This glyph is used for drawing features that consist of discontinuous
segments. Unlike "graded_segments" or "alignment", the segments are a
uniform color and not dependent on the score of the segment.
The following options are standard among all Glyphs. See
Bio::Graphics::Glyph for a full explanation.
Option Description Default
------ ----------- -------
-fgcolor Foreground color black
-outlinecolor Synonym for -fgcolor
-bgcolor Background color turquoise
-fillcolor Synonym for -bgcolor
-linewidth Line width 1
-height Height of glyph 10
-font Glyph font gdSmallFont
-connector Connector type 0 (false)
-connector_color
Connector color black
-label Whether to draw a label 0 (false)
-description Whether to draw a description 0 (false)
-strand_arrow Whether to indicate 0 (false)
strandedness
-hilite Highlight color undef (no color)
In addition, the following glyph-specific options are recognized:
-draw_dna If true, draw the dna residues 0 (false)
when magnification level
allows.
-draw_target If true, draw the dna residues 0 (false)
of the TARGET sequence when
magnification level allows.
See "Displaying Alignments".
-ragged_start When combined with -draw_target, 0 (false)
draw a few bases beyond the end
of the alignment. See "Displaying Alignments".
-show_mismatch When combined with -draw_target, 0 (false)
highlights mismatched bases in
pink. See "Displaying Alignments".
-true_target Show the true sequence of the 0 (false)
matched DNA, even if the match
is on the minus strand. See "Displaying Alignments".
-realign Attempt to realign sequences at 1 (true)
high mag to account for indels. See "Displaying Alignments".
The -draw_target and -ragged_start options only work with seqfeatures
that implement the hit() method (Bio::SeqFeature::SimilarityPair).
The -ragged_start option is mostly useful for looking for polyAs and
cloning sites at the beginning of ESTs and cDNAs. Currently there is
no way of activating ragged ends. The length of the ragged starts is
hard-coded at 25 bp, and the color of mismatches is hard-coded as
light pink.
At high magnifications, minus strand matches will automatically be
shown as their reverse complement (so that the match has the same
sequence as the plus strand of the source dna). If you prefer to see
the actual sequence of the target as it appears on the minus strand,
then set -true_target to true.
When the
-draw_target option is true, this glyph can be used to
display nucleotide alignments such as BLAST, FASTA or BLAT
similarities. At high magnification, this glyph will attempt to show
how the sequence of the source (query) DNA matches the sequence of the
target (the hit). For this to work, the feature must implement the
hit() method, and both the source and the target DNA must be
available. If you pass the glyph a series of
Bio::SeqFeature::SimilarityPair objects, then these criteria will be
satisified.
Without additional help, this glyph cannot display gapped alignments
correctly. To display gapped alignments, you can use the
Bio::Graphics::Brower::Realign module, which is part of the Generic
Genome Browser package (
http://www.gmod.org). If you wish to install
the Realign module and not the rest of the package, here is the
recipe:
cd Generic-Genome-Browser-1.XX
perl Makefile.PL DO_XS=1
make
make install_site
If possible, build the gbrowse package with the DO_XS=1 option. This
compiles a C-based DP algorithm that both gbrowse and gbrowse_details
will use if they can. If DO_XS is not set, then the scripts will use
a Perl-based version of the algorithm that is 10-100 times slower.
The display of alignments can be tweaked using the -ragged_start,
-show_mismatch, -true_target and -realign options. See the options
section for further details.
None available.
sub draw_component
{ my $self = shift;
my ($draw_dna,$draw_target) = ($self->option('draw_dna'),$self->option('draw_target'));
return $self->SUPER::draw_component(@_)
unless $draw_dna || $draw_target;
return $self->SUPER::draw_component(@_) unless $self->dna_fits;
my $dna = $draw_target ? eval {$self->feature->hit->seq}
: eval {$self->feature->seq};
return $self->SUPER::draw_component(@_) unless length $dna > 0;
my $show_mismatch = $draw_target && $self->option('show_mismatch');
my $genomic = eval {$self->feature->seq} if $show_mismatch;
my $gd = shift;
my ($x1,$y1,$x2,$y2) = $self->bounds(@_);
