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revision 1.59, Sat Sep 15 22:33:31 2007 UTC revision 1.60, Sun Sep 16 14:54:22 2007 UTC
# Line 561  Line 561 
561    
562  sub pegs_of {  sub pegs_of {
563      my($self) = @_;      my($self) = @_;
564      my $fam_dir  = $self->{dir};      return [$self->list_members];
     my @pegs     = map { chomp; $_ } `cut -f2 $fam_dir/PEGs`;  
     return [@pegs];  
565  }  }
566    
567    
# Line 635  Line 633 
633      my($fig,$func,$func2,$id2,$fam) = @_;      my($fig,$func,$func2,$id2,$fam) = @_;
634    
635      my $i;      my $i;
636      if ($func eq $fig->function_of($id2)) { return 1 }      $func  =~ s/^FIG\d{6}[^:]*:\s*//;
637        $func2 =~ s/^FIG\d{6}[^:]*:\s*//;
638    
639        if ($func eq $func2) { return 1 }
640      my @roles = split(/(\s*;\s+)|( [\@\/] )/,$func2);      my @roles = split(/(\s*;\s+)|( [\@\/] )/,$func2);
641      for ($i=0; ($i < @roles) && (! &in_sub($fig,$roles[$i],$fam)); $i++) {}      for ($i=0; ($i < @roles) && (! &in_sub($fig,$roles[$i],$fam)); $i++) {}
642      if ($i < @roles)  { return 0 }      if ($i < @roles)  { return 0 }
# Line 774  Line 775 
775  usage:  usage:
776  C<< if ( $figfam_obj->should_be_member( $seq ) ) { #...do something... } >>  C<< if ( $figfam_obj->should_be_member( $seq ) ) { #...do something... } >>
777    
778  Returns C<TRUE> if the protein sequence in C<$seq> is judged to be  Returns ($placed,$sims).  $placed will be
779    C<TRUE> if the protein sequence in C<$seq> is judged to be
780  "similar enough" to the members of a family to potentially be included.  "similar enough" to the members of a family to potentially be included.
781    
782  I have added the "loose" argument as an optional last argument.  This means that  I have added the "loose" argument as an optional last argument.  This means that

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