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revision 1.3, Thu Aug 11 03:10:35 2005 UTC revision 1.6, Thu Aug 11 05:16:46 2005 UTC
# Line 32  Line 32 
32  a copy of each transaction file in which the pseudo-IDs have been replaced by  a copy of each transaction file in which the pseudo-IDs have been replaced by
33  real IDs.  real IDs.
34    
35    =item annotate
36    
37    Annotate the features created by the transactions so as to indicate how they were
38    derived.
39    
40    =item fix
41    
42    Fix the locations of new features and verify the translations of new and changed
43    features.
44    
45  =back  =back
46    
47  =head2 The Transaction File  =head2 The Transaction File
# Line 140  Line 150 
150  Wrap each organism's processing in a database transaction. This makes the process  Wrap each organism's processing in a database transaction. This makes the process
151  slightly more restartable than it would be otherwise.  slightly more restartable than it would be otherwise.
152    
153    =item noAlias
154    
155    Assume that the transaction files do not contain aliases. This means that in CHANGE
156    records the translation will immediately follow the location.
157    
158  =cut  =cut
159    
160  use strict;  use strict;
# Line 158  Line 173 
173  use FixTransactions;  use FixTransactions;
174    
175  # Get the command-line options.  # Get the command-line options.
176  my ($options, @parameters) = Tracer::ParseCommand({ trace => 3, safe => 0 }, @ARGV);  my ($options, @parameters) = Tracer::ParseCommand({ trace => 3, safe => 0, noAlias => 0 }, @ARGV);
177  # Set up tracing.  # Set up tracing.
178  my $traceLevel = $options->{trace};  my $traceLevel = $options->{trace};
179  TSetup("$traceLevel Tracer DocUtils FIG", "TEXT");  TSetup("$traceLevel Tracer DocUtils FIG", "TEXT");
# Line 172  Line 187 
187      $controlBlock = CountTransactions->new($options, $mainCommand, @parameters);      $controlBlock = CountTransactions->new($options, $mainCommand, @parameters);
188  } elsif ($mainCommand eq 'process') {  } elsif ($mainCommand eq 'process') {
189      $controlBlock = ApplyTransactions->new($options, $mainCommand, @parameters);      $controlBlock = ApplyTransactions->new($options, $mainCommand, @parameters);
190    } elsif ($mainCommand eq 'annotate') {
191        $controlBlock = AnnotateTransactions->new($options, $mainCommand, @parameters);
192  } elsif ($mainCommand eq 'fix') {  } elsif ($mainCommand eq 'fix') {
193      $controlBlock = FixTransactions->new($options, $mainCommand, @parameters);      $controlBlock = FixTransactions->new($options, $mainCommand, @parameters);
194  } else {  } else {
# Line 225  Line 242 
242                  } elsif ($command eq 'delete') {                  } elsif ($command eq 'delete') {
243                      $controlBlock->Delete(@fields);                      $controlBlock->Delete(@fields);
244                  } elsif ($command eq 'change') {                  } elsif ($command eq 'change') {
245                        # Here we have a special case. If "noalias" is in effect, we need
246                        # to splice an empty field in before the translation.
247                        if ($controlBlock->Option("noAlias")) {
248                            splice @fields, 3, 0, "";
249                        }
250                      $controlBlock->Change(@fields);                      $controlBlock->Change(@fields);
251                  } else {                  } else {
252                      $controlBlock->AddMessage("Invalid command $command in line $tranCount for genome $genomeID");                      $controlBlock->AddMessage("Invalid command $command in line $tranCount for genome $genomeID");
# Line 233  Line 255 
255              }              }
256              # Terminate processing for this genome.              # Terminate processing for this genome.
257              my $orgStats = $controlBlock->EndGenome();              my $orgStats = $controlBlock->EndGenome();
258              Trace("Statistics for $genomeID\n\n" . $orgStats->Show()) if T(3);              Trace("Statistics for $genomeID\n\n" . $orgStats->Show() . "\n") if T(3);
259              # Close the transaction input file.              # Close the transaction input file.
260              close TRANS;              close TRANS;
261          }          }
262      }      }
263      # Terminate processing.      # Terminate processing.
264      $controlBlock->Teardown();      $controlBlock->Teardown();
265      Trace("Statistics for this run\n\n" . $controlBlock->Show()) if T(1);      Trace("Statistics for this run\n\n" . $controlBlock->Show() . "\n") if T(1);
266      Trace("Processing complete.") if T(1);      Trace("Processing complete.") if T(1);
267  }  }
268    

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