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.