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Bio::EnsEMBL::IdentityXref Class Reference
Inheritance diagram for Bio::EnsEMBL::IdentityXref:

List of all members.


Class Summary

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 24 of file IdentityXref.pm.

Available Methods

public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public void add_synonym ()
public Bio::EnsEMBL::Analysis analysis ()
public String cigar_line ()
public String comment ()
public String database ()
public String db_display_name ()
public Int dbID ()
public String dbname ()
public String description ()
public String display_id ()
public String ensembl_end ()
public String ensembl_id ()
public String ensembl_identity ()
public String ensembl_object_type ()
public String ensembl_start ()
public String evalue ()
public void flush_synonyms ()
public get_all_DAS_Features ()
public Listref get_all_dependents ()
public Listref get_all_masters ()
public Listref get_all_synonyms ()
public Bio::EnsEMBL::Mapper get_mapper ()
public get_synonyms ()
public String info_text ()
public String info_type ()
public Boolean is_stored ()
public String linkage_annotation ()
public List map_feature ()
public Bio::EnsEMBL::IdentityXref new ()
public Bio::EnsEMBL::DBEntry new_fast ()
public String optional_id ()
public String primary_id ()
public String priority ()
public query_end ()
public query_identity ()
public query_start ()
public String release ()
public String score ()
public secondary_db_name ()
public secondary_db_table ()
public String status ()
public target_identity ()
public transform_feature ()
public translation_end ()
public translation_start ()
public String type ()
public String version ()
public String xref_end ()
public String xref_identity ()
public String xref_start ()

Method Documentation

public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::Storable::adaptor ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBSQL::BaseAdaptor $adaptor
  Example    : none
  Description: get/set for this objects Adaptor
  Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable
 
Code:
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public void Bio::EnsEMBL::DBEntry::add_synonym ( ) [inherited]
  Arg [1]    : String $arg - synonym to add
  Example    : none
  Description: Add a synonym for the external object.
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Analysis Bio::EnsEMBL::DBEntry::analysis ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::Analysis $analysis
  Example    : none
  Description: get/set for attribute analysis
  Returntype : Bio::EnsEMBL::Analysis
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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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:
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public String Bio::EnsEMBL::DBEntry::comment ( ) [inherited]
  Args       : none
  Example    : none
  Description: Additional getter for attribute 'description'.
               The object's description.
               Only include for BioPerl interface compliance, please use
               $self->description().
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::DBEntry::database ( ) [inherited]
  Args       : none
  Example    : none
  Description: Additional getter for attribute 'dbname'.
               The name of the external database.
               Only include for BioPerl interface compliance, please use
               $self->dbname().
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::DBEntry::db_display_name ( ) [inherited]
  Arg [1]    : String $db_display_name
  Example    : none
  Description: Getter/setter for attribute 'db_display_name'.
               The preferred display name for the external database. Has
               "Projected " prepended if info_type='PROJECTION'.
  Returntype : String
  Exceptions : none
  Caller     : general
 
Code:
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public Int Bio::EnsEMBL::Storable::dbID ( ) [inherited]
  Arg [1]    : int $dbID
  Example    : none
  Description: getter/setter for the database internal id
  Returntype : int
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::Map::Ditag, and Bio::EnsEMBL::Map::DitagFeature.

