Bio::Ontology Term
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Summary
Bio::Ontology::Term - implementation of the interface for ontology terms
Package variables
No package variables defined.
Included modules
Bio::Annotation::DBLink
Bio::Ontology::Ontology
Bio::Ontology::OntologyStore
Data::Dumper
Inherit
Bio::DescribableI Bio::IdentifiableI Bio::Ontology::TermI Bio::Root::Root
Synopsis
#get Bio::Ontology::TermI somehow.
  print $term->identifier(), "\n";
print $term->name(), "\n";
print $term->definition(), "\n";
print $term->is_obsolete(), "\n";
print $term->comment(), "\n";
foreach my $synonym ( $term->each_synonym() ) { print $synonym, "\n"; }
Description
This is a simple implementation for ontology terms providing basic
methods (it provides no functionality related to graphs). It
implements the Bio::Ontology::TermI interface.
This class also implements Bio::IdentifiableI and
Bio::DescribableI.
Methods
newDescriptionCode
init
No description
Code
identifierDescriptionCode
nameDescriptionCode
definitionDescriptionCode
ontologyDescriptionCode
versionDescriptionCode
is_obsoleteDescriptionCode
commentDescriptionCode
get_synonymsDescriptionCode
add_synonymDescriptionCode
remove_synonymsDescriptionCode
get_dblinksDescriptionCode
get_dbxrefsDescriptionCode
get_dblink_contextDescriptionCode
get_dbxref_contextDescriptionCode
add_dblinkDescriptionCode
add_dbxrefDescriptionCode
has_dblinkDescriptionCode
has_dbxrefDescriptionCode
add_dblink_contextDescriptionCode
remove_dblinksDescriptionCode
remove_dbxrefsDescriptionCode
get_referencesDescriptionCode
add_referenceDescriptionCode
remove_referencesDescriptionCode
get_secondary_idsDescriptionCode
add_secondary_idDescriptionCode
remove_secondary_idsDescriptionCode
_is_true_or_false
No description
Code
object_idDescriptionCode
authorityDescriptionCode
namespaceDescriptionCode
display_nameDescriptionCode
descriptionDescriptionCode
each_dblink
No description
Code
add_dblinks
No description
Code
Methods description
newcode    nextTop
 Title   : new
Usage : $term = Bio::Ontology::Term->new(
-identifier => "16847",
-name => "1-aminocyclopropane-1-carboxylate synthase",
-definition => "Catalysis of ...",
-is_obsolete => 0,
-comment => "" );
Function: Creates a new Bio::Ontology::Term.
Returns : A new Bio::Ontology::Term object.
Args : -identifier => the identifier of this term [scalar]
-name => the name of this term [scalar]
-definition => the definition of this term [scalar]
-ontology => the ontology this term lives in
(a Bio::Ontology::OntologyI object)
-version => version information [scalar]
-is_obsolete => the obsoleteness of this term [0 or 1]
-comment => a comment [scalar]
-dblinks => Bio::Annotation::DBLink objects
[reference to array]
-references => Bio::Annotation::Reference objects
[reference to array]
See Bio::Ontology::OntologyI, Bio::Annotation::Reference,
Bio::Annotation::DBLink.
identifiercodeprevnextTop
 Title   : identifier
Usage : $term->identifier( "GO:0003947" );
or
print $term->identifier();
Function: Set/get for the identifier of this Term.
Returns : The identifier [scalar].
Args : The identifier [scalar] (optional).
namecodeprevnextTop
 Title   : name
Usage : $term->name( "N-acetylgalactosaminyltransferase" );
or
print $term->name();
Function: Set/get for the name of this Term.
Returns : The name [scalar].
Args : The name [scalar] (optional).
definitioncodeprevnextTop
 Title   : definition
Usage : $term->definition( "Catalysis of ..." );
or
print $term->definition();
Function: Set/get for the definition of this Term.
Returns : The definition [scalar].
Args : The definition [scalar] (optional).
ontologycodeprevnextTop
 Title   : ontology
Usage : $ont = $term->ontology();
or
$term->ontology( $ont );
Function: Get the ontology this term is in.
Note that with the ontology in hand you can query for all related terms etc. Returns : The ontology of this Term as a Bio::Ontology::OntologyI implementing object. Args : On set, the ontology of this Term as a Bio::Ontology::OntologyI implementing object or a string representing its name.
See Bio::Ontology::OntologyI.
versioncodeprevnextTop
 Title   : version
Usage : $term->version( "1.00" );
or
print $term->version();
Function: Set/get for version information.
Returns : The version [scalar].
Args : The version [scalar] (optional).
