NAME

Bio::Graphics::Browser2::Plugin -- Base class for gbrowse plugins.

SYNOPSIS

 package Bio::Graphics::Browser2::Plugin::MyPlugin;
 use Bio::Graphics::Browser2::Plugin;
 use CGI ':standard';
 @ISA = 'Bio::Graphics::Browser2::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 <form> 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;
 }

DESCRIPTION

This is the base class for Generic Genome Browser plugins. Plugins are perl .pm files that are stored in the gbrowse.conf/plugins directory. Plugins are activated in the gbrowse.conf/ configuration file by including them on the list indicated by the "plugins" setting:

 plugins = BatchDumper FastaDumper GFFDumper
	   OligoFinder RestrictionAnnotator

Site-specific plugins may be placed in one or more site-specific directories and added to the plugin search path using the plugin_path setting:

plugin_path = /usr/local/gbrowse_plugins

GBrowse currently recognizes five distinct types of plugins:

1) dumpers: These plugins receive the genomic segment object and generate a dump -- the output can be text, html or some other specialized format. Example: GAME dumper.
2) finders: These plugins accept input from the user and return a list of genomic regions. The main browser displays the found regions and allows the user to select among them. Example: BLAST search.
3) annotators: These plugins receive the genomic segment object and either 1) return a list of features which are overlayed on top of the detailed view (Example: restriction site annotator) or 2) update the database with new or modified features and return nothing (Example: basic editor)
4) trackfilters: These plugins can be used to reduce the complexity of sites that have many tracks, by providing search and filtering functions for the track table. When a trackfilter is active, its form-based user interface is positioned directly above the tracks table, and changes to the for cause the list of tracks to be updated dynamically.
5) highlighters: These plugins will color-highlight features based on user-defined attributes. For example, you could highlight all features that are in the positive strand.
6) filters: These plugins will filter features based on user-defined attributes. Only features that match the attributes will be displayed. For example, you could filter out RNA transcript features based on their size, so that only features that are less than 50 bp in length (e.g. short RNAs) are shown.

All plug-ins inherit from Bio::Graphics::Browser2::Plugin, which defines reasonable (but uninteresting) defaults for each of the methods. Specific behavior is then implemented by selectively overriding certain methods.

The best way to understand how this works is to look at the source code for some working plugins. Examples provided with the gbrowse distribution include:

GFFDumper.pm: A simple dumper which produces GFF format output representing the features of the currently-selected segment.
FastaDumper.pm: A more complex dumper that illustrates how to create and manage persistent user-modifiable settings.
SequenceDumper.pm: Another dumper that shows how plugins interact with the Bio::SeqIO system.
OligoFinder.pm: A finder that searches for short oligos in the entire database. (Only works with Bio::DB::GFF databases.)
RestrictionAnnotator.pm: An annotator that finds restriction sites in the currently selected region of the genome. It creates a new track for each type of restriction site selected.
RandomGene.pm: An example annotator that generates random gene-like structures in the currently displayed region of the genome. It's intended as a template for front-ends to gene prediction programs.
AttributeHiliter.pm: An example feature hiliter that works with Bio::DB::GFF and Bio::SeqFeature::Store databases.
FilterTest.pm: An example feature filter that filters based on strand of the feature.
SimpleTrackFinder.pm: An example track filter that filters tracks based on their name.
SourceTrackFinder.pm: Another example track filter that filters tracks based on the contents of their "track source" and "data source" options.

METHODS

The remainder of this document describes the methods available to the programmer.

INITIALIZATION

The initialization methods establish the human-readable name, description, and basic operating parameters of the plugin. They should be overridden in each plugin you write.

$name = $self->name()

Return a short human-readable name for the plugin. This will be displayed to the user in a menu using one of the following forms:

Dump <name>
Find <name>
Annotate <name>
plugin_defined_verb <name>

$description = $self->description()

This method returns a longer description for the plugin. The text may contain HTML tags, and should describe what the plugin does and who wrote it. This text is displayed when the user presses the "About..." button.

$verb = $self->verb()

This method returns a verb to be used in the plugin popup menu in cases where the main three don't fit. This method should be set return whitespace or an empty string (not undefined) if you do not want a descriptive verb for the menu

$suppress_title = $self->suppress_title()

The purpose of this methods is to suppress the 'Configure...' or 'Find...' title that is printed at the top of the page when the plugin is loaded. It will return false unless overriden by a plugin where this behaviour is desired.

$type = $self->type()

This tells gbrowse what the plugin's type is. It must return one of the scripts "dumper," "finder,", "annotator" as described in the introduction to this documentation. If the method is not overridden, type() will return "dumper."

$self->init()

This method is called before any methods are invoked and allows the plugin to do any run-time initialization it needs. The default is to do nothing. Ordinarily this method does not need to be implemented.

