Common pattern in different strings? Using KMP?
I think I solved the corresponding problem on rosalind.info. Here is my solution:
#!/usr/bin/perl
use strict;
use warnings;
sub kmp {
my @T = (-1, 0);
my ($pos, $cnd) = (2, 0);
while ( $pos <= @_ ) {
if ($_[$pos-1] eq $_[$cnd]) { $T[$pos++] = ++$cnd }
elsif ($cnd > 0) { $cnd = $T[$cnd] // 0 }
else { $T[$pos++] = 0 }
}
shift @T;
return @T;
}
use List::Util qw(max min);
sub lcs {
my @first = split //, my $first = shift;
my $n = @first;
my @string = map [ split //, $_ ], @_;
my ($pos, $length) = (0, 0);
SUFFIX: for my $p ( 0 .. $n - 1 ) {
shift @first if $p;
my @max;
for (@string) {
my @kmp = kmp @first, '$', @$_;
my $max = max @kmp;
next SUFFIX if $max < $length;
push @max, $max;
}
if ((my $min = min @max) > $length) {
($pos, $length) = ($p, $min);
}
}
return substr $first, $pos, $length;
}
open my $f, '< rosalind_lcs.txt' or die "could not open: $!";
say lcs <$f>;
Hope this will help
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