/ 
Bio-EnsEMBL-112.0.0_57
River stage zero No dependents
/ Bio::EnsEMBL::UnmappedObject

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.

NAME

Bio:EnsEMBL::UnmappedObject - A object representing why a particular entity was NOT mapped to the ensembl.

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.

METHODS

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

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

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

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

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

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

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

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

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

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

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

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

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