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revision 1.464, Tue May 2 16:09:44 2006 UTC revision 1.465, Thu May 4 20:05:54 2006 UTC
# Line 546  Line 546 
546  =cut  =cut
547  #: Return Type $;  #: Return Type $;
548  sub add_genome {  sub add_genome {
549      my($self,$genomeF, $force, $skipnr) = @_;      my($self,$genomeF, $force, $skipnr, $dont_mark_complete) = @_;
550    
551      &log_update("add_genome $genomeF $force $skipnr",$genomeF);      &log_update("add_genome $genomeF $force $skipnr $dont_mark_complete",$genomeF);
552    
553      my $rc = 0;      my $rc = 0;
554    
# Line 583  Line 583 
583    
584      if (-s "$FIG_Config::organisms/$genome/COMPLETE")      if (-s "$FIG_Config::organisms/$genome/COMPLETE")
585      {      {
586            if ($dont_mark_complete)
587            {
588                print STDERR "$genome was marked as \"complete\", but moving to WAS_MARKED_COMPLETE\n";
589                rename("$FIG_Config::organisms/$genome/COMPLETE", "$FIG_Config::organisms/$genome/WAS_MARKED_COMPLETE");
590            }
591            else
592            {
593          print STDERR "$genome was marked as \"complete\"\n";          print STDERR "$genome was marked as \"complete\"\n";
594      }      }
595        }
596      else      else
597      {      {
598          &run("assess_completeness $genome");          &run("assess_completeness $genome");
599          if (-s "$FIG_Config::organisms/$genome/PROBABLY_COMPLETE")          if (-s "$FIG_Config::organisms/$genome/PROBABLY_COMPLETE")
600          {          {
601              print STDERR "Assessed $genome to be probably complete\n";              print STDERR "Assessed $genome to be probably complete\n";
602                if (!$dont_mark_complete)
603                {
604                    print STDERR "Not copying PROBABLY_COMPLETE to COMPLETE; this will need to be done later\n";
605              &run("cp -p $FIG_Config::organisms/$genome/PROBABLY_COMPLETE $FIG_Config::organisms/$genome/COMPLETE");              &run("cp -p $FIG_Config::organisms/$genome/PROBABLY_COMPLETE $FIG_Config::organisms/$genome/COMPLETE");
606          }          }
607            }
608          else          else
609          {          {
610              print STDERR "Assessed $genome to not be probably complete\n";              print STDERR "Assessed $genome to not be probably complete\n";
# Line 6939  Line 6951 
6951      return expand_raw_sims( $self, \@raw_sims, $maxN, $maxP, $select, 1, $max_expand, $filters );      return expand_raw_sims( $self, \@raw_sims, $maxN, $maxP, $select, 1, $max_expand, $filters );
6952  }  }
6953    
6954    
6955  #  #
6956  # Choose the new sims code.  # Choose the old sims code.
6957  #  #
 *sims = \&nsims;  
6958    
6959    if ($FIG_Config::try_sim_server)
6960    {
6961  #  #
6962  # Choose the old sims code.      # Choose the new sims code.
6963  #  #
6964  #*sims = \&osims;      *sims = \&nsims;
6965    }
6966    else
6967    {
6968        *sims = \&osims;
6969    }
6970    
6971  sub get_local_sims {  sub get_local_sims {
6972      my ($self, $id, $filter_func) = @_;      my ($self, $id, $filter_func) = @_;

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