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gbrowse_syn
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gbrowse_syn
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#!/usr/bin/perl -w
eval 'exec /usr/bin/perl -w -S $0 ${1+"$@"}'
if 0; # not running under some shell
use constant DEFAULT_CONF => '/etc/gbrowse2/synteny';
our $CONF_DIR = $ENV{GBROWSE_CONF} ? "$ENV{GBROWSE_CONF}/synteny" : DEFAULT_CONF;
our $VERSION = 2.55;
our $BIOGRAPHICS_VERSION = 1.8;
use strict;
use CGI qw/:standard Map Area delete_all/;
use CGI::Carp 'fatalsToBrowser';
use CGI::Toggle;
use List::Util qw/min max sum/;
use Digest::MD5 'md5_hex';
use Bio::Graphics::Browser2;
use Bio::Graphics;
# Legacy libraries from 1.7 branch
# will slowly replace these
use Legacy::Graphics::Browser;
use Legacy::Graphics::Browser::Util;
use Legacy::Graphics::Browser::Synteny;
use Legacy::Graphics::Browser::PageSettings;
use Legacy::DB::SyntenyIO;
use Legacy::DB::SyntenyBlock;
use constant OVERVIEW_RATIO => 1.0;
use constant OVERVIEW_BGCOLOR => 'gainsboro';
use constant IMAGE_WIDTH => 800;
use constant INTERIMAGE_PAD => 5;
use constant VERTICAL_PAD => 40;
use constant ALIGN_HEIGHT => 6;
use constant MAX_SPAN => 0.3; # largest gap allowed for merging inset panels
use constant TOO_SMALL => 0.02; # minimum span for displayed alignments
use constant MAX_GAP => 50_001; # maximum gap for chaining
use constant MAX_SEGMENT => 2_000_001;
use constant EXTENSION => 'syn'; # extension for species conf files
use constant DEBUG => 0;
use constant HELP => 'http://gmod.org/wiki/GBrowse_syn_Help';
# Display options -- using a hash here so that
# $page_settings can be updated without using hard-coded
# keys (not counting this constant!).
use constant SETTINGS =>
(
aggregate => 0 , # chain alignments
pgrid => 1, # gridlines
shading => 1, # shaded polygons
tiny => 0, # ignore small alignments
pflip => 1, # flip (-) strand panels
edge => 1, # outline polygons
imagewidth => 800, # width of the image
display => 'expanded', # ref + 2 or all in one
ref => undef,
start => undef,
stop => undef,
end => undef,
name => undef,
search_src => undef,
species => undef
);
use vars qw($INVALID_SRC $CONF_DIR $SCONF $CONF $VERSION $MAP $BIOGRAPHICS_VERSION $SYNTENY_IO @hits);
# initialization
$CONF_DIR = conf_dir($CONF_DIR);
# error if no data sources configured
my $go;
while (<$CONF_DIR/*.synconf>) {
$go++;
}
unless ($go) {
print header, start_html('No data source');
print warning("No data source configured for GBrowse_syn\n");
print p('Please consult '.a({-href=>'http://gmod.org/wiki/GBrowse_syn'},'the documentation'));
print <<END;
<iframe style="frameborder:0;width:1280px;height:2000px" src="/gbrowse2/gbrowse_syn_help.html">
</iframe>
END
;
print end_html;
exit 0;
}
# search soure (general) configuration
$CONF = Legacy::Graphics::Browser::Synteny->new();
$CONF->read_configuration($CONF_DIR,'synconf');
# species-specific configuration
my $extension = $CONF->setting('config_extension') || EXTENSION;
$SCONF = open_config($CONF_DIR,$extension);
my ($page_settings,$session) = page_settings();
my $source = $page_settings->{source};
$CONF->page_settings($page_settings);
$CONF->search_src($page_settings->{search_src});
$CONF->source($page_settings->{source});
$MAP = db_map();
$SYNTENY_IO = Legacy::DB::SyntenyIO->new($CONF->setting('join'));
my $segment = landmark2segment($page_settings);
if ($segment) {
my $name = format_segment($segment);
if (ref $segment ne 'Bio::DB::GFF::RelSegment') {
redirect(url()."?name=$name");
}
$CONF->current_segment($segment);
param(name => $name);
$page_settings->{name} = $name;
}
my @reset = (0,0);
if (param('reset')) {
