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revision 1.72, Sat Apr 24 23:27:05 2004 UTC revision 1.73, Tue Apr 27 15:41:28 2004 UTC
# Line 2443  Line 2443 
2443      return @sims;      return @sims;
2444  }  }
2445    
2446    sub bbhs {
2447        my($self,$peg,$cutoff) = @_;
2448        my($sim,$peg2,$genome2,$i,@sims2);
2449    
2450        $cutoff = defined($cutoff) ? $cutoff : 1.0e-10;
2451        my @bbhs = ();
2452    
2453        my $genome1 = $self->genome_of($peg);
2454        foreach $sim ($self->sims($peg,10000,$cutoff,"fig"))
2455        {
2456            $peg2 = $sim->id2;
2457            $genome2 = $self->genome_of($peg2);
2458            @sims2 = $self->sims($peg2,10000,$cutoff,"fig");
2459            for ($i=0; ($i < @sims2) && ($self->genome_of($sims2[$i]->id2) ne $genome1); $i++) {}
2460            if (($i < @sims2) && ($sims2[$i]->id2 eq $peg))
2461            {
2462                push(@bbhs,[$peg2,$sim->psc]);
2463            }
2464        }
2465        return @bbhs;
2466    }
2467    
2468  =pod  =pod
2469    
2470  =head1 dsims  =head1 dsims

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