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revision 1.298, Wed Jun 22 21:00:24 2005 UTC revision 1.299, Thu Jun 23 19:35:07 2005 UTC
# Line 158  Line 158 
158      }      }
159      # Here we have the normal case. Check for default tracing. We only do this if      # Here we have the normal case. Check for default tracing. We only do this if
160      # the proper parameters are present and nobody else has set up tracing yet.      # the proper parameters are present and nobody else has set up tracing yet.
161      if (defined($FIG_Config::trace_levels) && Tracer::Setups() == 0) {      if (exists($ENV{Trace}))
162        {
163            my $trace_type = (defined $FIG_Config::trace_type ? $FIG_Config::trace_type : "WARN");
164            TSetup($ENV{Trace}, $trace_type);
165        }
166        elsif (defined($FIG_Config::trace_levels) && Tracer::Setups() == 0) {
167          # It's on, so we set it up. If the type is omitted, we default to WARN, which          # It's on, so we set it up. If the type is omitted, we default to WARN, which
168          # is the standard error output.          # is the standard error output.
169          my $trace_type = (defined $FIG_Config::trace_type ? $FIG_Config::trace_type : "WARN");          my $trace_type = (defined $FIG_Config::trace_type ? $FIG_Config::trace_type : "WARN");
# Line 4694  Line 4699 
4699    
4700  sub map_genome_to_id  sub map_genome_to_id
4701  {  {
4702        my($self, $genome) = @_;
4703    
4704        my $mapperc = $self->cached("_genome_mapper");
4705        my $mapper = $mapperc->{mapper_obj};
4706        if (!defined($mapper))
4707        {
4708            $mapper = new GenomeIDMap($self);
4709            $mapperc->{mapper_obj} = $mapper;
4710        }
4711    
4712        return $mapper->map_genome_id_to_gnum($genome);
4713    }
4714    
4715    sub map_id_to_genome
4716    {
4717        my($self, $id) = @_;
4718    
4719        my $mapperc = $self->cached("_genome_mapper");
4720        my $mapper = $mapperc->{mapper_obj};
4721        if (!defined($mapper))
4722        {
4723            $mapper = new GenomeIDMap($self);
4724            $mapperc->{mapper_obj} = $mapper;
4725        }
4726    
4727        return $mapper->map_gnum_to_gid($id);
4728  }  }
4729    
4730  ################ Routines to process functional coupling for PEGs  ##########################  ################ Routines to process functional coupling for PEGs  ##########################
# Line 7275  Line 7306 
7306                load_attributes                load_attributes
7307                load_bbhs                load_bbhs
7308                load_literature                load_literature
7309                load_couplings                load_coupling
7310             );             );
7311    
7312      push(@packages, "pegs_in_conflict | peg_to_subsystems > $FIG_Config::global/conflicted.pegs");      push(@packages, "pegs_in_conflict | peg_to_subsystems > $FIG_Config::global/conflicted.pegs");

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