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revision 1.73, Tue Apr 27 15:41:28 2004 UTC revision 1.74, Wed Apr 28 04:34:52 2004 UTC
# Line 2445  Line 2445 
2445    
2446  sub bbhs {  sub bbhs {
2447      my($self,$peg,$cutoff) = @_;      my($self,$peg,$cutoff) = @_;
2448      my($sim,$peg2,$genome2,$i,@sims2);      my($sim,$peg2,$genome2,$i,@sims2,%seen);
2449    
2450      $cutoff = defined($cutoff) ? $cutoff : 1.0e-10;      $cutoff = defined($cutoff) ? $cutoff : 1.0e-10;
2451      my @bbhs = ();      my @bbhs = ();
2452    
2453      my $genome1 = $self->genome_of($peg);      my $genome1 = $self->genome_of($peg);
2454        $seen{$genome1} = 1;
2455      foreach $sim ($self->sims($peg,10000,$cutoff,"fig"))      foreach $sim ($self->sims($peg,10000,$cutoff,"fig"))
2456      {      {
2457          $peg2 = $sim->id2;          $peg2 = $sim->id2;
2458          $genome2 = $self->genome_of($peg2);          $genome2 = $self->genome_of($peg2);
2459            next if ($seen{$genome2});
2460            $seen{$genome2} = 1;
2461          @sims2 = $self->sims($peg2,10000,$cutoff,"fig");          @sims2 = $self->sims($peg2,10000,$cutoff,"fig");
2462          for ($i=0; ($i < @sims2) && ($self->genome_of($sims2[$i]->id2) ne $genome1); $i++) {}          for ($i=0; ($i < @sims2) && ($self->genome_of($sims2[$i]->id2) ne $genome1); $i++) {}
2463          if (($i < @sims2) && ($sims2[$i]->id2 eq $peg))          if (($i < @sims2) && ($sims2[$i]->id2 eq $peg))

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