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revision 1.8, Wed Oct 12 03:01:41 2005 UTC revision 1.11, Wed Nov 2 21:45:08 2005 UTC
# Line 25  Line 25 
25    
26  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,  Loads B<Subsystem>, B<Role>, B<SSCell>, B<ContainsFeature>, B<IsGenomeOf>,
27  B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>,  B<IsRoleOf>, B<OccursInSubsystem>, B<ParticipatesIn>, B<HasSSCell>,
28  B<Catalyzes>, B<Reaction>, B<ConsistsOfRoles>, B<RoleSubset>, B<HasRoleSubset>,  B<Catalyzes>, B<ConsistsOfRoles>, B<RoleSubset>, B<HasRoleSubset>,
29  B<ConsistsOfGenomes>, B<GenomeSubset>, B<HasGenomeSubset>  B<ConsistsOfGenomes>, B<GenomeSubset>, B<HasGenomeSubset>
30    
31  =item Annotation  =item Annotation
# Line 60  Line 60 
60  =item Reaction  =item Reaction
61    
62  Loads B<ReactionURL>, B<Compound>, B<CompoundName>,  Loads B<ReactionURL>, B<Compound>, B<CompoundName>,
63  B<CompoundCAS>, B<IsAComponentOf>.  B<CompoundCAS>, B<IsAComponentOf>, B<Reaction>.
64    
65  =item *  =item *
66    
# Line 92  Line 92 
92    
93  Only generate the B<Feature> and B<IsLocatedIn> tables when processing the feature group.  Only generate the B<Feature> and B<IsLocatedIn> tables when processing the feature group.
94    
95    =item dbLoad
96    
97    If TRUE, the database tables will be loaded automatically from the load files created.
98    
99  =back  =back
100    
101  =cut  =cut
# Line 106  Line 110 
110  use File::Path;  use File::Path;
111  use SproutLoad;  use SproutLoad;
112  use Stats;  use Stats;
113    use SFXlate;
114    
115  # Get the command-line parameters and options.  # Get the command-line parameters and options.
116  my ($options, @parameters) = Tracer::ParseCommand({ geneFile => "", subsysFile => "",  my ($options, @parameters) = Tracer::ParseCommand({ geneFile => "", subsysFile => "",
117                                                      trace => 3, limitedFeatures => 0 },                                                      trace => 3, limitedFeatures => 0,
118                                                                 @ARGV);                                                      dbLoad => 0 }, @ARGV);
119  # Set up tracing.  # Set up tracing.
120  TSetup("$options->{trace} SproutLoad ERDBLoad ERDB Stats Tracer Load", "+>$FIG_Config::temp/trace.log");  TSetup("$options->{trace} SproutLoad ERDBLoad ERDB Stats Tracer Load", "+>$FIG_Config::temp/trace.log");
121  # Create the sprout loader object.  # Create the sprout loader object. Note that the Sprout object does not
122    # open the database unless the "dbLoad" option is turned on.
123  my $fig = FIG->new();  my $fig = FIG->new();
124  my $sprout = Sprout->new($FIG_Config::sproutDB, { noDBOpen => 1 });  my $sprout = SFXlate->new_sprout_only(undef, undef, undef, ! $options->{dbLoad});
125  my $spl = SproutLoad->new($sprout, $fig, $options->{geneFile}, $options->{subsysFile}, $options);  my $spl = SproutLoad->new($sprout, $fig, $options->{geneFile}, $options->{subsysFile}, $options);
126  # Process the parameters.  # Process the parameters.
127  for my $group (@parameters) {  for my $group (@parameters) {

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