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

##  dotmatrix1.pl takes a query string and a search string and uses the
##  dot-matrix method to find regions of alignment between the two.


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

#$query =  "AAGCGCGTCGCGATTGACATTATAGAAGGCGC";
#$search = "AAGTGCGACGCCATTCACAATATGGAACGCGA";

#$query =  "GGTAATA";
#$search = "GGTAATA";

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!!
                }
        }

        #$table[0][1] = "\\";
        
        
        
## 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, $window);
                if ($queryword eq $searchword)
                        {
                        $table[$i][$j] = "\\";
                        }
                }
        }

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

foreach (@table)
        {
        print @{$_}, " \n"  #{$table}[$i];
        }