From dadd5b121fda19c7411a99ddfbdc73ae9ee8bd72 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Tue, 18 Oct 2011 14:20:57 +0000
Subject: [PATCH] Reformat for readability.
---
.../IdMapping/InternalIdMapper/BaseMapper.pm | 213 ++++++++++--------
1 file changed, 117 insertions(+), 96 deletions(-)
diff --git a/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/BaseMapper.pm b/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/BaseMapper.pm
index 05920e1a44..ab1898e21a 100644
--- a/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/BaseMapper.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/BaseMapper.pm
@@ -1,3 +1,4 @@
+
=head1 LICENSE
Copyright (c) 1999-2011 The European Bioinformatics Institute and
@@ -41,41 +42,43 @@ 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 $self = shift;
+ my $matrix = shift;
my $mapping_name = shift;
# argument checks
- unless ($matrix and
- $matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
+ unless ($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,
- );
-
+ 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");
+ if ( $mappings->loaded ) {
+ $self->logger->info(
+ "Read existing mappings from ${mapping_name}.ser.\n");
return $mappings;
}
@@ -83,169 +86,187 @@ sub basic_mapping {
my $targets_done = {};
# sort scoring matrix entries by descending score
- my @sorted_entries = sort { $b->score <=> $a->score }
- @{ $matrix->get_all_Entries };
+ 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)) {
-
+ 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});
-
+ 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));
-
+ 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)) {
+ 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));
+ $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;
- }
+ $sources_done->{ $entry->source } = 1;
+ $targets_done->{ $entry->target } = 1;
+ } ## end while ( my $entry = shift...)
# create checkpoint
$mappings->write_to_file;
return $mappings;
-}
-
+} ## end sub basic_mapping
sub higher_score_exists {
- my ($self, $entry, $matrix, $sources_done, $targets_done) = @_;
+ 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;
+ 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;
+ 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, $other_target ) )
+ {
+ return 1;
}
}
return 0;
-}
-
+} ## end sub higher_score_exists
#
# find ambiguous mappings (see scores_similar() for definition)
#
sub ambiguous_mapping {
- my ($self, $entry, $matrix, $other_sources, $other_targets) = @_;
+ my ( $self, $entry, $matrix, $other_sources, $other_targets ) = @_;
my $source = $entry->source;
my $target = $entry->target;
- my $score = $entry->score;
+ 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_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;
+ 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 $retval;
-}
-
+} ## end sub ambiguous_mapping
-#
+#
# rule for similarity taken from java code...
#
sub scores_similar {
- my ($self, $s1, $s2) = @_;
+ 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);
-}
+ 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) = @_;
+ my ( $self, $other_sources, $sources_done ) = @_;
- unless (scalar(@$other_sources) and scalar(keys %$sources_done)) {
+ unless ( scalar(@$other_sources) and scalar( keys %$sources_done ) ) {
return $other_sources;
}
my @tmp = ();
- foreach my $e (@{ $other_sources }) {
- push @tmp, $e unless ($sources_done->{$e});
+ foreach my $e ( @{$other_sources} ) {
+ push @tmp, $e unless ( $sources_done->{$e} );
}
return \@tmp;
}
-
sub filter_targets {
- my ($self, $other_targets, $targets_done) = @_;
+ my ( $self, $other_targets, $targets_done ) = @_;
- unless (scalar(@{ $other_targets }) and scalar(keys %$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});
+ foreach my $e ( @{$other_targets} ) {
+ push @tmp, $e unless ( $targets_done->{$e} );
}
return \@tmp;
}
-
1;
-
--
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