use strict;
use warnings;
use Data::Dumper;

my @array1 = qw(l a r g e s t
   c o m m o n s e q u e n c i
   a l s u b s e t
);

my @array2 = qw(w h a t i s t
   h e l a r g e s t s e q u e
   n c i a l
);

my @array3 = qw(w h a t l a r
   g s e q c o m m o n
);

my @array4 = qw(w h a t l a r
  g s e q c o m m o n s e q u e
  n c i a l
);

my @array5 = qw( a b c d e f g h i j 
k l m n o p q r s t u v w x y z 
);

my @array6 = qw( a b c X f g h X l m 
n X j k a b c d 
);

print Dumper LCCOS(\@array1,\@array2);
print Dumper LCCOS(\@array2,\@array3);
print Dumper LCCOS(\@array3,\@array1);
print Dumper LCCOS(\@array1,\@array1);
print Dumper LCCOS(\@array2,\@array4);
print Dumper LCCOS(\@array5,\@array6);
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####################################
sub LCCOS {
####################################
 my ($array1,$array2) =  @_;
 my $current_largest = [];
 my $current_size;

 if ( @$array1 > @$array2 ) {
   ($array1,$array2) = ($array2,$array1)
 };

 my $count = 0;

 my %elements_in_longer;
  
 #create an HoA holding the locations of all elements
 #in the larger array so we only start at those places
 push @{$elements_in_longer{$_}},
    $count++ for @$array1;

 for my $pos_in_small ( 0 .. $#array2 ) {
   my $current_letter = $array2->[$pos_in_small];

   for my $possible_start(@{$elements_in_longer{$current_letter}}) {
     my $curr_pos_in_small = $pos_in_small;
     my $curr_pos_in_large = $possible_start;
     my @curr_matching_sequence;

     while ( defined $array1->[$curr_pos_in_large] 
             and 
             defined $array2->[$curr_pos_in_small] ) {
       if ($array1->[$curr_pos_in_large] 
           eq 
           $array2->[$curr_pos_in_small]) {
         push @curr_matching_sequence, 
           $array2->[$curr_pos_in_small];

         $curr_pos_in_large++;
         $curr_pos_in_small++;
       } else  { last; }
     }
     if ( @curr_matching_sequence > @{$current_largest} ) {
         $current_largest = \@curr_matching_sequence;
         $current_size = @curr_matching_sequence;
      }
    }

    #if the $current_size is longer that what is left to
    #check in the smaller array, then we are done.
    last if  $current_size > $#array2 - $pos_in_small;
  }
  return $current_largest;
}   ##LCCOS
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-enlil