@reset = (1, 'All settings have been reset to their default values');
}
$CONF->print_page_top($CONF->setting('description'),@reset,$session);
# warning if trying to search with no species
if (!$segment && param('name') && !$CONF->page_settings("search_src")) {
print warning("Error: select a species to search");
}
# Which aligned species have been asked for
my @requested_species = _unique(@{$page_settings->{species}});
if (!@requested_species) {
my $search_src = $page_settings->{search_src} || '';
unless ($search_src && $search_src ne 'nosrc' && $MAP->{$search_src}->{db}) {
$INVALID_SRC = $search_src;
}
@requested_species = grep {$_ ne $search_src} grep {$MAP->{$_}->{db}} keys %$MAP;
}
if ($segment) {
@hits = map {$SYNTENY_IO->get_synteny_by_range(-src => $page_settings->{search_src},
-ref => $segment->abs_ref,
-start => $segment->abs_start,
-end => $segment->abs_end,
-tgt => $_) } @requested_species;
}
my $header = $CONF->setting('header');
$header = &$header if ref $header;
print $header || h1($CONF->setting('description'));
if ($INVALID_SRC) {
print warning("Species '$INVALID_SRC' is not configured for this database");
}
search_form($segment);
print overview_panel($CONF->whole_segment($segment),$segment) if $segment;
if ($segment) {
# make sure no hits go off-screen
remap_coordinates($_) for @hits;
segment_info($page_settings,$segment);
my %species = map {$_->src2 => 1} @hits;
my @species = sort keys %species;
# either display ref species + 2 repeating or 'all in one'
if ($page_settings->{display} eq 'expanded') {
while (my @pair = splice @species, 0, 2) {
draw_image($page_settings,\@hits,@pair);
}
}
else {
draw_image($page_settings,\@hits,@species);
}
}
options_table();
print end_form();
print $CONF->footer || end_html();
# remember former source for the checkbox
$page_settings->{old_src} = $CONF->search_src;
exit 0;
sub species_chooser {
# pointless if < 3 species
return '' if keys %$MAP < 3;
my $src = $CONF->search_src();
my @species = grep {$_ ne $src} grep {$MAP->{$_}->{db}} keys %$MAP;
my $default = $CONF->page_settings->{species} || \@species;
push @$default, $CONF->page_settings('old_src');
if (!param('species')) {
$default = [keys %$MAP];
}
b(wiki_help('Aligned_Species',,$CONF->tr('Aligned Species'))) . ':' . br .
checkbox_group(
-id => 'speciesChooser',
-name => 'species',
-values => \@species,
-labels => { map {$_ => $MAP->{$_}->{desc} } @species },
-default => $default,
-multiple => 1,
-size => 8,
-override => 1,
);
}
sub expand_notice {
# pointless if < 4 species
return '' if keys %$MAP < 4;
my $state = param('display') || $CONF->page_settings->{display};
my $ref = $CONF->search_src;
my $title = b(wiki_help("Display_Mode",$CONF->tr("Display Mode")), ':');
my $url = url . "/" . $CONF->source;
if ($state eq 'expanded') {
return br, $title, br, "Three species/panel ",
a( {-href => $url.'?display=compact'}, 'Click to show all species in one panel');
}
else {
return br, $title, br, 'All species in one panel ',
a( {-href => $url.'?display=expanded'}, 'Click to show reference plus two species/panel');
}
}
sub landmark_search {
my $segment = shift;
my $default = format_segment($segment) if $segment;
return $CONF->setting('no search')
? '' : b(wiki_help('Landmark',$CONF->tr('Landmark'))).':'.br.
textfield(-name=>'name', -size=>25, -value=>$default);
}
sub species_search {
my $default = $CONF->page_settings("search_src");
my %labels = map {$_=>$MAP->{$_}{desc}} keys %$MAP;
my $values = [sort {$MAP->{$a}{desc} cmp $MAP->{$b}{desc}} grep {$MAP->{$_}{desc}} keys %labels];
unshift @$values, '';
my $onchange = "document.searchform.submit()";
return b(wiki_help('Reference_Species',$CONF->tr('Genome to Search'))) . ':' . br .