is_obsoletecodeprevnextTop
 Title   : is_obsolete
Usage : $term->is_obsolete( 1 );
or
if ( $term->is_obsolete() )
Function: Set/get for the obsoleteness of this Term.
Returns : the obsoleteness [0 or 1].
Args : the obsoleteness [0 or 1] (optional).
commentcodeprevnextTop
 Title   : comment
Usage : $term->comment( "Consider the term ..." );
or
print $term->comment();
Function: Set/get for an arbitrary comment about this Term.
Returns : A comment.
Args : A comment (optional).
get_synonymscodeprevnextTop
 Title   : get_synonyms
Usage : @aliases = $term->get_synonyms;
Function: Returns a list of aliases of this Term.
Returns : A list of aliases [array of [scalar]].
Args :
add_synonymcodeprevnextTop
 Title   : add_synonym
Usage : $term->add_synonym( @asynonyms );
or
$term->add_synonym( $synonym );
Function: Pushes one or more synonyms into the list of synonyms.
Returns :
Args : One synonym [scalar] or a list of synonyms [array of [scalar]].
remove_synonymscodeprevnextTop
 Title   : remove_synonyms()
Usage : $term->remove_synonyms();
Function: Deletes (and returns) the synonyms of this Term.
Returns : A list of synonyms [array of [scalar]].
Args :
get_dblinkscodeprevnextTop
 Title   : get_dblinks()
Usage : @ds = $term->get_dblinks();
Function: Returns a list of each dblinks of this GO term.
Returns : A list of dblinks [array of [scalars]].
Args : A scalar indicating the context (optional).
If omitted, all dblinks will be returned.
Note : deprecated method due to past use of mixed data types; use
get_dbxrefs() instead, which handles both strings and DBLink
instances
get_dbxrefscodeprevnextTop
 Title   : get_dbxrefs()
Usage : @ds = $term->get_dbxrefs();
Function: Returns a list of each link for this term.
If an implementor of this interface permits modification of this array property, the class should define at least methods add_dbxref() and remove_dbxrefs(), with obvious functionality. Returns : A list of Bio::Annotation::DBLink instances
Args : [optional] string which specifies context (default : returns all dbxrefs)
get_dblink_contextcodeprevnextTop
  Title   : get_dblink_context
Usage : @context = $term->get_dblink_context;
Function: Return all context existing in Term
Returns : a list of scalar
Args : [none]
Note : deprecated method due to past use of mixed data types; use
get_dbxref_context() instead
get_dbxref_contextcodeprevnextTop
  Title   : get_dbxref_context
Usage : @context = $term->get_dbxref_context;
Function: Return all context strings existing in Term
Returns : a list of scalars
Args : [none]
add_dblinkcodeprevnextTop
 Title   : add_dblink
Usage : $term->add_dblink( @dbls );
or
$term->add_dblink( $dbl );
Function: Pushes one or more dblinks onto the list of dblinks.
Returns :
Args : One or more Bio::Annotation::DBLink instances
Note : deprecated method due to past use of mixed data types; use
add_dbxref() instead, which handles both strings and
DBLink instances
add_dbxrefcodeprevnextTop
 Title   : add_dbxref
Usage : $term->add_dbxref( @dbls );
or
$term->add_dbxref( $dbl );
Function: Pushes one or more dblinks onto the list of dblinks.
Returns :
Args : -dbxrefs : array ref of Bio::Annotation::DBLink instances
-context : string designating the context for the DBLink
(default : '_default' - contextless)
has_dblinkcodeprevnextTop
  Title   : has_dblink
Usage : $term->has_dblink($dblink);
Function: Checks if a DBXref is already existing in the OBOterm object
Return : TRUE/FALSE
Args : [arg1] A DBxref identifier
Note : deprecated method due to past use of mixed data types; use
has_dbxref() instead, which handles both strings and
DBLink instances
has_dbxrefcodeprevnextTop
  Title   : has_dbxref
Usage : $term->has_dbxref($dbxref);
Function: Checks if a dbxref string is already existing in the OBOterm object
Return : TRUE/FALSE
Args : [arg1] A DBxref identifier (string).
Bio::Annotation::DBLink::display_text() is used for comparison
against the string.
add_dblink_contextcodeprevnextTop
  Title   : add_dblink_context
Usage : $term->add_dblink_context($db, $context);
Function: add a dblink with its context
Return : [none]
Args : [arg1] a Bio::Annotation::DBLink instance
[arg2] a string for context; if omitted, the
default/context-less one will be used.
Note : deprecated method due to past use of mixed data types; use
add_dbxref() instead
remove_dblinkscodeprevnextTop