public String Bio::EnsEMBL::DBEntry::dbname ( ) [inherited]
  Arg [1]    : (optional) String $arg - value to set
  Example    : none
  Description: Getter/setter for attribute 'dbname'.
               The name of the external database.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::DBEntry::description ( ) [inherited]
  Arg [1]    : (optional) String $arg - value to set
  Example    : none
  Description: Getter/setter for attribute 'description'.
               The object's description, from the xref table
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::DBEntry::display_id ( ) [inherited]
  Arg [1]    : (optional) String $arg - value to set
  Example    : none
  Description: Getter/setter for attribute 'display_id'.
               The object's preferred display name. This can be the same
               as primary_id or ensembl-specific.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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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:
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public String Bio::EnsEMBL::DBEntry::ensembl_id ( ) [inherited]
  Arg [1]    : (optional) String $arg - value to set
  Example    : none
  Description: Getter/setter for attribute ensembl_id.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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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:
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public String Bio::EnsEMBL::DBEntry::ensembl_object_type ( ) [inherited]
  Arg [1]    : (optional) String $arg - value to set
  Example    : none
  Description: Getter/setter for attribute ensembl_object_type.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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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:
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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:
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public void Bio::EnsEMBL::DBEntry::flush_synonyms ( ) [inherited]
  Args       : none
  Example    : none
  Description: Remove all synonyms from this object.
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Storable::get_all_DAS_Features ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::Gene, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Translation.

public Listref Bio::EnsEMBL::DBEntry::get_all_dependents ( ) [inherited]
  Args[1]    : (optional) Bio::EnsEMBL::Gene, Transcript or Translation object
  Example    : my @dependents = @{ $db_entry->get_all_dependents };
  Description: Get a list of DBEntrys that are depenednet on the DBEntry.
               if an ensembl gene transcript or translation is given then only
               the ones on that object will be given
  Returntype : listref of DBEntrys. May be empty.
  Exceptions : none
  Caller     : general
  Status     : UnStable
 
Code:
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public Listref Bio::EnsEMBL::DBEntry::get_all_masters ( ) [inherited]
  Args[1]    : (optional) Bio::EnsEMBL::Gene, Transcript or Translation object
  Example    : my @masters = @{ $db_entry->get_all_masters };
  Description: Get a list of DBEntrys that are the masters of the DBEntry.
               if an ensembl gene transcript or translation is given then only
               the ones on that object will be given.
  Returntype : listref of DBEntrys. May be empty.
  Exceptions : none
  Caller     : general
  Status     : UnStable
 
Code:
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public Listref Bio::EnsEMBL::DBEntry::get_all_synonyms ( ) [inherited]
  Args      : none
  Example    : my @synonyms = @{ $db_entry->get_all_synonyms };
  Description: Get a list of synonyms known for this object.
               Synonyms are lazy-loaded if required.
  Returntype : listref of strings. May be empty.
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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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:
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public Bio::EnsEMBL::DBEntry::get_synonyms ( ) [inherited]
  Description:

Deprecated:
use get_all_synonyms instead
 
Code:
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public String Bio::EnsEMBL::DBEntry::info_text ( ) [inherited]
  Arg [1]    : String $info_text
  Example    : none
  Description: Getter/setter for attribute 'info_text'.
  Returntype : String
  Exceptions : none
  Caller     : general
 
Code:
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public String Bio::EnsEMBL::DBEntry::info_type ( ) [inherited]
  Arg [1]    : String $info_type
  Example    : none
  Description: Getter/setter for attribute 'info_type'.
  Returntype : String
  Exceptions : none
  Caller     : general
 
Code:
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public Boolean Bio::EnsEMBL::Storable::is_stored ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBSQL::DBConnection 
             : or Bio::EnsEMBL::DBSQL::DBAdaptor
  Example    : do_something if($object->is_stored($db));
  Description: Returns true if this object is stored in the provided database.
               This works under the assumption that if the adaptor and dbID are
               set and the database of the adaptor shares the port, dbname and
               hostname with the provided database, this object is stored in
               that database.
  Returntype : 1 or 0
  Exceptions : throw if dbID is set but adaptor is not
               throw if adaptor is set but dbID is not
               throw if incorrect argument is passed
  Caller     : store methods
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::DBEntry::linkage_annotation ( ) [inherited]
  Arg [1]    : String $object_xref_text
  Example    : none
  Description: Getter/setter for attribute 'linkage_annotation'.
  Returntype : String
  Exceptions : none
  Caller     : general
 
