package EnsEMBL::Web::Configuration;
use strict;
use warnings;
no warnings qw(uninitialized);
use POSIX qw(floor ceil);
use CGI qw(escape);
use Time::HiRes qw(time);
use EnsEMBL::Web::Document::Panel;
use EnsEMBL::Web::OrderedTree;
use EnsEMBL::Web::DASConfig;
use EnsEMBL::Web::Cache;
use EnsEMBL::Web::TmpFile::Text;
use EnsEMBL::Web::TmpFile::Tar;
use EnsEMBL::Web::RegObj;
use EnsEMBL::Web::Component::Export qw(export_file);
use base qw(EnsEMBL::Web::Root);
our $MEMD = new EnsEMBL::Web::Cache;
sub object {
return $_[0]->{'object'};
}
sub populate_tree {
}
sub set_default_action {
}
sub new {
my( $class, $page, $object, $flag, $common_conf ) = @_;
my $self = {
'page' => $page,
'object' => $object,
'flag ' => $flag || '',
'cl' => {},
'_data' => $common_conf
};
bless $self, $class;
my $user = $ENSEMBL_WEB_REGISTRY->get_user;
my $session = $ENSEMBL_WEB_REGISTRY->get_session;
my $session_id = $session->get_session_id;
my $we_can_have_a_user_tree = $self->can('user_populate_tree') && ($user || $session_id);
## Trying to get user+session version of the tree from cache
my $tree = ($we_can_have_a_user_tree && $MEMD && $class->tree_cache_key($user, $session))
? $MEMD->get($class->tree_cache_key($user, $session))
: undef;
if ($tree) {
$self->{_data}{tree} = $tree;
} else {
## If no user+session tree found, build one
## Trying to get default tree from cache
$tree = $MEMD->get($class->tree_cache_key) if $MEMD && $class->tree_cache_key;
if ($tree) {
$self->{_data}{tree} = $tree;
} else {
$self->populate_tree;
## Cache default tree
$MEMD->set($class->tree_cache_key, $self->{_data}{tree}, undef, 'TREE')
if $MEMD && $class->tree_cache_key;
}
if ($we_can_have_a_user_tree) {
$self->user_populate_tree if $we_can_have_a_user_tree;
## Cache user+session tree version
$MEMD->set(
$class->tree_cache_key($user, $session),
$self->{_data}{tree},
undef,
'TREE', keys %{ $ENV{CACHE_TAGS}||{} }
) if $MEMD && $class->tree_cache_key($user, $session);
}
}
$self->set_default_action;
return $self;
}
## Each class might have different tree caching dependences
## See Configuration::Account and Configuration::Search for more examples
sub tree_cache_key {
my ($class, $user, $session) = @_;
my $key = "::${class}::$ENV{ENSEMBL_SPECIES}::TREE";
$key .= '::USER['. $user->id .']'
if $user;
$key .= '::SESSION['. $session->get_session_id .']'
if $session && $session->get_session_id;
return $key;
}
sub tree {
my $self = shift;
return $self->{_data}{tree};
}
sub configurable {
my $self = shift;
return $self->{_data}{configurable};
}
sub action {
my $self = shift;
return $self->{_data}{'action'};
}
sub set_action {
my $self = shift;
$self->{_data}{'action'} = $self->_get_valid_action(@_);
}
sub default_action {
### Default action for feature type...
my $self = shift;
unless( $self->{_data}{'default'} ) {
($self->{_data}{'default'}) = $self->{_data}{tree}->leaf_codes;
}
return $self->{_data}{'default'};
}
sub _get_valid_action {
my $self = shift;
my $action = shift;
my $func = shift;
return $action if $action eq 'Wizard';
# my %hash = map { $_ => 1 } $self->{_data}{tree}->get_node(';
return undef unless ref $self->{'object'};
my $node;
$node = $self->tree->get_node( $action."/".$func ) if $func;
$self->{'availability'} = ref($self->object) ? $self->object->availability : {};
return $action."/".$func if $node && $node->get('type') =~ /view/ &&
$self->is_available( $node->get('availability') );
$node = $self->tree->get_node( $action ) unless $node;
return $action if $node && $node->get('type') =~ /view/ &&
$self->is_available( $node->get('availability') );
my @nodes = ( $self->default_action, 'Idhistory', 'Chromosome', 'Genome' );
foreach( @nodes ) {
$node = $self->tree->get_node( $_ );
#warn( "H: $_:",$node->get('availability').'; '.join ("\t", grep { $self->{'availability'}{$_} } keys %{$self->{'availability'}||{} } ) ) if $node;
if( $node && $self->is_available( $node->get('availability') ) ) {
$self->{'object'}->problem( 'redirect', $self->{'object'}->_url({'action' => $_}) );
return $_;
}
}
return undef;
}
sub _ajax_content {
my $self = shift;
my $obj = $self->{'object'};
$self->{'page'}->renderer->{'r'}->headers_in->{'X-Requested-With'} = 'XMLHttpRequest';
## Force page type to be ingredient!
$self->{'page'}->{'_page_type_'} = 'ingredient';
my $panel = $self->new_panel( 'Ajax', 'code' => 'ajax_panel', 'object' => $obj);
$panel->add_component( 'component' => $ENV{'ENSEMBL_COMPONENT'} );
$self->add_panel( $panel );
}
sub _ajax_zmenu {
my $self = shift;
my $obj = $self->{'object'};
$self->{'page'}->renderer->{'r'}->headers_in->{'X-Requested-With'} = 'XMLHttpRequest';
my $panel = $self->new_panel( 'AjaxMenu', 'code' => 'ajax_zmenu', 'object' => $obj );
$self->add_panel( $panel );
return $panel;
}
sub _global_context {
my $self = shift;
return unless $self->{'page'}->can('global_context');
return unless $self->{'page'}->global_context;
my $type = $self->type;
my $co = $self->{object}->core_objects;
return unless $co;
my @data = (
['location', 'Location', 'View', $co->location_short_caption, $co->location, 0 ],
['gene', 'Gene', 'Summary', $co->gene_short_caption, $co->gene, 1 ],
['transcript', 'Transcript', 'Summary', $co->transcript_short_caption, $co->transcript, 1 ],
['variation', 'Variation', 'Summary', $co->variation_short_caption, $co->variation, 0 ],
);
my $qs = $self->query_string;
foreach my $row ( @data ) {
next unless $row->[4];
my $action =
$row->[4]->isa('EnsEMBL::Web::Fake') ? $row->[4]->view :
$row->[4]->isa('Bio::EnsEMBL::ArchiveStableId') ? 'idhistory' : $row->[2];
my $url = $self->{object}->_url({'type'=> $row->[1], 'action' => $action,'__clear'=>1 });
$url .="?$qs" if $qs;
my @class = ();
if( $row->[1] eq $type ) {
push @class, 'active';
}
$self->{'page'}->global_context->add_entry(
'type' => $row->[1],
'caption' => $row->[3],
'url' => $url,
'class' => (join ' ',@class),
);
}
$self->{'page'}->global_context->active( lc($type) );
}
sub _user_context {
my $self = shift;
my $type = $self->type;
my $obj = $self->{'object'};
my $qs = $self->query_string;
my $referer = $obj->param('_referer') ||
$obj->_url({ type => $type, action => $ENV{'ENSEMBL_ACTION'}, time => undef });
my $vc = $obj->get_viewconfig;
my $action = $type.'/'.$ENV{'ENSEMBL_ACTION'};
$action .= '/'.$ENV{'ENSEMBL_FUNCTION'} if $ENV{'ENSEMBL_FUNCTION'};
if( !$vc->real && $obj->parent->{'ENSEMBL_TYPE'} ) {
$vc = $obj->get_viewconfig( $obj->parent->{'ENSEMBL_TYPE'}, $obj->parent->{'ENSEMBL_ACTION'} );
$vc->form($obj);
$action = $obj->parent->{'ENSEMBL_TYPE'}.'/'.$obj->parent->{'ENSEMBL_ACTION'};
$action .= '/'.$obj->parent->{'ENSEMBL_FUNCTION'} if $obj->parent->{'ENSEMBL_FUNCTION'};
