## TITLE('Polymerase Chain Reaction (PCR) Components')
## DESCRIPTION
## Select the statement that is TRUE or FALSE about polymerase chain reaction (PCR) components.
## ENDDESCRIPTION
## KEYWORDS('polymerase chain reaction (PCR) components','true/false','multiple choice')
## DBsubject('Laboratory Techniques')
## DBchapter('')
## DBsection('')
## Date('2026-08-19')
## Author('Neil R. Voss')
## Institution('Roosevelt University')

DOCUMENT();

loadMacros(
  "PGstandard.pl",
  "PGML.pl",
  "PGchoicemacros.pl",
  "parserRadioButtons.pl",
  "PGcourse.pl",
);

TEXT(beginproblem());
$showPartialCorrectAnswers = 1;

#==========================================================
# AUTO-GENERATED GROUPS FROM YAML
#==========================================================

@true_groups = (
  [
    'Taq DNA Polymerase',
    'Thermostable DNA Polymerase',
    'Heat stable DNA Polymerase',
  ],
  [
    'Deoxynucleotide triphosphates',
    'dNTPs',
    'dATP, dTTP, dCTP, and dGTP',
  ],
  [
    'Magnesium ions (Mg<sup>2+</sup>)',
    'positively charged metal ions',
  ],
  [
    'Oligonucleotide primers',
    'Primers complementary to each end of the sequence to be amplified',
  ],
  [
    'Reaction Buffer',
    'pH Buffer',
  ],
  [
    'Template DNA',
    'DNA containing the sequences to be amplified',
  ],
  [
    'Thermal Cycler',
  ],
);
@false_groups = (
  [
    'E. coli DNA Polymerase',
    'Thermolabile DNA Polymerase',
  ],
  [
    'DNA Ligase',
  ],
  [
    'DNA Helicase',
  ],
  [
    'mRNA template',
    'messenger RNA template',
  ],
  [
    'reverse transciptase (RT)',
  ],
  [
    'Restriction enzymes',
  ],
  [
    'DNA Primase',
  ],
  [
    'Single-stranded DNA binding proteins (SSB)',
  ],
  [
    'DNA Gyrase',
  ],
  [
    '5&prime;&rarr;3&prime; exonuclease',
  ],
  [
    'Okazaki fragments',
  ],
  [
    'DNA sliding &beta;-clamp protein',
  ],
  [
    'ATP synthase complex',
  ],
);

#==========================================================
# GLOBAL SETTINGS
#==========================================================

$topic = 'polymerase chain reaction (PCR) components';
my $local_random = PGrandom->new();
$local_random->srand($problemSeed);
my @mode_choices = ("TRUE", "FALSE");
$mode = $mode_choices[$local_random->random(0, $#mode_choices, 1)];
$num_distractors = 4;
# Question text with FALSE override
$question_false = 'Which one of the following is NOT a component in a typical modern polymerase chain reaction (PCR) experiment?';
#==========================================================
# SELECT GROUP
#==========================================================

my (@selected_group, @opposite_groups);

if ($mode eq "TRUE") {
  $group_index      = $local_random->random(0, scalar(@true_groups)-1, 1);
  @selected_group   = @{ $true_groups[$group_index] };
  @opposite_groups  = @false_groups;
} else {
  $group_index      = $local_random->random(0, scalar(@false_groups)-1, 1);
  @selected_group   = @{ $false_groups[$group_index] };
  @opposite_groups  = @true_groups;
}

#==========================================================
# PICK CORRECT + DISTRACTORS
#==========================================================

my $correct_index = $local_random->random(0, $#selected_group, 1);
$correct = $selected_group[$correct_index];

my @available_group_indices = (0 .. $#opposite_groups);
my @selected_distractor_indices = ();

while (@selected_distractor_indices < $num_distractors && @available_group_indices > 0) {
  my $random_index = $local_random->random(0, scalar(@available_group_indices)-1, 1);
  push @selected_distractor_indices, splice(@available_group_indices, $random_index, 1);
}

@distractors = ();
foreach my $group_idx (@selected_distractor_indices) {
  my @group = @{ $opposite_groups[$group_idx] };
  my $distractor_index = $local_random->random(0, $#group, 1);
  my $distractor = $group[$distractor_index];
  push @distractors, $distractor;
}

@choices = ($correct, @distractors);

#==========================================================
# SHUFFLE CHOICES (SEED-STABLE)
#==========================================================

my @choice_indices = (0 .. $#choices);
my @choice_shuffled = ();
while (@choice_indices) {
  my $pick = $local_random->random(0, $#choice_indices, 1);
  push @choice_shuffled, splice(@choice_indices, $pick, 1);
}
@choices = @choices[@choice_shuffled];

#==========================================================
# RADIO BUTTONS WITH A/B/C/D/E LABELS
#==========================================================

$rb = RadioButtons(
  [@choices],
  $correct,
  labels        => ['A','B','C','D','E'],
  displayLabels => 1,
  randomize     => 0,
  separator     => '<div style="margin-bottom: 0.7em;"></div>',
);

#==========================================================
# PGML
#==========================================================

BEGIN_PGML

[@ $mode eq "TRUE" ? "Which one of the following statements is <span style='color: #127663;'><strong>TRUE</strong></span> about $topic?" : $question_false @]*

[_]{$rb}

END_PGML

ENDDOCUMENT();