Look at the various IPC modules (Inter Process Communication) . You can try this simple example, but various glitches can occur like needing a pty or something. You should try to run your java program instead of bash, and see what happens.

#!/usr/bin/perl 
use warnings;
use strict;
use IPC::Open3;

$|=1;

#my $pid=open3(\*IN,\*OUT,\*ERR,'/bin/bash'); # or your java program
my $pid=open3(\*IN,\*OUT,0,'/bin/bash');
# set \*ERR to 0 to send STDERR to STDOUT

my $cmd = 'date';

#send cmd to bash
print IN "$cmd\n";

# assuming your program understands it

print IN "l";
print IN "m";
print IN "t";
print IN "\n";
#getresult

my $result = <OUT>;
print $result;
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