}
## Do we have a View Config for this display?
# Get view configuration...!
## Do we have any image configs for this display?
my %ics = $vc->image_configs;
## Can user data be added to this page?
my $flag = $obj->param('config') ? 0 : 1;
my $active_config = $obj->param('config') || $vc->default_config();
my $active = $type ne 'Account' && $type ne 'UserData' && $active_config eq '_page';
my $upload_data = $vc->can_upload;
if( $vc->has_form ) {
$self->{'page'}->global_context->add_entry(
'type' => 'Config',
'id' => "config_page",
'caption' => 'Configure page',
$active ? ( 'class' => 'active' ) : ( 'url' => $obj->_url({
'time' => time,
'type' => 'Config',
'action' => $action,
'config' => '_page',
'_referer' => $referer,
}))
);
$flag = 0;
}
foreach my $ic_code (sort keys %ics) {
my $ic = $obj->get_imageconfig( $ic_code );
$active = $type ne 'Account' && $type ne 'UserData' && $active_config eq $ic_code || $flag;
$self->{'page'}->global_context->add_entry(
'type' => 'Config',
'id' => "config_$ic_code",
'caption' => $ic->get_parameter('title'),
$active ? ( 'class' => 'active' ) : ( 'url' => $obj->_url({
'time' => time,
'type' => 'Config',
'action' => $action,
'config' => $ic_code,
'_referer' => $referer,
}))
);
$flag = 0;
}
$active = $type eq 'UserData';
my $module = $vc->can_upload ? 'Upload' : 'ManageData';
$self->{'page'}->global_context->add_entry(
'type' => 'UserData',
'id' => 'user_data',
'caption' => 'Custom Data',
$active ? ( 'class' => 'active' ) : ( 'url' => $obj->_url({
'time' => time,
'_referer' => $referer,
'__clear' => 1,
'type' => 'UserData',
'action' => $module,
}))
);
## Now the user account link - varies depending on whether the user is logged in or not!
$active = $type eq 'Account';
if( $obj->species_defs->ENSEMBL_LOGINS) {
my $user_action = $ENSEMBL_WEB_REGISTRY->get_user ? 'Links' : 'Login';
$self->{'page'}->global_context->add_entry(
'type' => 'Account',
'id' => 'account',
'caption' => 'Your account',
$active ? ( 'class' => 'active') : ( 'url' => $obj->_url({
'_referer' => $referer,
'time' => time,
'__clear' => 1,
'type' => 'Account',
'action' => $user_action,
}))
);
}
$self->{'page'}->global_context->active( lc($type) );
}
sub _reset_config_panel {
my( $self, $title, $action, $config ) = @_;
my $obj = $self->{'object'};
my $panel = $self->new_panel( 'Configurator',
'code' => 'x',
'object' => $obj
);
my $url = $obj->_url({'type'=>'Config','action'=>$action,'reset'=>1,'config'=>$config,'time'=>time});
my $c = sprintf '
<p>
To update this configuration, select your tracks and other options in the box above and close
this popup window. Your view will then be updated automatically.
</p>
<p>
<a class="modal_link reset-button" href="%s">Reset configuration for %s to default settings</a>.
</p>', $url, CGI::escapeHTML( $title ) || 'this page';
if( $title ) {
$c .= '
<p>
Notes:
</p>
<ul>
<li>
To change whether a track is drawn OR how it is drawn, click on the icon by the track name and
then select the way the track is to be rendered.
</li>
<li>
On the left hand side of the page the number of tracks in a menu, and the number of tracks
currently turned on from that menu are shown by the two numbers in parentheses <span style="white-space:nowrap">(tracks on/total tracks)</span>.
</li>
<li>
<p>
Certain tracks displayed come from user-supplied or external data sources, these are clearly
marked as <strong><img src="/i/track-das.gif" alt="DAS" style="vertical-align:top; width:40px;height:16px" title="DAS" /></strong> (Distributed Annotation Sources),
<strong><img src="/i/track-url.gif" alt="URL" style="vertical-align:top; width:40px;height:16px" title="URL" /></strong> (UCSC style web resources) or <strong><img src="/i/track-user.gif" alt="User" style="vertical-align:top; width:40px;height:16px" title="User" /></strong> data uploaded by
yourself or another user.
</p>
<p>
Please note that the content of these tracks is not the responsibility of the Ensembl project.
</p>
<p>In the case of URL based or DAS tracks may either slow down your ensembl browsing experience OR may be unavailable as these are served and stored from other servers elsewhere on the Internet.
</p>
</li>
</ul>';
}
$panel->set_content( $c );
$self->add_panel( $panel );
}
sub _export_configurator {
my ($self, $options) = @_;
my $object = $self->{'object'};
my $type = $object->type;
my $content;
my $text;
$self->tree->_flush_tree;
my $vc = $object->get_viewconfig($type, 'Export');
my $config = {
'fasta' => {
'label' => 'FASTA sequence',
'formats' => [
[ 'fasta', 'FASTA sequence' ]
],
'params' => [
[ 'cdna', 'cDNA' ],
[ 'coding', 'Coding sequence', $options->{'translation'} ],
[ 'peptide', 'Peptide sequence', $options->{'translation'} ],
[ 'utr5', "5' UTR", $options->{'five'} ],
[ 'utr3', "3' UTR", $options->{'three'} ],
[ 'exons', 'Exons' ],
[ 'introns', 'Introns' ]
]
},
'features' => {
'label' => 'Feature File',
'formats' => [
[ 'csv', 'CSV (Comma separated values)' ],
[ 'gff', 'GFF Format' ],
[ 'tab', 'Tab separated values' ]
],
'params' => [
[ 'similarity', 'Similarity features' ],
[ 'repeat', 'Repeat features' ],
[ 'genscan', 'Prediction features (genscan)' ],
[ 'variation', 'Variation features' ],
[ 'gene', 'Gene Information' ]
]
},
'flat' => {
'label' => 'Flat File',
'formats' => [
[ 'embl', 'EMBL' ],
[ 'genbank', 'GenBank' ]
],
'params' => [
[ 'similarity', 'Similarity features' ],
[ 'repeat', 'Repeat features' ],
[ 'genscan', 'Prediction features (genscan)' ],
[ 'contig', 'Contig Information' ],
[ 'variation', 'Variation features' ],
[ 'marker', 'Marker features' ],
[ 'gene', 'Gene Information' ],
[ 'vegagene', 'Vega Gene Information' ],
[ 'estgene', 'EST Gene Information' ]
]
},
'pip' => {
'label' => 'PIP (%age identity plot)',
'formats' => [
[ 'pipmaker', 'Pipmaker / zPicture format' ],
[ 'vista', 'Vista Format' ]
]
}
};
if ($options->{'config_merge'}) {
for (keys %{$options->{'config_merge'}}) {
$config->{$_} = { %{$config->{$_}}, %{$options->{'config_merge'}->{$_}} };
}
}
$options->{'strand_values'} ||= [
{ value => 'feature', name => 'Feature strand' },
{ value => '1', name => 'Forward strand' },
{ value => '-1', name => 'Reverse strand' }
];
# Second page
if ($object->param('save')) {
my $output = $object->param('output');
my $href = $object->_url({
'time' => time,
'action' => 'Export',
'strand' => $object->param('strand'),
'output' => $output
});
my $map = {
'csv' => 'features',
'gff' => 'features',
'tab' => 'features',
'embl' => 'flat',
'genbank' => 'flat',
'pipmaker' => 'pip',
'vista' => 'pip'
};
my $key = $map->{$output} || $output;
my @formats;
if ($key eq 'pip') {
my $seq_file = EnsEMBL::Web::TmpFile::Text->new(
extension => 'fa',
prefix => '',
content_type => 'text/plain; charset=utf-8',
);
my $anno_file = EnsEMBL::Web::TmpFile::Text->new(
filename => $seq_file->filename,
extension => 'txt',
prefix => '',
content_type => 'text/plain; charset=utf-8',
);
export_file($seq_file, $object, 'seq');
export_file($anno_file, $object, $output);
$seq_file->save;
$anno_file->save;
my $tar_file = EnsEMBL::Web::TmpFile::Tar->new(
filename => $seq_file->filename,
prefix => '',
use_short_names => 1
);
$tar_file->add_file($seq_file);
$tar_file->add_file($anno_file);
$tar_file->save;
$text = qq{<p>Your export has been processed successfully. You can download the exported data by following the links below</p>};
@formats = (
[ 'Sequence data', '', ' rel="external"', ' [FASTA format]', $seq_file->URL ],
[ 'Annotation data', '', ' rel="external"', ' [pipmaker format]', $anno_file->URL ],
[ 'Combined file', '', '', '', $tar_file->URL ]
);
} else {
@formats = (
[ 'HTML', 'HTML', ' rel="external"' ],
[ 'Text', 'Text', ' rel="external"' ],
[ 'Compressed text (.gz)', 'TextGz' ]
);
}
my $checked_params = {};
foreach (@{$config->{$key}->{'params'}}) {
$checked_params->{"${output}_$_->[0]"} = 1;
if ($object->param("${output}_$_->[0]") eq 'yes') {
$_->[0] =~ s/(miscset_)//;
$href .= $1 ? ";miscset=$_->[0]" : ";st=$_->[0]";
}
}
foreach (grep { /${output}_/ } $object->param) {
(my $param = $_) =~ s/${output}_//;
$href .= ";$param=" . $object->param($_) unless $checked_params->{$_};
}
# How confusing!
my $form_action = $object->_url({ 'action' => $type, 'type' => 'Export', 'function' => $object->action }, 1);
my $hidden_params;
foreach (keys %{$form_action->[1]||{}}) {
$hidden_params .= qq{
<input type="hidden" name="$_" value="$form_action->[1]->{$_}" />};
}
$content = qq{
<h2>Export Configuration - Output Format</h2>
<form id="export_output_configuration" class="std check" method="get" action="$form_action->[0]">
<fieldset>
$text
<ul>};
foreach (@formats) {
my $format = ";_format=$_->[1]" if $_->[1];
my $link = $_->[4] || $href;
$content .= qq{
<li><a class="modal_close" href="$link$format"$_->[2]>$_->[0]</a>$_->[3]</li>};
}
$content .= qq{
</ul>
<input type="submit" value="< Back" class="submit" />
$hidden_params
</form>};
} else { # First page
$vc->{'_temp'} = { config => $config, options => $options }; # Hack to get it through to ViewConfig
$vc->form($object, 1);
delete $vc->{'_temp'};
$content = qq{
<h2>Export Configuration - Feature List</h2>};
$content .= $vc->get_form->render;
}
my $panel = $self->new_panel(
'Configurator',
'code' => 'configurator',
'object'=> $object
);
$panel->set_content($content);
$self->add_panel($panel);
}
sub _configurator {
my $self = shift;
my $obj = $self->{'object'};
my $vc = $obj->get_viewconfig();
warn "... $vc ...";
warn ">>>>> ", $vc->has_form ," <<<<<";
my $conf;
my $config_key = $obj->param('config');
eval {
$conf = $obj->image_config_hash( $obj->param('config') ) if $obj->param('config');
};
my $action = $ENV{'ENSEMBL_TYPE'}.'/'.$ENV{'ENSEMBL_ACTION'};
$action .= '/'.$ENV{'ENSEMBL_FUNCTION'} if $ENV{'ENSEMBL_FUNCTION'};
my $referer = $obj->param('_referer') || $ENV{'REQUEST_URI'};
my $url = $obj->_url({'type'=>'Config','action'=>$action,'_referer'=>$referer},1);
