I think you are seriously underestimating the performance of disk I/O.
I wrote a test program to read an array of ints between 100 and 1000
bytes long out of a file that is 170mb of ints.  Even with my slow
computer it averages 10ms or less per array read.  I don't think 10ms
would be too long to wait.

import java.io.*;
import java.util.*;

public class test10 {
    public static void main(String[] args) throws Exception {
        /* creates 170mb file of ints
        RandomAccessFile file = new RandomAccessFile("ran.dat","rw");
        for (int i=0; i<42500000; i++)
            file.writeInt(i);
        file.close();
        */
        int iterations = 10000;
        Random random = new Random(System.currentTimeMillis());
        RandomAccessFile file = new RandomAccessFile("ran.dat","r");
        long start = System.currentTimeMillis();
        for (int i=0; i<iterations; i++) {
            int arrayLength = random.nextInt(900) + 100;
            int[] buf = new int[arrayLength];
            int where = random.nextInt(42500000);
            file.seek(where * 4);
            try {
                for (int j=0; j<arrayLength; j++)
                    buf[j] = file.readInt();
            } catch (EOFException eofe) {
                System.out.println(eofe);
            }
        }
        file.close();
        long end = System.currentTimeMillis();
        System.out.println((end-start)/1.0/iterations);

        /* this is slightly faster than above
        int iterations = 10000;
        Random random = new Random(System.currentTimeMillis());
        long start = System.currentTimeMillis();
        for (int i=0; i<iterations; i++) {
            FileInputStream fis = new FileInputStream("ran.dat");
            BufferedInputStream bis = new BufferedInputStream(fis);
            DataInputStream dis = new DataInputStream(bis);
            int arrayLength = random.nextInt(900) + 100;
            int[] buf = new int[arrayLength];
            int where = random.nextInt(42500000);
            dis.skip(where * 4);
            try {
                for (int j=0; j<arrayLength; j++)
                    buf[j] = dis.readInt();
            } catch (EOFException eofe) {
                System.out.println(eofe);
            }
            dis.close();
        }
        long end = System.currentTimeMillis();
        System.out.println((end-start)/1.0/iterations);
        */
    }
}

Why not read the data in from disk (you should be able to know where in the
file the int[] that you want is located, so you don't need to read the whole
(large) file) and leave soft references to the arrays that you've already
read in?

Alun Harford