popup_menu(
-onchange => $onchange,
-name =>'search_src',
-values => $values,
-labels => \%labels,
-default => $default,
-override => 1
);
}
sub search_form {
my $segment = shift;
print start_form(-name=>'searchform',-method => 'post');
navigation_table($segment);
}
sub db_map {
my %map;
my @map = shellwords($CONF->setting('source_map'));
while (my($symbol,$db,$desc) = splice(@map,0,3)) {
$map{$symbol}{db} = $db;
$map{$symbol}{desc} = $desc;
}
\%map;
}
sub _type_from_box {
my $box = shift;
my @type = split ':', $box->[0];
my ($feature,$fname) = @type[0,-1];
return ($feature,$fname);
}
sub draw_image {
my ($page_settings,$hits,@species) = @_;
my ($toggle_section,@hits);
for my $species (@species) {
push @hits, grep {$_->src2 eq $species} @$hits;
}
my $src = $CONF->page_settings("search_src");
my $segment = $CONF->current_segment or return;
my $max_segment = $CONF->setting('max_segment') || MAX_SEGMENT;
if ( $segment->length > $max_segment) {
my $units = $CONF->unit_label($max_segment);
print h2("Sorry: the size of region $segment exceeds the maximum ($units)");
exit;
}
my $max_gap = $segment->length * ($CONF->setting('max_span') || MAX_SPAN);
# dynamically create synteny blocks
@hits = aggregate(\@hits) if $CONF->page_settings("aggregate");
# save the hits by name so we can access them from the name alone
for (@hits) {
$CONF->name2hit( $_->name => $_ );
}
# relate hits into "span" sorted by target contig/chromosomes
# %span = ( target_database,target_contig => { target, contig, start, end } } )
my (%span,$hit2span,%instance);
for my $h (sort {$a->tstart <=> $b->tstart} @hits) {
my $src = $h->src2;
my $contig = $h->target;
$instance{$src,$contig} ||= 0;
my $key = join $;,$src,$contig,$instance{$src,$contig};
# start a new span if the gap is too large
if ($span{$key} && ($h->tstart >= $span{$key}{end}+$max_gap)) {
$key = join $;,$src,$contig,++$instance{$src,$contig};
}
# Tally the plus and minus strand total. We will flip the panel
# if more aligned sequence is on the minus strand than the plus strand.
# only count actual alignmnts (not aggregates).
my $panel_flip = $CONF->panel_flip($key);
if ($h->parts) {
for my $p (@{$h->parts}) {
$panel_flip->{$key}{yes} += ($p->tend - $p->tstart) if $p->tstrand eq '-';
$panel_flip->{$key}{no} += ($p->tend - $p->tstart) if $p->tstrand eq '+';
}
}
else {
$panel_flip->{$key}{yes} += ($h->tend - $h->tstart) if $h->tstrand eq '-';
$panel_flip->{$key}{no} += ($h->tend - $h->tstart) if $h->tstrand eq '+';
}
$span{$key}{start} = $h->tstart
if !defined $span{$key}{start} or $span{$key}{start} > $h->tstart;
$span{$key}{end} = $h->tend
if !defined $span{$key}{end} or $span{$key}{end} < $h->tend;
$contig =~ s/Superc/C/;
$span{$key}{src} ||= $src;
$span{$key}{contig} ||= $contig;
$span{$key}{tstart} ||= $h->start;
$span{$key}{tend} ||= $h->end;
($span{$key}{tstart}) = sort {$a<=>$b} ($h->start,$span{$key}{tstart});
($span{$key}{tend}) = sort {$b<=>$a} ($h->end,$span{$key}{tend});
$hit2span->{$h} = $key;
$hit2span->{$h->name} = $key;
}
# get rid of tiny spans
my $src_fraction = ($CONF->setting('min_alignment_size') || TOO_SMALL || 0) * $segment->length;
my @unused_hits;
unless ($CONF->page_settings("tiny")) {
for my $key (keys %span) {
my $too_short = ($span{$key}{end} - $span{$key}{start}) < $src_fraction
&& ($span{$key}{tend} - $span{$key}{tstart}) < $src_fraction;
if ($too_short) {
delete $span{$key};
push @unused_hits, grep { $hit2span->{$_} eq $key } @hits;
@hits = grep { $hit2span->{$_} ne $key } @hits;
}
}
}
# sort hits into upper and lower hits, based on this pattern:
#
# 1 3 5 7 upper spans
#
# - - - - - - - - - upper hits
#
# - - - - - - - - - lower hits
#
# 0 2 4 6 lower spans
#
my (%hit_positions);
my $pidx = 0;
my %species = map {$_->src2 => 1} @hits;
my %position = map {$_ => ++$pidx} sort keys %species;
for my $h (sort {($b->end-$b->start)<=>($a->end-$a->start)} @hits) {
my $src = $h->src2;
my $span_key = $hit2span->{$h};
$span{$span_key}{position} = $position{$src};
$hit_positions{$h} ||= $span{$span_key}{position};
}
# Create the middle (reference) panel
my ($upper_ff,$lower_ff,%is_upper);
# restrict segment to aligned sequence
my $only_aligned = 0;
if ($only_aligned && @hits) {
my @coords = map {$_->start, $_->end} @hits;
my $new_name = $segment->ref .':'.(min @coords).'..'.(max @coords);
$segment = landmark2segment($page_settings,$new_name,$CONF->page_settings('search_src'));
}
for my $h (@hits) {
