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

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NAME

Bio::EnsEMBL::IdMapping::ScoreBuilder - score builder base class

SYNOPSIS

This class is not instantiated. Please see subclasses for usage examples (e.g. GeneScoreBuilder).

DESCRIPTION

This is the base class for the score builders used in the stable Id mapping application. It contains methods which are used by more than one ScoreBuilder.

METHODS

  create_shrinked_matrix
  internal_id_rescore
  log_matrix_stats

create_shrinked_matrix

  Arg[1]      : Bio::EnsEMBL::Idmapping::ScoredMappingMatrix $matrix - a scoring
                matrix
  Arg[2]      : Bio::EnsEMBL::Idmapping::MappingList $mappings - mappings
  Arg[3]      : String $cache_file - base name of a cache file (extension '.ser'
                will be added automatically) for the returned matrix
  Example     : my $new_scores = $score_builder->create_shrinked_matrix(
                  $gene_scores, $mappings, "gene_matrix1");
  Description : Create a shrinked scoring matrix which doesn't contain entries
                which were already mapped. It also logs how many new mappings
                were added in this process.
  Return type : Bio::EnsEMBL::IdMapping::ScoredMappingMatrix
  Exceptions  : thrown on wrong or missing arguments
  Caller      : InternalIdMapper plugin
  Status      : At Risk
              : under development

internal_id_rescore

  Arg[1]      : Bio::EnsEMBL::Idmapping::ScoredMappingMatrix $matrix - a scoring
                matrix
  Example     : $score_builder->internal_id_rescore($gene_scores);
  Description : Rescore ambiguous mappings based on internal Ids. This is the
                last disambiguation step and is only useful if objects with the
                same internal Id were used in source and target dbs (e.g. in
                patch builds or if objects were copied from source to target).

                If a source and target gene have the same internal Id and there
                are mappings to other target genes then these *other* mappings
                are penalised.
  Return type : none
  Exceptions  : thrown on wrong or missing argument
  Caller      : InternalIdMapper plugins
  Status      : At Risk
              : under development

log_matrix_stats

  Arg[1]      : Bio::EnsEMBL::Idmapping::ScoredMappingMatrix $matrix - a scoring
                matrix
  Example     : $score_builder->log_matrix_stats;
  Description : Logs scoring matrix statistics (number of entries, min/max/avg
                scores).
  Return type : none
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development