SYNOPSIS

DESCRIPTION

METHODS

userdata()

$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.

$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.