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revision 1.100, Sun May 30 15:04:26 2004 UTC revision 1.101, Tue Jun 1 00:45:38 2004 UTC
# Line 2810  Line 2810 
2810    
2811    
2812  sub bbhs {  sub bbhs {
2813      my($self,$peg,$cutoff) = @_;      my($self,$peg,$cutoff,$frac_match) = @_;
2814      my($sim,$peg2,$genome2,$i,@sims2,%seen);      my($sim,$peg2,$genome2,$i,@sims2,%seen);
2815    
2816        $frac_match = defined($frac_match) ? $frac_match : 0;
2817    
2818      $cutoff = defined($cutoff) ? $cutoff : 1.0e-10;      $cutoff = defined($cutoff) ? $cutoff : 1.0e-10;
2819      my @bbhs = ();      my @bbhs = ();
2820      my @precomputed = ();      my @precomputed = ();
# Line 2836  Line 2838 
2838      foreach $sim ($self->sims($peg,10000,$cutoff,"fig"))      foreach $sim ($self->sims($peg,10000,$cutoff,"fig"))
2839      {      {
2840          $peg2 = $sim->id2;          $peg2 = $sim->id2;
2841          if ($bbhs{$peg2})          my $frac = &FIG::min(($sim->e1+1 - $sim->b1) / $sim->ln1, ($sim->e2+1 - $sim->b2) / $sim->ln2);
2842            if ($bbhs{$peg2} && ($frac >= $frac_match))
2843          {          {
2844              push(@bbhs,[$peg2,$sim->psc]);              push(@bbhs,[$peg2,$sim->psc]);
2845          }          }

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