Code:
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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:
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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:
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Reimplemented from Bio::EnsEMBL::DBEntry.

public Bio::EnsEMBL::DBEntry Bio::EnsEMBL::DBEntry::new_fast ( ) [inherited]
  Arg [1]    : Hashref $hashref - hash reference to bless as new DBEntry object
  Description: A very quick constructor that requires internal knowledge of
               the class. This is used in speed critical sections of the code
               where many objects need to be created quickly.
  Returntype : Bio::EnsEMBL::DBEntry
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::DBEntry::optional_id ( ) [inherited]
  Args       : none
  Example    : none
  Description: Additional getter for attribute 'display_id'.
               The object's preferred display name.
               Only include for BioPerl interface compliance, please use
               $self->display_id().
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::DBEntry::primary_id ( ) [inherited]
  Arg [1]    : (optional) String $arg - value to set
  Example    : none
  Description: Getter/setter for attribute 'primary_id'.
               This is the object's primary id in the external database.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::DBEntry::priority ( ) [inherited]
  Arg [1]    : int $priority
  Example    : none
  Priority   : Getter/setter for attribute 'priority'. Note this
               is the priority from the external_db table.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : At Risk
             : due to it being under development
 
Code:
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public Bio::EnsEMBL::IdentityXref::query_end ( )
  Description:

Deprecated:
. Use xref_end() instead. Status : At Risk
 
Code:
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public Bio::EnsEMBL::IdentityXref::query_identity ( )
  Description:

Deprecated:
. Use xref_identity() instead. Status : At Risk
 
Code:
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public Bio::EnsEMBL::IdentityXref::query_start ( )
  Description:

Deprecated:
. Use xref_start() instead. Status : At Risk
 
Code:
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public String Bio::EnsEMBL::DBEntry::release ( ) [inherited]
  Arg [1]    : (optional) String $arg - value to set
  Example    : none
  Description: Getter/setter for attribute 'release'.
               The external database release name.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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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
 
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public Bio::EnsEMBL::DBEntry::secondary_db_name ( ) [inherited]
  Arg [1]    : String $secondary_db_name
  Example    : none
  Description: Getter/setter for attribute 'secondary_db_name'.
  Returnsecondary_db_name : String
  Exceptions : none
  Caller     : general
 
Code:
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public Bio::EnsEMBL::DBEntry::secondary_db_table ( ) [inherited]
  Arg [1]    : String $secondary_db_table
  Example    : none
  Description: Getter/setter for attribute 'secondary_db_table'.
  Returnsecondary_db_table : String
  Exceptions : none
  Caller     : general
 
Code:
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public String Bio::EnsEMBL::DBEntry::status ( ) [inherited]
  Arg [1]    : (optional) String $arg - value to set
  Example    : none
  Description: Getter/setter for attribute 'status'.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::IdentityXref::target_identity ( )
  Description:

Deprecated:
. Use ensembl_identity() instead. Status : At Risk
 
Code:
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public Bio::EnsEMBL::IdentityXref::transform_feature ( )

Undocumented method

Code:
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public Bio::EnsEMBL::IdentityXref::translation_end ( )
  Description:

Deprecated:
. Use ensembl_end() instead. Status : At Risk
 
Code:
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public Bio::EnsEMBL::IdentityXref::translation_start ( )
  Description:

Deprecated:
. Use ensembl_start() instead. Status : At Risk
 
Code:
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public String Bio::EnsEMBL::DBEntry::type ( ) [inherited]
  Arg [1]    : String $type
  Example    : none
  Description: Getter/setter for attribute 'type'.
  Returntype : String
  Exceptions : none
  Caller     : general
 
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public String Bio::EnsEMBL::DBEntry::version ( ) [inherited]
  Arg [1]    : (optional) String $arg - value to set
  Example    : none
  Description: Getter/setter for attribute 'version'.
               The object's version in the external database.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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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:
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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:
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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:
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The documentation for this class was generated from the following file: