Bio::Ontology InterProTerm
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Summary
Bio::Ontology::InterProTerm - Implementation of InterProI term interface
Package variables
No package variables defined.
Included modules
Bio::Annotation::Reference
Inherit
Bio::Ontology::Term
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";
Description
This is a simple extension of Bio::Ontology::Term for InterPro terms.
Methods
newDescriptionCode
initDescriptionCode
_check_interpro_idDescriptionCode
interpro_idDescriptionCode
short_nameDescriptionCode
protein_countDescriptionCode
get_membersDescriptionCode
add_memberDescriptionCode
remove_membersDescriptionCode
get_examplesDescriptionCode
add_exampleDescriptionCode
remove_examplesDescriptionCode
get_external_documentsDescriptionCode
add_external_documentDescriptionCode
remove_external_documentsDescriptionCode
class_listDescriptionCode
to_stringDescriptionCode
secondary_idsDescriptionCode
Methods description
newcode    nextTop
 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]
initcodeprevnextTop
 Title   : init
 Usage   : $term->init();
 Function: Initializes this InterProTerm to all "" and empty lists.
 Example :
 Returns : 
 Args    :
_check_interpro_idcodeprevnextTop
 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
interpro_idcodeprevnextTop
 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)
short_namecodeprevnextTop
 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)
protein_countcodeprevnextTop
 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)
get_memberscodeprevnextTop
 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    :
add_membercodeprevnextTop
 Title   : add_member
 Usage   :
 Function: Add one or more member(s) to this object.
 Example :
 Returns : 
 Args    : One or more Bio::Annotation::DBLink objects.
remove_memberscodeprevnextTop
 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    :
get_examplescodeprevnextTop
 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    :
add_examplecodeprevnextTop
 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.
remove_examplescodeprevnextTop
 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    :
get_external_documentscodeprevnextTop
 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    :
add_external_documentcodeprevnextTop
 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.
remove_external_documentscodeprevnextTop
 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    :
class_listcodeprevnextTop
 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
to_stringcodeprevnextTop
 Title   : to_string()
 Usage   : print $term->to_string();
 Function: to_string method for InterPro terms.
 Returns : A string representation of this InterPro term.
 Args    :
secondary_idscodeprevnextTop
 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
Methods code
newdescriptionprevnextTop
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;
}
initdescriptionprevnextTop
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 );
    $self->short_name("");
}
_check_interpro_iddescriptionprevnextTop
sub _check_interpro_id {
  my ($self, $value) = @_;

  $self->throw( "InterPro ID ".$value." is incorrect\n" )
    unless ( $value =~ /^IPR\d{6}$/ ||
	     $value eq INTERPRO_ID_DEFAULT );

  return $value;
}
interpro_iddescriptionprevnextTop
sub interpro_id {
  my ($self, $value) = @_;

  if( defined $value) {
    $value = $self->_check_interpro_id($value);
    return $self->identifier($value);
  }

  return $self->identifier();
}
short_namedescriptionprevnextTop
sub short_name {
  my ($self, $value) = @_;

  if( defined $value) {
    $self->{'short_name'} = $value ? $value : undef;
  }

  return $self->{'short_name'};
}
protein_countdescriptionprevnextTop
sub protein_count {
  my ($self,$value) = @_;

  if( defined $value) {
    $self->{'protein_count'} = $value ? $value : undef;
  }

  return $self->{'protein_count'};
}
get_membersdescriptionprevnextTop
sub get_members {
    my $self = shift;
    return $self->get_dbxrefs('member_list');
}
add_memberdescriptionprevnextTop
sub add_member {
    my $self = shift;
    $self->add_dbxref(-dbxrefs =>\@ _, -context => 'member_list');
}
remove_membersdescriptionprevnextTop
sub remove_members {
    my $self = shift;
    return $self->remove_dbxrefs('member_list');
}
get_examplesdescriptionprevnextTop
sub get_examples {
    my $self = shift;
    return $self->get_dbxrefs('example_list');
}
add_exampledescriptionprevnextTop
sub add_example {
    my $self = shift;
    return $self->add_dbxref(-dbxrefs =>\@ _, -context => 'example_list');
}
remove_examplesdescriptionprevnextTop
sub remove_examples {
    my $self = shift;
    return $self->remove_dbxrefs('example_list');
}
get_external_documentsdescriptionprevnextTop
sub get_external_documents {
    my $self = shift;
    return $self->get_dbxrefs('external_doc_list');
}
add_external_documentdescriptionprevnextTop
sub add_external_document {
    my $self = shift;
    return $self->add_dbxref(-dbxrefs =>\@ _, -context => 'external_doc_list');
}
remove_external_documentsdescriptionprevnextTop
sub remove_external_documents {
    my $self = shift;
    return $self->remove_dbxrefs('external_doc_list');
}
class_listdescriptionprevnextTop
sub class_list {
    my ($self, $value) = @_;
    if( defined $value && ref $value eq 'ARRAY') {
        if (!@$value) {
            # passing an empty array ref is essentially same as remove_dbxrefs,
            # so do that
            $self->remove_dbxrefs('class_list');
        } else {
            $self->add_dbxref(-dbxrefs => $value, -context => 'class_list');
        }
    }
    return [$self->get_dbxrefs('class_list')];
}
to_stringdescriptionprevnextTop
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->get_references ) {
            $s .= "-- References:\n";
            foreach my $ref ( $self->get_references ) {
                $s .=
                    $ref->authors . "\n"
                  . $ref->title . "\n"
                  . $ref->location . "\n\n";
            }
            $s .= "\n";
        }
        if ( defined $self->get_members ) {
            $s .= "-- Member List:\n";
            foreach my $ref ( $self->get_members ) {
                $s .= $ref->database . "\t" . $ref->primary_id . "\n";
            }
            $s .= "\n";
        }
        if ( defined $self->get_external_documents ) {
            $s .= "-- External Document List:\n";
            foreach my $ref ( $self->get_external_documents ) {
                $s .= $ref->database . "\t" . $ref->primary_id . "\n";
            }
            $s .= "\n";
        }
        if ( defined $self->get_examples ) {
            $s .= "-- Examples:\n";
            foreach my $ref ( $self->get_examples ) {
                $s .= join( "\t",
                    map { $ref->$_ || '' } qw(database primary_id 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 ( $self->get_secondary_ids() ) {
                # TODO: getting undef here in some cases, needs to be checked
                next unless defined ($ref);
                $s .= $ref . "\n";
            }
            $s .= "\n";
        }
    }
    else {
        $s .= "InterPro term not fully instantiated\n";
    }
    return $s;
}
secondary_idsdescriptionprevnextTop
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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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/wiki/Mailing_lists  - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
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
the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Peter DimitrovTop
Email dimitrov@gnf.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
get_referencesTop
 Title   : get_references
 Usage   :
 Function: Get the references for this InterPro term.
 Example :
 Returns : An array of Bio::Annotation::Reference objects
 Args    :
add_referenceTop
 Title   : add_reference
 Usage   :
 Function: Add one or more references to this InterPro term.
 Example :
 Returns : 
 Args    : One or more Bio::Annotation::Reference objects.
remove_referencesTop
 Title   : remove_references
 Usage   :
 Function: Remove all references for this InterPro term.
 Example :
 Returns : The list of previous references as an array of
           Bio::Annotation::Reference objects.
 Args    :
Deprecated methodsTop
These are here for backwards compatibility.