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

List of all members.


Class Summary

Synopsis

  use Bio::EnsEMBL::UnmappedObject;

  my $uo = Bio::EnsEMBL::UnmappedObject-\>new(
    -type           =\> 'xref',
    -analysis       =\> $analysis,
    -external_db_id =\> 4100,
    -identifier     =\> "Q12345",
    -query_score    =\> 45.5,
    -target_score   =\> 29.2,
    -ensembl_id     =\> 122346,
    -ensembl_type   =\> "Translation",
    -summary        =\> "match failed for exonerate",
    -full_desc      =\> "match failed for the xref exonerate run "
      . "as match was below threshold of 90"
  );

Description

UnmappedObjects represent entities NOT mapped to ensembl. Therefore this
should help users to find out why certain accessions etc can not be
found.
 

Definition at line 33 of file UnmappedObject.pm.

Available Methods

public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public Bio::EnsEMBL::Analysis analysis ()
public Int dbID ()
public String description ()
public String ensembl_id ()
public String ensembl_object_type ()
public Int external_db_id ()
public Int external_db_name ()
public get_all_DAS_Features ()
public String identifier ()
public Boolean is_stored ()
public Bio::EnsEMBL::UnmappedObject new ()
public Bio::EnsEMBL::UnmappedObject new_fast ()
public Float query_score ()
public stable_id ()
public String summary ()
public Float target_score ()
public String type ()
public Int unmapped_reason_id ()

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 Bio::EnsEMBL::Analysis Bio::EnsEMBL::UnmappedObject::analysis ( )
  Arg [1]     : (optional) analysis to be set to
  Example     : print $unmappedObject->analysis->logic_name."\\n";
  Description : Basic getter/setter for analysis
  ReturnType  : Bio::EnsEMBL::Analysis
  Exceptions  : none
  Caller      : general
  Status      : At Risk
 
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::UnmappedObject::description ( )
  Arg [1]     : (optional) * to be set to
  Example     : print $unmappedObject->description."\\n";
  Description : Basic getter/setter for description
  ReturnType  : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
 
Code:
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public String Bio::EnsEMBL::UnmappedObject::ensembl_id ( )
  Arg [1]     : (optional) ensembl id to be set to
  Example     : print $unmappedObject->ensembl_id."\\n";
  Description : Basic getter/setter for ensembl id
  ReturnType  : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
 
Code:
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public String Bio::EnsEMBL::UnmappedObject::ensembl_object_type ( )
  Arg [1]     : (optional) ensembl object type to be set to
  Example     : print $unmappedObject->ensembl_object_type."\\n";
  Description : Basic getter/setter for ensembl object type
  ReturnType  : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
 
Code:
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public Int Bio::EnsEMBL::UnmappedObject::external_db_id ( )
  Arg [1]     : (optional) external_db_id to be set to
  Example     : print $unmappedObject->external_db_id."\\n";
  Description : Basic getter/setter for external_db_id
  ReturnType  : int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
 
Code:
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public Int Bio::EnsEMBL::UnmappedObject::external_db_name ( )
  Example     : print $unmappedObject->external_db_name()."\\n";
  Description : Basic getter for external_db_name
  ReturnType  : int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
 
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 String Bio::EnsEMBL::UnmappedObject::identifier ( )
  Arg [1]     : (optional) identifier to be set to
  Example     : print $unmappedObject->identifier."\\n";
  Description : Basic getter/setter for identifier
  ReturnType  : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
 
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 Bio::EnsEMBL::UnmappedObject Bio::EnsEMBL::UnmappedObject::new ( )
  Arg [TYPE]           : the type of mapping i.e. 'xref','cDNA' 
  Arg [ANALYSIS]       : Analysis object. 
  Arg [EXTERNAL_DB_ID] : id for the external db id this identifier is from
  Arg [IDENTIFIER]     : name of the identifier i.e. accession
  Arg [QUERY_SCORE]    : (optional) The query score
  Arg [TARGET_SCORE]   : (optional) The target score
  Arg [SUMMARY]        : The summary reason for not mapping.
  Arg [FULL_DESC]      : The Full description of why it did not map.
  Arg [ENSEMBL_ID]     : (optional) internal ensembl id for the best match
  Arg [ENSEMBL_OBJECT_TYPE] : (optional) the type of object for the best match
  Example              : see SYNOPSIS
  Returntype           : Bio::EnsEMBL::UnmappedObject
  Exceptions           : If any of the none optional args are missing
  Caller               : general
  Status               : At Risk
 
Code:
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Reimplemented from Bio::EnsEMBL::Storable.

public Bio::EnsEMBL::UnmappedObject Bio::EnsEMBL::UnmappedObject::new_fast ( )
  Arg [...]  : none
  Example    : $feature = Bio::EnsEMBL::UnmappedObject->new_fast();
  Description: Creates a new Unmapped Object.
  Returntype : Bio::EnsEMBL::UnmappedObject
  Exceptions : none
  Caller     : general
  Status     : At Risk
 
Code:
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public Float Bio::EnsEMBL::UnmappedObject::query_score ( )
  Arg [1]     : (optional) query_score to be set to
  Example     : print $unmappedObject->query_score."\\n";
  Description : Basic getter/setter for query_score
  ReturnType  : float
  Exceptions  : none
  Caller      : general
  Status      : At Risk
 
Code:
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public Bio::EnsEMBL::UnmappedObject::stable_id ( )

Undocumented method

Code:
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public String Bio::EnsEMBL::UnmappedObject::summary ( )
  Arg [1]     : (optional) summary to be set to
  Example     : print $unmappedObject->summary."\\n";
  Description : Basic getter/setter for summary
  ReturnType  : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
 
Code:
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public Float Bio::EnsEMBL::UnmappedObject::target_score ( )
  Arg [1]     : (optional) target_score to be set to
  Example     : print $unmappedObject->target_score."\\n";
  Description : Basic getter/setter for target_score
  ReturnType  : float
  Exceptions  : none
  Caller      : general
  Status      : At Risk
 
Code:
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public String Bio::EnsEMBL::UnmappedObject::type ( )
  Arg [1]     : (optional) type to be set to
  Example     : print $unmappedObject->type."\\n";
  Description : Basic getter/setter for type
  ReturnType  : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
 
Code:
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public Int Bio::EnsEMBL::UnmappedObject::unmapped_reason_id ( )
  Arg [1]     : (optional) unmapped_reason_id to be set to
  Example     : print $unmappedObject->unmapped_reason_id."\\n";
  Description : Basic getter/setter for unmapped_reason_id
  ReturnType  : int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
 
Code:
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The documentation for this class was generated from the following file: