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added track filtering functionality as well as ability to select trac…
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,99 @@ | ||
| package Bio::Graphics::Browser::Plugin::SimpleTrackFinder; | ||
| # $Id: SimpleTrackFinder.pm,v 1.1 2009-05-20 20:36:20 lstein Exp $ | ||
| use strict; | ||
| use CGI qw(:standard *table); | ||
| use base 'Bio::Graphics::Browser::Plugin'; | ||
| our $VERSION = '0.25'; | ||
|
|
||
| sub name { "Simple Track Finder" } | ||
|
|
||
| sub description { | ||
| return p("The simple track finder filters the track table by the name of the track."); | ||
| } | ||
|
|
||
| sub type { 'trackfilter' } | ||
|
|
||
| sub init { } | ||
|
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||
| sub config_defaults { | ||
| my $self = shift; | ||
| return { | ||
| track_name => undef, | ||
| }; | ||
| } | ||
|
|
||
| sub reconfigure { | ||
| my $self = shift; | ||
| my $current_config = $self->configuration; | ||
| $current_config->{track_name} = $self->config_param('track_name'); | ||
| } | ||
|
|
||
| sub configure_form { | ||
| my $self = shift; | ||
| my $current_config = $self->configuration; | ||
| my $name = $current_config->{track_name}; | ||
| return | ||
| b('Partial or full track name:'). | ||
| textfield(-id => 'track_name_filter', | ||
| -name => $self->config_name('track_name'), | ||
| -default => $name, | ||
| -override => 1, | ||
| -onKeyDown=>'if (event.keyCode==13) doPluginUpdate()', | ||
| ). | ||
| button(-value => 'Clear', | ||
| -onClick => "\$('track_name_filter').clear(); doPluginUpdate()"); | ||
| } | ||
|
|
||
| sub filter_tracks { | ||
| my $self = shift; | ||
| my $tracks = shift; | ||
| my $source = shift; | ||
|
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||
| my $config = $self->configuration; | ||
| my $name = $config->{track_name} or return @$tracks; | ||
|
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| my @filtered = grep { | ||
| my $key = $source->setting($_=>'key') || $_; | ||
| $key =~ m/$name/i | ||
| } @$tracks; | ||
| warn "name = $name, filtered = @filtered"; | ||
| return @filtered; | ||
| } | ||
|
|
||
| 1; | ||
|
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||
| __END__ | ||
| =head1 NAME | ||
| Bio::Graphics::Browser::Plugin::SimpleTrackFinder - Limit list of tracks to those that match a name pattern | ||
| =head1 SYNOPSIS | ||
| In the appropriate gbrowse configuration file: | ||
| track filter = SimpleTrackFinder | ||
| =head1 DESCRIPTION | ||
| =head1 OPTIONS | ||
| =head1 BUGS | ||
| None known yet. | ||
| =head1 SEE ALSO | ||
| L<Bio::Graphics::Browser::Plugin> | ||
| =head1 AUTHOR | ||
| Lincoln Stein E<lt>lincoln.stein@gmail.comE<gt>. | ||
| Copyright (c) 2009 Ontario Institute for Cancer Research | ||
| This library is free software; you can redistribute it and/or modify | ||
| it under the same terms as Perl itself. | ||
| =cut |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,136 @@ | ||
| package Bio::Graphics::Browser::Plugin::SourceTrackFinder; | ||
| # $Id: SourceTrackFinder.pm,v 1.1 2009-05-20 20:36:20 lstein Exp $ | ||
| use strict; | ||
| use CGI qw(:standard *table); | ||
| use base 'Bio::Graphics::Browser::Plugin'; | ||
| use Bio::Graphics::Browser::Util 'shellwords'; | ||
| our $VERSION = '0.25'; | ||
|
|
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| sub name { "Source Track Finder" } | ||
|
|
||
| sub description { | ||
| return p("The source track finder filters the track table by the data and config source the track."); | ||
| } | ||
|
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| sub type { 'trackfilter' } | ||
|
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| sub init { } | ||
|
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| sub config_defaults { | ||
| my $self = shift; | ||
|
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| # this line gets all the options defined in the "[SourceTrackFinder:plugin]" stanza | ||
| my %fields = map {$_=>undef} $self->get_fields; | ||
|
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| return \%fields; | ||
| } | ||
|
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|
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| # this method gets all the options defined in the "[SourceTrackFinder:plugin]" stanza | ||
| sub get_fields { | ||
| my $self = shift; | ||
| return $self->browser_config->plugin_setting; | ||
| } | ||
|
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| sub reconfigure { | ||
| my $self = shift; | ||
| my $current_config = $self->configuration; | ||
|
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| for my $f ($self->get_fields) { | ||
| $current_config->{lc $f} = $self->config_param($f); | ||
| } | ||
| } | ||
|
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||
| sub configure_form { | ||
| my $self = shift; | ||
| my $current_config = $self->configuration; | ||
| my $source = $self->browser_config; | ||
|
|
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| my @fields = $self->get_fields; | ||
| my @elements; | ||
|
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| for my $f (@fields) { | ||
| my @options = ('',shellwords($source->plugin_setting($f))); | ||
| push @elements,b(ucfirst $f.':'); | ||
| push @elements, | ||
| popup_menu( | ||
| -id => "plugin_$f", | ||
| -class => "SourceTrackFinderPopup", | ||
| -name => $self->config_name($f), | ||
| -values => \@options, | ||
| -default => $current_config->{$f}, | ||
| -override => 1, | ||
| -onChange => 'doPluginUpdate()', | ||
| ) | ||
| } | ||
| push @elements, | ||
| button(-value => 'Clear', | ||
| -onClick => q($$('.SourceTrackFinderPopup').each(function(m) {m.selectedIndex=0}); doPluginUpdate();) | ||
| ); | ||
| return join ' ',@elements; | ||
|
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|
|
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| } | ||
|
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| sub filter_tracks { | ||
| my $self = shift; | ||
| my $track_labels = shift; | ||
| my $source = shift; | ||
|
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| my $config = $self->configuration; | ||
| my @fields = $self->get_fields; | ||
| my %filters = map {lc $_ => $config->{lc $_}} @fields; | ||
|
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| my @result; | ||
|
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| LABEL: | ||
| for my $l (@$track_labels) { | ||
| do {push @result,$l; next LABEL} if $l =~ /^(plugin|file|http|das)/; | ||
|
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| for my $f (keys %filters) { | ||
| my %values = map {lc $_=>1} shellwords $source->fallback_setting($l=>$f); | ||
| next LABEL if length $filters{$f} && !$values{lc $filters{$f}}; | ||
| } | ||
|
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| push @result,$l; | ||
| } | ||
| return @result; | ||
| } | ||
|
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| 1; | ||
|
|
||
| __END__ | ||
| =head1 NAME | ||
| Bio::Graphics::Browser::Plugin::SimpleTrackFinder - Limit list of tracks to those that match a name pattern | ||
| =head1 SYNOPSIS | ||
| In the appropriate gbrowse configuration file: | ||
| track filter = SimpleTrackFinder | ||
| =head1 DESCRIPTION | ||
| =head1 OPTIONS | ||
| =head1 BUGS | ||
| None known yet. | ||
| =head1 SEE ALSO | ||
| L<Bio::Graphics::Browser::Plugin> | ||
| =head1 AUTHOR | ||
| Lincoln Stein E<lt>lincoln.stein@gmail.comE<gt>. | ||
| Copyright (c) 2009 Ontario Institute for Cancer Research | ||
| This library is free software; you can redistribute it and/or modify | ||
| it under the same terms as Perl itself. | ||
| =cut |
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