 Title   : remove_dblinks()
Usage : $term->remove_dblinks();
Function: Deletes (and returns) the definition references of this GO term.
Returns : A list of definition references [array of [scalars]].
Args : Context. If omitted or equal to 'all', all dblinks
will be removed.
Note : deprecated method due to past use of mixed data types; use
remove_dblinks() instead, which handles both strings and
DBLink instances
remove_dbxrefscodeprevnextTop
 Title   : remove_dbxrefs()
Usage : $term->remove_dbxrefs();
Function: Deletes (and returns) the definition references of this GO term.
Returns : A list of definition references [array of [scalars]].
Args : Context. If omitted or equal to 'all', all dblinks
will be removed.
get_referencescodeprevnextTop
  Title   : get_references
Usage : @references = $self->get_references
Fuctnion: Returns a list of references
Return : A list of objects
Args : [none]
add_referencecodeprevnextTop
  Title   : add_reference
Usage : $self->add_reference($reference);
$self->add_reference($reference1, $reference2);
Fuctnion: Add one or more references
Returns : [none]
remove_referencescodeprevnextTop
  Title   : remove_references
Usage : $self->remove_references;
Function: Deletes (and returns) all references
Returns : A list of references
Args : [none]
get_secondary_idscodeprevnextTop
 Title   : get_secondary_ids
Usage : @ids = $term->get_secondary_ids();
Function: Returns a list of secondary identifiers of this Term.
Secondary identifiers mostly originate from merging terms, or possibly also from splitting terms. Returns : A list of secondary identifiers [array of [scalar]] Args :
add_secondary_idcodeprevnextTop
 Title   : add_secondary_id
Usage : $term->add_secondary_id( @ids );
or
$term->add_secondary_id( $id );
Function: Adds one or more secondary identifiers to this term.
Returns :
Args : One or more secondary identifiers [scalars]
remove_secondary_idscodeprevnextTop
 Title   : remove_secondary_ids
Usage : $term->remove_secondary_ids();
Function: Deletes (and returns) the secondary identifiers of this Term.
Returns : The previous list of secondary identifiers [array of [scalars]]
Args :
object_idcodeprevnextTop
 Title   : object_id
Usage : $string = $obj->object_id()
Function: a string which represents the stable primary identifier
in this namespace of this object.
This is a synonym for identifier(). Returns : A scalar
authoritycodeprevnextTop
 Title   : authority
Usage : $authority = $obj->authority()
Function: a string which represents the organisation which
granted the namespace, written as the DNS name for
organisation (eg, wormbase.org)
This forwards to ontology()->authority(). Note that you cannot set the authority before having set the ontology or the namespace (which will set the ontology). Returns : A scalar Args : on set, the new value (a scalar)
namespacecodeprevnextTop
 Title   : namespace
Usage : $string = $obj->namespace()
Function: A string representing the name space this identifier
is valid in, often the database name or the name
describing the collection.
This forwards to ontology() (set mode) and ontology()->name() (get mode). I.e., setting the namespace will set the ontology to one matching that name in the ontology store, or to one newly created. Returns : A scalar Args : on set, the new value (a scalar)
display_namecodeprevnextTop
 Title   : display_name
Usage : $string = $obj->display_name()
Function: A string which is what should be displayed to the user.
The definition in Bio::DescribableI states that the string should not contain spaces. As this is not very sensible for ontology terms, we relax this here. The implementation just forwards to name(). Returns : A scalar Args : on set, the new value (a scalar)
descriptioncodeprevnextTop
 Title   : description
Usage : $string = $obj->description()
Function: A text string suitable for displaying to the user a
description. This string is likely to have spaces, but
should not have any newlines or formatting - just plain
text.
This forwards to definition(). The caveat is that the text will often be longer for ontology term definitions than the 255 characters stated in the definition in Bio::DescribableI. Returns : A scalar Args : on set, the new value (a scalar)
Methods code
newdescriptionprevnextTop
sub new {
    my( $class,@args ) = @_;

