The Eliminator reads in two files, the first containing the set of “potential duplicates”, the second containing the “baseline” set, and outputs only those lines which exist in the first file but not the second.

Eliminator.java

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.HashSet;
import java.util.Set;
import java.util.TreeSet;

public class Eliminator
{
    private TreeSet<String> potentialDuplicates = new TreeSet<>();
    private HashSet<String> baseline = new HashSet<>();

    public Eliminator(File potentialDuplicateSource, File baselineSource) throws IOException
    {
        populateHashSetFromFile(potentialDuplicateSource, this.potentialDuplicates);
        populateHashSetFromFile(baselineSource, this.baseline);
    }

    public TreeSet<String> unique()
    {
        TreeSet<String> unique = new TreeSet<>();

        for (String potential : this.potentialDuplicates)
            if (!this.baseline.contains(potential))
                unique.add(potential);

        return unique;
    }

    private static void populateHashSetFromFile(File source, Set<String> set) throws IOException
    {
        BufferedReader reader = new BufferedReader(new FileReader(source));

        String line;
        while ((line = reader.readLine()) != null)
            set.add(line);
    }

    public static void main(String[] args) throws Exception
    {
        if (args.length < 2)
        {
            System.err.printf("Usage: java Eliminator <potential_duplicates> <baseline>\n");
            System.exit(1);
        }

        Eliminator eliminator = new Eliminator(new File(args[0]), new File(args[1]));
        for (String unique : eliminator.unique())
            System.out.printf("%s\n", unique);
    }
}