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lib/Bio/WebService/LANL/SequenceLocator.pm  view on Meta::CPAN

        unbroken_text => 1,
    );

    my $expect_alignment = 0;

    while (my $tag = $doc->get_tag("b", "pre")) {
        my $name = lc $tag->[0];
        my $text = $doc->get_text;
        next unless defined $text;

        # <pre>s are preceeded by a bold header, which we use as an indicator
        if ($name eq 'b') {
            $expect_alignment = $text =~ /Alignment\s+of\s+the\s+query\s+sequence\s+to\s+HXB2/i;
        } elsif ($name eq 'pre') {
            if ($text =~ /^\s*Query\b/m and $text =~ /^\s*HXB2\b/m) {
                push @alignments, $text;
                warn "Not expecting alignment, but found one‽"
                    unless $expect_alignment;
            }
            elsif ($text =~ /^\s+$/ and $expect_alignment) {
                push @alignments, undef;    # We appear to have found an unaligned sequence.