more progress on the inside side of Render; passes all regression tes…

…ts; work on Render::HTML needs to start

cgi-bin/gbrowse_img.PLS

@@ -45,7 +45,7 @@ print OUT "use lib '$OPTIONS{LIB}';\n" if defined $OPTIONS{LIB};
 # In the following, perl variables are not expanded during extraction.
 
 print OUT <<'!NO!SUBS!';
-# $Id: gbrowse_img.PLS,v 1.30 2005-12-09 22:19:09 mwz444 Exp $
+# $Id: gbrowse_img.PLS,v 1.31 2007-02-14 23:54:39 lstein Exp $
 
 use strict;
 use CGI qw(param redirect header start_html end_html
@@ -269,7 +269,7 @@ elsif ($image_class =~ /SVG/) {
   } else {
     print_cached (
 		  $newpagecache,
-		  header('image/svg-xml'),
+		  header('image/svg+xml'),
 		  $img->svg
 		 );
   }

conf/plugins/TestFinder.pm

@@ -0,0 +1,18 @@
+package Bio::Graphics::Browser::Plugin::TestFinder;
+
+use strict;
+use warnings;
+use base 'Bio::Graphics::Browser::Plugin';
+
+sub name { 'TypeFinder'}
+
+# return all objects of type 'motif'
+sub find {
+  my $self     = shift;
+  my $db       = $self->database;
+  my $query    = $self->page_settings->{name} or return;
+  my @features = $db->features(-type=>$query);
+  return \@features;
+}
+
+1;

lib/Bio/Graphics/Browser/Plugin.pm

@@ -1,5 +1,5 @@
 package Bio::Graphics::Browser::Plugin;
-# $Id: Plugin.pm,v 1.14 2006-08-21 15:36:32 sheldon_mckay Exp $
+# $Id: Plugin.pm,v 1.15 2007-02-14 23:54:39 lstein Exp $
 # base class for plugins for the Generic Genome Browser
 
 =head1 NAME
@@ -382,21 +382,18 @@ described in this section.
 
 =over 4
 
-=item $features = $self->find($segment);
+=item $features = $self->find();
 
-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 an arrayref of
-Bio::SeqFeatureI objects (see L<Bio::SeqFeatureI>).  These synthetic
-feature objects should indicate the position, name and type of the
-features found.
+The find() method is called to search for features of interest. It
+should return an arrayref of Bio::SeqFeatureI objects (see
+L<Bio::SeqFeatureI>).  These synthetic feature objects should indicate
+the position, name and type of the features found.
 
-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.
+Depending on the type of find you are performing, you might search for
+preexisting features on the currently named segment for matches, or
+create your own features from scratch in the way that the annotator
+plugins do.  In most cases you'll do 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
@@ -412,7 +409,6 @@ 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 $database = $self->database;

libnew/Bio/Graphics/Browser.pm

@@ -1,5 +1,5 @@
 package Bio::Graphics::Browser;
-# $Id: Browser.pm,v 1.3 2007-01-05 22:34:04 lstein Exp $
+# $Id: Browser.pm,v 1.4 2007-02-14 23:54:39 lstein Exp $
 # Globals and utilities for GBrowse and friends
 
 use strict;
@@ -137,7 +137,7 @@ sub url_fetch_max_size     { shift->setting(general=>'url_fetch_max_size')     }
 sub session_driver         { shift->setting(general=>'session driver') || 'driver:file;serializer:default' }
 sub session_args    {
   my $self = shift;
-  my %args = shellwords($self->setting(general=>'session_args'));
+  my %args = shellwords($self->setting(general=>'session args'));
   return \%args if %args;
   my ($url,$path) = $self->tmpdir('sessions');
   return {Directory=>$path};
@@ -204,7 +204,7 @@ sub update_data_source {
 }
 
 ## methods for dealing with the session
-sub new_session {
+sub session {
   my $self = shift;
   my $id   = shift;
   return Bio::Graphics::Browser::Session->new($self->session_driver,

libnew/Bio/Graphics/Browser/DataSource.pm

@@ -367,4 +367,16 @@ sub make_link {
   croak "Do not call make_link() on the DataSource. Call it on the Render object";
 }
 
+# this is an aggregator-aware way of retrieving all the named types
+sub _all_types {
+  my $self  = shift;
+  my $db    = shift;
+  return $self->{_all_types} if exists $self->{_all_types}; # memoize
+  my %types = map {$_=>1} (
+			   (map {$_->get_method}        eval {$db->aggregators}),
+			   (map {$self->label2type($_)} $self->labels)
+			   );
+  return $self->{_all_types} = \%types;
+}
+
 1;