    my $self = $class->SUPER::new( @args );
    my ( $identifier, $name, $definition, $category, $ont, $version,
        $is_obsolete, $comment, $dblinks, $dbxrefs, $references)
        = $self->_rearrange( [
        qw(IDENTIFIER NAME DEFINITION CATEGORY ONTOLOGY VERSION IS_OBSOLETE
        COMMENT DBLINKS DBXREFS REFERENCES) ], @args );

    $self->init();

    defined($identifier)   && $self->identifier( $identifier );
    defined($name)         && $self->name( $name );
    defined($definition)   && $self->definition( $definition );
    defined($category)     && $self->category( $category );
    defined($ont)          && $self->ontology( $ont );
    defined($version)      && $self->version( $version );
    defined($is_obsolete)  && $self->is_obsolete( $is_obsolete );
    defined($comment)      && $self->comment( $comment  );
    defined($dbxrefs)      && $self->add_dbxref(-dbxrefs => $dbxrefs);
    # deprecated methods, allow to pass on to get the dep. notification
ref($dblinks) && $self->add_dblink(@$dblinks); ref($references) && $self->add_reference(@$references); return $self; } # new
}
initdescriptionprevnextTop
sub init {
    my $self = shift;

    $self->identifier(undef);
    $self->name(undef);
    $self->comment(undef);
    $self->definition(undef);
    $self->ontology(undef);
    $self->is_obsolete(0);
    $self->remove_synonyms();
    $self->remove_dbxrefs();
    $self->remove_references;
    $self->remove_secondary_ids();

} # init
}
identifierdescriptionprevnextTop
sub identifier {
    my $self = shift;

    return $self->{'identifier'} = shift if @_;
    return $self->{'identifier'};
} # identifier
}
namedescriptionprevnextTop
sub name {
    my $self = shift;

    return $self->{'name'} = shift if @_;
    return $self->{'name'};
} # name
}
definitiondescriptionprevnextTop
sub definition {
    my $self = shift;

    return $self->{'definition'} = shift if @_;
    return $self->{'definition'};
} # definition
}
ontologydescriptionprevnextTop
sub ontology {
    my $self = shift;
    my $ont;

    if(@_) {
        $ont = shift;
        if($ont) {
            $ont = Bio::Ontology::Ontology->new(-name => $ont) if ! ref($ont);
            if(! $ont->isa("Bio::Ontology::OntologyI")) {
                $self->throw(ref($ont)." does not implement ".
                             "Bio::Ontology::OntologyI. Bummer.");
            }
        }
        return $self->{"_ontology"} = $ont;
    }
    return $self->{"_ontology"};
} # ontology
}
versiondescriptionprevnextTop
sub version {
    my $self = shift;

    return $self->{'version'} = shift if @_;
    return $self->{'version'};
} # version
}
is_obsoletedescriptionprevnextTop
sub is_obsolete {
    my $self = shift;

    return $self->{'is_obsolete'} = shift if @_;
    return $self->{'is_obsolete'};
} # is_obsolete
}
commentdescriptionprevnextTop
sub comment {
    my $self = shift;

    return $self->{'comment'} = shift if @_;
    return $self->{'comment'};
} # comment
}
get_synonymsdescriptionprevnextTop
sub get_synonyms {
    my $self = shift;

    return @{ $self->{ "_synonyms" } } if exists($self->{ "_synonyms" });
    return ();
} # get_synonyms
}
add_synonymdescriptionprevnextTop
sub add_synonym {
    my ( $self, @values ) = @_;

    return unless( @values );

    # avoid duplicates
foreach my $syn (@values) { next if grep { $_ eq $syn; } @{$self->{ "_synonyms" }}; push( @{ $self->{ "_synonyms" } }, $syn ); } } # add_synonym
}
remove_synonymsdescriptionprevnextTop
sub remove_synonyms {
    my ( $self ) = @_;

    my @a = $self->get_synonyms();
    $self->{ "_synonyms" } = [];
    return @a;

