/>
               <secondaryRef db="pubmed" id="14755292"/>
             </xref>
           </participantDetection>
           <attributeList>
             <attribute name="exp-modification">MAPPIT bait construct - a chimeric cytokine receptor composed of the extracellular region of homodimeric EpoR, fused to the transmembrane and cytosolic domains of the leptin receptor wherein all the tyr...
             <attribute name="figure-legend">2b, 2c, 5</attribute>
             <attribute name="contact-email">jan.tavernier@ugent.be</attribute>
             <attribute name="author-list">Eyckerman S., Verhee A., der Heyden JV., Lemmens I., Ostade XV., Vandekerckhove J., Tavernier J.</attribute>
           </attributeList>
         </experimentDescription>
       </experimentList>
       <interactorList>
         <proteinInteractor id="EBI-617698">
           <names>
             <shortLabel>tala_sv40</shortLabel>
             <fullName>Large T antigen</fullName>

t/data/tol-2010-02-18.nhx view on Meta::CPAN

(((aquifex[&&NHX:TOL=59615],calderobacterium[&&NHX:TOL=59616],hydrogenobacter[&&NHX:TOL=59617],thermocrinis[&&NHX:TOL=59618],hydrogenothermus[&&NHX:TOL=59619],persephonella[&&NHX:TOL=59620],sulfurihydrogenibium[&&NHX:TOL=59621],balnearium[&&NHX:TOL=5...

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