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.\" ========================================================================
.\"
.IX Title "Bio::DB::Tagger 3pm"
.TH Bio::DB::Tagger 3pm "2018-10-03" "perl v5.26.2" "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::DB::Tagger \-\- Simple object tagging system
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\& use Bio::DB::Tagger;
\& my $tagger = Bio::DB::Tagger\->new(\-dsn    => \*(Aqdbi:mysql:tagdb\*(Aq,
\&                                   \-create => 1);
\&
\& $tagger\->add_tags(\-object => $object_name,
\&                   \-tags   => \e@tags);
\&
\& $tagger\->set_tags(\-object => $object_name,
\&                   \-key    => $object_key,
\&                   \-tags   => \e@tags);
\&
\& $tagger\->add_tag(\-object  => $object_name,
\&                  \-tag     => \*(Aqvenue\*(Aq,
\&                  \-value   => \*(Aqmermaid parade\*(Aq,
\&                  \-author  => \*(Aqlincoln.stein@gmail.com\*(Aq);
\&
\& $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 = $tags[0]\en";              # Tag stringify interface
\& print "tag value = ",$tags[0]\->value,"\en";   # object interface
\& print "tag author= ",$tags[0]\->author,"\en";  # 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(\*(Aqprefix\*(Aq);
\& while (my $tag = $iterator\->next_tag) { }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a simple object tagger interface that provides relational
support for tagging objects (identified by string IDs) with arbitrary
string tags.
.SS "\s-1METHODS\s0"
.IX Subsection "METHODS"
.ie n .IP "$tagger = Bio::DB::Tagger\->new(@args)" 4
.el .IP "\f(CW$tagger\fR = Bio::DB::Tagger\->new(@args)" 4
.IX Item "$tagger = Bio::DB::Tagger->new(@args)"
Constructor for the tagger class. Arguments are:
.Sp
.Vb 2
\&  \-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.
.Ve
.Sp
The dsn can be a preopened database handle or a dbi: data source
string.
.ie n .IP "@objects = $tagger\->search_tag($tag [,$value])" 4
.el .IP "\f(CW@objects\fR = \f(CW$tagger\fR\->search_tag($tag [,$value])" 4
.IX Item "@objects = $tagger->search_tag($tag [,$value])"
.PD 0
.ie n .IP "$object_arrayref = $tagger\->search_tag($tag [,$value])" 4
.el .IP "\f(CW$object_arrayref\fR = \f(CW$tagger\fR\->search_tag($tag [,$value])" 4
.IX Item "$object_arrayref = $tagger->search_tag($tag [,$value])"
.PD
Return all object names and keys that are tagged with \*(L"$tag\*(R",
optionally qualified by tag value \f(CW$value\fR.
.ie n .IP "$boolean = $tagger\->has_tag($object,$tag [,$value])" 4
.el .IP "\f(CW$boolean\fR = \f(CW$tagger\fR\->has_tag($object,$tag [,$value])" 4
.IX Item "$boolean = $tagger->has_tag($object,$tag [,$value])"
Returns true if indicated object has the indicated tag, or the
indicated combination of tag and value.
.ie n .IP "@tags = $tagger\->get_tag($object,$tag)" 4
.el .IP "\f(CW@tags\fR = \f(CW$tagger\fR\->get_tag($object,$tag)" 4
.IX Item "@tags = $tagger->get_tag($object,$tag)"
Returns all the tags of type \f(CW$tag\fR.
.ie n .IP "$tags = $tagger\->\fItags()\fR" 4
.el .IP "\f(CW$tags\fR = \f(CW$tagger\fR\->\fItags()\fR" 4
.IX Item "$tags = $tagger->tags()"
.PD 0
.ie n .IP "@tags = $tagger\->\fItags()\fR" 4
.el .IP "\f(CW@tags\fR = \f(CW$tagger\fR\->\fItags()\fR" 4
.IX Item "@tags = $tagger->tags()"
.PD
Return a list of all tags in the database. In a list context, returns
the list of tags. In an array context, returns an array ref.
