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lib/Bio/MUST/Apps/HmmCleaner.pm  view on Meta::CPAN

    my %matrix;
    for my $cleaner ($self->all_cleaners) {
        my $seqid = $cleaner->seq->full_id;
        $matrix{$seqid} = $cleaner->get_seqmask;
    }

    return \%matrix;
}

sub update_cleaners {
    my $self = shift;
    my $threshold = shift;
    $self->_set_threshold($threshold);
    my $costs = shift // $self->_get_default_cost;

    for my $cleaner ($self->all_cleaners) {
        $cleaner->update($threshold,$costs);
    }

    return;

lib/Bio/MUST/Apps/HmmCleaner/Cleaner.pm  view on Meta::CPAN

sub _build_shifts {
    return shift->_get_shifts;
}

## use critic


# METHOD

sub update {
    my $self = shift;
    my $threshold = shift;
    my $costs = shift;

    $self->_set_costs($costs);
    $self->_set_threshold($threshold);
    # watch out, the order is important here
    $self->_set_nogap_shifts($self->_get_nogap_shifts);
    $self->_set_shifts($self->_get_shifts);