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revision 1.1, Mon Jun 22 19:35:59 2009 UTC revision 1.3, Thu Jun 25 22:28:43 2009 UTC
# Line 23  Line 23 
23    
24  use Data::Dumper;  use Data::Dumper;
25  use Carp;  use Carp;
26    use gjoalignment;
27    
28  sub context_tags {  sub context_tags {
29      my($pegs,$dist) = @_;      my($pegs,$dist) = @_;
# Line 153  Line 154 
154    
155          foreach my $sim (@blastout)          foreach my $sim (@blastout)
156          {          {
157              if (! $pegs{$sim->id2})              if ((! $pegs{$sim->id2}) && $fig->is_real_feature($sim->id2))
158              {              {
159                  $pegs{$sim->id2} = $fig->function_of($sim->id2);                  $pegs{$sim->id2} = $fig->function_of($sim->id2);
160                  my $gs = $fig->genus_species(&FIG::genome_of($sim->id2));                  my $gs = $fig->genus_species(&FIG::genome_of($sim->id2));
# Line 163  Line 164 
164      }      }
165      push(@seqs,@to_add);      push(@seqs,@to_add);
166      if (@seqs < 2) { return undef }      if (@seqs < 2) { return undef }
167      return &align_with_muscle(\@seqs);      return &gjoalignment::align_with_muscle(\@seqs);
168  }  }
169    
170  sub role_in {  sub role_in {

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