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revision 1.5, Mon Mar 2 22:12:29 2009 UTC revision 1.7, Tue Jun 30 19:53:00 2009 UTC
# Line 50  Line 50 
50    
51  =item source  =item source
52    
53  [[FigPm]] object used to access the source data.  L<FIG> object used to access the source data.
54    
55  =item options  =item options
56    
# Line 192  Line 192 
192          my @subs = $fig->all_subsystems();          my @subs = $fig->all_subsystems();
193          for my $sub (@subs) {          for my $sub (@subs) {
194              # Only keep NMPDR subsystems that exist on disk.              # Only keep NMPDR subsystems that exist on disk.
195              if ($fig->nmpdr_subsystem($sub) && defined $fig->get_subsystem($sub)) {              if ($fig->nmpdr_subsystem($sub) && ! $fig->is_experimental_subsystem($sub)) {
196                  push @retVal, $sub;                  push @retVal, $sub;
197              }              }
198          }          }
199          Tracer::PutFile($subFileName, \@retVal);          Tracer::PutFile($subFileName, \@retVal);
200      }      }
201        Trace(scalar(@retVal) . " subsystems in list.") if T(ERDBLoadGroup => 3);
202      # Return the result.      # Return the result.
203      my %retVal = map { $_ => 1 } @retVal;      my %retVal = map { $_ => 1 } @retVal;
204      return \%retVal;      return \%retVal;
# Line 206  Line 207 
207    
208  =head3 GetSectionList  =head3 GetSectionList
209    
210      my @sections = BaseSproutLoader::GetSectionList($sprout, fig);      my @sections = BaseSproutLoader::GetSectionList($sprout, fig, $directory);
211    
212  Return a list of the sections for a Sprout load. The section list is  Return a list of the sections for a Sprout load. The section list is
213  normally determined by retrieving a list of all the complete genomes and  normally determined by retrieving a list of all the complete genomes and
# Line 223  Line 224 
224    
225  =item fig  =item fig
226    
227  [[FigPm]] object from which the data is being retrieved.  L<FIG> object from which the data is being retrieved.
228    
229    =item directory (optional)
230    
231    Directory from which the Sprout tables are being loaded.
232    
233  =item RETURN  =item RETURN
234    
# Line 234  Line 239 
239  =cut  =cut
240    
241  sub GetSectionList {  sub GetSectionList {
242      my ($sprout, $fig) = @_;      my ($sprout, $fig, $directory) = @_;
243      # Declare the return variable.      # Declare the return variable.
244      my @retVal;      my @retVal;
245        # Insure we have a data directory.
246        $directory ||= $sprout->LoadDirectory();
247      # Look for the section list in the data directory.      # Look for the section list in the data directory.
248      my $sectionFileName = $sprout->LoadDirectory() . "/" .      my $sectionFileName = $directory . "/" .
249          ERDBGenerate::CreateFileName('section_master', undef, 'control');          ERDBGenerate::CreateFileName('section_master', undef, 'control');
250      if (-f $sectionFileName) {      if (-f $sectionFileName) {
251          # It's there. Get the list from it.          # It's there. Get the list from it.

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