Bio::Graphics::Browser2::DataSource -- DataSource to access data
$path = $source->userdata(@path_components)
Returns a path to somewhere in the tmp file system for the
$setting = $source->global_setting('option')
except that it is only for 'general' options. If the
option is not found in the datasource config file, then looks in the global
Returns "open" "closed" or "off" for the named
section. Named sections are:
This is called at initialization time to add track configs for the automatic
"scale" (arrow) tracks for details, overview and regionview
- $db = $dsn->databases
- Return all named databases from [name:database]
- ($adaptor,@argv) = $dsn->db2args('databasename')
- Given a database named by ['databasename':database], return
its adaptor and arguments.
- ($dbid,$adaptor,@argv) =
- 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 = $dsn->dbs
- Return the names of all the sections that define dbs in the
datasource: both track sections that define dbargs and named database
sections. Note that we do not uniquify the case in which the same adaptor
and dbargs are defined twice in two different sections.
- Empty out our cache of database settings and fetch anew
from config file
($url,$path) = generate_image($gd);
Given a GD::Image object, this method calls its png()
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
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.
Search through all stanzas for those with a matching "data source"
option. Data sources look like this:
data source = FlyBase
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.
Search through all stanzas for those with a matching "track source"
option. Track sources look like this:
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.
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