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Bio-EnsEMBL-112.0.0_58
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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