## DESCRIPTION
## Match each of the following DNA replication enzymes with their corresponding functions.
## ENDDESCRIPTION
## KEYWORDS('DNA replication enzymes','functions')
## DBsubject('Molecular Biology')
## DBchapter('')
## DBsection('')
## Date('2026-07-12')
## Author('Neil R. Voss')
## Institution('Roosevelt University')

DOCUMENT();

loadMacros(
    'PGstandard.pl',
    'PGML.pl',
    'PGchoicemacros.pl',
    'parserPopUp.pl',
    'parserUtils.pl',
    'PGgraders.pl',
    'PGcourse.pl'
);
our @ALPHABET = ('A' .. 'Z');

# ================================
# Full matching data
# ================================
%match_data = (
  'DNA topoisomerase' => [
    'this enzyme relieves strain in the parental <span style="color: #228822; font-weight:700;">DNA double helix</span> caused by the supercoiling',
    'this enzyme releases the supercoiling tension in the <span style="color: #228822; font-weight:700;">DNA double helix</span>',
  ],
  'primase' => [
    'this enzyme builds <span style="color: #b33000; font-weight:700;">RNA primers</span> using the parental <span style="color: #228822; font-weight:700;">DNA strand</span> as a template',
    'this enzyme creates the <span style="color: #b33000; font-weight:700;">RNA primers</span> that serve as a starting point for DNA synthesis',
  ],
  'DNA&nbsp;helicase' => [
    'this enzyme unwinds the parental <span style="color: #228822; font-weight:700;">DNA double helix</span>',
    'this enzyme separates the two strands of the <span style="color: #228822; font-weight:700;">DNA double helix</span>',
  ],
  'DNA&nbsp;ligase' => [
    'this enzyme joins <span style="color: #3b7600; font-weight:700;">Okazaki fragments</span> together to create one continuous <span style="color: #228822; font-weight:700;">DNA strand</span>',
    'this enzyme seals the gaps between the <span style="color: #3b7600; font-weight:700;">Okazaki fragments</span> to create one continuous <span style="color: #228822; font-weight:700;">DNA strand</span>',
  ],
  'single-strand binding proteins' => [
    'this protein holds the <span style="color: #228822; font-weight:700;">DNA strand</span>s apart while they are being replicated',
    'this protein stabilizes the open conformation of the unwound DNA',
  ],
  'DNA&nbsp;polymerase&nbsp;&#8544;' => [
    'this enzyme replaces the <span style="color: #b33000; font-weight:700;">RNA primers</span> with DNA in the <span style="color: #3b7600; font-weight:700;">Okazaki fragments</span>',
    'this enzyme removes <span style="color: #b33000; font-weight:700;">RNA primers</span> and fills the gaps with DNA between <span style="color: #3b7600; font-weight:700;">Okazaki fragments</span>',
    'this enzyme removes the <span style="color: #b33000; font-weight:700;">RNA primers</span> at the beginning of each Okazaki fragment and replaces them with DNA',
  ],
  'DNA&nbsp;polymerase&nbsp;&#8546;' => [
    'this enzyme produces the majority of DNA polymer during DNA replications',
    'this enzyme is responsible for the synthesis of most of the bacterial chromosome',
    'this enzyme synthesizes DNA on both the <span style="color: #002699; font-weight:700;">leading strand</span> and the <span style="color: #995c00; font-weight:700;">lagging strand</span>',
    'this enzyme is responsible for synthesizing the entire <span style="color: #002699; font-weight:700;">leading strand</span>',
  ],
  'DNA sliding clamp' => [
    'this enzyme is a ring that tethers certain enzymes to DNA',
    'this enzyme prevents certain enzymes from falling off of the DNA',
  ],
);

# -------------------------------
# Select N random keys
# -------------------------------
my $n = 4;
@all_keys = PGsort(sub { $_[0] lt $_[1] }, keys %match_data);
my $local_seed = (defined($problemSeed) && $problemSeed ne '') ? $problemSeed : 1;
my $local_random = new PGrandom($local_seed);

my @indices = (0 .. $#all_keys);
my @shuffled = ();
while (@indices) {
  my $pick = $local_random->random(0, $#indices, 1);
  push @shuffled, splice(@indices, $pick, 1);
}
my @selected_keys = @all_keys[@shuffled[0..$n-1]];

# -------------------------------
# Build question/answer pairs
# -------------------------------
# Each entry: [prompt, choice]
@q_and_a = ();
foreach my $key (@selected_keys) {
  my $values_ref = $match_data{$key};
  my $i = $local_random->random(0, $#$values_ref, 1);
  my $value = $values_ref->[$i];
  push @q_and_a, [ $value, $key ];
}