my $src = $h->src2;
# keep track of the hits for mapping purposes
$is_upper{$src} ||= $hit_positions{$h} % 2;
my $ff = $is_upper{$src} ? \$upper_ff : \$lower_ff;
$$ff ||= Bio::Graphics::FeatureFile->new;
add_hit_to_ff($segment,$$ff,$h,$hit2span);
}
my $orphan_hit = 0;
for my $h (@unused_hits) {
warn "I am an orphan! ".$h->start."..".$h->end."\n" if DEBUG;
my $is_upper = ++$orphan_hit % 2;
my $ff = $is_upper ? \$upper_ff : \$lower_ff;
$$ff ||= Bio::Graphics::FeatureFile->new;
add_hit_to_ff($segment,$$ff,$h,$hit2span);
}
# base image width
my $width = $CONF->page_settings('imagewidth') || $CONF->setting("imagewidth") || IMAGE_WIDTH;
# but also allow for padding
my $ip = $SCONF->setting('image_padding') || 0;
my $pl = $SCONF->setting('pad_left') || 0;
my $pr = $SCONF->setting('pad_right') || 0;
my $padding = ($pl || $ip) + ($pr || $ip);
my ($ref_img,$ref_boxes) = segment2image($segment,
$src,
{
width => $width - $padding,
features_top => $upper_ff,
features_bottom => $lower_ff,
background => 'white',
}
) or die("no image");
$width = $ref_img->width;
my $ref_title = $MAP->{$src}{desc} . ' ' . format_segment($segment);
# pad all of the span coordinates for a bit of regional context
for my $key (keys %span) {
my $width = $span{$key}{end} - $span{$key}{start};
$span{$key}{start} -= int $width/20;
$span{$key}{end } += int $width/20;
}
# we now create panels and corresponding hit feature files for each of the small
# panels
my $refwidth = $width;
my $panel_count = keys %span;
my $panels_above = my @panels_above = grep { $span{$_}{position} % 2 } keys %span;
my $panels_below = my @panels_below = grep {!($span{$_}{position} % 2) } keys %span;
my $bases_above = sum( map {$span{$_}{end} - $span{$_}{start}} @panels_above );
my $bases_below = sum( map {$span{$_}{end} - $span{$_}{start}} @panels_below );
my ($pad_top,$pad_bottom) = (0,0);
my ($img,$boxes);
my $im_pad = $CONF->setting('interimage_pad') || INTERIMAGE_PAD;
for my $key (keys %span) {
my $panel_position = $span{$key}{position};
my $is_above = $panel_position % 2;
my $total_bases = $is_above ? $bases_above : $bases_below;
my $panels = $is_above ? $panels_above : $panels_below;
my $total_width = $refwidth - $panels*3*$im_pad + $im_pad;
my $src = $span{$key}{src};
my $contig = $span{$key}{contig};
my $end = $span{$key}{end};
my $start = $span{$key}{start};
my $bases = $end - $start;
my $name = "$contig:$start..$end";
my $segment = landmark2segment($page_settings,$name,$src);
my @relevant_hits = grep {$hit2span->{$_} eq $key} @hits;
my $rsegment = landmark2segment($page_settings,"$contig:$start..$end",$src);
# width of inset panels scaled by size of target sequence
$bases or next;
my $scale = $bases/$total_bases;
my $width = $total_width*$scale;
my $ff = Bio::Graphics::FeatureFile->new;
add_hit_to_ff($rsegment,$ff,$_,$hit2span,'invert') foreach @relevant_hits;
my $segment_args = {width => $width};
if ($is_above) {
$segment_args->{features_bottom} = $ff;
$segment_args->{noscale} = 1;
}
else {
$segment_args->{features_top} = $ff;
}
$segment_args->{flip}++ if panel_is_flipped($key,1);
($img,$boxes) = segment2image($segment, $src, $segment_args);
$img or next;
$span{$key}{image} = $img;
$span{$key}{boxes} = $boxes;
$span{$key}{title} = $MAP->{$src}{desc};
$span{$key}{title} .= ' (reverse)' if panel_is_flipped($key);
$pad_top = $img->height if $is_above && $pad_top < $img->height;
$pad_bottom = $img->height if !$is_above && $pad_bottom < $img->height;
}
# total height is height of reference + pad_top + pad_bottom + VERTICAL_PAD pixels of spacing
my $total_height = $ref_img->height + $pad_top + $pad_bottom;
my $vertical_pad = $CONF->setting('vertical_pad') || VERTICAL_PAD;
$total_height += $vertical_pad if $panels_above;
$total_height += $vertical_pad if $panels_below;
$total_height += $im_pad;
# create a master image for all panels
my $gd = GD::Image->new($ref_img->width+2*$im_pad,$total_height+1,1) or return;
$gd->saveAlpha(0);
$gd->alphaBlending(1);
my $white = $gd->colorAllocate(255,255,255);
my $black = $gd->colorAllocate(0,0,0);
my $cyan = $gd->colorAllocate(0,255,255);
$gd->filledRectangle(0,0,$gd->width,$gd->height,$white);
my $translucent = $gd->colorAllocateAlpha(0,0,255,90);
for my $key (keys %span) {
my $color = $CONF->setting($MAP->{$span{$key}{src}}{db}=>'color');
# report missing config for the species if no color is found
$color || die <<END;
No color configured for $MAP->{$span{$key}{src}}{db}.
