Raw content of Bio::Ontology::InterProTerm
<![CDATA[# $Id: InterProTerm.pm,v 1.4.2.2 2003/03/25 12:32:16 heikki Exp $
#
# BioPerl module for Bio::Ontology::InterProTerm
#
# Cared for by Peter Dimitrov <dimitrov@gnf.org>
#
# Copyright Peter Dimitrov
# (c) Peter Dimitrov, dimitrov@gnf.org, 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# POD documentation - main docs before the code
=head1 NAME
InterProTerm - Implementation of InterProI term interface
=head1 SYNOPSIS
my $term = Bio::Ontology::InterProTerm->new( -interpro_id => "IPR000001",
-name => "Kringle",
-definition => "Kringles are autonomous structural domains ...",
-ontology => "Domain"
);
print $term->interpro_id(), "\n";
print $term->name(), "\n";
print $term->definition(), "\n";
print $term->is_obsolete(), "\n";
print $term->ontology->name(), "\n";
=head1 DESCRIPTION
This is a simple extension of L<Bio::Ontology::Term> for InterPro terms.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Peter Dimitrov
Email dimitrov@gnf.org
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Ontology::InterProTerm;
use vars qw(@ISA);
use strict;
use Bio::Ontology::Term;
use Bio::Annotation::Reference;
use constant INTERPRO_ID_DEFAULT => "IPR000000";
@ISA = qw( Bio::Ontology::Term );
=head2 new
Title : new
Usage : $term = Bio::Ontology::InterProTerm->new( -interpro_id => "IPR000002",
-name => "Cdc20/Fizzy",
-definition => "The Cdc20/Fizzy region is almost always ...",
-ontology => "Domain"
);
Function: Creates a new Bio::Ontology::InterProTerm.
Example :
Returns : A new Bio::Ontology::InterProTerm object.
Args :
-interpro_id => the InterPro ID of the term. Has the form IPRdddddd, where dddddd is a zero-padded six digit number
-name => the name of this InterPro term [scalar]
-definition => the definition/abstract of this InterPro term [scalar]
-ontology => ontology of InterPro terms [Bio::Ontology::OntologyI]
-comment => a comment [scalar]
=cut
sub new{
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ( $interpro_id,
$short_name)
= $self->_rearrange( [qw( INTERPRO_ID
SHORT_NAME
)
], @args );
$interpro_id && $self->interpro_id( $interpro_id );
$short_name && $self->short_name( $short_name );
return $self;
}
=head2 init
Title : init
Usage : $term->init();
Function: Initializes this InterProTerm to all "" and empty lists.
Example :
Returns :
Args :
=cut
sub init{
my $self = shift;
# first call the inherited version to properly chain up the hierarchy
$self->SUPER::init(@_);
# then only initialize what we implement ourselves here
$self->interpro_id( INTERPRO_ID_DEFAULT );
$self->short_name("");
}
=head2 _check_interpro_id
Title : _check_interpro_id
Usage :
Function: Performs simple check in order to validate that its argument has the form IPRdddddd, where dddddd is a zero-padded six digit number.
Example :
Returns : Returns its argument if valid, otherwise throws exception.
Args : String
=cut
sub _check_interpro_id{
my ($self, $value) = @_;
$self->throw( "InterPro ID ".$value." is incorrect\n" )
unless ( $value =~ /^IPR\d{6}$/ ||
$value eq INTERPRO_ID_DEFAULT );
return $value;
}
=head2 interpro_id
Title : interpro_id
Usage : $obj->interpro_id($newval)
Function: Set/get for the interpro_id of this InterProTerm
Example :
Returns : value of interpro_id (a scalar)
Args : new value (a scalar, optional)
=cut
sub interpro_id{
my ($self, $value) = @_;
if( defined $value) {
$value = $self->_check_interpro_id($value);
}
return $self->identifier($value);
}
=head2 short_name
Title : short_name
Usage : $obj->short_name($newval)
Function: Set/get for the short name of this InterProTerm.
Example :
Returns : value of short_name (a scalar)
Args : new value (a scalar, optional)
=cut
sub short_name{
my ($self, $value) = @_;
if( defined $value) {
$self->{'short_name'} = $value ? $value : undef;
}
return $self->{'short_name'};
}
=head2 protein_count
Title : protein_count
Usage : $obj->protein_count($newval)
Function: Set/get for the protein count of this InterProTerm.
