NAME

       Bio::Graphics::Browser2::DataSource -- DataSource to access data

SYNOPSIS

DESCRIPTION

   METHODS
         $path = $source->userdata(@path_components)

         Returns a path to somewhere in the tmp file system for the
         indicated userdata.

   global_setting()
         $setting = $source->global_setting('option')

       Like code_setting() except that it is only for 'general' options. If the option is not found in the
       datasource config file, then looks in the global file.

   $section_setting = $data_source->section_setting($section_name)
       Returns "open" "closed" or "off" for the named section. Named sections are:

        instructions
        search
        overview
        details
        tracks
        display
        upload_tracks

   add_scale_tracks()
       This is called at initialization time to add track configs for the automatic "scale" (arrow) tracks for
       details, overview and regionview

       $db = $dsn->databases
           Return all named databases from [name:database] tracks.

       ($adaptor,@argv) = $dsn->db2args('databasename')
           Given a database named by ['databasename':database], return its adaptor and arguments.

       ($dbid,$adaptor,@argv) = $dsn->db_settings('track_label')
           Return the adaptor and arguments suitable for the database identified by the given track label. If no
           track label is given then the "general" default database is used.

       $db = $dsn->open_database('track')
           Return the database handle specified by the given track label or 'general' if not given. The
           databases are cached and so it is ok to call repeatedly.

       @ids   = $dsn->db2id($db)
       $dbid  = $dsn->db2id($db)
           Given a database handle, return all dbids that correspond to that database. In a scalar context,
           returns just the first dbid that uses it. It is less confusing to call in a scalar context.

       @ids   = $dsn->dbs
           Return the names of all the sections that define dbs in the datasource: both track sections that
           define dbargs and named database sections. Note that we do not uniquify the case in which the same
           adaptor and dbargs are defined twice in two different sections.

       $dsn->clear_cache
           Empty out our cache of database settings and fetch anew from config file

   generate_image
         ($url,$path) = generate_image($gd);

       Given a GD::Image object, this method calls its png() or gif() methods (depending on GD version), stores
       the output into the temporary "images" subdirectory of the directory given by the "tmp_base" option in
       the configuration file. It returns a two element list consisting of the URL to the image and the physical
       path of the image.

   $source->add_dbid_to_feature($feature,$dbid_hashref)
       This adds a new method called gbrowse_dbid() to a feature. Do not call it if the method is already in the
       feature's class. The hashref should be populated by feature memory locations (overload::StrVal($feature))
       as keys and database symbolic IDs as values.

   @labels = $source->data_source_to_label(@data_sources)
       Search through all stanzas for those with a matching "data source" option. Data sources look like this:

        [stanzaLabel1]
        data source = FlyBase

        [stanzaLabel2]
        data source = FlyBase

       Now searching for $source->data_source_to_label('FlyBase') will return "stanzaLabel1" and "stanzaLabel2"
       along with others that match. A track may have several data sources, separated by spaces.

   @labels = $source->track_source_to_label(@track_sources)
       Search through all stanzas for those with a matching "track source" option. Track sources look like this:

        [stanzaLabel]
        track source = UCSC EBI NCBI

       Now searching for $source->track_source_to_label('UCSC','EBI') will return "stanzaLabel" along with
       others that match. A track may have several space-delimited track sources.

   $boolean = $source->use_inline_imagemap($label=>$length)
       Given a track label and length (for semantic zooming) return true if we should generate an inline
       clickable imagemap vs one in which the actions are generated by Ajax callbacks