Check the \[$MAP->{$span{$key}{src}}{db}\] stanza in your main configuration file;
END
;
my @colrgb = Bio::Graphics::Panel->color_name_to_rgb($color);
$span{$key}{tcolor} = $gd->colorAllocateAlpha(@colrgb,110);
$span{$key}{bgcolor} = $gd->colorAllocateAlpha(@colrgb,115);
$span{$key}{border} = $gd->colorResolve(@colrgb);
}
my $ref_top = $panels_above ? $pad_top + $vertical_pad : $im_pad;
my $ref_bottom = $ref_top + $ref_img->height;
# paste the individual panels into the picture
my @map_items;
my %x = ( above => $im_pad, below => $im_pad);
# order the panels by hit order
my (@sorted_spans,%seen_span);
for my $h (sort {$a->start <=> $b->start} @hits) {
my $span = $hit2span->{$h};
push @sorted_spans, $span if ++$seen_span{$span} == 1;
}
my $max_height_above = max( map {eval{$span{$_}{image}->height}} grep {$span{$_}{position} % 2} @sorted_spans);
my $max_height_below = max( map {eval{$span{$_}{image}->height}} grep {! ($span{$_}{position} % 2)} @sorted_spans);
for my $key (@sorted_spans) {
my $is_above = $span{$key}{position} % 2;
my $img = $span{$key}{image} or next;
my $xi = $is_above ? 'above' : 'below';
my $max_height = $is_above ? $max_height_above : $max_height_below;
my $img_y = $is_above ? $ref_top-$vertical_pad-$img->height : $ref_bottom+$vertical_pad ;
my $msk_y = $is_above ? $ref_top-$vertical_pad-$max_height : $img_y;
$span{$key}{offsets} = [$x{$xi},$img_y];
my @rect = ($x{$xi},$msk_y,$x{$xi}+$img->width,$msk_y+$max_height);
$gd->copy($img,$x{$xi},$img_y,0,0,$img->width,$img->height);
$gd->filledRectangle(@rect,$span{$key}{bgcolor});
$gd->rectangle(@rect,$span{$key}{border});
$gd->string(GD::gdSmallFont,$x{$xi}+5,$msk_y,$span{$key}{title},$black)
if $img->width > 75;
$x{$xi} += $img->width + $im_pad;
my $name = "$span{$key}{contig}:$span{$key}{start}..$span{$key}{end}";
push @map_items,Area({shape=>'rect',
coords=>join(',',@rect),
href=>"?search_src=$span{$key}{src};name=$name",
title=>$span{$key}{title}});
}
# middle row (reference)
my @rect = ($im_pad,$ref_top,$im_pad+$ref_img->width,$ref_top+$ref_img->height);
$gd->copy($ref_img,$im_pad,$ref_top,0,0,$ref_img->width,$ref_img->height);
my $color = $CONF->setting($MAP->{$src}{db}=>'color');
$color ||= 'blue';
my $bgcolor = $gd->colorAllocateAlpha(Bio::Graphics::Panel->color_name_to_rgb($color),110);
my $border = $gd->colorResolve(Bio::Graphics::Panel->color_name_to_rgb($color));
$gd->filledRectangle(@rect,$bgcolor);
$gd->rectangle(@rect,$border);
my $title = $MAP->{$src}{desc} . ' (reference)';
$gd->string(GD::gdSmallFont,$rect[0]+5,$rect[1],$title,$black);
push @map_items,Area({shape=>'rect',
coords=>join(',',@rect),
title=>$ref_title});
# sort out the coordinates of all the hits so that we can join them
# first the hits in the reference panel
my (%ref_boxes,%panel_boxes);
for my $box (@$ref_boxes) {
ref $box or next;
my ($feature,$fname) = _type_from_box($box);
my @rect = ($im_pad+$box->[1],$ref_top+$box->[2],$im_pad+$box->[3],$ref_top+$box->[4]);
if ($feature =~ /^match(_part)?$/) {
$ref_boxes{$fname} = \@rect;
}
else {
my %atts = %{$box->[5]};
my $url = url();
$url =~ s/gbrowse_syn.*$//;
$atts{href} =~ s/\.\.\/\.\.\//$url/ if $atts{href};
push @map_items,Area({shape=>'rect',coords=>join(',',@rect),%atts});
