[Bio] / FigKernelScripts / TransactFeatures.pl Repository:
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revision 1.4, Thu Aug 11 03:19:31 2005 UTC revision 1.5, Thu Aug 11 04:14:45 2005 UTC
# Line 150  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 168  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("$traceLevel Tracer DocUtils FIG", "TEXT");
# Line 235  Line 240 
240                  } elsif ($command eq 'delete') {                  } elsif ($command eq 'delete') {
241                      $controlBlock->Delete(@fields);                      $controlBlock->Delete(@fields);
242                  } elsif ($command eq 'change') {                  } elsif ($command eq 'change') {
243                        # Here we have a special case. If "noalias" is in effect, we need
244                        # to splice an empty field in before the translation.
245                        if ($controlBlock->Option("noAlias")) {
246                            splice @fields, 3, 0, "";
247                        }
248                      $controlBlock->Change(@fields);                      $controlBlock->Change(@fields);
249                  } else {                  } else {
250                      $controlBlock->AddMessage("Invalid command $command in line $tranCount for genome $genomeID");                      $controlBlock->AddMessage("Invalid command $command in line $tranCount for genome $genomeID");

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