Bio::Graphics::Browser2::RegionSearch

NAME

Bio::Graphics::Browser2::RegionSearch -- Search through multiple databases for feature matches.

SYNOPSIS

  my $dbs = Bio::Graphics::Browser2::RegionSearch->new(
              { source => $data_source, 
                state  => $session_state
              });
  $dbs->init_databases();
  my $features = $dbs->search_features({-search_term=>'sma-3'});

DESCRIPTION

This implements a feature search based on the heuristics in Bio::Graphics::Browser2::Region. The search is distributed across all local and remote databases as specified in the data source.

METHODS

The remainder of this document describes the methods available to the programmer.

$db = Bio::Graphics::Browser2::RegionSearch->new({opts})

Create a new RegionSearch object. Required parameters are:

        Parameter     Description
        source        The Bio::Graphics::Browser2::DataSource
                      object describing the local and remote
                      databases for this source.
        state         The page_settings document describing the
                      current state of the user session (for
                      looking up search_options and the like in the
                      future).

This method will initialize all the databases in preparation for a search. Pass it a list of track labels to search only in the databases defined by those tracks. Otherwise it will sort all tracks into local and remote ones.

$source = source()

Return the data source.

state()

remote_dbs()

local_dbs()

@features = $db->features(@args)

Pass @args to the underlying db adaptors' features() methods and return all matching features. Example:

   @features = $db->features(-type=>'CDS')

$meta_segment = $db->segment($segment)

Given an existing segment, return a Bio::Graphics::Browser2::MetaSegment object, which behaves more or less like a regular Bio::Das::SegmentI object, but searches multiple databases. Both iterative and non-iterative feature fetching is supported.

(The class definitions for Bio::Graphics::Browser2::MetaSegment are located in the Bio/Graphics/Browser/RegionSearch.pm file.)

$segment = $db->feature2segment($feature)

Converts a feature into a segment in the database that the feature corresponds to.

@segments = $db->features2segments($feature)

As above, but takes an arrayref of features and returns an array of segments.

$found = $db->search_features($args)

This method will search all the databases for features matching the search term and will return the results as an array ref of Bio::SeqFeatureI objects. The arguments are a hash ref containing the various options passed to the db adaptors' features() method (e.g. "-type"), or a hashref with the key "-search_term", in which case the search term is parsed as any of gbrowse's heuristic keyword searches.

If no args are provided, then the search term is taken from the "name" field of the settings object.

$found = $db->search_features_locally($args)

Search only the local databases for the term.

$Args is a hashref:

   Key             Value
   ---             -----
   -search_term    term to search for
   -shortcircuit   stop searching if term is found in default db

If -shortcircuit is not provided, it defaults to true.

$found = $db->search_features_remotely($args)

Search only the remote databases for the term.

$db->add_dbid_to_features($db,$features)

Add a gbrowse_dbid() method to each of the features in the list.

$mapper = $search->coordinate_mapper($segment,$optimize)

Create a Bio::Graphics coordinator mapper on the current segment. If optimize set to true, then features that map outside the current segment's seqid and region are nulled.

AUTHOR

Lincoln Stein <[email protected]>.

This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text. In addition, please see DISCLAIMER.txt for disclaimers of warranty.

2022-09-30

perl v5.34.0