GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  BIO::DAS::TYPE (3)

.ds Aq ’

NAME

Bio::Das::Type - A sequence annotation type

CONTENTS

SYNOPSIS



  use Bio::Das;

  # contact a DAS server using the "elegans" data source
  my $das      = Bio::Das->new(http://www.wormbase.org/db/das => elegans);

  # find out what feature types are available
  my @types       = $db->types;

  # get information on each one
  for my $t (@types) {
    my $id          = $t->id;
    my $method      = $t->method;
    my $category    = $t->category;
    my $isreference = $t->reference;
    my $label       = $t->label;
    my $method_label = $t->method_label;
  }



DESCRIPTION

The Bio::Das::Type class provides information about the type of an annotation. Each type has a category, which is a general description of the type, a unique ID, which names the type, and an optional method, which describes how the type was derived. A type may also be marked as being a landmark that can be used as a reference sequence.

Optionally, types can have human readable labels. There is one label for the type itself, and another for the type’s method.

    OBJECT CREATION

Bio::Das::Type objects are created by calling the types() method of a Bio::Das or Bio::Das::Segment object. They are also created implicity when a Bio::Das::Segment::Feature is created.

If needed, there is a simple constructor which can be called directly:
$type = Bio::Das::Type->new($id,$method,$category) Create and return a Bio::Das::Type object with the indicated typeID, method and category.

    OBJECT METHODS

The following methods are public. Most of them use an accessor calling style. Called without an argument, they return the current value of the attribute. Called with an argument, they change the attribute and return its previous value.
$id = $type->id([$newid]) Get or set the ID for the type;
$label = $type->label([$newlabel]) Get or set the label for the type;
$method = $type->method([$newmethod]) Get or set the method ID for the type.
$label = $type->method_label([$newlabel]) Get or set the method label for the type.
$category = $type->category([$newcategory]) Get or set the category for the type.
$reference = $type->reference([$newreference]) Get or set the value of the reference attribute. If the attribute is true, then features of this type can be used as reference sequences. However, see LIMITATIONSbelow.

    LIMITATIONS

Due to the requirements of the DAS spec, the reference() method will always return false for types returned by the Bio::Das->types() or Bio::Das::Segment->types() methods. As currently specified, the reference attribute is an attribute of an individual feature, and not of a generic type.

AUTHOR

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. See DISCLAIMER.txt for disclaimers of warranty.

SEE ALSO

Bio::Das, Bio::Das::Segment, Bio::Das::Segment::Feature
Search for    or go to Top of page |  Section 3 |  Main Index


perl v5.20.3 DAS::TYPE (3) 2009-08-25

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.