} # remove_synonyms
}
get_dblinksdescriptionprevnextTop
sub get_dblinks {
    my ($self, $context) = @_;
    $self->deprecated("Use of get_dblinks is deprecated.  Note that prior use\n".
                      "of this method could return either simple scalar values\n".
                      "or Bio::Annotation::DBLink instances; only\n ".
                      "Bio::Annotation::DBLink is now supported.\n ".
                      "Use get_dbxrefs() instead");
    $self->get_dbxrefs($context);
} # get_dblinks
}
get_dbxrefsdescriptionprevnextTop
sub get_dbxrefs {
    my ($self, $context) = shift;
    my @dbxrefs;
    if (defined($context)) {
        if (exists($self->{_dblinks}->{$context})) {
            @dbxrefs =  @{$self->{_dblinks}->{$context}};
        }
    } else {
        @dbxrefs = map { @$_ } values %{$self->{_dblinks}} ;
    }
    return @dbxrefs;
} # get_dbxrefs
}
get_dblink_contextdescriptionprevnextTop
sub get_dblink_context {
    my $self=shift;
    $self->deprecated("Use of get_dblink_context() is deprecated; use get_dbxref_context() instead");
    return $self->get_dbxref_context(@_);
}
get_dbxref_contextdescriptionprevnextTop
sub get_dbxref_context {
    my $self=shift;
    return keys %{$self->{_dblinks}};
}
add_dblinkdescriptionprevnextTop
sub add_dblink {
    my $self = shift;
    $self->deprecated("Use of simple strings and add_dblink() is deprecated; use\n".
                      "Bio::Annotation::DBLink instances and add_dbxref() instead");
    # here we're assuming the data is in a simple DB:ID format
my @dbxrefs; for my $string (@_) { my ($db, $id) = split(':',$string); push @dbxrefs, Bio::Annotation::DBLink->new(-database => $db, -primary_id => $id); } return $self->add_dbxref(-dbxrefs =>\@ dbxrefs, -context => '_default'); } # add_dblink
}
add_dbxrefdescriptionprevnextTop
sub add_dbxref {
    my $self = shift;
    my ($links, $context) = $self->_rearrange([qw(DBXREFS CONTEXT)],@_);
    return unless defined $links;
    $context ||= '_default';
    $self->throw("DBLinks must be passed as an array reference") if ref $links ne 'ARRAY';
    foreach my $dbxref (@{$links}) {
        $self->throw("$dbxref is not a DBLink") unless ref $dbxref &&
            $dbxref->isa('Bio::Annotation::DBLink');
        $self->throw("'all' is a reserved word for context.") if $context eq 'all';
        if (! exists($self->{_dblinks}->{$context})) {
            $self->{_dblinks}->{$context} = [];
        }
        my $linktext = ref $dbxref ? $dbxref->display_text : $dbxref;
        if (grep {$_->display_text eq $linktext}
            @{$self->{_dblinks}->{$context}})
        {
            $self->warn("DBLink exists in the dblink of $context");
        }
        push @{$self->{_dblinks}->{$context}}, $dbxref;
    }
} # add_dbxref
# alias, for consistency
*add_dbxrefs =\& add_dbxref;
}
has_dblinkdescriptionprevnextTop
sub has_dblink {
    my ( $self, $value ) = @_;
    $self->deprecated("use of has_dblink() is deprecated; use has_dbxref() instead");
    return $self->has_dbxref($value);
}
has_dbxrefdescriptionprevnextTop
sub has_dbxref {
    my ( $self, $value ) = @_;
    return unless defined $value;
    my $context = "_default";
    $self->throw("'all' is a reserved word for context.") if $context eq 'all';
    $context ||= '_default';
    if ( ( $self->{_dblinks}->{$context} ) &&
        grep { $_->display_text eq $value } 
        @{ $self->{_dblinks}->{$context} } )
    {
        return TRUE;
    }
    else {
        return FALSE;
    }
}
add_dblink_contextdescriptionprevnextTop
sub add_dblink_context {
    my ($self, $value, $context) = @_;
    $self->deprecated("Use of simple strings and add_dblink_context() is deprecated; use\n
                      Bio::Annotation::DBLink instances and add_dbxref() instead");
    return $self->add_dbxref([$value],$context);
}
remove_dblinksdescriptionprevnextTop
sub remove_dblinks {
    my ($self, $context) = @_;
    $self->deprecated("use of remove_dblinks() is deprecated; use remove_dbxrefs() instead");
    return $self->remove_dbxrefs(@_);
} # remove_dblinks
}
remove_dbxrefsdescriptionprevnextTop
sub remove_dbxrefs {
    my ($self, $context) = @_;
    $context = undef if $context && ($context eq "all");
    my @old = $self->get_dbxrefs($context);
    if (defined($context)) {
        $self->{_dblinks}->{$context}=[];
    } else {
        $self->{_dblinks} = {};
    }
    return @old;
} # remove_dbxrefs
}
get_referencesdescriptionprevnextTop
sub get_references {
    my $self=shift;
    return @{$self->{_references}} if exists $self->{_references};
    return ();
}
add_referencedescriptionprevnextTop
sub add_reference {
    my ($self, @values) =@_;
    return unless @values;
    # avoid duplicates and undefs
foreach my $reference (@values){ $self->throw("Passed data not an Bio::Annotation::Reference") unless ref $reference && $reference->isa('Bio::AnnotationI'); next unless defined $reference; next if grep{$_ eq $reference} @{$self->{_references}}; push @{$self->{_references}}, $reference; }
}
remove_referencesdescriptionprevnextTop
sub remove_references {
    my $self=shift;
    my @references=$self->get_references;
    $self->{_references}=[];
    return @references;
}
get_secondary_idsdescriptionprevnextTop
sub get_secondary_ids {
    my $self = shift;

