Bio::Ontology
InterProTerm
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Summary
InterProTerm - Implementation of InterProI term interface
Package variables
No package variables defined.
Included modules
Inherit
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
Methods
Methods description
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 |
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. |
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. |
Title : add_member
Usage :
Function: Add one or more member(s) to this object.
Example :
Returns :
Args : One or more Bio::Annotation::DBLink objects. |
Title : add_reference
Usage :
Function: Add one or more references to this InterPro term.
Example :
Returns :
Args : One or more Bio::Annotation::Reference objects. |
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 |
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 : |
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 : |
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 : |
Title : get_references
Usage :
Function: Get the references for this InterPro term.
Example :
Returns : An array of Bio::Annotation::Reference objects
Args : |
Title : init
Usage : $term->init();
Function: Initializes this InterProTerm to all "" and empty lists.
Example :
Returns :
Args : |
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) |
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] |
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) |
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 : |
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 : |
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 : |
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 : |
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 |
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) |
Title : to_string()
Usage : print $term->to_string();
Function: to_string method for InterPro terms.
Returns : A string representation of this InterPro term.
Args : |
Methods code
sub _check_interpro_id
{ my ($self, $value) = @_;
$self->throw( "InterPro ID ".$value." is incorrect\n" )
unless ( $value =~ /^IPR\d{6}$/ ||
$value eq INTERPRO_ID_DEFAULT );
return $value;} | sub add_example
{ my $self = shift;
$self->{'_examples'} = [] unless exists($self->{'_examples'});
push(@{$self->{'_examples'}}, @_);} | sub add_external_document
{ my $self = shift;
$self->{'_external_documents'} = [] unless exists($self->{'_external_documents'});
push(@{$self->{'_external_documents'}}, @_);} | sub add_member
{ my $self = shift;
$self->{'_members'} = [] unless exists($self->{'_members'});
push(@{$self->{'_members'}}, @_);} | sub add_reference
{ my $self = shift;
$self->{"_references"} = [] unless exists($self->{"_references"});
push(@{$self->{"_references"}}, @_);} | sub class_list
{ my ($self, $value) = @_;
if( defined $value) {
$self->{'class_list'} = $value;
}
return $self->{'class_list'};} | sub get_examples
{ my $self = shift;
return @{$self->{'_examples'}} if exists($self->{'_examples'});
return ();} | sub get_external_documents
{ my $self = shift;
return @{$self->{'_external_documents'}} if exists($self->{'_external_documents'});
return ();} | sub get_members
{ my $self = shift;
return @{$self->{'_members'}} if exists($self->{'_members'});
return ();} | sub get_references
{ my $self = shift;
return @{$self->{"_references"}} if exists($self->{"_references"});
return ();} | sub init
{ my $self = shift;
$self->SUPER::init(@_);
$self->interpro_id( INTERPRO_ID_DEFAULT );
$self->short_name("");} | sub interpro_id
{ my ($self, $value) = @_;
if( defined $value) {
$value = $self->_check_interpro_id($value);
}
return $self->identifier($value);} | 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 $self;} | sub protein_count
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'protein_count'} = $value ? $value : undef;
}
return $self->{'protein_count'};} | sub remove_examples
{ my $self = shift;
my @arr = $self->get_examples();
$self->{'_examples'} = [];
return @arr;} | sub remove_external_documents
{ my $self = shift;
my @arr = $self->get_external_documents();
$self->{'_external_documents'} = [];
return @arr;} | sub remove_members
{ my $self = shift;
my @arr = $self->get_members();
$self->{'_members'} = [];
return @arr;} | sub remove_references
{ my $self = shift;
my @arr = $self->get_references();
$self->{"_references"} = [];
return @arr;} | sub secondary_ids
{ my $self = shift;
my @ids;
$self->warn("secondary_ids is deprecated. Use ".
"get_secondary_ids/add_secondary_id instead.");
if(@_) {
my $sids = shift;
if($sids) {
$self->add_secondary_id(@$sids);
@ids = @$sids;
} else {
$self->remove_secondary_ids();
}
} else {
@ids = $self->get_secondary_ids();
}
return\@ ids;
}
1;} | sub short_name
{ my ($self, $value) = @_;
if( defined $value) {
$self->{'short_name'} = $value ? $value : undef;
}
return $self->{'short_name'};} | sub to_string
{ my($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;} | General documentation
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
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/
| AUTHOR - Peter Dimitrov | Top |
Additional contributors names and emails here
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
These are here for backwards compatibility.