}
$gd->rectangle(@rect,$black) if DEBUG;
}
# now for the hits in each individual panel
my %tcolors;
for my $key (keys %span) {
defined $span{$key}{offsets} or next;
my ($left,$top) = @{$span{$key}{offsets}};
my $boxes = $span{$key}{boxes};
for my $box (@$boxes) {
ref $box or next;
my ($feature,$fname) = _type_from_box($box);
#next unless $feature =~ /^match(_part)?$/;
my @rect = ($left+$box->[1],$top+$box->[2],$left+$box->[3],$top+$box->[4]);
if ($feature =~ /^match(_part)?$/) {
$panel_boxes{$fname} = \@rect;
}
else {
push @map_items, Area( {
shape => 'rect',
coords => join(',',@rect),
%{$box->[5]}});
}
$tcolors{$fname} = $span{$key}{tcolor};
$gd->rectangle(@rect,$black) if DEBUG;
}
}
my %grid_line;
my %gc;
$gc{1} = $CONF->page_settings("pgrid") ? $gd->colorResolveAlpha(10,10,10,100) : $gd->colorResolveAlpha(10,10,10,70);
$gc{3} = $gd->colorResolveAlpha(10,10,255,100);
my $thickness = 3;
my $grid_upper;
for my $feature (keys %ref_boxes) {
next unless defined $ref_boxes{$feature} && defined $panel_boxes{$feature};
my $hit = $CONF->name2hit($feature);
next unless defined $hit;
my $span = $hit2span->{$feature};
my $flip = !panel_is_flipped($span) && $CONF->flip($feature)
|| panel_is_flipped($span) && !$CONF->flip($feature);
my ($rx1,$ry1,$rx2,$ry2) = @{$ref_boxes{$feature}};
my ($px1,$py1,$px2,$py2) = @{$panel_boxes{$feature}};
my $upper = $py2 < $ry1;
if ($CONF->page_settings("shading")) {
my $poly = GD::Polygon->new();
$upper = $py2 < $ry1;
($rx1,$rx2) = ($rx2,$rx1) if $flip;
if ($upper) {
$grid_upper ||= $ry2;
$poly->addPt($px1,$py2);
$poly->addPt($px2,$py2);
$poly->addPt($rx2,$ry1);
$poly->addPt($rx1,$ry1);
}
else {
$poly->addPt($px1,$py1);
$poly->addPt($px2,$py1);
$poly->addPt($rx2,$ry2);
$poly->addPt($rx1,$ry2);
}
$gd->filledPolygon($poly,$tcolors{$feature});
}
}
my %within_a_pixel;
# reloop to avoid mysterious alpha-channel interaction
# between shading and grid-lines
for my $feature (keys %ref_boxes) {
next unless defined $ref_boxes{$feature} && defined $panel_boxes{$feature};
next if $feature =~ /aggregate/;
my $exact = $CONF->setting('grid coordinates');
$exact = $exact && $exact eq 'exact';
next unless my $hit = $CONF->name2hit($feature);
my $span = $hit2span->{$feature};
my $flip = !panel_is_flipped($span) && $CONF->flip($feature)
|| panel_is_flipped($span) && !$CONF->flip($feature);
my ($rx1,$ry1,$rx2,$ry2) = @{$ref_boxes{$feature}};
my ($px1,$py1,$px2,$py2) = @{$panel_boxes{$feature}};
my $upper = $py2 < $ry1;
my @grid_coords = $CONF->page_settings("pgrid")
? grid_coords( $hit,
$ref_boxes{$feature},
$panel_boxes{$feature},
panel_is_flipped($span),
$segment) : ();
# add edges
if ($CONF->page_settings("edge")) {
unshift @grid_coords, $flip ? [$rx1,$px2] : [$rx1,$px1];
push @grid_coords, $flip ? [$rx2,$px1] : [$rx2,$px2];
}
my $tidx = 0;
for my $pair (@grid_coords) {
my ($x1,$x2) = @$pair;
$grid_line{$x1}{thickness} = 1 if $exact;
unless ($grid_line{$x1}{thickness}) {
$thickness = ++$tidx == 5 ? 3 : 1;
$tidx = 0 if $tidx == 5;
}
else {
$thickness = $grid_line{$x1}{thickness};
}
$gd->setThickness($thickness);
if ($upper) {
$gd->line($x1,$ry1,$x2,$py2,$gc{$thickness});
$gd->line($x2,$py2,$x2,0,$gc{$thickness});
