Permalink
Browse files

Minor edits

  • Loading branch information...
Brian O
Brian O committed Mar 23, 2007
1 parent dca8444 commit 095b1f38325e72e3f7d66f0233aaae25bdaec662
Showing with 17 additions and 16 deletions.
  1. +14 −14 docs/pod/PLUGINS_HOWTO.pod
  2. +3 −2 docs/pod/README-berkeley-gadfly.pod
View
@@ -105,7 +105,6 @@ These plugins take filtering options from the user and are converted into
a filter closure. Every feature from the track is passed to this closure.
All features for which a true value is returned by the filter closure show
up in the track.
=back
@@ -153,9 +152,10 @@ template for front-ends to gene prediction programs.
=item FilterTest.pm
An example filter that filters the features from the 'ORFs' track (yeast example database).
The user can pass options to filter the ORFs based on strand or length.
Only those ORFs meeting the passed criteria are displayed.
An example filter that filters the features from the 'ORFs' track
(yeast example database). The user can pass options to filter
the ORFs based on strand or length. Only those ORFs meeting the
passed criteria are displayed.
=back
@@ -277,9 +277,9 @@ configuration section.
You can now access these settings from within the plugin by using
the following idiom:
my $browser_config = $self->browser_config;
my $traverse_isa = $browser_config->plugin_setting('traverse_isa');
my $server = $browser_config->plugin_setting('use_server');
my $browser_config = $self->browser_config;
my $traverse_isa = $browser_config->plugin_setting('traverse_isa');
my $server = $browser_config->plugin_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
@@ -530,7 +530,7 @@ 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'));
$html .= textfield(-name => $self->config_name('query'));
=item $self->reconfigure()
@@ -546,11 +546,11 @@ 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');
}
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
@@ -562,7 +562,7 @@ function.
=head1 SEE ALSO
the Bio::Graphics::Browser manpage
The Bio::Graphics::Browser manpage.
=head1 AUTHOR
@@ -11,5 +11,6 @@ We hope to eventually merge the branches, and use an adapter bridge to
transparently connect to GadFly. The gadfly adaptor located in the
lib directory is incomplete and nonfunctional.
Questions -
Chris Mungall <cjm@fruitfly.org>
=head1 Questions
Chris Mungall <cjm@fruitfly.org> or the gmod-gbrowse mailing list.

0 comments on commit 095b1f3

Please sign in to comment.