Bio::Graphics::Browser::Plugin A base class for gbrowse plugins
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Bio::Graphics::Browser::Plugin Tags

Perl module perl graphics gbrowse plugins gbrowse

Bio::Graphics::Browser::Plugin Description

A base class for gbrowse plugins Bio::Graphics::Browser::Plugin is a Perl module for gbrowse plugins.SYNOPSIS package Bio::Graphics::Browser::Plugin::MyPlugin; use Bio::Graphics::Browser::Plugin; use CGI ':standard'; @ISA = 'Bio::Graphics::Browser::Plugin'; # called by gbrowse to return name of plugin for popup menu sub name { 'Example Plugin' } # called by gbrowse to return the descriptive verb for popup menu sub verb { 'Demonstrate' } # called by gbrowse to return description of plugin sub description { 'This is an example plugin' } # called by gbrowse to return type of plugin sub type { 'annotator' } # called by gbrowse to configure default settings for plugin sub config_defaults { my $self = shift; return {foo => $value1, bar => $value2} } # called by gbrowse to reconfigure plugin settings based on CGI parameters sub reconfigure { my $self = shift; my $current = $self->configuration; $current->{foo} = $self->config_param('foo'); $current->{bar} = $self->config_param('bar'); } # called by gbrowse to create a fragment for changing settings sub configure_form { my $self = shift; my $current = $self->configuration; my $form = textfield(-name => $self->config_name('foo'), -value => $current->{foo}) . textfield(-name => $self->config_name('bar'), -value => $current->{bar}); return $form; } # called by gbrowse to annotate the DNA, returning features sub annotate { my $self = shift; my ($segment,$coordinate_mapper) = @_; my $config = $self->configuration; my $feature_list = $self->new_feature_list; $feature_list->add_type('my_type' => {glyph => 'generic', key => 'my type', bgcolor => 'green', link => 'http://www.google.com/search?q=$name' } ); # do something with the sequence segment my @features = do_something(); $feature_list->add_feature($_ => 'my_type') foreach @features; return $feature_list; }This is the base class for Generic Genome Browser plugins. Plugins are perl .pm files that are stored in the gbrowse.conf/plugins directory. Requirements: · Perl

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