# -------------------------------
# Randomize the questions
# -------------------------------
my @q_indices = (0 .. $#q_and_a);
my @q_shuffled = ();
while (@q_indices) {
  my $pick = $local_random->random(0, $#q_indices, 1);
  push @q_shuffled, $q_and_a[splice(@q_indices, $pick, 1)];
}
@q_and_a = @q_shuffled;

# -------------------------------
# Sort the choices alphabetically
# -------------------------------
@answers = ();
push(@answers, (map { $_->[1] } @q_and_a));
@answers_sorted = PGsort(sub { $_[0] lt $_[1] }, @answers);

# -------------------------------
# HTML-safe answer labels
# -------------------------------
%answer_html = (
  'DNA&nbsp;topoisomerase' => '<span style="color: #935d00; font-weight:700;">DNA&nbsp;topoisomerase</span>',
  'primase' => '<span style="color: #6c6c00; font-weight:700;">primase</span>',
  'DNA&nbsp;helicase' => '<span style="color: #d40000; font-weight:700;">DNA&nbsp;helicase</span>',
  'DNA&nbsp;ligase' => '<span style="color: #b74300; font-weight:700;">DNA&nbsp;ligase</span>',
  'single-strand binding proteins' => '<span style="color: #7b7737; font-weight:700;">single-strand binding proteins</span>',
  'DNA&nbsp;polymerase&nbsp;&#8544;' => '<span style="color: #b45918; font-weight:700;">DNA&nbsp;polymerase&nbsp;&#8544;</span>',
  'DNA&nbsp;polymerase&nbsp;&#8546;' => '<span style="color: #3e3ec4; font-weight:700;">DNA&nbsp;polymerase&nbsp;&#8546;</span>',
  'DNA sliding clamp' => 'DNA sliding clamp',
);

@answers_sorted_html = map { $answer_html{$_} || $_ } @answers_sorted;

# -------------------------------
# Create answer index lookup
# -------------------------------
our %answer_index;
for (my $i = 0; $i <= $#answers_sorted; $i++) {
  $answer_index{$answers_sorted[$i]} = $i;
}

# -------------------------------
# PopUp/DropDown compatibility
# -------------------------------
sub make_popup {
  return defined &DropDown ? DropDown(@_) : PopUp(@_);
}

# -------------------------------
# Create popup objects (blank default)
# -------------------------------
my @answer_letters = @ALPHABET[0 .. $#answers_sorted];
my @answer_letters_with_blank = ('', @answer_letters);
@answer_dropdowns =
  map { make_popup([ @answer_letters_with_blank ], $answer_index{$q_and_a[$_][1]} + 1 ) }
  0 .. $#q_and_a;

# -------------------------------
# Render the question
# -------------------------------
HEADER_TEXT(<<END_STYLE);
<style>
.pgml-bold { font-weight: 700; }
.two-column {
    display: flex;
	flex-wrap: wrap;
	gap: 2rem;
	align-items: center;
	justify-content: space-evenly;
}
</style>
END_STYLE

$question_text = 'Match each of the following DNA replication enzymes with their corresponding functions.';
$note_text = 'Note: Each choice will be used exactly once.';

BEGIN_PGML
[$question_text]*
[$note_text]*

[@ MODES(HTML => '<div class="two-column"><div>') @]*
[@ join(
    "\n\n",
    map {
        '[_]{$answer_dropdowns[' . $_ . ']} '
            . '*' . ($_ + 1) . '.* '
            . '[$q_and_a[' . $_ . '][0]]*'
    } 0 .. $#q_and_a
) @]**
[@ MODES(HTML => '</div><div class="right-col">') @]*
[@ join(
    "\n\n",
    map {
        chr(65 + $_) . '\\.' . ' ' . '[$answers_sorted_html[' . $_ . ']]*'
    } 0 .. $#answers_sorted
) @]**
[@ MODES(HTML => '</div></div>') @]*
END_PGML

# -------------------------------
# Dynamic Partial Credit Based on $n
# -------------------------------
$showPartialCorrectAnswers = 0;
my @thresholds;
my @scores;
for (my $i = 1; $i <= $n; $i++) {
  push @thresholds, $i;
  push @scores, sprintf("%.2f", $i / $n);
}

install_problem_grader(~~&custom_problem_grader_fluid);
$ENV{grader_numright} = [@thresholds];
$ENV{grader_scores}   = [@scores];
$ENV{grader_message} = 'You can earn partial credit.';

# -------------------------------
# Solution
# -------------------------------
$answer_list = join(', ', map { ($_ + 1) . '-' . $ALPHABET[$answer_index{$q_and_a[$_][1]}] } 0 .. $#q_and_a);
BEGIN_PGML_SOLUTION
The correct answers are: [$answer_list].
END_PGML_SOLUTION

ENDDOCUMENT();