unless( $conf ) {
## This must be the view config....
if( $vc->has_form ) {
$vc->get_form->{'_attributes'}{'action'} = $url->[0];
if( $ENV{'ENSEMBL_ACTION'} ne 'ExternalData' ) {
my $vc_2 = $obj->get_viewconfig( undef, 'ExternalData' );
if( $vc_2 ) {
$vc_2->{'_form'} = $vc->{'_form'};
$vc_2->form( undef, 1 );
}
}
foreach( keys %{$url->[1]}) {
$vc->add_form_element({'type'=>'Hidden','name'=>$_,'value' => $url->[1]{$_}});
}
$self->tree->_flush_tree();
$self->create_node( 'form_conf', 'Configure', [], {
'url' => '', 'availability' => 0, 'id' => 'form_conf_id', 'caption' => 'Configure'
} );
$self->{'page'}->{'_page_type_'} = 'configurator';
$self->{'page'}->local_context->tree( $self->{_data}{'tree'} );
$self->{'page'}->local_context->active( 'form_conf' );
$self->{'page'}->local_context->caption( 'Configure view' );
$self->{'page'}->local_context->class( 'view_configuration' );
$self->{'page'}->local_context->counts( {} );
my $panel = $self->new_panel( 'Configurator',
'code' => 'configurator',
'object' => $obj
);
my $content = '';
$content .= sprintf '<h2>Configuration for: "%s"</h2>', CGI::escapeHTML($vc->title) if $vc->title;
$content .= $vc->get_form->render;
$panel->set_content( $content );
$self->add_panel( $panel );
$self->_reset_config_panel( $vc->title, $action );
return;
}
my %T = $vc->image_configs;
my @Q = sort keys %T;
if(@Q) {
$config_key = $Q[0];
$conf = $obj->image_config_hash( $Q[0] );
}
}
return unless $conf;
$self->{'page'}->{'_page_type_'} = 'configurator';
$self->tree->_flush_tree();
my $rhs_content = sprintf '
<form id="configuration" action="%s" method="post">
<div>', $url->[0];
foreach( keys %{ $url->[1] } ) {
$rhs_content .= sprintf '
<input type="hidden" name="%s" value="%s" />', $_, CGI::escapeHTML( $url->[1]{$_} );
}
$rhs_content .= sprintf '
<input type="hidden" name="config" value="%s" />
</div>', $obj->param('config') ;
my $active = '';
$self->create_node(
'active_tracks',
'Active tracks',
[], # configurator EnsEMBL::Web::Component::Configurator ],
{ 'url' => "#active_tracks", 'id' => 'active_tracks', 'availability' => 1 }
);
foreach my $node ($conf->tree->top_level) {
next unless $node->get('caption');
next if $node->is_leaf;
my $count = 0;
my $link_key = 'link_'.$node->key;
my $menu_key = 'menu_'.$node->key;
$rhs_content .= sprintf '
<div id="%s">
<h2>%s</h2>
<dl class="config_menu">', $menu_key, CGI::escapeHTML( $node->get('caption') );
# <dl class="config_menu" id="%s">
# <dt class="title">%s</dt>', $menu_key, CGI::escapeHTML( $node->get('caption') );
my $available = 0;
my $on = 0;
foreach my $track_node ( $node->descendants ) {
next if $track_node->get('menu') eq 'no';
$rhs_content .= sprintf '
<dt%s><select id="%s" name="%s">',
'', # $track_node->get('glyphset') =~ /_(prot)?das/ ? ' class="das_menu_entry"' : '',
$track_node->key, $track_node->key;
my $display = $track_node->get( 'display' ) || 'off';
my @states = @{ $track_node->get( 'renderers' ) || [qw(off Off normal Normal)] };
while( my($K,$V) = splice(@states,0,2) ) {
$rhs_content .= sprintf '
<option value="%s"%s>%s</option>', $K, $K eq $display ? ' selected="selected"' : '', CGI::escapeHTML($V);
}
$count ++;
$on ++ if $display ne 'off';
my $t = CGI::escapeHTML( $track_node->get('name') );
if( $track_node->get('_class') ) {
my $class = $track_node->get('_class');
$t = sprintf '<img src="/i/track-%s.gif" style="width:40px;height:16px" title="%s" alt="[%s]" /> %s', lc($class), $class, $class, $t;
}
$rhs_content .= sprintf '
</select> %s</dt>', $t;
my $desc = $track_node->get('description');
if( $desc ) {
$desc =~ s/&(?!\w+;)/&/g;
$desc =~ s/href="?([^"]+?)"?([ >])/href="$1"$2/g;
$desc =~ s/<a>/<\/a>/g;
$desc =~ s/"[ "]*>/">/g;
$rhs_content .= sprintf '
<dd>%s</dd>', $desc;
}
}
$rhs_content .= '
</dl>
</div>';
$active ||= $link_key if $count > 0;
$self->create_node(
$link_key,
( $count ? "($on/$count) " : '' ).$node->get('caption'),
[], # configurator EnsEMBL::Web::Component::Configurator ],
{ 'url' => "#$menu_key", 'availability' => ($count>0), 'id' => $link_key }
);
}
$rhs_content .= '
</form>';
$self->{'page'}->local_context->tree( $self->{_data}{'tree'} );
$self->{'page'}->local_context->active( 'active_tracks' );
$self->{'page'}->local_context->caption( $conf->get_parameter('title') );
$self->{'page'}->local_context->class( 'track_configuration' );
$self->{'page'}->local_context->counts( {} );
my $search_panel = $self->new_panel(
'Configurator',
'code' => 'configurator_search',
'object' => $obj
);
$search_panel->set_content( '
<form id="configuration_search" action="" method="get">
Search display: <input id="configuration_search_text" />
</form>'
);
$self->add_panel( $search_panel );
my $panel = $self->new_panel(
'Configurator',
'code' => 'configurator',
'object' => $obj
);
$panel->set_content( $rhs_content );
$self->add_panel( $panel );
$self->_reset_config_panel( $conf->get_parameter('title'), $action, $config_key );
return $panel;
}
sub _local_context {
my $self = shift;
return unless $self->{'page'}->can('local_context') && $self->{'page'}->local_context;
my $hash = {}; # $self->obj->get_summary_counts;
$self->{'page'}->local_context->tree( $self->{_data}{'tree'} );
my $action = $self->_get_valid_action( $ENV{'ENSEMBL_ACTION'}, $ENV{'ENSEMBL_FUNCTION'} );
$self->{'page'}->local_context->active( $action );#$self->{_data}{'action'} );
$self->{'page'}->local_context->caption( ref($self->{object}) ? $self->{object}->short_caption : $self->{object} );
$self->{'page'}->local_context->counts( ref( $self->{object}) ? $self->{object}->counts : {} );
$self->{'page'}->local_context->availability( ref($self->{object}) ? $self->{object}->availability : {} );
}
sub _local_tools {
my $self = shift;
return unless $self->{'page'}->can('local_tools');
return unless $self->{'page'}->local_tools;
