Lines Matching refs:masker
503 $mask_file, $mask_data, $mask_make_args, $masker,
559 if ($masker) {
560 $self->throw("Masker '$masker' not available") unless
561 grep /^$masker$/, keys %AVAILABLE_MASKERS;
562 $self->{_masker} = $masker;
643 sub masker { shift->{_masker} } subroutine
766 elsif ($self->masker && $self->mask_data) { # build the mask
801 my ($data, $mask_db, $make_args, $masker) = $self->_rearrange([qw(
809 $masker ||= $self->masker;
811 unless $masker;
814 unless (grep /^$masker$/, keys %AVAILABLE_MASKERS) {
815 $self->throw("Masker '$masker' not available");
818 unless ($masker eq 'segmasker') {
819 $self->throw("Masker '$masker' can't use a blastdb as primary input");
822 $AVAILABLE_MASKERS{$masker}) {
823 $self->throw("Masker '$masker' is incompatible with input db sequence type");
841 unless ($type eq $AVAILABLE_MASKERS{$masker}) {
842 $self->throw("Masker '$masker' is incompatible with sequence type '$type'");
869 for ($masker) {
872 $mask_args{'-outfmt'} = $MASKER_ENCODING{$masker};
873 $self->{_factory} = $bp_class->new(-command => $masker,
892 $self->{_factory} = $bp_class->new(-command => $masker,
900 $mask_args{'-outfmt'} = $MASKER_ENCODING{$masker};
913 $mask_args{'-outfmt'} = $MASKER_ENCODING{$masker};
914 $self->{_factory} = $bp_class->new(-command => $masker,
921 $self->throw("Masker program '$masker' not recognized");