Printing a 2500 x 2500 dimensional matrix using Perl - perl

Question

I am very new to Perl. Recently I wrote a code to calculate the coefficient of correlation between the atoms between two structures. This is a brief summary of my program.
for($i=1;$i<=2500;$i++)
{
for($j=1;$j<=2500;$j++)
{
calculate the correlation (Cij);
print $Cij;
}
}
This program prints all the correlations serially in a single column. But I need to print the correlations in the form of a matrix, something like..
Atom1 Atom2 Atom3 Atom4
Atom1 0.5 -0.1 0.6 0.8
Atom2 0.1 0.2 0.3 -0.5
Atom3 -0.8 0.9 1.0 0.0
Atom4 0.3 1.0 0.8 -0.8
I don't know, how it can be done. Please help me with a solution or suggest me how to do it !

Answer 1

Simple issue you're having. You need to print a NL after you finish printing a row. However, while i have your attention, I'll prattle on.
You should store your data in a matrix using references. This way, the way you store your data matches the concept of your data:
my #atoms; # Storing the data in here
my $i = 300;
my $j = 400;
my $value = ...; # Calculating what the value should be at column 300, row 400.
# Any one of these will work. Pick one:
my $atoms[$i][$j] = $value; # Looks just like a matrix!
my $atoms[$i]->[$j] = $value; # Reminds you this isn't really a matrix.
my ${$atoms[$1]}[$j] = $value; # Now this just looks ridiculous, but is technically correct.
My preference is the second way. It's just a light reminder that this isn't actually a matrix. Instead it's an array of my rows, and each row points to another array that holds the column data for that particular row. The syntax is still pretty clean although not quite as clean as the first way.
Now, let's get back to your problem:
my #atoms; # I'll store the calculated values here
....
my $atoms[$i]->[$j] = ... # calculated value for row $i column $j
....
# And not to print out my matrix
for my $i (0..$#atoms) {
for my $j (0..$#{ $atoms[$i] } ) {
printf "%4.2f ", $atoms[$i]->[$j]; # Notice no "\n".
}
print "\n"; # Print the NL once you finish a row
}
Notice I use for my $i (0..$#atoms). This syntax is cleaner than the C style three part for which is being discouraged. (Python doesn't have it, and I don't know it will be supported in Perl 6). This is very easy to understand: I'm incrementing through my array. I also use $#atom which is the length of my #atoms array -- or the number of rows in my Matrix. This way, as my matrix size changes, I don't have to edit my program.
The columns [$j] is a bit tricker. $atom[$i] is a reference to an array that contains my column data for row $i, and doesn't really represent a row of data directly. (This is why I like $atoms[$i]->[$j] instead of $atoms[$i][$j]. It gives me this subtle reminder.) To get the actual array that contains my column data for row $i, I need to dereference it. Thus, the actual column values are stored in row $i in the array array #{$atoms[$i]}.
To get the last entry in an array, you replace the # sigil with $#, so the last index in my
array is $#{ $atoms[$i] }.
Oh, another thing because this isn't a true matrix: Each row could have a different numbers of entries. You can't have that with a real matrix. This makes using an Array of Arrays in Perl a bit more powerful, and a bit more dangerous. If you need a consistent number of columns, you have to manually check for that. A true matrix would automatically create the required columns based upon the largest $j value.

Answer 2

Disclaimer: Pseudo Code, you might have to take care of special cases and especially the headers yourself.
for($i=1;$i<=2500;$i++)
{
print "\n"; # linebreak here.
for($j=1;$j<=2500;$j++)
{
calculate the correlation (Cij);
printf "\t%4f",$Cij; # print a tab followed by your float giving it 4
# spaces of room. But no linebreak here.
}
}
This is of course a very crude and quick and dirty solution. But if you save the output into a .csv file, most csv-able spreadsheet programs (OpenOfice) should easily be able to read it into a proper table. If the spreadsheet viewer of your choice can not understand tabs as delimeter, you could easily add ; or / or whatever it can use into the printf string.