    return @{$self->{"_secondary_ids"}} if exists($self->{"_secondary_ids"});
    return ();
} # get_secondary_ids
}
add_secondary_iddescriptionprevnextTop
sub add_secondary_id {
    my $self = shift;

    return unless @_;

    # avoid duplicates
foreach my $id (@_) { next if grep { !$_ or $_ eq $id; } @{$self->{ "_secondary_ids" }}; push( @{ $self->{ "_secondary_ids" } }, $id ); } } # add_secondary_id
}
remove_secondary_idsdescriptionprevnextTop
sub remove_secondary_ids {
    my $self = shift;

    my @a = $self->get_secondary_ids();
    $self->{ "_secondary_ids" } = [];
    return @a;

} # remove_secondary_ids
# Title :_is_true_or_false
# Function: Checks whether the argument is TRUE or FALSE.
# Returns :
# Args : The value to be checked.
}
_is_true_or_falsedescriptionprevnextTop
sub _is_true_or_false {
    my ( $self, $value ) = @_;
    unless ( $value !~ /\D/ && ( $value == TRUE || $value == FALSE ) ) {
        $self->throw( "Found [" . $value
        . "] where " . TRUE . " or " . FALSE . " expected" );
    }
} # _is_true_or_false
}
object_iddescriptionprevnextTop
sub object_id {
    return shift->identifier(@_);
}
authoritydescriptionprevnextTop
sub authority {
    my $self = shift;
    my $ont = $self->ontology();

    return $ont->authority(@_) if $ont;
    $self->throw("cannot manipulate authority prior to ".
                 "setting the namespace or ontology") if @_;
    return;
}
namespacedescriptionprevnextTop
sub namespace {
    my $self = shift;

    $self->ontology(@_) if(@_);
    my $ont = $self->ontology();
    return defined($ont) ? $ont->name() : undef;
}
display_namedescriptionprevnextTop
sub display_name {
    return shift->name(@_);
}
descriptiondescriptionprevnextTop
sub description {
    return shift->definition(@_);
}

#################################################################
# aliases or forwards to maintain backward compatibility
#################################################################
}
each_dblinkdescriptionprevnextTop
sub each_dblink {
shift->throw("use of each_dblink() is deprecated; use get_dbxrefs() instead")
}
add_dblinksdescriptionprevnextTop
sub add_dblinks {
shift->throw("use of add_dblinks() is deprecated; use add_dbxref() instead")
}
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 one
of the Bioperl mailing lists. 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
the bugs and their resolution. Bug reports can be submitted via the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORTop
Christian M. Zmasek
Email: czmasek-at-burnham.org or cmzmasek@yahoo.com
WWW: http://monochrome-effect.net/
Address:
  Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121
APPENDIXTop
The rest of the documentation details each of the object
methods.
Methods implementing L<Bio::IdentifiableI> and Bio::DescribableITop
Deprecated methodsTop
Used for looking up the methods that supercedes them.