Inheritance diagram for Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper:

Public Member Functions
public	basic_mapping ()

public	higher_score_exists ()

public	ambiguous_mapping ()

public	scores_similar ()

public	filter_sources ()

public	filter_targets ()

Public Member Functions inherited from Bio::EnsEMBL::IdMapping::BaseObject
public $this	new ()

public Filehandle	get_filehandle ()

public Boolean	file_exists ()

public SQLStatement	fetch_value_from_db ()

public Int	dump_table_to_file ()

public Int	upload_file_into_table ()

public Bio::EnsEMBL::Utils::Logger	logger ()

public Bio::EnsEMBL::Utils::ConfParser	conf ()

public Bio::EnsEMBL::IdMapping::Cache	cache ()

Detailed Description

Synopsis

Description

Definition at line 17 of file BaseMapper.pm.

Member Function Documentation

◆ ambiguous_mapping()

public Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper::ambiguous_mapping ( )

Undocumented method

Code:

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◆ basic_mapping()

public Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper::basic_mapping ( )

Undocumented method

Code:

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sub basic_mapping {
  my $self         = shift;
  my $matrix       = shift;
  my $mapping_name = shift;
 
  # argument checks
  unless ($matrix
      and $matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix') )
  {
    throw('Need a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }
 
  throw('Need a name for serialising the mapping.')
    unless ($mapping_name);
 
  # Create a new MappingList object. Specify AUTO_LOAD to load
  # serialised existing mappings if found
  my $dump_path =
    path_append( $self->conf->param('basedir'), 'mapping' );
 
  my $mappings =
    Bio::EnsEMBL::IdMapping::MappingList->new(
                                   -DUMP_PATH  => $dump_path,
                                   -CACHE_FILE => "${mapping_name}.ser",
                                   -AUTO_LOAD  => 1, );
 
  # checkpoint test: return a previously stored MappingList
  if ( $mappings->loaded ) {
    $self->logger->info(
                  "Read existing mappings from ${mapping_name}.ser.\n");
    return $mappings;
  }
 
  my $sources_done = {};
  my $targets_done = {};
 
  # sort scoring matrix entries by descending score
  my @sorted_entries =
    sort { $b->score <=> $a->score } @{ $matrix->get_all_Entries };
 
  # debug
  #my $idx = substr($mapping_name, -1);
 
  while ( my $entry = shift(@sorted_entries) ) {
 
    #$self->logger->debug("\nxxx$idx ".$entry->to_string." ");
 
    # we already found a mapping for either source or target
    next
      if (    $sources_done->{ $entry->source }
           or $targets_done->{ $entry->target } );
 
    #$self->logger->debug('d');
 
    # there's a better mapping for either source or target
    next
      if ( $self->higher_score_exists(
                           $entry, $matrix, $sources_done, $targets_done
           ) );
 
    #$self->logger->debug('h');
 
    # check for ambiguous mappings; they are dealt with later
    my $other_sources = [];
    my $other_targets = [];
 
    if ( $self->ambiguous_mapping( $entry,         $matrix,
                                   $other_sources, $other_targets ) )
    {
      #$self->logger->debug('a');
 
      $other_sources =
        $self->filter_sources( $other_sources, $sources_done );
      $other_targets =
        $self->filter_targets( $other_targets, $targets_done );
 
      next if ( scalar(@$other_sources) or scalar(@$other_targets) );
    }
 
    #$self->logger->debug('A');
 
    # this is the best mapping, add it
    $mappings->add_Entry($entry);
 
    $sources_done->{ $entry->source } = 1;
    $targets_done->{ $entry->target } = 1;
  } ## end while ( my $entry = shift...)
 
  # create checkpoint
  $mappings->write_to_file;
 
  return $mappings;
} ## end sub basic_mapping

◆ filter_sources()

public Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper::filter_sources ( )

Undocumented method

Code:

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◆ filter_targets()

public Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper::filter_targets ( )

Undocumented method

Code:

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◆ higher_score_exists()

public Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper::higher_score_exists ( )

Undocumented method

Code:

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◆ scores_similar()

public Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper::scores_similar ( )

Undocumented method

Code:

click to view

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

ensembl/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/BaseMapper.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ ambiguous_mapping()

◆ basic_mapping()

◆ filter_sources()

◆ filter_targets()

◆ higher_score_exists()

◆ scores_similar()