Bio::EnsEMBL::IdentityXref Class Reference

Inheritance diagram for Bio::EnsEMBL::IdentityXref:

Public Member Functions
public Bio::EnsEMBL::IdentityXref	new ()
public String	xref_identity ()
public String	ensembl_identity ()
public String	cigar_line ()
public String	ensembl_start ()
public String	ensembl_end ()
public String	xref_start ()
public String	xref_end ()
public String	score ()
public String	evalue ()
public Bio::EnsEMBL::Mapper	get_mapper ()
public	transform_feature ()
public List	map_feature ()
Public Member Functions inherited from Bio::EnsEMBL::DBEntry
public Bio::EnsEMBL::DBEntry	new ()
public String	primary_id ()
public String	display_id ()
public String	optional_id ()
public String	dbname ()
public String	database ()
public String	release ()
public String	version ()
public String	db_version ()
public String	description ()
public Bio::EnsEMBL::Analysis	analysis ()
public String	comment ()
public String	priority ()
public String	db_display_name ()
public String	info_type ()
public String	info_text ()
public String	linkage_annotation ()
public String	type ()
public String	secondary_db_name ()
public String	secondary_db_table ()
public void	add_synonym ()
public Listref	get_all_synonyms ()
public Listref	get_all_dependents ()
public Listref	get_all_masters ()
public void	flush_synonyms ()
public String	status ()
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

my $xref = Bio::EnsEMBL::IdentityXref->new(
  -XREF_IDENTITY    => 80.4,
  -ENSEMBL_IDENTITY => 90.1,
  -SCORE            => 90,
  -EVALUE           => 12,
  -CIGAR_LINE       => '23MD3M2I40M',
  -XREF_START       => 1,
  -XREF_END         => 68,
  -ENSEMBL_START    => 10,
  -ENSEMBL_END      => 77,
  -ADAPTOR          => $adaptor,
  -PRIMARY_ID       => $primary_id,
  -DBNAME           => 'SwissProt'
);

Definition at line 23 of file IdentityXref.pm.

Member Function Documentation

cigar_line()

public String Bio::EnsEMBL::IdentityXref::cigar_line

(

)

  Arg [1]    : string $cigar_line
  Example    :

none

  Description: get/set for attribute cigar_line
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

ensembl_end()

public String Bio::EnsEMBL::IdentityXref::ensembl_end

(

)

  Arg [1]    : string $ensembl_end
  Example    :

none

  Description: get/set for attribute ensembl_end
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

ensembl_identity()

public String Bio::EnsEMBL::IdentityXref::ensembl_identity

(

)

  Arg [1]    : (optional) string $value
  Example    :

$ensembl_identity = $id_xref->ensembl_identity;

  Description: Getter/Setter for ensembl identity
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

ensembl_start()

public String Bio::EnsEMBL::IdentityXref::ensembl_start

(

)

  Arg [1]    : string $ensembl_start
  Example    :

none

  Description: get/set for attribute ensembl_start
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

evalue()

public String Bio::EnsEMBL::IdentityXref::evalue

(

)

  Arg [1]    : string $evalue
  Example    :

none

  Description: get/set for attribute evalue
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_mapper()

public Bio::EnsEMBL::Mapper Bio::EnsEMBL::IdentityXref::get_mapper

(

)

  Args       : none
  Example    :

none

  Description: produces a mapper object that takes coordinates from one side 
               of the alignment to the other side. "ensembl" and "external" 
               are the two coordinate systems contained.
  Returntype : Bio::EnsEMBL::Mapper
  Exceptions : none
  Caller     : general, ProteinDAS subsystem
  Status     : Stable

Code:

map_feature()

public List Bio::EnsEMBL::IdentityXref::map_feature

(

)

  Arg [1]    : a start,end capable feature object
  Example    :

none

  Description: 
  Returntype : list of Coordinates/Gaps which represents the mapping
  Exceptions : none
  Caller     : another way of doing ProteinDAS
  Status     : Stable

Code:

new()

public Bio::EnsEMBL::IdentityXref Bio::EnsEMBL::IdentityXref::new

(

)

  Arg [...]  : XREF_IDENTITY ENSEMBL_IDENTITY SCORE EVALUE CIGAR_LINE
             : XREF_START XREF_END ENSEMBL_START ENSEMBL_END
             : ANALYSIS pairs
  Example    :

see synopsis 

  Description: Create a new Bio::EnsEMBL::IdentityXref object
  Returntype : Bio::EnsEMBL::IdentityXref
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

score()

public String Bio::EnsEMBL::IdentityXref::score

(

)

  Arg [1]    : string $score
  Example    :

none

  Description: get/set for attribute score
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

transform_feature()

public Bio::EnsEMBL::IdentityXref::transform_feature

(

)

Undocumented method

Code:

xref_end()

public String Bio::EnsEMBL::IdentityXref::xref_end

(

)

  Arg [1]    : string $xref_end
  Example    :

none

  Description: get/set for attribute xref_end
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

xref_identity()

public String Bio::EnsEMBL::IdentityXref::xref_identity

(

)

  Arg [1]    : (optional) string $value
  Example    :

$xref_identity = $id_xref->xref_identity;

  Description: Getter/Setter for xref identity
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

xref_start()

public String Bio::EnsEMBL::IdentityXref::xref_start

(

)

  Arg [1]    : string $xref_start
  Example    :

none

  Description: get/set for attribute xref_start
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

---

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

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