ACCESS TO THE ENVIRONMENT

The following methods give the plugin access to the environment, including the gbrowse page settings, the sequence features database, and the plugin's own configuration settings.

These methods do not generally need to be overridden.

$config = $self->configuration()

Call this method to retrieve the persistent configuration for this plugin. The configuration is a hashref containing the default configuration settings established by config_defaults(), possibly modified by the user. Due to cookie limitations, the values of the hashref must be scalars or array references.

See CONFIGURATION METHODS for instructions on how to create and maintain the plugin's persistent configuration information.

$renderer = $self->renderer

This method returns a copy of the Render object, which provides access to the internal workings of the page layout engine. You will need to troll the Bio::Graphics::Browser2::Render source code to understand how to use this object.

$database = $self->database

This method returns a copy of the default database. Depending on the data source chosen by the gbrowse administrator, this may be a Bio::DB::GFF database, a Bio::DB::Das::Chado database, a Bio::Das database, a Bio::DB::Das::BioSQL database, or any of the other Das-like databases that gbrowse supports.

@dbs = $self->all_databases

This method returns copies of all the databases defined for this data source. Most useful for Finder plugins.

@track_names = $self->selected_tracks

This method returns the list of track names that the user currently has turned on. Track names are the internal names identified in gbrowse configuration file stanzas, for example "ORFs" in the 01.yeast.conf example file.

@feature_types = $self->selected_features

This method returns the list of feature types that the user currently has turned on. Feature types are the feature identifiers indicated by the "feature" setting in each track in the gbrowse configuration file, for example "ORF:sgd" in the 01.yeast.conf [ORFs] track.

$gbrowse_settings = $self->page_settings

This method returns a big hash containing the current gbrowse persistent user settings. These settings are documented in the gbrowse executable source code. You will not ordinarily need to access the contents of this hash, and you should *not* change its values.

$browser_config = $self->browser_config

This method returns a copy of the Bio::Graphics::Browser2::DataSource object that drives gbrowse. This object allows you to interrogate (and change!) the values set in the current gbrowse configuration file.

$value = $self->setting('setting name')

The recommended use for this object is to recover plugin-specific settings from the gbrowse configuration file. These can be defined by the gbrowse administrator by placing the following type of stanza into the gbrowse config file:

[GOSearch:plugin]
traverse_isa = 1
use_server   = http://amigo.geneontology.org

"GOSearch" is the package name of the plugin, and the ":plugin" part of the stanza name tells gbrowse that this is a plugin-private configuration section.

You can now access these settings from within the plugin by using the following idiom:

my $traverse_isa   = $self->setting('traverse_isa');
my $server         = $self->setting('use_server');

This facility is intended to be used for any settings that should not be changed by the end user. Persistent user preferences should be stored in the hash returned by configuration().

If your plugin inherits from another one, then the inheritance path will be searched for settings. For example, if the GOSearch plugin inherits from the OntologySearch plugin, then setting() will search first for a stanza named "GOSearch:plugin" and then for "OntologySearch:plugin".

$search = $self->db_search

This method returns a Bio::Graphics::Browser2::RegionSearch object, which you can use to search all local and remote databases. The interface is this:

$features = $search->search_features(\%args);

where \%args are the various arguments (e.g. -type, -seq_id, -name) passed to the dbadaptors' search_features() method. Alternatively:

$features = $search->search_features('keyword string')

which implements GBrowse's heuristic search.

The result is an array reference of features found.

The search object also has a get_seq_stream() method that accepts the same arguments as search_features() but returns an iterator. The iterator implements a next_seq() method.

$language = $self->language

This method returns the current I18n language file. You can use this to make translations with the tr() method:

print $self->language->tr('WELCOME');

$segments = $self->segments

This method returns the current segments in use by gbrowse. The active segments are set from within gbrowse

$plugin->segments(\@segments);

The active segments can then be retrieved from within the plugin. This is useful in cases where segment-specific information is required by plugin methods that are not passed a segment object.

$config_path = $self->config_path

This method returns the path to the directory in which gbrowse stores its configuration files. This is very useful for storing plugin-specific configuration files. See the sourcecode of RestrictionAnnotator for an exmaple of this.

$feature_file = $self->new_feature_file

This method creates a new Bio::Graphics::FeatureFile for use by annotators. The annotate() method must invoke this method, configure the resulting feature file, and then add one or more Bio::Graphics::Feature objects to it.

This method is equivalent to calling Bio::Graphics::FeatureFile->new(-smart_features=>1), where the -smart_features argument allows features to be turned into imagemap links.

METHODS TO BE IMPLEMENTED IN DUMPERS

All plugins that act as feature dumpers should override one or more of the methods described in this section.

$self->dump($segment)

Given a Bio::Das::SegmentI object, produce some output from its sequence and/or features. This can be used to dump something as simple as a FASTA file, or as complex as a motif analysis performed on the sequence.

