LICENSE

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

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

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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