my $obj = $self->{object};
my $referer = $ENV{'REQUEST_URI'};
my $vc = $obj->get_viewconfig;
my $config = $vc->default_config;
my $disabled_upload = 1;
if( $vc->real && $config ) {
my $action = $obj->type.'/'.$obj->action;
$action .= '/'.$obj->function if $obj->function;
$self->{'page'}->local_tools->add_entry(
'caption' => 'Configure this page',
'class' => 'modal_link',
'url' => $obj->_url({ 'time' => time, 'type' => 'Config', 'action' => $action,
'config' => $config, '_referer' => $referer })
);
if( $vc->can_upload ) {
my $caption = 'Add custom data to page';
my $action = 'Upload';
my $user = $ENSEMBL_WEB_REGISTRY->get_user;
my @temp_uploads = $self->object->get_session->get_data(type => 'upload');
my @user_uploads = $user ? $user->uploads : ();
if (@temp_uploads || @user_uploads) {
$caption = 'Add/manage custom data';
$action = 'ManageData';
}
$self->{'page'}->local_tools->add_entry(
'caption' => $caption,
'class' => 'modal_link',
'url' => $obj->_url({'time' => time, 'type' => 'UserData', 'action' => $action,
'_referer' => $referer, '__clear' => 1 })
);
$disabled_upload = 0;
}
} else {
$self->{'page'}->local_tools->add_entry(
'caption' => 'Configure this page',
'class' => 'disabled',
'url' => undef,
'title' => 'There are no options for this page'
);
}
if( $disabled_upload ) {
$self->{'page'}->local_tools->add_entry(
'caption' => 'Add custom data to page',
'class' => 'disabled',
'url' => undef,
'title' => 'You cannot add custom data to this page'
);
}
if ($obj->can_export) {
my $action = $obj->type.'/'.$obj->action;
$action .= '/'.$obj->function if $obj->function;
$self->{'page'}->local_tools->add_entry(
'caption' => 'Export data',
'class' => 'modal_link',
'url' => $obj->_url({ 'time' => time, 'type' => 'Export', 'action' => $action, '_referer' => $referer })
);
} else {
$self->{'page'}->local_tools->add_entry(
'caption' => 'Export data',
'class' => 'disabled',
'url' => undef,
'title' => 'You cannot export data from this page'
);
}
if( $ENV{'ENSEMBL_USER_ID'} ) {
$self->{'page'}->local_tools->add_entry(
'caption' => 'Bookmark this page',
'class' => 'modal_link',
'url' => $obj->_url({ 'type' => 'Account', 'action' => 'Bookmark/Add',
'_referer' => $ENV{'REQUEST_URI'}, '__clear' =>1,
'name' => $self->{'page'}->title->get,
'url' => $obj->species_defs->ENSEMBL_BASE_URL.$ENV{'REQUEST_URI'} })
);
} else {
$self->{'page'}->local_tools->add_entry(
'caption' => 'Bookmark this page',
'class' => 'disabled',
'url' => undef,
'title' => 'You must be logged in to bookmark pages'
);
}
}
sub _user_tools {
my $self = shift;
my $obj = $self->{object};
my $sitename = $obj->species_defs->ENSEMBL_SITETYPE;
my @data = (
['Back to '.$sitename, '/index.html'],
);
my $type;
foreach my $row ( @data ) {
if( $row->[1] =~ /^http/ ) {
$type = 'external';
}
$self->{'page'}->local_tools->add_entry(
'type' => $type,
'caption' => $row->[0],
'url' => $row->[1],
);
}
}
sub _context_panel {
my $self = shift;
my $raw = shift;
my $obj = $self->{'object'};
my $panel = $self->new_panel( 'Summary',
'code' => 'summary_panel',
'object' => $obj,
'raw_caption' => $raw,
'caption' => $obj->caption
);
$panel->add_component( 'summary' => sprintf( 'EnsEMBL::Web::Component::%s::Summary', $self->type ) );
$self->add_panel( $panel );
}
sub _content_panel {
my $self = shift;
my $obj = $self->{'object'};
my $action = $self->_get_valid_action( $ENV{'ENSEMBL_ACTION'}, $ENV{'ENSEMBL_FUNCTION'} );
my $node = $self->get_node( $action );
return unless $node;
my $title = $node->data->{'concise'}||$node->data->{'caption'};
$title =~ s/\s*\(.*\[\[.*\]\].*\)\s*//;
$title = join ' - ', '', $title, ( $obj ? $obj->caption : () );
$self->set_title( $title ) if $self->can('set_title');
my $previous_node = $node->previous;
## don't show tabs for 'no_menu' nodes
$self->{'availability'} = $obj->availability;
while(
defined($previous_node) && ( $previous_node->get('type') ne 'view' || ! $self->is_available( $previous_node->get('availability') ) )
) {
$previous_node = $previous_node->previous;
}
my $next_node = $node->next;
while(
defined($next_node) && ( $next_node->get('type') ne 'view' || ! $self->is_available( $next_node->get('availability') ) )
) {
$next_node = $next_node->next;
}
my %params = (
'object' => $obj,
'code' => 'main',
'caption' => $node->data->{'full_caption'} || $node->data->{'concise'} || $node->data->{'caption'}
);
$params{'previous'} = $previous_node->data if $previous_node;
$params{'next' } = $next_node->data if $next_node;
## Check for help
my %help = $self->{object}->species_defs->multiX('ENSEMBL_HELP');
$params{'help'} = $help{$ENV{'ENSEMBL_TYPE'}}{$ENV{'ENSEMBL_ACTION'}} if keys %help;
$params{'omit_header'} = $self->{doctype} eq 'Popup' ? 1 : 0;
my $panel = $self->new_panel( 'Navigation', %params );
if( $panel ) {
$panel->add_components( '__messages', 'EnsEMBL::Web::Component::Messages', @{$node->data->{'components'}} );
$self->add_panel( $panel );
}
}
sub get_node {
my ( $self, $code ) = @_;
return $self->{_data}{tree}->get_node( $code );
}
sub species { return $ENV{'ENSEMBL_SPECIES'}; }
sub type { return $ENV{'ENSEMBL_TYPE'}; }
sub query_string {
my $self = shift;
return unless defined $self->{object}->core_objects;
my %parameters = (%{$self->{object}->core_objects->{parameters}},@_);
my @S = ();
foreach (sort keys %parameters) {
push @S, "$_=$parameters{$_}" if defined $parameters{$_};
}
push @S, '_referer='.CGI::escape($self->object->param('_referer'))
if $self->object->param('_referer');
return join ';', @S;
}
sub create_node {
my ( $self, $code, $caption, $components, $options ) = @_;
my $details = {
caption => $caption,
components => $components,
code => $code,
type => 'view',
};
foreach ( keys %{$options||{}} ) {
$details->{$_} = $options->{$_};
}
if( $self->tree ) {
return $self->tree->create_node( $code, $details );
