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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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NAME

Bio::EnsEMBL::DBSQL::KaryotypeBand

SYNOPSIS

use Bio::EnsEMBL::KaryotypeBand;

# Create and populate a karyotype band (normally done by adaptor)
$kb = Bio::EnsEMBL::KaryotyeBand(
  -START   => 1,
  -END     => 1_000_000,
  -SLICE   => $chrX_slice,
  -NAME    => 'q31',
  -STAIN   => 'gpos50',
  -ADAPTOR => $db->get_KaryotypeBandAdaptor(),
  -DBID    => 10
);

# Can tranform this band into other coord systems, just like other
# features
$kb = $kb->transform('supercontig');

$start      = $kb->start();
$end        = $kb->end();
$seq_region = $kb->slice->seq_region_name();

# Karyotypes have internal ids as well
$kary_id = $kb->dbID();

DESCRIPTION

KaryotypeBand objects encapsulate data pertaining to a single karyotype band. Access these objects through a Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor.

KarytoypeBand inherits from Bio::EnsEMBL::Feature and can be used just as any other feature can be.

METHODS

new

Arg [NAME] : string (optional)
             The name of this band
Arg [STAIN]: string (optional)
             The stain of this band
Arg [...]  : Arguments passed to superclass constructor.
             See Bio::EnsEMBL::Feature
Example    : $kb = Bio::EnsEMBL::KaryotypeBand->new(-START => $start,
                                                    -END   => $end,
                                                    -SLICE => $slice,
                                                    -NAME  => 'q11.21',
                                                    -STAIN => 'gneg');
Description: Constructor.  Creates a new KaryotypeBand object, which can be
             treated as any other feature object. Note that karyotypes
             bands always have strand = 0.
Returntype : Bio::EnsEMBL::KarytotypeBand
Exceptions : none
Caller     : Bio::EnsEMBL::KaryotypeBandAdaptor
Status     : Stable

name

Arg [1]    : (optional) string $value
Example    : my $band_name = $band->name(); 
Description: Getter/Setter for the name of this band
Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

stain

Arg [1]    : (optional) string $value
Example    : my $band_stain = $band->stain();
Description: get/set for the band stain (e.g. 'gpos50')
Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

strand

  Arg [1]    : none
	Example    : $strand = $karyotype_feat->strand();
  Description: Overrides the Feature strand method to always return a
               value of 0 for karyotype features (they are unstranded features)
  Returntype : int (always 0)
  Exceptions : none
  Caller     : general
  Status     : Stable

move

Arg [1]    : $start - The new end of this band
Arg [2]    : $end - The new start of this band
Arg [3]    : $strand - ignored always set to 0
Example    : $kb->move(1, 10_000);
Description: Overrides superclass move() method to ensure strand is always 0.
             See Bio::EnsEMBL::Feature::move
Returntype : none
Exceptions : none
Caller     : general
Status     : Stable

display_id

Arg [1]    : none
Example    : print $kb->display_id();
Description: This method returns a string that is considered to be
             the 'display' identifier.  For karyotype bands this is the
             name of the karyotype band or '' if no name is defined.
Returntype : string
Exceptions : none
Caller     : web drawing code
Status     : Stable

summary_as_hash

Example       : $karyotype_band_summary = $band->summary_as_hash();
Description   : Extends Feature::summary_as_hash
                Retrieves a summary of this Karyotype object.
                  
Returns       : hashref of arrays of descriptive strings
Status        : Intended for internal use