.ie n .IP "$iterator = $tagger\->tag_match('prefix')" 4
.el .IP "\f(CW$iterator\fR = \f(CW$tagger\fR\->tag_match('prefix')" 4
.IX Item "$iterator = $tagger->tag_match('prefix')"
Returns an iterator that matches all tags beginning with 'prefix'
(case insensitive). Call \f(CW$iterator\fR\->\fInext_tag()\fR to get the next match.
.ie n .IP "$iterator = $tagger\->tag_match('prefix')" 4
.el .IP "\f(CW$iterator\fR = \f(CW$tagger\fR\->tag_match('prefix')" 4
.IX Item "$iterator = $tagger->tag_match('prefix')"
Returns an iterator that matches all tags beginning with 'prefix'
(case insensitive). Call \f(CW$iterator\fR\->\fInext_tag()\fR to get the next match.
.ie n .IP "$tags = $tagger\->\fItag_counts()\fR" 4
.el .IP "\f(CW$tags\fR = \f(CW$tagger\fR\->\fItag_counts()\fR" 4
.IX Item "$tags = $tagger->tag_counts()"
.PD 0
.ie n .IP "@tags = $tagger\->\fItag_counts()\fR" 4
.el .IP "\f(CW@tags\fR = \f(CW$tagger\fR\->\fItag_counts()\fR" 4
.IX Item "@tags = $tagger->tag_counts()"
.PD
Return a set of Bio::DB::Tagger::Tag objects representing all known
tags. The tag values correspond to the number of times that tag has
been used to tag objects.
.ie n .IP "$result = $tagger\->add_tag(@args);" 4
.el .IP "\f(CW$result\fR = \f(CW$tagger\fR\->add_tag(@args);" 4
.IX Item "$result = $tagger->add_tag(@args);"
Add a tag to the database. The following forms are accepted:
.Sp
.Vb 1
\& $tagger\->add_tag($object_name=>$tag);
.Ve
.Sp
Add a Bio::DB::Tagger::Tag to the object named \*(L"$object_name\*(R".
.Sp
.Vb 2
\& $tagger\->add_tag(\-object => $object_name,
\&                  \-tag    => $tag);
.Ve
.Sp
The same as above using \-option syntax.
.Sp
.Vb 4
\& $tagger\->add_tag(\-object => $object_name,
\&                  \-tag    => $tagname,
\&                  \-value  => $tagvalue,
\&                  \-author => $authorname);
.Ve
.Sp
Generate the tag from the options provided in \fB\-tag\fR, \fB\-value\fR
(optional) and \fB\-author\fR (optional), and then add the tag to the
object.
.Sp
Returns true on success.
.ie n .IP "$result = $tagger\->set_tags(@args);" 4
.el .IP "\f(CW$result\fR = \f(CW$tagger\fR\->set_tags(@args);" 4
.IX Item "$result = $tagger->set_tags(@args);"
Set the tags of an object, replacing all previous tags.
.Sp
Arguments: \fB\-object\fR  Name of the object to tag.
           \fB\-tags\fR    List of Bio::DB::Tagger::Tag objects
.Sp
Returns true on success.
.ie n .IP "$result = $tagger\->set_tag(@args);" 4
.el .IP "\f(CW$result\fR = \f(CW$tagger\fR\->set_tag(@args);" 4
.IX Item "$result = $tagger->set_tag(@args);"
Set a tag, replacing all previous tags of the same name.
.Sp
Arguments: \fB\-object\fR  Name of the object to tag.
           \fB\-tag\fR     A Bio::DB::Tagger::Tag object, or tag name
.Sp
Returns true on success.
.ie n .IP "$result = $tagger\->clear_tags($objectname);" 4
.el .IP "\f(CW$result\fR = \f(CW$tagger\fR\->clear_tags($objectname);" 4
.IX Item "$result = $tagger->clear_tags($objectname);"
Clear all tags from the indicated object. Returns true if the
operation was successful.
