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/ Bio::DB::Tagger

NAME

Bio::DB::Tagger -- Simple object tagging system

SYNOPSIS

use Bio::DB::Tagger;
my $tagger = Bio::DB::Tagger->new(-dsn    => 'dbi:mysql:tagdb',
                                  -create => 1);

$tagger->add_tags(-object => $object_name,
                  -tags   => \@tags);

$tagger->set_tags(-object => $object_name,
                  -key    => $object_key,
                  -tags   => \@tags);

$tagger->add_tag(-object  => $object_name,
                 -tag     => 'venue',
                 -value   => 'mermaid parade',
                 -author  => 'lincoln.stein@gmail.com');

$tagger->add_tag(-object  => $object_name,
                 -tag     => $tag);

$tagger->add_tag($object_name => $tag);

$tagger->clear_tags($object_name);                      # delete all tags attached to object
$tagger->delete_tag($object_name,$tag_name [,$value]);  # delete one tag attached to object

$tagger->nuke_tag($tag_name);                           # delete this tag completely
$tagger->nuke_object($object_name);
$tagger->nuke_author($author_name);

my @tags  = $tagger->get_tags($object_name [,$author]);
print "first tag = $tags[0]\n";              # Tag stringify interface
print "tag value = ",$tags[0]->value,"\n";   # object interface
print "tag author= ",$tags[0]->author,"\n";  # object interface

my $hasit    = $tagger->has_tag($object_name,$tag);

my @objects  = $tagger->search_tag($tag);

my @tags  = $tagger->tags;

my $iterator = $tagger->tag_match('prefix');
while (my $tag = $iterator->next_tag) { }

DESCRIPTION

This is a simple object tagger interface that provides relational support for tagging objects (identified by string IDs) with arbitrary string tags.

METHODS

$tagger = Bio::DB::Tagger->new(@args)

Constructor for the tagger class. Arguments are:

-dsn    <dsn>    A DBI data source, possibly including host and
                  password information

-create <0|1>    If true, then database will be initialized with a
                  new schema. Database must already exist.

The dsn can be a preopened database handle or a dbi: data source string.

@objects = $tagger->search_tag($tag [,$value])
$object_arrayref = $tagger->search_tag($tag [,$value])

Return all object names and keys that are tagged with "$tag", optionally qualified by tag value $value.

$boolean = $tagger->has_tag($object,$tag [,$value])

Returns true if indicated object has the indicated tag, or the indicated combination of tag and value.

@tags = $tagger->get_tag($object,$tag)

Returns all the tags of type $tag.

$tags = $tagger->tags()
@tags = $tagger->tags()

Return a list of all tags in the database. In a list context, returns the list of tags. In an array context, returns an array ref.

$iterator = $tagger->tag_match('prefix')

Returns an iterator that matches all tags beginning with 'prefix' (case insensitive). Call $iterator->next_tag() to get the next match.

$iterator = $tagger->tag_match('prefix')

Returns an iterator that matches all tags beginning with 'prefix' (case insensitive). Call $iterator->next_tag() to get the next match.

$tags = $tagger->tag_counts()
@tags = $tagger->tag_counts()

Return a set of Bio::DB::Tagger::Tag objects representing all known tags. The tag values correspond to the number of times that tag has been used to tag objects.

$result = $tagger->add_tag(@args);

Add a tag to the database. The following forms are accepted:

$tagger->add_tag($object_name=>$tag);

Add a Bio::DB::Tagger::Tag to the object named "$object_name".

$tagger->add_tag(-object => $object_name,
                 -tag    => $tag);

The same as above using -option syntax.

$tagger->add_tag(-object => $object_name,
                 -tag    => $tagname,
                 -value  => $tagvalue,
                 -author => $authorname);

Generate the tag from the options provided in -tag, -value (optional) and -author (optional), and then add the tag to the object.

Returns true on success.

$result = $tagger->set_tags(@args);

Set the tags of an object, replacing all previous tags.

Arguments: -object Name of the object to tag. -tags List of Bio::DB::Tagger::Tag objects

Returns true on success.

$result = $tagger->set_tag(@args);

Set a tag, replacing all previous tags of the same name.

Arguments: -object Name of the object to tag. -tag A Bio::DB::Tagger::Tag object, or tag name

Returns true on success.

$result = $tagger->clear_tags($objectname);

Clear all tags from the indicated object. Returns true if the operation was successful.

$result = $tagger->delete_tag($objectname,$tagname [,$tagvalue]);

Clear the one tag from the indicated object, filtering by tagname, optionally by value.

$result = $tagger->nuke_object($objectname);

Removes the object named $objectname. Returns true if the operation was successful.

$result = $tagger->nuke_author($authorname);

Removes the author named $authorname. Returns true if the operation was successful.

$result = $tagger->nuke_tag($tagname);

Removes the tag named $tagname. Returns true if the operation was successful.

@tags = $tagger->get_tags($object_name [,$author])

Return all tags assigned to the indicated object, optionally filtering by the author.

$oid = $tagger->object_to_id($objectname [,$create] [,$key])

Fetch the object id (oid) of the object named "$objectname". If the object doesn't exist, and $create is true, will create a new entry for the object in the database.

$tid = $tagger->tag_to_id($tagname [,$create])

Fetch the tag id (tid) of the object named "$tagname". If the tag doesn't exist, and $create is true, will create a new entry for the tag in the database.

$aid = $tagger->author_to_id($authorname [,$create])

Fetch the author id (aid) of the object named "$authorname". If the tag doesn't exist, and $create is true, will create a new entry for the author in the database.

$dbh = $tagger->dbh

Return underlying DBI handle.

$tagger->initialize

Initialize the database with a fresh schema.

SEE ALSO

Bio::Graphics::Browser, Bio::DB::SeqFeature::Store

AUTHOR

Lincoln Stein <lincoln.stein@gmail.com>.

Copyright (c) 2009 Ontario Institute for Cancer Research

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.