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revision 1.10, Thu Apr 21 16:28:21 2005 UTC revision 1.11, Sun Apr 24 16:33:26 2005 UTC
# Line 673  Line 673 
673      my($self, $directive, $rest) = @_;      my($self, $directive, $rest) = @_;
674    
675      $directive = lc($directive);      $directive = lc($directive);
676      my @rest=split /\t/, $rest;      # this should catch both #seed and ##seed :-)
677        if ($directive eq "seed")
     if ($directive eq "genome")  
678      {      {
679          $self->current_file->genome_id($rest[0]);        return $self->parse_seed_directive($rest);
         $self->current_file->genome_name($rest[1]);  
     }  
     elsif ($directive eq "genome_md5")  
     {  
         $self->current_file->set_genome_checksum(@rest[0,1]);  
680      }      }
681      elsif ($directive eq "origin")  
682        my @rest=split /\t/, $rest;
683    
684        # removed genome, genome_md5, origin, taxnomy as they are not real gff directives. These are in seed_directives below
685        if ($directive eq "project")
686      {      {
687          print STDERR "We have a directive called origin but this should be changed as it will conflict with NCBI's ORIGIN indicating beginning of the sequence\n";          # I am not sure if PROJECT is a seed directive or a GFF directive
         print STDERR "At the moment ORIGIN is returned by \$feat->project\n";  
688          $self->current_file->project($rest[0]);          $self->current_file->project($rest[0]);
689      }      }
     elsif ($directive eq "taxonomy")  
     {  
         $self->current_file->taxonomy($rest);  
     }  
690      elsif ($directive eq "sequence-region")      elsif ($directive eq "sequence-region")
691      {      {
692          $self->current_file->contigs($rest[0]);          $self->current_file->contigs($rest[0]);
# Line 715  Line 708 
708      my($verb, @rest) = split(/\t/, $rest);      my($verb, @rest) = split(/\t/, $rest);
709    
710      # are we case sensitive? I don't think so      # are we case sensitive? I don't think so
711      $verb-lc($verb);      $verb=lc($verb);
712    
713      if ($verb eq "anno_start")      if ($verb eq "genome")
714        {
715            $self->current_file->genome_id($rest[0]);
716            $self->current_file->genome_name($rest[1]);
717        }
718        elsif ($verb eq "genome_md5")
719        {
720            $self->current_file->set_genome_checksum(@rest[0,1]);
721        }
722        elsif ($verb eq "project")
723        {
724            # I am not sure if PROJECT is a seed directive or a GFF directive
725            $self->current_file->project($rest[0]);
726        }
727        elsif ($verb eq "taxonomy")
728        {
729            $self->current_file->taxonomy($rest);
730        }
731        elsif ($verb eq "anno_start")
732      {      {
733          $self->current_file->anno_start($rest[0]);          $self->current_file->anno_start($rest[0]);
734      }      }

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