}
}
sub create_subnode {
my ( $self, $code, $caption, $components, $options ) = @_;
my $details = {
caption => $caption,
components => $components,
code => $code,
type => 'subview',
%{ $options || {} },
};
return $self->tree->create_node( $code, $details )
if $self->tree;
}
sub create_submenu {
my ($self, $code, $caption, $options ) = @_;
my $details = {
caption => $caption,
url => '',
type => 'menu',
%{ $options || {} },
};
return $self->tree->create_node( $code, $details )
if $self->tree;
}
sub delete_node {
my ($self, $code) = @_;
if ($code && $self->tree) {
my $node = $self->tree->get_node($code);
$node->remove_node if $node;
}
}
sub delete_submenu {
my ($self, $code) = @_;
if ($code && $self->tree) {
my $node = $self->tree->get_node($code);
$node->remove_subtree if $node;
}
}
sub update_configs_from_parameter {
my( $self, $parameter_name, @imageconfigs ) = @_;
my $val = $self->{object}->param( $parameter_name );
my $rst = $self->{object}->param( 'reset' );
my $wsc = $self->{object}->get_viewconfig();
my @das = $self->{object}->param( 'add_das_source' );
foreach my $config_name ( @imageconfigs ) {
$self->{'object'}->attach_image_config( $self->{'object'}->script, $config_name );
$self->{'object'}->image_config_hash( $config_name );
}
foreach my $URL ( @das ) {
my $das = EnsEMBL::Web::DASConfig->new_from_URL( $URL );
$self->{object}->get_session( )->add_das( $das );
}
return unless $val || $rst;
if( $wsc ) {
$wsc->reset() if $rst;
$wsc->update_config_from_parameter( $val ) if $val;
}
foreach my $config_name ( @imageconfigs ) {
my $wuc = $self->{'object'}->image_config_hash( $config_name );
# my $wuc = $self->{'object'}->get_imageconfig( $config_name );
if( $wuc ) {
$wuc->reset() if $rst;
$wuc->update_config_from_parameter( $val ) if $val;
$self->{object}->get_session->_temp_store( $self->{object}->script, $config_name );
}
}
}
sub add_panel { $_[0]{page}->content->add_panel( $_[1] ); }
sub set_title { $_[0]{page}->set_title( $_[1] ); }
sub add_form { my($self,$panel,@T)=@_; $panel->add_form( $self->{page}, @T ); }
sub add_block {
my $self = shift;
return unless $self->{page}->can('menu');
return unless $self->{page}->menu;
my $flag = shift;
$flag =~s/#/($self->{flag} || '')/ge;
# $flag =~s/#/$self->{flag}/g;
$self->{page}->menu->add_block( $flag, @_ );
}
sub delete_block {
my $self = shift;
return unless $self->{page}->can('menu');
return unless $self->{page}->menu;
my $flag = shift;
$flag =~s/#/$self->{flag}/g;
$self->{page}->menu->delete_block( $flag, @_ );
}
sub add_entry {
my $self = shift;
return unless $self->{page}->can('menu');
return unless $self->{page}->menu;
my $flag = shift;
$flag =~s/#/($self->{flag} || '')/ge;
$self->{page}->menu->add_entry( $flag, @_ );
}
sub new_panel {
my( $self, $panel_type, %params ) = @_;
my $module_name = "EnsEMBL::Web::Document::Panel";
$module_name.= "::$panel_type" if $panel_type;
$params{'code'} =~ s/#/$self->{'flag'}||0/eg;
if( $panel_type && !$self->dynamic_use( $module_name ) ) {
my $error = $self->dynamic_use_failure( $module_name );
my $message = "^Can't locate EnsEMBL/Web/Document/Panel/$panel_type\.pm in";
if( $error =~ /$message/ ) {
$error = qq(<p>Unrecognised panel type "<b>$panel_type</b>");
} else {
$error = sprintf( "<p>Unable to compile <strong>$module_name</strong></p><pre>%s</pre>",
$self->_format_error( $error ) );
}
$self->{page}->content->add_panel(
new EnsEMBL::Web::Document::Panel(
'object' => $self->{'object'},
'code' => "error_$params{'code'}",
'caption' => "Panel compilation error",
'content' => $error,
'has_header' => $params{'has_header'},
)
);
return undef;
}
no strict 'refs';
my $panel;
eval {
$panel = $module_name->new( 'object' => $self->{'object'}, %params );
};
return $panel unless $@;
my $error = "<pre>".$self->_format_error($@)."</pre>";
$self->{page}->content->add_panel(
new EnsEMBL::Web::Document::Panel(
'object' => $self->{'object'},
'code' => "error_$params{'code'}",
'caption' => "Panel runtime error",
'content' => "<p>Unable to compile <strong>$module_name</strong></p>$error"
)
);
return undef;
}
sub mapview_possible {
my( $self, $location ) = @_;
my @coords = split(':', $location);
my %chrs = map { $_,1 } @{$self->{object}->species_defs->ENSEMBL_CHROMOSOMES || []};
return 1 if exists $chrs{$coords[0]};
}
sub ajax_zmenu_variation {
# Specific zmenu for variation features
my $self = shift;
my $panel = $self->_ajax_zmenu;
my $obj = $self->object;
my $db_adaptor = $obj->database('variation');
my $var_adaptor = $db_adaptor->get_VariationAdaptor();
my $var_feat_adaptor = $db_adaptor->get_VariationFeatureAdaptor();
my $v_id = $obj->param('v');
my $var = $var_adaptor->fetch_by_name($v_id);
my @vf = @{$var_feat_adaptor->fetch_all_by_Variation($var)};
my $feature;
if ( scalar @vf == 1) { $feature = $vf[0];}
else {
foreach (@vf) {
if ($_->dbID eq $obj->param('vf') ) {$feature = $_;}
}
}
my $tvar_adaptor = $db_adaptor->get_TranscriptVariationAdaptor();
my $trans_variation = $tvar_adaptor->fetch_by_dbID($obj->param('vf'));
## alternate way to retrieve transcript_variation_feature if there are more than one with the same variation_feature id;
unless ($trans_variation){
my $trans_id = $obj->param('vt');
if ($trans_id){
my $trans_adaptor = $obj->database('core')->get_TranscriptAdaptor;
my $transcript = $trans_adaptor->fetch_by_stable_id($trans_id);
foreach my $trv (@{$tvar_adaptor->fetch_all_by_Transcripts([$transcript])}) {
if ($trv->variation_feature->variation_name() eq $feature->variation_name){
$trans_variation = $trv;
}
}
}
}
my $type;
if ($obj->param('snp_fake') && $feature) { $type = $feature->display_consequence; }
elsif ($trans_variation){ $type = join ", ", @{$trans_variation->consequence_type || [] };}
elsif ($obj->param('consequence')){$type = $obj->param('consequence') || '';}