.ie n .IP "$result = $tagger\->delete_tag($objectname,$tagname [,$tagvalue]);" 4
.el .IP "\f(CW$result\fR = \f(CW$tagger\fR\->delete_tag($objectname,$tagname [,$tagvalue]);" 4
.IX Item "$result = $tagger->delete_tag($objectname,$tagname [,$tagvalue]);"
Clear the one tag from the indicated object, filtering by tagname,
optionally by value.
.ie n .IP "$result = $tagger\->nuke_object($objectname);" 4
.el .IP "\f(CW$result\fR = \f(CW$tagger\fR\->nuke_object($objectname);" 4
.IX Item "$result = $tagger->nuke_object($objectname);"
Removes the object named \f(CW$objectname\fR. Returns true if the operation
was successful.
.ie n .IP "$result = $tagger\->nuke_author($authorname);" 4
.el .IP "\f(CW$result\fR = \f(CW$tagger\fR\->nuke_author($authorname);" 4
.IX Item "$result = $tagger->nuke_author($authorname);"
Removes the author named \f(CW$authorname\fR. Returns true if the operation
was successful.
.ie n .IP "$result = $tagger\->nuke_tag($tagname);" 4
.el .IP "\f(CW$result\fR = \f(CW$tagger\fR\->nuke_tag($tagname);" 4
.IX Item "$result = $tagger->nuke_tag($tagname);"
Removes the tag named \f(CW$tagname\fR. Returns true if the operation was
successful.
.ie n .IP "@tags = $tagger\->get_tags($object_name [,$author])" 4
.el .IP "\f(CW@tags\fR = \f(CW$tagger\fR\->get_tags($object_name [,$author])" 4
.IX Item "@tags = $tagger->get_tags($object_name [,$author])"
Return all tags assigned to the indicated object, optionally
filtering by the author.
.ie n .IP "$oid = $tagger\->object_to_id($objectname [,$create] [,$key])" 4
.el .IP "\f(CW$oid\fR = \f(CW$tagger\fR\->object_to_id($objectname [,$create] [,$key])" 4
.IX Item "$oid = $tagger->object_to_id($objectname [,$create] [,$key])"
Fetch the object id (oid) of the object named \*(L"$objectname\*(R". If the
object doesn't exist, and \f(CW$create\fR is true, will create a new entry for
the object in the database.
.ie n .IP "$tid = $tagger\->tag_to_id($tagname [,$create])" 4
.el .IP "\f(CW$tid\fR = \f(CW$tagger\fR\->tag_to_id($tagname [,$create])" 4
.IX Item "$tid = $tagger->tag_to_id($tagname [,$create])"
Fetch the tag id (tid) of the object named \*(L"$tagname\*(R". If the tag
doesn't exist, and \f(CW$create\fR is true, will create a new entry for the
tag in the database.
.ie n .IP "$aid = $tagger\->author_to_id($authorname [,$create])" 4
.el .IP "\f(CW$aid\fR = \f(CW$tagger\fR\->author_to_id($authorname [,$create])" 4
.IX Item "$aid = $tagger->author_to_id($authorname [,$create])"
Fetch the author id (aid) of the object named \*(L"$authorname\*(R". If the
tag doesn't exist, and \f(CW$create\fR is true, will create a new entry for
the author in the database.
.ie n .IP "$dbh = $tagger\->dbh" 4
.el .IP "\f(CW$dbh\fR = \f(CW$tagger\fR\->dbh" 4
.IX Item "$dbh = $tagger->dbh"
Return underlying \s-1DBI\s0 handle.
.ie n .IP "$tagger\->initialize" 4
.el .IP "\f(CW$tagger\fR\->initialize" 4
.IX Item "$tagger->initialize"
Initialize the database with a fresh schema.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::Graphics::Browser, Bio::DB::SeqFeature::Store
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln Stein <lincoln.stein@gmail.com>.
.PP
Copyright (c) 2009 Ontario Institute for Cancer Research
.PP
This package and its accompanying libraries is free software; you can
redistribute it and/or modify it under the terms of the \s-1GPL\s0 (either
version 1, or at your option, any later version) or the Artistic
License 2.0.  Refer to \s-1LICENSE\s0 for the full license text. In addition,
please see \s-1DISCLAIMER\s0.txt for disclaimers of warranty.