As described in Bio::Das::SegmentI, the segment object represents the region of the genome currently on display in the gbrowse "detail" panel. You may call its seq() method to return the sequence as a string, or its features() method to return a list of all features that have been annotated onto this segment of the genome.

At the time that dump() is called, gbrowse will already have set up the HTTP header and performed other initialization. The dump() method merely needs to begin printing output using the appropriate MIME type. By default, the MIME type is text/plain, but this can be changed with the mime_type() method described next.

The following trivial example shows a dump() method that prints the name and length of the segment:

sub dump {
   my $self = shift;
   my $segment = shift;
   print "name   = ",$segment->seq_id,"\n";
   print "length = ",$segment->length,"\n";
}

$type = $self->mime_type

Return the MIME type of the information produced by the plugin. By default, this method returns "text/plain". Override it to return another MIME type, such as "text/xml".

METHODS TO BE IMPLEMENTED IN FINDERS

All finder plugins will need to override one or more of the methods described in this section.

$features = $self->find($segment);

The find() method will be passed a Bio::Das::SegmentI segment object, as described earlier for the dump() method. Your code should search the segment for features of interest, and return a two element list. The first element should be an arrayref of Bio::SeqFeatureI objects (see Bio::SeqFeatureI), or an empty list if nothing was found. These synthetic feature objects should indicate the position, name and type of the features found. The second element of the returned list should be a (possibly shortened) version of the search string for display in informational messages.

Depending on the type of find you are performing, you might search the preexisting features on the segment for matches, or create your own features from scratch in the way that the annotator plugins do. You may choose to ignore the passed segment and perform the search on the entire database, which you can obtain using the database() method call.

To create features from scratch I suggest you use either Bio::Graphics::Feature, or Bio::SeqFeature::Generic to generate the features. See their respective manual pages for details, and the OligoFinder.pm plugin for an example of how to do this.

If the plugin requires user input before it can perform its task, find() should return undef. Gbrowse will invoke configure_form() followed by reconfigure() in order to prompt the user for input. If nothing is found, the plugin should return an empty list. The following is an example of how to prompt the user for input -- in this case, a gene ontology term:

sub find {
   my $self = shift;
   my $segment  = shift;  # we ignore this!
   my $config   = $self->configuration;
   my $query    = $config->{query} or return undef;  # PROMPT FOR INPUT
   my $search   = $self->db_search;
   my @features = $search->features(-attributes=>{GO_Term => $query});
   return (\@features,$query); 
}

sub configure_form {
   my $self = shift;
   return "Enter a GO Term: "
          . textfield(-name=>$self->config_name('query'));
}

sub reconfigure {
   my $self = shift;
   my $config = $self->configuration;
   $config->{query} = $self->config_param('query');
}

See the sections below for more description of the configure_form() and reconfigure() methods.

NOTE: If you need to use auxiliary files like BLAST files, you can store the location of those files in the gbrowse .conf file under the stanza [YourPlugin:plugin]:

[YourPlugin:plugin]
blast_path = /usr/local/blast/databases

sub find {
   my $self = shift;
   my $segment = shift;  # ignored
   my $blast_path = $self->browser_config->plugin_setting('blast_path');
   # etc etc etc  
}

$features = $self->auto_find($search_string)

If the plugin has an "auto_find" method, then the method will be invoked whenever the user types a string into GBrowse's search box. The plugin may search any of the current data source's databases (which you can get using $self->all_databases), or its own databases.

Return an arrayref containing the features found. Return an empty arrayref to indicate that no features were found. Return undef to indicate that the plugin declines to perform the search, in which case GBrowse will default to its own search algorithm.

You may also choose to merge your search results with GBrowse's. To do this, you can initiate the default search by calling:

$default_features 
   = $self->db_search->search_features({-search_term => 'searchterm'})

Then do what you need to do to merge your customized search with the default terms.

METHODS TO BE IMPLEMENTED IN ANNOTATORS

All annotator plugins will need to override the method described in this section.

$feature_file = $plugin->annotate($segment[,$coordinate_mapper])

The annotate() method will be invoked with a Bio::Das::SegmentI segment representing the region of the genome currently on view in the gbrowse detail panel. The method should first call its own new_feature_list() to create a Bio::Graphics::FeatureFile feature set object, and define one or more feature types to added to the feature set. The method should then create one or more Bio::Graphics::Feature objects and add them to the feature set using add_feature.

The reason that annotate() returns a Bio::Graphics::FeatureFile rather than an array of features the way that find() does is because Bio::Graphics::FeatureFile also allows you to set up how the features will be rendered; you can define tracks, assign different feature types to different tracks, and assign each feature type a glyph, color, and other options.