else { $type = $feature->display_consequence; }
my $var_link = $obj->_url({'type' => 'Variation', 'action' => 'Summary', 'v' => $feature->variation_name, 'vf' => $feature->dbID, 'source' => $feature->source });
my $chr_start = $feature->start();
my $chr_end = $feature->end();
my $bp = $chr_start;
if( $chr_end < $chr_start ) {
$bp = "between $chr_end & $chr_start";
} elsif($chr_end > $chr_start ) {
$bp = "$chr_start - $chr_end";
}
my $source = (join ", ", @{$feature->get_all_sources ||[] });
my $allele = $feature->allele_string;
my $alleles = (length($allele)<16 ? $allele : substr($allele,0,14).'..');
$panel->{'caption'} = 'Variation: ' . $feature->variation_name;
$panel->add_entry({
'label_html' => 'Variation Properties',
'link' => $var_link,
'priority' => 15,
});
$panel->add_entry({
'type' => 'bp:',
'label' => $bp,
'priority' => 13,
});
$panel->add_entry({
'type' => 'class:',
'label' => $feature->var_class,
'priority' => 11,
});
$panel->add_entry({
'type' => 'ambiguity code:',
'label' => $feature->ambig_code,
'priority' => 9,
});
$panel->add_entry({
'type' => 'alleles:',
'label' => $alleles,
'priority' => 7,
});
$panel->add_entry({
'type' => 'source:',
'label' => $source,
'priority' => 5,
});
$panel->add_entry({
'type' => 'type:',
'label' => $type,
'priority' => 2,
});
if ($obj->param('snp_fake')){
my $status = join(', ', @{$feature->get_all_validation_states||[]} );
$panel->add_entry({
'type' => 'status:',
'label' => $status || '-',
'priority' => 12,
});
$panel->add_entry({
'type' => 'mapweight:',
'label' => $feature->map_weight,
'priority' => 8,
});
} elsif ($obj->param('var_box')){
unless ( $obj->param('var_box') eq '-' ){
$panel->add_entry({
'type' => 'amino acid:',
'label' => $obj->param('var_box'),
'priority' => 8,
});
}
} elsif ($obj->type eq 'Variation'){
my $status = join(', ', @{$feature->get_all_validation_states||[]} );
$panel->add_entry({
'type' => 'status:',
'label' => $status || '-',
'priority' => 12,
});
}
return;
}
sub ajax_zmenu_variation_protein {
# Specific zmenu for variation features
my $self = shift;
my $panel = $self->_ajax_zmenu;
my $obj = $self->object;
my $db_adaptor = $obj->database('variation');
my $var_adaptor = $db_adaptor->get_VariationAdaptor();
my $var_feat_adaptor = $db_adaptor->get_VariationFeatureAdaptor();
my $v_id = $obj->param('v');
my $var = $var_adaptor->fetch_by_name($v_id);
my @vf = @{$var_feat_adaptor->fetch_all_by_Variation($var)};
my $feature;
if ( scalar @vf == 1) { $feature = $vf[0];}
else {
foreach (@vf) {
if ($_->dbID eq $obj->param('vf') ) {$feature = $_;}
}
}
my $var_link = $obj->_url({'type' => 'Variation', 'action' => 'Summary', 'v' => $feature->variation_name, 'vf' => $feature->dbID, 'source' => $feature->source });
$panel->{'caption'} = 'Variation Information ' ;
$panel->add_entry({
'type' => 'Variation ID:',
'label_html' => $feature->variation_name,
'link' => $var_link,
'priority' => 15,
});
if ($obj->param('vtype')){
my $type = lc($obj->param('vtype'));
$type =~s/e$//;
$type .= 'ion';
$panel->add_entry({
'type' => ucfirst($type),
'label' => $obj->param('indel'),
'priority' => 13,
});
$panel->add_entry({
'type' => 'Position:',
'label' => $obj->param('pos'),
'priority' => 11,
});
$panel->add_entry({
'type' => 'Length:',
'label' => $obj->param('len'),
'priority' => 11,
});
} else {
$panel->add_entry({
'type' => 'Variation type:',
'label' => $feature->display_consequence,
'priority' => 13,
});
}
$panel->add_entry({
'type' => 'Residue:',
'label' => $obj->param('res'),
'priority' => 11,
}) if $obj->param('res');
$panel->add_entry({
'type' => 'Alternative Residues:',
'label' => $obj->param('ar'),
'priority' => 11,
}) if $obj->param('ar');
$panel->add_entry({
'type' => 'Codon:',
'label' => $obj->param('cod'),
'priority' => 9,
}) if $obj->param('cod');
$panel->add_entry({
'type' => 'Alleles:',
'label' => $obj->param('al'),
'priority' => 7,
}) if $obj->param('al') ;
return;
}
sub ajax_zmenu_variation_transcript {
# Specific zmenu for transcripts on variation image
my $self = shift;
my $panel = $self->_ajax_zmenu;
my $obj = $self->object;
my $trans_id = $obj->param('vt') || die( "No transcript stable ID value in params" );
my $exon_id = $obj->param('e') || die( "No exon stable ID value in params" );
my $trans_adaptor = $obj->database('core')->get_TranscriptAdaptor;
my $transcript = $trans_adaptor->fetch_by_stable_id($trans_id);
my $protein_id = $transcript->translation ? $transcript->translation->stable_id() : '';
my $id = $transcript->external_name() eq '' ? $trans_id : ( $transcript->external_db.": ".$transcript->external_name() );
$panel->{'caption'} = $obj->species_defs->AUTHORITY." Gene";
$panel->add_entry({
'label' => $id,
'priority' => 15,
});
unless ($obj->type eq 'Transcript'){
$panel->add_entry({
'type' => 'Gene:',
'label_html' => $obj->stable_id,
'link' => $obj->_url({'type' => 'Gene', 'action' => 'Summary', 'g' =>$obj->stable_id }),
'priority' => 10,
});
}
$panel->add_entry({
'type' => 'Transcript:',
'label_html' => $trans_id,
'link' => $obj->_url({'type' => 'Transcript', 'action' => 'Summary', 't' => $trans_id }),
'priority' => 9,
});
if ($protein_id ){
$panel->add_entry({
'type' => 'Protein product:',
'label_html' => $protein_id,
'link' => $obj->_url({'type' => 'Transcript', 'action' => 'ProteinSummary', 't' => $trans_id }),
'priority' => 8,
});
$panel->add_entry({
'label_html' => 'Export Protein',
'link' => $obj->_url({'type' => 'Transcript', 'action' => 'Export/fasta', 't' => $trans_id, 'st' => 'peptide', '_format' =>'Text' }),
'priority' => 5,
});
}
$panel->add_entry({
'type' => 'Exon:',
'label' => $exon_id,
'priority' => 7,
});
$panel->add_entry({
'label_html' => 'Export cDNA',
'link' => $obj->_url({'type' => 'Transcript', 'action' => 'Export/fasta', 't' => $trans_id, 'st' => 'cdna', '_format' =>'Text' }),