Example :
Returns : value of protein_count (a scalar)
Args : new value (a scalar, optional)
=cut
sub protein_count{
my ($self,$value) = @_;
if( defined $value) {
$self->{'protein_count'} = $value ? $value : undef;
}
return $self->{'protein_count'};
}
=head2 get_references
Title : get_references
Usage :
Function: Get the references for this InterPro term.
Example :
Returns : An array of L<Bio::Annotation::Reference> objects
Args :
=cut
sub get_references{
my $self = shift;
return @{$self->{"_references"}} if exists($self->{"_references"});
return ();
}
=head2 add_reference
Title : add_reference
Usage :
Function: Add one or more references to this InterPro term.
Example :
Returns :
Args : One or more L<Bio::Annotation::Reference> objects.
=cut
sub add_reference{
my $self = shift;
$self->{"_references"} = [] unless exists($self->{"_references"});
push(@{$self->{"_references"}}, @_);
}
=head2 remove_references
Title : remove_references
Usage :
Function: Remove all references for this InterPro term.
Example :
Returns : The list of previous references as an array of
L<Bio::Annotation::Reference> objects.
Args :
=cut
sub remove_references{
my $self = shift;
my @arr = $self->get_references();
$self->{"_references"} = [];
return @arr;
}
=head2 get_members
Title : get_members
Usage : @arr = get_members()
Function: Get the list of member(s) for this object.
Example :
Returns : An array of Bio::Annotation::DBLink objects
Args :
=cut
sub get_members{
my $self = shift;
return @{$self->{'_members'}} if exists($self->{'_members'});
return ();
}
=head2 add_member
Title : add_member
Usage :
Function: Add one or more member(s) to this object.
Example :
Returns :
Args : One or more Bio::Annotation::DBLink objects.
=cut
sub add_member{
my $self = shift;
$self->{'_members'} = [] unless exists($self->{'_members'});
push(@{$self->{'_members'}}, @_);
}
=head2 remove_members
Title : remove_members
Usage :
Function: Remove all members for this class.
Example :
Returns : The list of previous members as an array of
Bio::Annotation::DBLink objects.
Args :
=cut
sub remove_members{
my $self = shift;
my @arr = $self->get_members();
$self->{'_members'} = [];
return @arr;
}
=head2 get_examples
Title : get_examples
Usage : @arr = get_examples()
Function: Get the list of example(s) for this object.
This is an element of the InterPro xml schema.
Example :
Returns : An array of Bio::Annotation::DBLink objects
Args :
=cut
sub get_examples{
my $self = shift;
return @{$self->{'_examples'}} if exists($self->{'_examples'});
return ();
}
=head2 add_example
Title : add_example
Usage :
Function: Add one or more example(s) to this object.
This is an element of the InterPro xml schema.
Example :
Returns :
Args : One or more Bio::Annotation::DBLink objects.
=cut
sub add_example{
my $self = shift;
$self->{'_examples'} = [] unless exists($self->{'_examples'});
push(@{$self->{'_examples'}}, @_);
}
=head2 remove_examples
Title : remove_examples
Usage :
Function: Remove all examples for this class.
This is an element of the InterPro xml schema.
Example :
Returns : The list of previous examples as an array of
Bio::Annotation::DBLink objects.
Args :
=cut
sub remove_examples{
my $self = shift;
my @arr = $self->get_examples();
$self->{'_examples'} = [];
return @arr;
}
=head2 get_external_documents
Title : get_external_documents
Usage : @arr = get_external_documents()
Function: Get the list of external_document(s) for this object.
This is an element of the InterPro xml schema.
Example :
Returns : An array of Bio::Annotation::DBLink objects
Args :
=cut
sub get_external_documents{
my $self = shift;
return @{$self->{'_external_documents'}} if exists($self->{'_external_documents'});
return ();
}
=head2 add_external_document
Title : add_external_document
Usage :
Function: Add one or more external_document(s) to this object.
This is an element of the InterPro xml schema.
Example :
Returns :
Args : One or more Bio::Annotation::DBLink objects.
