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revision 1.26, Tue Mar 30 16:44:51 2004 UTC revision 1.27, Wed Mar 31 10:52:25 2004 UTC
# Line 506  Line 506 
506    
507  sub package_assignments {  sub package_assignments {
508      my($fig,$user,$who,$date,$genomes,$file) = @_;      my($fig,$user,$who,$date,$genomes,$file) = @_;
509      my($genome,$x,$org,$curr);      my($genome,$x,$org,$curr,$peg);
510      $who   = $who ? $who : "master";      $who   = $who ? $who : "master";
511      $date  = $date ? $date : 0;      $date  = $date ? $date : 0;
512    
513      if (open(ASSIGNMENTS,">$file"))      if (open(ASSIGNMENTS,">$file"))
514      {      {
515          print ASSIGNMENTS "$user\t$who\t$date\n";          print ASSIGNMENTS "$user\t$who\t$date\n";
516          foreach $x (sort { $a->[0] cmp $b->[0] } $fig->assignments_made($genomes,$who,$date))          my @assignments = sort { $a->[0] cmp $b->[0] } $fig->assignments_made($genomes,$who,$date);
517            foreach $x (@assignments)
518          {          {
519              print ASSIGNMENTS join("\t",@$x),"\n";              print ASSIGNMENTS join("\t",@$x),"\n";
520          }          }
521            print ASSIGNMENTS "//\n";
522    
523            foreach $x (@assignments)
524            {
525                ($peg,undef) = @$x;
526                my $seq = $self->get_translation($peg);
527                &FIG::display_id_and_seq($peg,\$seq,\*ASSIGNMENTS);
528      }      }
529      close(ASSIGNMENTS);      close(ASSIGNMENTS);
530  }  }
531    }
532    
533  =pod  =pod
534    
# Line 630  Line 640 
640  }  }
641    
642  sub package_subsystems {  sub package_subsystems {
643      my($file) = @_;      my($file,$just_exchangable) = @_;
644      my($ssa);      my($ssa);
645    
646        $just_exchangable = defined($just_exchangable) ? $just_exchangable : 1;
647        my @exchangable = grep { (! $just_exchangable) || $fig->is_exchangable_subsystem($_) }
648                          $fig->all_subsystems;
649    
650      my $fig = new FIG;      my $fig = new FIG;
     my @exchangable = $fig->all_exchangable_subsystems;  
651      if ((@exchangable > 0) && open(SUB,">$file"))      if ((@exchangable > 0) && open(SUB,">$file"))
652      {      {
653          foreach $ssa (@exchangable)          foreach $ssa (@exchangable)

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