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

cpanm Bio::EnsEMBL::CDS

perl -MCPAN -e shell
install Bio::EnsEMBL::CDS