$grid_line{$x1}{top} ||= $ry2;
}
else {
my $pad = $im_pad;
$gd->line($x1,$ry2,$x2,$py1,$gc{$thickness});
$gd->line($x2,$py1,$x2,$gd->height-$pad-1,$gc{$thickness});
$grid_line{$x1}{bottom} ||= $ry1;
}
$grid_line{$x1}{thickness} ||= $thickness;
}
}
for my $g (keys %grid_line) {
# skip the line if there is one already drawn
# a pixel to the left or right;
next if $within_a_pixel{$g-1} || $within_a_pixel{$g+1} || $within_a_pixel{$g};
$within_a_pixel{$g} = 1;
my $thickness = $grid_line{$g}{thickness};
$gd->setThickness($thickness);
$grid_line{$g}{top} ||= $grid_upper;#$ref_top;
$grid_line{$g}{bottom} ||= $ref_bottom;
$gd->line($g,$grid_line{$g}{top},$g,$grid_line{$g}{bottom},$gc{$thickness});
}
my $url = $SCONF->generate_image($gd);
my $label = $CONF->page_settings->{display} eq 'compact' ? # all
'Details' : # or a sub-set
join(', ',@species);
my $map_name = md5_hex($label);
print toggle( $label,
table( {-width=>'100%'},
Tr( td( {-align=>'center', -class => 'databody'},
img({-src=>$url,-border=>0,-usemap=>'#'.$map_name} )))
),
);
my $map = Map({-name=>$map_name},reverse @map_items);
$map =~ s/\</\n\</g;
print $map;
}
sub segment2image {
my ($segment,$src,$options) = @_;
$segment or return;
my $width = $options->{width};
my $hits_top = $options->{features_top};
my $hits_bottom = $options->{features_bottom};
my $background = $options->{background} || 'white';
my $flip = $options->{flip};
my $dsn = $MAP->{$src}{db} or return;
$SCONF->source($dsn);
# make sure balloon tooltips are turned on
$SCONF->setting('GENERAL','balloon tips',1);
my @tracks = shellwords($CONF->setting($dsn => 'tracks'));
my $ff_scale = Bio::Graphics::FeatureFile->new;
$ff_scale->add_type( SCALE => { fgcolor => 'black',
glyph => 'arrow',
tick => 2,
double => 0,
description => 0} );
$ff_scale->add_feature(segment2feature($segment,$ff_scale));
my @labels;
if ($hits_top && $hits_bottom) {
@labels = ('ff_top','ff_scale',@tracks,'ff_bottom');
}
elsif ($hits_top) {
@labels = ('ff_top','zz_scale',@tracks);
}
elsif ($hits_bottom) {
@labels = (@tracks,'ff_scale','ff_bottom');
}
else {
@labels = ('ff_scale',@tracks);
}
my %ff_hash;
$ff_hash{ff_top} = $hits_top if $hits_top;
$ff_hash{ff_bottom} = $hits_bottom if $hits_bottom;
# coerce correct track order in bottom panel
my $scale_label = $hits_bottom && !$hits_bottom ? 'zz_scale' : 'ff_scale';
$ff_hash{$scale_label} = $ff_scale;
$SCONF->width($width);
my $im_pad = $CONF->setting('interimage_pad') || INTERIMAGE_PAD;
# padding must be temporarily overridden for inset panels
my ($pl,$pr);
unless ($src eq $CONF->search_src()) {
$pl = $SCONF->setting('pad_left');
$pr = $SCONF->setting('pad_right');
$SCONF->setting('general','pad_left' => $im_pad);
$SCONF->setting('general','pad_right' => $im_pad);
}
$SCONF->setting('general','detail bgcolor'=> $background);
my $title = $MAP->{$src}{desc};
# cache no panels if some params change
my $no_cache = [md5_hex(url(-query_string=>1))];
landmark2segment() if _isref($segment);
my ($img,$boxes) = $SCONF->render_panels(
{
drag_n_drop => 0,
image_and_map => 1,
keystyle => 'none',
segment => $segment,
labels => \@labels,
title => $title,
-grid => 0,
do_map => 1,
noscale => 1,
feature_files=>\%ff_hash,