=cut
sub add_external_document{
my $self = shift;
$self->{'_external_documents'} = [] unless exists($self->{'_external_documents'});
push(@{$self->{'_external_documents'}}, @_);
}
=head2 remove_external_documents
Title : remove_external_documents
Usage :
Function: Remove all external_documents for this class.
This is an element of the InterPro xml schema.
Example :
Returns : The list of previous external_documents as an array of
Bio::Annotation::DBLink objects.
Args :
=cut
sub remove_external_documents{
my $self = shift;
my @arr = $self->get_external_documents();
$self->{'_external_documents'} = [];
return @arr;
}
=head2 class_list
Title : class_list
Usage : $obj->class_list($newval)
Function: Set/get for class list element of the InterPro xml schema
Example :
Returns : reference to an array of Bio::Annotation::DBLink objects
Args : reference to an array of Bio::Annotation::DBLink objects
=cut
sub class_list{
my ($self, $value) = @_;
if( defined $value) {
$self->{'class_list'} = $value;
}
return $self->{'class_list'};
}
=head2 to_string
Title : to_string()
Usage : print $term->to_string();
Function: to_string method for InterPro terms.
Returns : A string representation of this InterPro term.
Args :
=cut
sub to_string {
my($self) = @_;
my $s = "";
$s .= "-- InterPro id:\n";
$s .= $self->interpro_id()."\n";
if (defined $self->name) {
$s .= "-- Name:\n";
$s .= $self->name()."\n";
$s .= "-- Definition:\n";
$s .= $self->definition()."\n";
$s .= "-- Category:\n";
if ( defined( $self->ontology() ) ) {
$s .= $self->ontology()->name()."\n";
} else {
$s .= "\n";
}
$s .= "-- Version:\n";
$s .= $self->version()."\n";
$s .= "-- Is obsolete:\n";
$s .= $self->is_obsolete()."\n";
$s .= "-- Comment:\n";
$s .= $self->comment()."\n";
if (defined $self->references) {
$s .= "-- References:\n";
foreach my $ref ( @{$self->references} ) {
$s .= $ref->authors."\n".$ref->title."\n".$ref->location."\n\n";
};
$s .= "\n";
}
if (defined $self->member_list) {
$s .= "-- Member List:\n";
foreach my $ref ( @{$self->member_list} ) {
$s .= $ref->database."\t".$ref->primary_id."\n";
};
$s .= "\n";
}
if (defined $self->external_doc_list) {
$s .= "-- External Document List:\n";
foreach my $ref ( @{$self->external_doc_list} ) {
$s .= $ref->database."\t".$ref->primary_id."\n";
};
$s .= "\n";
}
if (defined $self->examples) {
$s .= "-- Examples:\n";
foreach my $ref ( @{$self->examples} ) {
$s .= $ref->database."\t".$ref->primary_id."\t".$ref->comment."\n";
};
$s .= "\n";
}
if (defined $self->class_list) {
$s .= "-- Class List:\n";
foreach my $ref ( @{$self->class_list} ) {
$s .= $ref->primary_id."\n";
};
$s .= "\n";
}
if ($self->get_secondary_ids) {
$s .= "-- Secondary IDs:\n";
foreach my $ref ( $self->get_secondary_ids() ) {
$s .= $ref."\n";
};
$s .= "\n";
}
}
else {
$s .= "InterPro term not fully instantiated\n";
}
return $s;
}
=head1 Deprecated methods
These are here for backwards compatibility.
=cut
=head2 secondary_ids
Title : secondary_ids
Usage : $obj->secondary_ids($newval)
Function: This is deprecated. Use get_secondary_ids() or
add_secondary_id() instead.
Example :
Returns : reference to an array of strings
Args : reference to an array of strings
=cut
sub secondary_ids{
my $self = shift;
my @ids;
$self->warn("secondary_ids is deprecated. Use ".
"get_secondary_ids/add_secondary_id instead.");
# set mode?
if(@_) {
my $sids = shift;
if($sids) {
$self->add_secondary_id(@$sids);
@ids = @$sids;
} else {
# we interpret setting to undef as removing the array
$self->remove_secondary_ids();
}
} else {
# no; get mode
@ids = $self->get_secondary_ids();
}
return \@ids;
}
1;
]]>