my $offset = 0;
eval {
if ($draw_target && $self->option('ragged_start')){
my $target = $self->feature->hit;
if ($target->start < $target->end && $target->start < RAGGED_START_FUZZ
&& $self->{partno} == 0) {
$offset = $target->start - 1;
if ($offset > 0) {
$dna = $target->subseq(1-$offset,0)->seq . $dna;
$genomic = $self->feature->subseq(1-$offset,0)->seq . $genomic;
$x1 -= $offset * $self->scale;
}
}
elsif ($target->end < $target->start &&
$target->end < RAGGED_START_FUZZ && $self->{partno} == $self->{total_parts}) {
$offset = $target->end - 1;
if ($offset > 0) {
$dna .= $target->factory->get_dna($target,$offset,1);
$genomic = $self->feature->subseq(-$offset,0)->seq . $genomic;
$x2 += $offset * $self->scale;
$offset = 0;
}
}
}
};
$self->draw_dna($gd,$offset,lc $dna,lc $genomic,$x1,$y1,$x2,$y2);} | sub draw_dna
{ my $self = shift;
my ($gd,$start_offset,$dna,$genomic,$x1,$y1,$x2,$y2) = @_;
my $pixels_per_base = $self->scale;
my $feature = $self->feature;
my $target = $feature->target;
my $strand = $feature->strand;
my @segs;
if ($strand < 0) {
$dna = $self->reversec($dna);
$genomic = $self->reversec($genomic);
$strand = 1;
}
my $complement = $strand < 0;
if ($self->{flip}) {
$dna = $self->reversec($dna);
$genomic = $self->reversec($genomic);
$strand *= -1;
}
warn "strand = $strand, complement = $complement" if DEBUG;
warn "feature = $feature: length(dna) = ",length($dna)," length(genomic) = ",length($genomic),
" target = ",$feature->target->start,'..',$feature->target->end if DEBUG;
my $realign = !defined($self->option('realign')) || $self->option('realign');
if ($realign && eval { require Bio::Graphics::Browser::Realign}) {
warn "$genomic\n$dna\n" if DEBUG;
warn "strand = $strand" if DEBUG;
@segs = Bio::Graphics::Browser::Realign::align_segs($genomic,$dna);
for my $seg (@segs) {
my $src = substr($genomic,$seg->[0],$seg->[1]-$seg->[0]+1);
my $tgt = substr($dna, $seg->[2],$seg->[3]-$seg->[2]+1);
warn "@$seg\n$src\n$tgt" if DEBUG;
}
} else {
@segs = [0,length($genomic)-1,0,length($dna)-1];
}
my $color = $self->fgcolor;
my $font = $self->font;
my $lineheight = $font->height;
my $fontwidth = $font->width;
$y1 -= $lineheight/2 - 3;
my $pink = $self->factory->translate_color('lightpink');
my $panel_end = $self->panel->right;
my $start = $self->map_no_trunc($self->feature->start- $start_offset);
my $end = $self->map_no_trunc($self->feature->end - $start_offset);
my $true_target = $self->option('true_target');
my $show_complement = $true_target && $feature->strand < 0;
my ($last,$tlast);
for my $seg (@segs) {
if (defined $last) {
my $delta = $seg->[0] - $last - 1;
my $tdelta = $seg->[2] - $tlast - 1;
warn "src gap [$last,$seg->[0]], tgt gap [$tlast,$seg->[2]], delta = $delta, tdelta = $tdelta\n" if DEBUG;
my $gaps = $delta - $tdelta;
my @fill_in = split '',substr($dna,$tlast+1,$tdelta) if $tdelta > 0;
unshift @fill_in,('-')x$gaps if $gaps > 0;
warn "gaps = $gaps, fill_in = @fill_in\n" if DEBUG;
my $distance = $pixels_per_base * ($delta+1);
my $pixels_per_target = $gaps >= 0 ? $pixels_per_base : $distance/(@fill_in+1);
warn "pixels_per_base = $pixels_per_base, pixels_per_target=$pixels_per_target\n" if DEBUG;
my $offset = $self->{flip} ? $end + ($last-1)*$pixels_per_base : $start + $last*$pixels_per_base;
for (my $i=0; $i<@fill_in; $i++) {
my $x = $self->{flip} ? int($offset + ($i+1)*$pixels_per_target + 0.5)
: int($offset + ($i+1)*$pixels_per_target + 0.5);
$self->filled_box($gd,$x,$y1+3,$x+$fontwidth,$y1+$lineheight-3,$pink,$pink) unless $gaps;
$gd->char($font,$x,$y1,$show_complement ? $complement{$fill_in[$i]} : $fill_in[$i],$color);
}
}
my @genomic = split '',substr($genomic,$seg->[0],$seg->[1]-$seg->[0]+1);
my @bases = split '',substr($dna, $seg->[2],$seg->[3]-$seg->[2]+1);
for (my $i = 0; $i<@bases; $i++) {
my $x = $self->{flip} ? int($end + ($seg->[0] + $i - 1)*$pixels_per_base + 0.5)
: int($start + ($seg->[0] + $i) *$pixels_per_base + 0.5);
next if $x+1 < $x1;
last if $x+1 > $x2;
if ($genomic[$i] && lc($bases[$i]) ne lc($complement ? $complement{$genomic[@genomic - $i - 1]} : $genomic[$i])) {
$self->filled_box($gd,$x,$y1+3,$x+$fontwidth,$y1+$lineheight-3,$pink,$pink);
}
$gd->char($font,$x,$y1,$show_complement ? $complement{$bases[$i]} || $bases[$i] : $bases[$i],$color);
}
$last = $seg->[1];
$tlast = $seg->[3];
}} | Please report them.