-flip => $flip,
cache_extra => $no_cache,
}
);
# restore original padding
unless ($src eq $CONF->search_src()) {
$SCONF->setting('general','pad_left' => $pl);
$SCONF->setting('general','pad_right' => $pr);
}
return ($img,$boxes,$segment);
}
sub _isref {
my $segment = shift;
return $segment->ref eq $CONF->page_settings('ref') &&
$segment->start == $CONF->page_settings('start') &&
$segment->stop == $CONF->page_settings('stop');
}
sub format_segment {
my $seg = shift;
return $seg->ref.':'.$seg->start.'..'.$seg->end;
}
sub landmark2segment {
my $settings = shift || $CONF->page_settings;
my ($name,$source) = @_;
if ($name && $source) {
}
elsif ($CONF->page_settings("name")) {
$name = $CONF->page_settings("name");
}
elsif ($CONF->page_settings("ref")) {
$name = $CONF->page_settings("ref") . ':';
$name .= $CONF->page_settings("start") . ':';
$name .= $CONF->page_settings("stop");
}
$source ||= $CONF->page_settings("search_src");
my $segment = _do_search($name,$source) if $name && $source;
# Did not find our segment? Try the other species
if (!$segment) {
for my $src (grep {defined $_} @{$settings->{species}}) {
next if $src eq $source;
$segment = _do_search($name,$src) if $name;
if ($segment) {
$settings->{search_src} = $src;
$CONF->search_src($src);
last;
}
}
}
# remember our search!
if ($segment && $source && $source eq $settings->{search_src}) {
$settings->{"ref"} = $segment->ref;
$settings->{"start"} = $segment->start;
$settings->{"stop"} = $segment->end;
$settings->{"name"} = format_segment($segment);
}
return $segment;
}
sub _do_search {
my ($landmark,$src) = @_;
my $dsn = $MAP->{$src}{db} or return undef;
$SCONF->source($dsn);
my $db = open_database();
my ($segment) = grep {$_} $SCONF->name2segments($landmark,$db);
return $segment;
}
sub warning {
h2({-style=>'color:red'},@_);
}
sub add_hit_to_ff {
my ($segment,$ff,$hit,$hit2span,$invert) = @_;
my $flip_hit = $hit->tstrand eq '-';
$CONF->flip($hit->name => 1) if $flip_hit;
my @attributes = $flip_hit ? (-attributes => {flip=>1}) : ();
my $src = $hit->src2;
my $setcolor = $CONF->setting($MAP->{$src}->{db} => 'color');
$ff->add_type(
"match:$src" => {
bgcolor => $setcolor,
fgcolor => $setcolor,
height => $CONF->setting('align_height') || ALIGN_HEIGHT,
glyph => 'segments',
label => 0,
box_subparts => 1,
connector => 'dashed',
},
);
my $seqid = $invert ? $hit->target : $hit->seqid;
my $strand = $invert ? $hit->tstrand : $hit->strand;
my $start = $invert ? $hit->tstart : $hit->start;
my $end = $invert ? $hit->tend : $hit->end;
my $feature = Bio::Graphics::Feature->new(
-source => $src,
-type => 'match',
-name => $hit->name,
-seq_id => $seqid,
-strand => $strand eq '-' ? -1 : 1,
-configurator => $ff
);
my $parts = $CONF->{parts}->{$hit->name};
if ($parts) {
for my $part (@$parts) {
$CONF->flip($part->name => 1) if $flip_hit;
$hit2span->{$part->name} = $hit2span->{$hit};
$CONF->name2hit($part->name => $part);
my $start = $invert ? $part->tstart : $part->start;
my $end = $invert ? $part->tend : $part->end;
my $subfeat = Bio::Graphics::Feature->new(
-type => 'match_part',
-name => $part->name,
-start => $start,
-end => $end,
-strand => $strand
);
$feature->add_segment($subfeat,'EXPAND');