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revision 1.63, Thu Oct 18 03:27:35 2007 UTC revision 1.64, Wed Oct 24 14:25:28 2007 UTC
# Line 792  Line 792 
792  =cut  =cut
793    
794  sub should_be_member {  sub should_be_member {
795      my($self,$seq,$debug,$loose) = @_;      my($self,$seq,$debug,$loose,$debug_peg) = @_;
796    
797      if ($debug) {      if ($debug) {
798          $ENV{DEBUG}   = 1;          $ENV{DEBUG}   = 1;
# Line 804  Line 804 
804      my $dir = $self->{dir};      my $dir = $self->{dir};
805    
806      if ($ENV{DEBUG}) { print STDERR &Dumper([$self->family_id,$seq]) }      if ($ENV{DEBUG}) { print STDERR &Dumper([$self->family_id,$seq]) }
807  #    return &ross_hack($self,$fig,$loose,$seq,$dir);  
808    
809      my($in);      my($in);
810      if (open(DEC,"<$dir/decision.procedure") && ($in = <DEC>) && ($in =~ /^(\S+)\s+(\S.*\S)/))      if (open(DEC,"<$dir/decision.procedure") && ($in = <DEC>) && ($in =~ /^(\S+)(\s+(\S.*\S))?/))
811      {      {
812          no strict 'refs';          no strict 'refs';
813    
814          my $procedure = $1;          my $procedure = $1;
815          my @args      = split(/\s+/,$2);          my @args      = $3 ? split(/\s+/,$3) : ();
816          return &{$procedure}($self,$fig,$loose,$seq,$dir,@args);          return &{$procedure}($self,$fig,$loose,$seq,$dir,$debug_peg,@args);
817      }      }
818      else      else
819      {      {
820          print STDERR $self->family_id," is missing a decision procedure\n";          return &ross_hack($self,$fig,$loose,$seq,$dir,$debug_peg);
         return 0;  
821      }      }
822  }  }
823    
824  sub blast_vote {  sub blast_vote {
825      my($self,$fig,$loose,$seq,$dir,$partition,$min_bsc) = @_;      my($self,$fig,$loose,$seq,$dir,$debug_peg,$partition,$min_bsc) = @_;
826    
827      (-s "$dir/PEGs") || return undef;      (-s "$dir/PEGs") || return undef;
828      if ($ENV{DEBUG}) { print STDERR "checking: min_bsc=$min_bsc\n" }      if ($ENV{DEBUG}) { print STDERR "checking: min_bsc=$min_bsc\n" }
# Line 851  Line 850 
850    
851          my $sim = [split(/\t/,$_)];          my $sim = [split(/\t/,$_)];
852          my $peg = $sim->[1];          my $peg = $sim->[1];
853          next if (($_ = $ENV{IGNORE}) && (&FIG::genome_of($peg) eq $_)); # for debugging          next if ($debug_peg && ($debug_peg eq $peg));
854          my $bit_score = $sim->[11];          my $bit_score = $sim->[11];
855          my $matched1 = abs($sim->[7] - $sim->[6]) + 1;          my $matched1 = abs($sim->[7] - $sim->[6]) + 1;
856          my $matched2 = abs($sim->[9] - $sim->[8]) + 1;          my $matched2 = abs($sim->[9] - $sim->[8]) + 1;
# Line 892  Line 891 
891  }  }
892    
893  sub ross_hack {  sub ross_hack {
894      my($self,$fig,$loose,$seq,$dir,$min_bsc) = @_;      my($self,$fig,$loose,$seq,$dir,$debug_peg) = @_;
895    
896      my $tmpF = "$FIG_Config::temp/tmp$$.fasta";      my $tmpF = "$FIG_Config::temp/tmp$$.fasta";
897      open(TMP,">$tmpF")      open(TMP,">$tmpF")
# Line 921  Line 920 
920    
921          my $sim = [split(/\t/,$_)];          my $sim = [split(/\t/,$_)];
922          my $peg = $sim->[1];          my $peg = $sim->[1];
923          next if (($_ = $ENV{IGNORE}) && (&FIG::genome_of($peg) eq $_)); # for debugging          next if ($debug_peg && ($debug_peg eq $peg));
924    
925          my $sc = $sim->[10];          my $sc = $sim->[10];
926          my $bit_score = $sim->[11];          my $bit_score = $sim->[11];

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