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{
    for my $stk ( qw(cbs upsk) ) {
        my $infile = file('test', "$stk.stockholm");
        my $ali = $class->load_stockholm($infile);
        is $ali->filename, $infile, 'got expected filename from stockholm file';
        my $flag = $ali->is_protein;
        ok( $stk eq 'cbs' ? $flag : !$flag,
            "rightly detected alignment type: $infile" );
        cmp_store(
            obj => $ali, method => 'store',
            file => "$stk.ali",
            test => 'wrote expected Ali from stockholm',
        );
    }
}

{
    for my $ks (0, 1) {
        my $infile = file('test', 'tinyseq.xml');
        my $ali = $class->load_tinyseq($infile, { keep_strain => $ks } );
        is $ali->filename, $infile, 'got expected filename from tinyseq file';
        my $flag = not $ali->is_protein;
        ok( $flag, "rightly detected alignment type: $infile" );
        cmp_store(
            obj => $ali, method => 'store',
            file => "tinyseq_ks$ks.ali",
            test => 'wrote expected Ali from tinyseq (keeping strains)',
        );
    }
}

{
    my $infile = file('test', 'uniq.ali');
    my $ali = $class->load($infile);
    ok not($ali->has_uniq_ids), 'rightly detected duplicate ids';
    cmp_store(
        obj => $ali, method => 'store',
        file => 'uniq.ali',
        test => 'wrote expected Ali in spite of duplicate ids',
    );
}

{
    my $infile = file('test', 'unaligned.ali');
    my $ali = $class->load($infile);
    ok not($ali->is_aligned), 'rightly detected lack of alignment';
    cmp_ok $ali->width, '==', 25, 'got expected unaligned Ali width';
    cmp_store(
        obj => $ali, method => 'store',
        file => 'unaligned.ali',
        test => 'wrote expected unaligned Ali',
    );
}

my @exp_nomiss_lens = (56, 54, 48, 54, 44, 50, 48, 50, 52, 34);

{
    my $infile = file('test', 'complete.ali');
    my $ali = $class->load($infile);

    $ali->dont_guess;
    ok !$ali->is_aligned, 'rightly overrided guessing of alignment';
    cmp_store(
        obj => $ali, method => 'store_fasta',
        file => 'complete.fasta',
        test => 'wrote expected unaltered FASTA from non-guessing Ali',
    );

    $ali->guess;
    ok $ali->is_aligned, 'rightly detected alignment';
    cmp_ok $ali->width, '==', 56, 'got expected Ali width';
    is_deeply [ map { $_->nomiss_seq_len } $ali->all_seqs ], \@exp_nomiss_lens,
        'got expected seq lengths (excluding gaps and missing chars)';
}

{
    my $infile = file('test', 'AhHMA4_clustalw.ali');
    my $ali = $class->load($infile);

    cmp_store(
        obj => $ali, method => 'temp_fasta',
        file => 'temp_degap.fasta',
        test => 'wrote expected temp degapped .fasta file',
        args => { degap => 1 },
    );

    is_deeply [ map { $_->full_id } $ali->all_seq_ids ], \@exp_full_ids,
        'rightly restored original ids after temp file creation';

    cmp_store(
        obj => $ali, method => 'temp_fasta',
        file => 'temp_degap_nowrap.fasta',
        test => 'wrote expected temp degapped and unwrapped.fasta file',
        args => { degap => 1, chunk => -1 },
    );

    cmp_store(
        obj => $ali, method => 'temp_fasta',
        file => 'temp.fasta',
        test => 'wrote expected temp .fasta file (no degapping side-effect)',
    );

    cmp_store(
        obj => $ali, method => 'temp_fasta',
        file => 'temp_prefix.fasta',
        test => 'wrote expected temp .fasta file (custom std_mapper prefix)',
        args => { id_prefix => 'myseq' },
    );
}

# TODO: check that mutators indeed return the Ali object?

# TODO: consider keeping empty seqs when parsing Ali (not that easy)
# {
#     my $infile = file('test', 'empty_seqs.ali');
#     my $ali = $class->load($infile);
#     explain $ali;
#     cmp_ok $ali->count_seqs, '==', 3;
#     ok(List::AllUtils::all { $_->seq_len == 0 } $ali->all_seqs),
#         'rightly read an Ali full of empty seqs';
# }

# uc_seqs
{
    my $infile = file('test', 'seqs4uc.ali');
    my $ali = $class->load($infile);

    my $ali_uc = $ali->uc_seqs;