'priority' => 6,
});
return;
}
sub ajax_zmenu_id_history_tree_node {
# Specific zmenu for idhistory tree nodes
my $self = shift;
my $panel = $self->_ajax_zmenu;
my $obj = $self->object;
my $a_id = $obj->param('node') || die( "No node value in params" );
my $db = $obj->param('db') || 'core';
my $db_adaptor = $obj->database($db);
my $arch_adaptor = $db_adaptor->get_ArchiveStableIdAdaptor;
my $db_name = $obj->param('db_name');
my $arch_obj = $arch_adaptor->fetch_by_stable_id_dbname( $a_id, $db_name);
my $id = $arch_obj->stable_id .".". $arch_obj->version;
my $type = $arch_obj->type eq 'Translation' ? 'Protein' : $arch_obj->type;
my $url = $id;
my $link;
unless ($arch_obj->release <= $obj->species_defs->EARLIEST_ARCHIVE){ $link = _archive_link($obj, $arch_obj, $obj->species_defs->ENSEMBL_ARCHIVES, $obj->species_defs->ENSEMBL_VERSION); }
$panel->{'caption'} = $id;
$panel->add_entry({
'type' => $type,
'label_html' => $id,
'link' => $link,
'priority' => 10,
});
$panel->add_entry({
'type' => 'Release',
'label' => $arch_obj->release,
'priority' => 9,
});
$panel->add_entry({
'type' => 'Assembly',
'label' => $arch_obj->assembly,
'priority' => 8,
});
$panel->add_entry({
'type' => 'Database',
'label' => $arch_obj->db_name,
'priority' => 7,
});
return;
}
sub ajax_zmenu_id_history_tree_branch {
# Specific zmenu for idhistory tree branch lines
my $self = shift;
my $panel = $self->_ajax_zmenu;
my $obj = $self->object;
my $old_id = $obj->param('old') || die( "No old id value in params" );
my $new_id = $obj->param('new') || die( "No new id value in params" );
my $db = $obj->param('db') || 'core';
my $db_adaptor = $obj->database($db);
my $arch_adaptor = $db_adaptor->get_ArchiveStableIdAdaptor;
my $old_arch_obj = $arch_adaptor->fetch_by_stable_id_dbname( $old_id, $obj->param('old_db'));
my $new_arch_obj = $arch_adaptor->fetch_by_stable_id_dbname( $new_id, $obj->param('new_db') );
my %types = ( 'Old' => $old_arch_obj, 'New' => $new_arch_obj);
my $priority = 15;
$panel->{'caption'} = 'Similarity Match';
foreach ( sort { $types{$a} <=> $types{$b} } keys %types) {
my $version = $_;
my $object = $types{$_};
my $id = $object->stable_id .".".$object->version;
my $url = $id;
my $link;
unless ($old_arch_obj->release <= $obj->species_defs->EARLIEST_ARCHIVE){ $link = _archive_link($obj, $object); }
$panel->add_entry({
'type' => $version." ".$object->type,
'label_html' => $object->stable_id .".".$object->version,
'link' => $link,
'priority' => $priority,
});
$panel->add_entry({
'type' => $version." ".'Release',
'label' => $object->release,
'priority' => $priority--,
});
$panel->add_entry({
'type' => $version." ".'Assembly',
'label' => $object->assembly,
'priority' => $priority--,
});
$panel->add_entry({
'type' => $version." ".'Database',
'label' => $object->db_name,
'priority' => $priority--,
});
$priority--;
}
my $score = $obj->param('score');
if ($score ==0 ){$score = 'Unknown';}
else { $score = sprintf("%.2f", $score);}
$panel->add_entry({
'type' => 'Score',
'label' => $score,
'priority' => $priority--,
});
return
}
sub ajax_zmenu_id_history_tree_label {
# Specific zmenu for idhistory tree feature labels
my $self = shift;
my $panel = $self->_ajax_zmenu;
my $obj = $self->object;
my $id = $obj->param('label') || die( "No label value in params" );
my $type = ucfirst($obj->param('feat_type'));
my ($action, $p, $url);
if ($type eq 'Gene') {
$p = 'g';
$action = 'Idhistory';
$url = $obj->_url({'type' => $type, 'action' => $action, $p => $id, 't' => undef, 'protein' => undef, 'p' => undef, 'r' => undef });
} elsif ($type eq 'Transcript'){
$p = 't';
$action = 'Idhistory';
$url = $obj->_url({'type' => $type, 'action' => $action, $p => $id, 'protein' => undef, 'p' => undef, 'g' => undef, 'r' => undef });
} else {
$type = 'Transcript';
$p = 'protein';
$action = 'Idhistory/Protein';
$url = $obj->_url({'type' => $type, 'action' => $action, $p => $id, 't' => undef, 'g' => undef, 'r' => undef });
}
#Âmy $url = $obj->_url({'type' => $type, 'action' => $action, $p => $id });
$panel->add_entry({
'label_html' => $id,
'link' => $url,
'priority' => 1,
});
return
}
sub _archive_link {
my ($OBJ, $obj) = @_;
my $type = $obj->type eq 'Translation' ? 'peptide' : lc($obj->type);
my $name = $obj->stable_id . "." . $obj->version;
my $url;
my $current = $OBJ->species_defs->ENSEMBL_VERSION;
my $view = $type."view";
if ($type eq 'peptide') {
$view = 'protview';
} elsif ($type eq 'transcript') {
$view = 'transview';
}
my ($action, $p);
### Set parameters for new style URLs post release 50
if ($obj->release >= 51 ){
if ($type eq 'gene') {
$type = 'Gene';
$p = 'g';
$action = 'Summary';
} elsif ($type eq 'transcript'){
$type = 'Transcript';
$p = 't';
$action = 'Summary';
} else {
$type = 'Transcript';
$p = 'p';
$action = 'ProteinSummary';
}
}
if ($obj->release == $current){
$url = $OBJ->_url({'type' => $type, 'action' => $action, $p => $name });
return $url;
} else {
my $release_info = EnsEMBL::Web::Data::Release->new($obj->release);
my $archive_site = $release_info->archive;
$url = "http://$archive_site.archive.ensembl.org";
if ($obj->release >=51){
$url .= $OBJ->_url({'type' => $type, 'action' => $action, $p => $name });
} else {
$url .= "/".$ENV{'ENSEMBL_SPECIES'};
$url .= "/$view?$type=$name";
}
}
return $url;
}
sub ajax_zmenu_read_coverage {
my $self = shift;
my $panel = shift;
my $obj = $self->object;
return unless $obj->param('disp_level');
$panel->{'caption'} = "Resequencing read coverage: ". $obj->param('disp_level');
$panel->add_entry({
'type' => 'bp:',
'label' => $obj->param('pos'),
'priority' => 12,
});
$panel->add_entry({
'type' => 'Sample:',
'label' => $obj->param('sp'),
'priority' => 8,
});
$panel->add_entry({
'type' => 'Source:',
'label' => "Sanger",
'priority' => 4,
});
return;
}
1;