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revision 1.3, Thu Jun 25 22:28:43 2009 UTC revision 1.4, Sat Jun 27 18:55:29 2009 UTC
# Line 111  Line 111 
111  }  }
112    
113  sub reference_set_for_paralogs {  sub reference_set_for_paralogs {
114      my($genomes,$roles,$keep_multifunctional,$max_sc) = @_;      my($genomes,$roles,$parms) = @_;
115    
116        $parms ||= {};
117    
118        my $keep_multifunctional = $parms->{'keep_multifunctional'};
119        if (! defined($keep_multifunctional)) { $keep_multifunctional = 1 };
120    
121        my $max_sc               = $parms->{'max_sc'};
122        if (! defined($max_sc))  { $max_sc = 1.0e-5 }
123    
124        my $min_cov              = $parms->{'min_cov'};
125        if (! defined($min_cov)) { $min_cov = 0.7 }
126    
127      if (! $max_sc) { $max_sc = 1.0e-5 }      if (! $max_sc) { $max_sc = 1.0e-5 }
128      my %ref_genomes = map { $_ => 1 } @$genomes;      my %ref_genomes = map { $_ => 1 } @$genomes;
# Line 154  Line 165 
165    
166          foreach my $sim (@blastout)          foreach my $sim (@blastout)
167          {          {
168              if ((! $pegs{$sim->id2}) && $fig->is_real_feature($sim->id2))              if ((! $pegs{$sim->id2}) && $fig->is_real_feature($sim->id2) &&
169                    ((($sim->e2 + 1 - $sim->b2) /$sim->ln2) >= $min_cov))
170              {              {
171                  $pegs{$sim->id2} = $fig->function_of($sim->id2);                  $pegs{$sim->id2} = $fig->function_of($sim->id2);
172                  my $gs = $fig->genus_species(&FIG::genome_of($sim->id2));                  my $gs = $fig->genus_species(&FIG::genome_of($sim->id2));

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