The annotate() function will also be passed a coordinate_mapper variable. This is a code ref to a function that will transform coordinates from relative to absolute coordinates. The function takes a reference sequence name and a list of [$start,$end] coordinate pairs, and returns a similar function result, except that the sequence name and coordinates are all in absolute coordinate space. Currently there are no plugins that make use of this facility.

See Bio::Graphics::FeatureFile for details, and the RestrictionAnnotator.pm plugin for an example.

METHODS TO BE IMPLEMENTED IN TRACKFILTERS

@track_names = $plugin->filter_tracks($tracks,$source)

Given a list of track names and a Bio::Graphics::Browser2::DataSource object, identify the track names to display and return them as a list. The tracks are passed as a reference to a list of all possible track names.

To make the form interactive, you may wish to pepper the plugin's configuration form methods with calls to the javascript routine doPluginUpdate(). This causes GBrowse to update the plugin's configuration and refresh the tracks table as a side effect.

@terms = $plugin->hilite_terms

Returns a list of terms to hilight in the tracks table, or empty if none.

METHODS TO BE IMPLEMENTED IN FEATURE HILITERS

$color = $self->highlight($feature): This method is passed a feature. It returns a color name (or any Bio::Graphics color string) to highlight the feature with that color, or undef if the feature should not be highlighted at all.

METHODS TO BE IMPLEMENTED IN FEATURE FILTERS

($filter,$newkey) = $self->filter($track_label,$key)

This method is passed a track label and the original key of the label. It is expected to return a two-element list consisting of a coderef and a new key for the track. The coderef should be a subroutine that takes a feature as its single argument and returns true to include the feature in the track and false to exclude the feature from the track.

sub {
    my $feature = shift;
    return do_something() ? 1 : 0;
}

The filter() method should return an updated string for the track key to indicate that the track is being filtered. This is to inform the user that the track is not showing all possible features.

The filter() method should return an empty list if it does not wish to install or filter, or to remove a filter that was previously installed.

PERSISTENT CONFIGURATION METHODS

The following methods can be called to retrieve data about the environment in which the plugin is running. These methods are also used by gbrowse to change the plugin state.

$config = $self->config_defaults()

This method will be called once at plugin startup time to give the plugin a chance to set up its default configuration state. If you implement this method you should return the configuration as a hash reference in which the values of the hash are either scalar values or array references. The contents of this hash will be placed in a CGI::Session.

You will wish to implement this method if the plugin has user-modifiable settings.

NOTE ON FILEHANDLES: You are not allowed to permanently store a filehandle in the persistent configuration data structure because the session-handling code will try to serialize and store the filehandle, which is not allowed by the default serializer. If you must store a filehandle in the configuration data structure, be sure to delete it within the annotate(), find() or dump() methods once you are finished using it.

$self->configure_form()

This method will be called when the user presses the "Configure plugin" button. You should return the HTML for a fill-out form that allows the user to change the current settings. The HTML should contain the contents of an HTML <form> section, but not the actual <form> and </form> tags. These tags, along with the Submit and Cancel buttons, will be added automatically. Typically you will build up the HTML to return using a series of .= append operations.

It is highly recommended that you use the CGI module to generate the fill-out form. In order to avoid clashing with other parts of gbrowse, plugin fill-out forms must respect a namespacing convention in which the name of each form field is preceded by the plugin package name and a dot. The package name is the last component of the plugin's package; for example "GoSearch" is the package name for Bio::Graphics::Browser2::Plugin::GoSearch. To represent the "query" field of the plugin named "GOSearch", the text field must be named "GOSearch.query".

To make this easier to do right, the Plugin module provides a method named config_name() which will add the prefix for you. Here is how to use it with the "query" example:

$html .= textfield(-name  => $self->config_name('query'));

$self->reconfigure()

If you implement a configure_form() method, you must also implement a reconfigure() method. This method is called after the user submits the form and should be used to integrate the form values with the current configuration.

Remember that the form fields are namespaced. You may recover them using the CGI param() method by preceding them with the proper prefix. To make this easier to manage, this module provides a config_param() method that manages the namespaces transparently.

Here is a working example:

sub reconfigure {
    my $self = shift;
    my $current_configuration = $self->configuration;
    $current_configuration->{query} = $self->config_param('query');
}

All this does is to retrieve the current configuration by calling the configuration() method. The value of the "query" key is then replaced by a fill-out form parameter named "query", using config_param() instead of the more familiar CGI module's param() function.

AUTHOR

Lincoln Stein <lstein@cshl.org>.

This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text. In addition, please see DISCLAIMER.txt for disclaimers of warranty.

To install CGI::Toggle, copy and paste the appropriate command in to your terminal.

cpanm

cpanm CGI::Toggle

CPAN shell

perl -MCPAN -e shell
install CGI::Toggle

For more information on module installation, please visit the detailed CPAN module installation guide.

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