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revision 1.52, Thu Sep 1 18:14:53 2005 UTC revision 1.53, Thu Sep 1 18:23:49 2005 UTC
# Line 387  Line 387 
387  =cut  =cut
388    
389  sub package_annotations {  sub package_annotations {
390      my($fig,$who,$date,$genomes,$file) = @_;      my($fig,$who,$date,$genomes,$file, %options) = @_;
391      my $fig_base = "$FIG_Config::fig_disk/FIG";      my $fig_base = "$FIG_Config::fig_disk/FIG";
392    
393      if (!open(ANNOTATIONS,">$file"))      if (!open(ANNOTATIONS,">$file"))
# Line 421  Line 421 
421          }          }
422    
423      }      }
     for my $gent (@annos)  
     {  
         my($genome, $alist) = @$gent;  
   
         for my $peg (sort { &FIG::by_fig_id($a, $b) } keys %$alist)  
         {  
             for my $aent (@{$alist->{$peg}})  
             {  
                 chomp $aent->[$#$aent];  
                 print ANNOTATIONS join("\n", @$aent) . "\n///\n";  
             }  
         }  
424    
     }  
425      print ANNOTATIONS "//\n";      print ANNOTATIONS "//\n";
426    
427        if (!$options{skip_aliases})
428        {
429      for my $gent (@annos)      for my $gent (@annos)
430      {      {
431          my($genome, $alist) = @$gent;          my($genome, $alist) = @$gent;
# Line 447  Line 437 
437              print ANNOTATIONS join("\t",($peg,join(",",@aliases),$gs,scalar $fig->function_of($peg))) . "\n";              print ANNOTATIONS join("\t",($peg,join(",",@aliases),$gs,scalar $fig->function_of($peg))) . "\n";
438          }          }
439      }      }
440        }
441    
442      print ANNOTATIONS "//\n";      print ANNOTATIONS "//\n";
443        if (!$options{skip_sequences})
444        {
445      for my $gent (@annos)      for my $gent (@annos)
446      {      {
447          my($genome, $alist) = @$gent;          my($genome, $alist) = @$gent;
# Line 459  Line 453 
453          }          }
454    
455      }      }
456        }
457    
458      close(ANNOTATIONS);      close(ANNOTATIONS);
459  }  }

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