#!/usr/local/bin/perl
#use strict;
#use warnings;

##  dotmatrix2.pl takes a query string and a search string and uses the
##  dot-matrix method to find regions of alignment between the two.

sub compare;  ## a subrouting declaration - to be defined later

my $window =  4;
my $match = 4;
my $similarity;
my $query =  "AAGCGCGTCGCGATTGACATTATAGAAGGCGC";
my $search = "ATGTTCGCGATTGACATTCAAAAGCGAGTCAG";

$query =  "AAGCGCGTCGCGATTGACATTATAGAAGGCGCAG";
$search = "AAGTGCGACGCCATTCACAATATGGAACGCGCAG";

my $querylen  = length($query);
my $searchlen = length($search);
my $queryword;
my $searchword;
my $i;
my $j;

my @table;


## Define a two-dimensional array consisting of an array of references
## to a series of anonymous arrays of scalars in the second dimension
## and initialize the two-dimensional array with zeros

for ($i = 0; $i < $querylen; $i++)
        {
        for ($j = 0; $j < $searchlen; $j++)
                {
                $table[$i][$j] = 0;  # perl "autovivifies" the anonymous arrays
                                     # indexed my $j!!
                }
        }

        
## Now step through the matrix using "sliding window" substrings of the query
## and search sequences and check off those positions where the substrings are
## identical.

for ($i = 0; $i < $querylen; $i++)
        {
        for ($j = 0; $j < $searchlen; $j++)
                {
                $queryword  = substr($query, $i, $window);
                $searchword = substr($search,$j, $window);

                #print $queryword, " ", $searchword, " Line \n";
                $similarity = compare($queryword,$searchword);

                if ($similarity >= $match)
                        {
                        $table[$i][$j] = "\\";
                        }
                }
        }

## Now that we have "scored" the matrix, let's print it out and see how we did

foreach (@table)
        {
        print @{$_}, " \n";
        }
        
 ## compare is a simple subroutine that takes two strings
 ## as input and returns the number of exact matches at each position


sub compare
        {
        my $similar = 0;
        my $string1 = shift;
        my $string2 = shift;
        my $minlength;
        
        if (length($string1) < length($string2) )
                {
                $minlength = length($string1);
                }
        else
                {
                $minlength = length($string2);
                }

        
        for (my $i = 0; $i < $minlength; $i++)
                {
                if (substr($string1,$i,1) eq substr($string2, $i, 1))
                        {
                        $similar++;
                        }
                }

        #print $string1, " ", $string2, " ", $similar, " func\n";

                        
        return $similar;
        }