BaseMapper.pm 6.03 KB
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=head1 LICENSE
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  Copyright (c) 1999-2011 The European Bioinformatics Institute and
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  Genome Research Limited.  All rights reserved.
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  This software is distributed under a modified Apache license.
  For license details, please see
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    http://www.ensembl.org/info/about/code_licence.html
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=head1 CONTACT
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  Please email comments or questions to the public Ensembl
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  developers list at <dev@ensembl.org>.
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  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.
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=cut
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=head1 NAME
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=head1 SYNOPSIS
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=head1 DESCRIPTION
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=head1 METHODS
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=cut

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package Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper;
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use strict;
use warnings;
no warnings 'uninitialized';

use Bio::EnsEMBL::IdMapping::BaseObject;
our @ISA = qw(Bio::EnsEMBL::IdMapping::BaseObject);

use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::ScriptUtils qw(path_append);
use Bio::EnsEMBL::IdMapping::MappingList;


# scores are considered the same if (2.0 * (s1-s2))/(s1 + s2) < this
use constant SIMILAR_SCORE_RATIO => 0.01;

    
#
# find the highest unambiguous score for all sources and targets in a scoring
# matrix
#
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;
  }

  # create checkpoint
  $mappings->write_to_file;

  return $mappings;
}


sub higher_score_exists {
  my ($self, $entry, $matrix, $sources_done, $targets_done) = @_;

  my $source = $entry->source;
  my $target = $entry->target;
  my $score = $entry->score;

  foreach my $other_source (@{ $matrix->get_sources_for_target($target) }) {
    if ($other_source != $source and !$sources_done->{$other_source} and
        $score < $matrix->get_score($other_source, $target)) {
          return 1;
    }
  }

  foreach my $other_target (@{ $matrix->get_targets_for_source($source) }) {
    if ($other_target != $target and !$targets_done->{$other_target} and
        $score < $matrix->get_score($source, $other_target)) {
          return 1;
    }
  }

  return 0;
}


#
# find ambiguous mappings (see scores_similar() for definition)
#
sub ambiguous_mapping {
  my ($self, $entry, $matrix, $other_sources, $other_targets) = @_;

  my $source = $entry->source;
  my $target = $entry->target;
  my $score = $entry->score;

  my $retval = 0;

  foreach my $other_source (@{ $matrix->get_sources_for_target($target) }) {
    my $other_score = $matrix->get_score($other_source, $target);
    
    if ($other_source != $source and
      ($self->scores_similar($score, $other_score) or $score < $other_score)) {
        $retval = 1;
        push @{ $other_sources }, $other_source;
    }
  }

  foreach my $other_target (@{ $matrix->get_targets_for_source($source) }) {
    my $other_score = $matrix->get_score($source, $other_target);

    if ($other_target != $target and
      ($self->scores_similar($score, $other_score) or $score < $other_score)) {
        $retval = 1;
        push @{ $other_targets }, $other_target;
    }
  }

  return $retval;
}


# 
# rule for similarity taken from java code...
#
sub scores_similar {
  my ($self, $s1, $s2) = @_;

  # always give priority to exact matches over very similar ones
  return 0 if ($s1 == 1 and $s2 < 1);

  my $diff = $s1 -$s2;
  $diff = -$diff if ($diff < 0);
  
  my $pc = 2 * $diff / ($s1 + $s2);
  
  return ($pc < SIMILAR_SCORE_RATIO);
}


sub filter_sources {
  my ($self, $other_sources, $sources_done) = @_;

  unless (scalar(@$other_sources) and scalar(keys %$sources_done)) {
    return $other_sources;
  }

  my @tmp = ();

  foreach my $e (@{ $other_sources }) {
    push @tmp, $e unless ($sources_done->{$e}); 
  }

  return \@tmp;
}


sub filter_targets {
  my ($self, $other_targets, $targets_done) = @_;

  unless (scalar(@{ $other_targets }) and scalar(keys %$targets_done)) {
    return $other_targets;
  }

  my @tmp = ();

  foreach my $e (@{ $other_targets }) {
    push @tmp, $e unless ($targets_done->{$e}); 
  }

  return \@tmp;
}


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