Bio::EnsEMBL::UnmappedObject Class Reference

Inheritance diagram for Bio::EnsEMBL::UnmappedObject:

Public Member Functions
public Bio::EnsEMBL::UnmappedObject	new ()
public String	description ()
public String	summary ()
public String	type ()
public String	ensembl_object_type ()
public String	ensembl_id ()
public Int	external_db_id ()
public Int	external_db_name ()
public	stable_id ()
public String	identifier ()
public Float	query_score ()
public Float	target_score ()
public Int	unmapped_reason_id ()
public Bio::EnsEMBL::Analysis	analysis ()
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::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.

Member Function Documentation

analysis()

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:

description()

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:

ensembl_id()

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:

ensembl_object_type()

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:

external_db_id()

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:

external_db_name()

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:

identifier()

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:

new()

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:

query_score()

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:

stable_id()

public Bio::EnsEMBL::UnmappedObject::stable_id

(

)

Undocumented method

Code:

summary()

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:

target_score()

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:

type()

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:

unmapped_reason_id()

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:

---

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

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