Bio::EnsEMBL::KaryotypeBand Class Reference

Inheritance diagram for Bio::EnsEMBL::KaryotypeBand:

Public Member Functions
public Bio::EnsEMBL::KarytotypeBand	new ()
public String	name ()
public String	stain ()
public Int	strand ()
public void	move ()
public String	display_id ()
public Hashref	summary_as_hash ()
Public Member Functions inherited from Bio::EnsEMBL::Feature
public Bio::EnsEMBL::Feature	new ()
public Int	start ()
public Int	end ()
public Int	strand ()
public void	move ()
public Int	length ()
public Bio::EnsEMBL::Analysis	analysis ()
public Bio::EnsEMBL::Slice	slice ()
public Boolean Or Undef	equals ()
public Bio::EnsEMBL::Feature	transform ()
public Bio::EnsEMBL::Feature	transfer ()
public Listref	project_to_slice ()
public Listref	project ()
public String	seqname ()
public String	display_id ()
public String	version ()
public Bio::EnsEMBL::Slice	feature_Slice ()
public String	seq_region_name ()
public Int	seq_region_length ()
public Boolean	seq_region_strand ()
public Int	seq_region_start ()
public Int	seq_region_end ()
public String	coord_system_name ()
public String	seq ()
public Listref	get_all_alt_locations ()
public Boolean	overlaps ()
public Boolean	overlaps_local ()
public List	get_overlapping_Genes ()
public Bio::EnsEMBL::Gene	get_nearest_Gene ()
public String	feature_so_acc ()
public String	feature_so_term ()
public Hashref	summary_as_hash ()
public String	species ()
public	sub_SeqFeature ()
public	add_sub_SeqFeature ()
public	flush_sub_SeqFeature ()
Public Member Functions inherited from Bio::EnsEMBL::Storable
public Bio::EnsEMBL::Storable	new ()
public Instance	new_fast ()
public Int	dbID ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()
public Boolean	is_stored ()
public	get_all_DAS_Features ()

Detailed Description

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.

Definition at line 45 of file KaryotypeBand.pm.

Member Function Documentation

display_id()

public String Bio::EnsEMBL::KaryotypeBand::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

Code:

move()

public void Bio::EnsEMBL::KaryotypeBand::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

Code:

name()

public String Bio::EnsEMBL::KaryotypeBand::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

Code:

new()

public Bio::EnsEMBL::KarytotypeBand Bio::EnsEMBL::KaryotypeBand::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

Code:

stain()

public String Bio::EnsEMBL::KaryotypeBand::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

Code:

strand()

public Int Bio::EnsEMBL::KaryotypeBand::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

Code:

summary_as_hash()

public Hashref Bio::EnsEMBL::KaryotypeBand::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
 

Code:

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The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/KaryotypeBand.pm