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.\" ========================================================================
.\"
.IX Title "Bio::Graphics::Browser2::DataSource 3pm"
.TH Bio::Graphics::Browser2::DataSource 3pm "2023-12-07" "perl v5.36.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Graphics::Browser2::DataSource \-\- DataSource to access data
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
.SS "\s-1METHODS\s0"
.IX Subsection "METHODS"
.Vb 1
\&  $path = $source\->userdata(@path_components)
\&
\&  Returns a path to somewhere in the tmp file system for the 
\&  indicated userdata.
.Ve
.SS "\fBglobal_setting()\fP"
.IX Subsection "global_setting()"
.Vb 1
\&  $setting = $source\->global_setting(\*(Aqoption\*(Aq)
.Ve
.PP
Like \fBcode_setting()\fR except that it is only for 'general' options. If the
option is not found in the datasource config file, then looks in the
global file.
.ie n .SS "$section_setting = $data_source\->section_setting($section_name)"
.el .SS "\f(CW$section_setting\fP = \f(CW$data_source\fP\->section_setting($section_name)"
.IX Subsection "$section_setting = $data_source->section_setting($section_name)"
Returns \*(L"open\*(R" \*(L"closed\*(R" or \*(L"off\*(R" for the named section. Named sections are:
.PP
.Vb 7
\& instructions
\& search
\& overview
\& details
\& tracks
\& display
\& upload_tracks
.Ve
.SS "\fBadd_scale_tracks()\fP"
.IX Subsection "add_scale_tracks()"
This is called at initialization time to add track configs
for the automatic \*(L"scale\*(R" (arrow) tracks for details, overview and regionview
.ie n .IP "$db = $dsn\->databases" 4
.el .IP "\f(CW$db\fR = \f(CW$dsn\fR\->databases" 4
.IX Item "$db = $dsn->databases"
Return all named databases from [name:database] tracks.
.ie n .IP "($adaptor,@argv) = $dsn\->db2args('databasename')" 4
.el .IP "($adaptor,@argv) = \f(CW$dsn\fR\->db2args('databasename')" 4
.IX Item "($adaptor,@argv) = $dsn->db2args('databasename')"
Given a database named by ['databasename':database], return its
adaptor and arguments.
.ie n .IP "($dbid,$adaptor,@argv) = $dsn\->db_settings('track_label')" 4
.el .IP "($dbid,$adaptor,@argv) = \f(CW$dsn\fR\->db_settings('track_label')" 4
.IX Item "($dbid,$adaptor,@argv) = $dsn->db_settings('track_label')"
Return the adaptor and arguments suitable for the database identified
by the given track label. If no track label is given then the
\&\*(L"general\*(R" default database is used.
.ie n .IP "$db = $dsn\->open_database('track')" 4
.el .IP "\f(CW$db\fR = \f(CW$dsn\fR\->open_database('track')" 4
.IX Item "$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.
.ie n .IP "@ids   = $dsn\->db2id($db)" 4
.el .IP "\f(CW@ids\fR   = \f(CW$dsn\fR\->db2id($db)" 4
.IX Item "@ids = $dsn->db2id($db)"
.PD 0
.ie n .IP "$dbid  = $dsn\->db2id($db)" 4
.el .IP "\f(CW$dbid\fR  = \f(CW$dsn\fR\->db2id($db)" 4
.IX Item "$dbid = $dsn->db2id($db)"
.PD
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.
.ie n .IP "@ids   = $dsn\->dbs" 4
.el .IP "\f(CW@ids\fR   = \f(CW$dsn\fR\->dbs" 4
.IX Item "@ids = $dsn->dbs"
Return the names of all the sections that define dbs in the datasource: both track sections
that define dbargs and named database sections. Note that we do not
uniquify the case in which the same adaptor and dbargs are defined twice in two different
sections.
.ie n .IP "$dsn\->clear_cache" 4
.el .IP "\f(CW$dsn\fR\->clear_cache" 4
.IX Item "$dsn->clear_cache"
Empty out our cache of database settings and fetch anew from config file
.SS "generate_image"
.IX Subsection "generate_image"
.Vb 1
\&  ($url,$path) = generate_image($gd);
.Ve
.PP
Given a GD::Image object, this method calls its \fBpng()\fR or \fBgif()\fR methods
(depending on \s-1GD\s0 version), stores the output into the temporary
\&\*(L"images\*(R" subdirectory of the directory given by the \*(L"tmp_base\*(R" option
in the configuration file. It returns a two element list consisting of
the \s-1URL\s0 to the image and the physical path of the image.
.ie n .SS "$source\->add_dbid_to_feature($feature,$dbid_hashref)"
.el .SS "\f(CW$source\fP\->add_dbid_to_feature($feature,$dbid_hashref)"
.IX Subsection "$source->add_dbid_to_feature($feature,$dbid_hashref)"
This adds a new method called \fBgbrowse_dbid()\fR 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.
.ie n .SS "@labels = $source\->data_source_to_label(@data_sources)"
.el .SS "\f(CW@labels\fP = \f(CW$source\fP\->data_source_to_label(@data_sources)"
.IX Subsection "@labels = $source->data_source_to_label(@data_sources)"
Search through all stanzas for those with a matching \*(L"data source\*(R"
option. Data sources look like this:
.PP
.Vb 2
\& [stanzaLabel1]
\& data source = FlyBase
\&
\& [stanzaLabel2]
\& data source = FlyBase
.Ve
.PP
Now searching for \f(CW$source\fR\->data_source_to_label('FlyBase') will return
\&\*(L"stanzaLabel1\*(R" and \*(L"stanzaLabel2\*(R" along with others that match. A
track may have several data sources, separated by spaces.
.ie n .SS "@labels = $source\->track_source_to_label(@track_sources)"
.el .SS "\f(CW@labels\fP = \f(CW$source\fP\->track_source_to_label(@track_sources)"
.IX Subsection "@labels = $source->track_source_to_label(@track_sources)"
Search through all stanzas for those with a matching \*(L"track source\*(R"
option. Track sources look like this:
.PP
.Vb 2
\& [stanzaLabel]
\& track source = UCSC EBI NCBI
.Ve
.PP
Now searching for \f(CW$source\fR\->track_source_to_label('\s-1UCSC\s0','\s-1EBI\s0') will
return \*(L"stanzaLabel\*(R" along with others that match. A track may have
several space-delimited track sources.
.ie n .SS "$boolean = $source\->use_inline_imagemap($label=>$length)"
.el .SS "\f(CW$boolean\fP = \f(CW$source\fP\->use_inline_imagemap($label=>$length)"
.IX Subsection "$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