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lib/Bio/BLAST/Database.pm  view on Meta::CPAN

			      #add seqid indexes if called for
			      $self->indexed_seqs ? qw/sd si/ : (),
			     );

  #add protein/nucleotide prefix to extensions
  my $norp = $self->type eq 'protein' ? '.p' : '.n';
  $_ = $norp.$_ foreach @necessary_extensions;

  #deal with large, split databases
  if( $self->is_split ) {
    #if the database is split, add all of the fragment numbers to
    #the extensions we have to have

    #maximum index number of all fragments present
    my $max_frag_num = 0 + max( map { /\.(\d{2,3})\.[np]\w\w$/ ? $1 : 0 } @files);

    #make extensions with all of the necessary fragment numbers
    @necessary_extensions = map { my $ext = $_;
				  map {sprintf(".%02d$ext",$_)} (0..$max_frag_num)
				} @necessary_extensions;

    #also remember that we have to have an alias file for split dbs
    push @necessary_extensions, $norp.'al';
  }

  #now that we have our list of all the file extensions we need to have,
  #check if they are actually there
  my $ffbn = $self->full_file_basename;
  return all {