Bio::DB::GFF Typename
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Summary
Bio::DB::GFF::Typename -- The name of a feature type
Package variables
Privates (from "my" definitions)
%OBJECT_CACHE;
Inherit
Bio::Das::FeatureTypeI Bio::Root::Root
Synopsis
  use Bio::DB::GFF;
my $type = Bio::DB::GFF::Typename->new(similarity => 'BLAT_EST_GENOME'); my $segment = $segment->features($type);
Description
Bio::DB::GFF::Typename objects encapsulate the combination of feature
method and source used by the GFF flat file format. They can be used
in the Bio::DB::GFF modules wherever a feature type is called for.
Since there are relatively few types and many features, this module
maintains a memory cache of unique types so that two features of the
same type will share the same Bio::DB::GFF::Typename object.
Methods
newDescriptionCode
methodDescriptionCode
sourceDescriptionCode
asStringDescriptionCode
cloneDescriptionCode
matchDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : $type = Bio::DB::GFF::Typename->new($method,$source)
Function: create a new Bio::DB::GFF::Typename object
Returns : a new Bio::DB::GFF::Typename object
Args : method and source
Status : Public
methodcodeprevnextTop
 Title   : method
Usage : $method = $type->method([$newmethod])
Function: get or set the method
Returns : a method name
Args : new method name (optional)
Status : Public
sourcecodeprevnextTop
 Title   : source
Usage : $source = $type->source([$newsource])
Function: get or set the source
Returns : a source name
Args : new source name (optional)
Status : Public
asStringcodeprevnextTop
 Title   : asString
Usage : $string = $type->asString
Function: get the method and source as a string
Returns : a string in "method:source" format
Args : none
Status : Public
This method is used by operator overloading to overload the '""'
operator.
clonecodeprevnextTop
 Title   : clone
Usage : $new_clone = $type->clone;
Function: clone this object
Returns : a new Bio::DB::GFF::Typename object
Args : none
Status : Public
This method creates an exact copy of the object.
matchcodeprevnextTop
 Title   : match
Usage : $boolean = $type->match($type_or_string)
Function: fuzzy match on types
Returns : a flag indicating that the argument matches the object
Args : a Bio::DB::GFF::typename object, or a string in method:source format
Status : Public
This match allows Sequence:Link and Sequence: to match, but not
Sequence:Link and Sequence:Genomic_canonical.
Methods code
newdescriptionprevnextTop
sub new {
  my $package = shift;
  my ($method,$source) = @_;
  $method ||= '';
  $source ||= '';
  if ($source eq '' && $method =~ /^([\w-]+):([\w-]*)$/) {
    $method = $1;
    $source = $2;
  }
  return $OBJECT_CACHE{"$method:$source"} ||= bless [$method,$source],$package;
}
methoddescriptionprevnextTop
sub method {
  my $self = shift;
  my $d = $self->[0];
  $self->[0] = shift if @_;
  $d;
}
sourcedescriptionprevnextTop
sub source {
  my $self = shift;
  my $d = $self->[1];
  $self->[1] = shift if @_;
  $d;
}
asStringdescriptionprevnextTop
sub asString {
  $_[0]->[1] ? join ':',@{$_[0]} : $_[0]->[0];
}
clonedescriptionprevnextTop
sub clone {
  my $self = shift;
  return bless [@$self],ref $self;
}
matchdescriptionprevnextTop
sub match {
  my $self   = shift;
  my $target = shift;
  my ($method,$source);

  if (UNIVERSAL::isa($target,'Bio::DB::GFF::Typename')) {
    ($method,$source) = ($target->method,$target->source);
  } else {
    ($method,$source) = split /:/,$target;
  }

  $source ||= ''; # quash uninit variable warnings
return if $method ne '' && $self->method ne '' && $method ne $self->method; return if $source ne '' && $self->source ne '' && $source ne $self->source; 1; } 1;
}
General documentation
BUGSTop
This module is still under development.
SEE ALSOTop
bioperl, Bio::DB::GFF, Bio::DB::RelSegment
AUTHORTop
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2001 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.