| 2853 |
|
|
| 2854 |
my $genomeQ = $genome ? quotemeta $genome : ""; |
my $genomeQ = $genome ? quotemeta $genome : ""; |
| 2855 |
|
|
|
$peg = ""; |
|
| 2856 |
$rdbH = $self->db_handle; |
$rdbH = $self->db_handle; |
| 2857 |
if (($relational_db_response = $rdbH->SQL("SELECT id FROM ext_alias WHERE ( alias = \'$alias\' )")) && |
if (($relational_db_response = $rdbH->SQL("SELECT id FROM ext_alias WHERE ( alias = \'$alias\' )")) && |
| 2858 |
(@$relational_db_response > 0)) |
(@$relational_db_response > 0)) |
| 2859 |
{ |
{ |
| 2860 |
|
@pegs = map { $_->[0] } @$relational_db_response; |
| 2861 |
if (@$relational_db_response == 1) |
if (@$relational_db_response == 1) |
| 2862 |
{ |
{ |
| 2863 |
$peg = $relational_db_response->[0]->[0]; |
$peg = $relational_db_response->[0]->[0]; |
| 2864 |
|
return wantarray() ? ($peg) : $peg; |
| 2865 |
} |
} |
| 2866 |
elsif (wantarray()) |
elsif (wantarray()) |
| 2867 |
{ |
{ |
| 2868 |
return map { $_->[0] } @$relational_db_response; |
return map { $_->[0] } @$relational_db_response; |
| 2869 |
} |
} |
|
} |
|
| 2870 |
else |
else |
| 2871 |
{ |
{ |
| 2872 |
my @poss = grep { $_ =~ /^fig\|/ } map { $_->[0] } $self->mapped_prot_ids($alias); |
return wantarray() ? () : ""; |
|
if ($genomeQ) |
|
|
{ |
|
|
@poss = grep { $_ =~ /^fig\|$genomeQ/ } @poss; |
|
| 2873 |
} |
} |
|
|
|
|
if (@poss == 1) |
|
|
{ |
|
|
$peg = $poss[0]; |
|
| 2874 |
} |
} |
|
elsif (wantarray()) |
|
|
{ |
|
|
return @poss; |
|
|
} |
|
|
else |
|
|
{ |
|
|
return ""; |
|
|
} |
|
|
} |
|
|
return wantarray() ? ($peg) : $peg; |
|
| 2875 |
} |
} |
| 2876 |
|
|
| 2877 |
sub to_alias { |
sub to_alias { |
| 2878 |
my($self,$fid,$type) = @_; |
my($self,$fid,$type) = @_; |
| 2879 |
|
|
| 2880 |
my @aliases = grep { $_ =~ /^$type\|/ } $self->feature_aliases($fid); |
my @aliases = grep { $_ =~ /^$type\|/ } $self->feature_aliases($fid); |
|
if (@aliases == 0) |
|
|
{ |
|
|
@aliases = grep { $_ =~ /^$type\|/ } map { $_->[0] } $self->mapped_prot_ids($fid); |
|
|
} |
|
| 2881 |
|
|
| 2882 |
if (wantarray()) |
if (wantarray()) |
| 2883 |
{ |
{ |
| 3188 |
my($ev,$sc,$i,$j); |
my($ev,$sc,$i,$j); |
| 3189 |
|
|
| 3190 |
$ev = []; |
$ev = []; |
|
$sc = 0; |
|
| 3191 |
|
|
| 3192 |
$i = 0; |
$i = 0; |
| 3193 |
$j = 0; |
$j = 0; |
| 3203 |
} |
} |
| 3204 |
else |
else |
| 3205 |
{ |
{ |
| 3206 |
$sc += $self->accumulate_ev($genome1,$sim1->[$i]->[1],$sim2->[$j]->[1],$bound,$ev); |
$self->accumulate_ev($genome1,$sim1->[$i]->[1],$sim2->[$j]->[1],$bound,$ev); |
| 3207 |
$i++; |
$i++; |
| 3208 |
$j++; |
$j++; |
| 3209 |
} |
} |
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