Package com.googlecode.gaal.suffix.impl

Source Code of com.googlecode.gaal.suffix.impl.LinearizedSuffixTreeImplTest

package com.googlecode.gaal.suffix.impl;

import static org.junit.Assert.assertArrayEquals;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;

import java.util.Iterator;

import org.junit.Before;
import org.junit.Test;

import com.googlecode.gaal.data.api.IntSequence;
import com.googlecode.gaal.data.impl.ArraySequence;
import com.googlecode.gaal.suffix.api.IntervalTree.Interval;
import com.googlecode.gaal.suffix.api.LinearizedSuffixTree;
import com.googlecode.gaal.suffix.api.LinearizedSuffixTree.BinaryInterval;
import com.googlecode.gaal.suffix.impl.LinearizedSuffixTreeImpl;
import com.googlecode.gaal.suffix.impl.EnhancedSuffixArrayImplTest.IntervalImpl;

public class LinearizedSuffixTreeImplTest {

    // caggtcagtcacggtatca#
    private static final int[] text = { 2, 1, 3, 3, 4, 2, 1, 3, 4, 2, 1, 2, 3, 3, 4, 1, 4, 2, 1, 5 };
    private static final String[] alphabet = { null, "a", "c", "g", "t", "#" };

    private static final int[] suffixTable = { 10, 1, 6, 15, 18, 9, 0, 5, 17, 11, 12, 2, 13, 7, 3, 14, 8, 4, 16, 19 };
    private static final int[] prefixTable = { 18, 1, 9, 13, 4, 19, 8, 2, 10, 14, 17, 12, 7, 16, 6, 3, 11, 15, 5, 0 };

    private static final int[] sLcpTable = { -1, 1, 2, 1, 1, 0, 2, 3, 2, 1, 0, 3, 1, 2, 4, 0, 1, 3, 3, 0 };
    private static final int[] pLcpTable = { -1, 2, 3, 4, 1, 0, 1, 1, 2, 3, 0, 3, 1, 1, 2, 0, 1, 2, 3, 0 };

    private static final int[] sExtendedLcpTable = { 0, 6, 10, 5, 6, 2, 11, 15, 10, 5, 1, 15, 5, 10, 20, 0, 5, 16, 15,
            1 };

    private static final int[] pExtendedLcpTable = { 0, 10, 15, 20, 5, 2, 6, 5, 10, 15, 1, 15, 6, 5, 10, 0, 5, 10, 15,
            1 };

    private static final int[] sNewChildTable = { 15, 2, 1, 4, 3, 9, 7, 6, 8, 5, 12, 11, 13, 14, 10, 19, 18, 17, 16, 0 };

    private static final int[] pNewChildTable = { 15, 2, 3, 1, 4, 7, 6, 8, 9, 5, 13, 11, 12, 14, 10, 19, 17, 18, 16, 0 };

    private static final IntervalImpl[] preOrder = { new IntervalImpl(0, 19, 0), new IntervalImpl(0, 14, 0),
            new IntervalImpl(0, 9, 0), new IntervalImpl(0, 4, 1), new IntervalImpl(0, 2, 1),
            new IntervalImpl(0, 0, -1), new IntervalImpl(1, 2, 2), new IntervalImpl(1, 1, -1),
            new IntervalImpl(2, 2, -1), new IntervalImpl(3, 4, 1), new IntervalImpl(3, 3, -1),
            new IntervalImpl(4, 4, -1), new IntervalImpl(5, 9, 1), new IntervalImpl(5, 8, 2),
            new IntervalImpl(5, 7, 2), new IntervalImpl(5, 5, -1), new IntervalImpl(6, 7, 3),
            new IntervalImpl(6, 6, -1), new IntervalImpl(7, 7, -1), new IntervalImpl(8, 8, -1),
            new IntervalImpl(9, 9, -1), new IntervalImpl(10, 14, 1), new IntervalImpl(10, 11, 3),
            new IntervalImpl(10, 10, -1), new IntervalImpl(11, 11, -1), new IntervalImpl(12, 14, 2),
            new IntervalImpl(12, 12, -1), new IntervalImpl(13, 14, 4), new IntervalImpl(13, 13, -1),
            new IntervalImpl(14, 14, -1), new IntervalImpl(15, 19, 0), new IntervalImpl(15, 18, 1),
            new IntervalImpl(15, 15, -1), new IntervalImpl(16, 18, 3), new IntervalImpl(16, 17, 3),
            new IntervalImpl(16, 16, -1), new IntervalImpl(17, 17, -1), new IntervalImpl(18, 18, -1),
            new IntervalImpl(19, 19, -1) };

    private LinearizedSuffixTree lst;
    private LinearizedSuffixTree lpt;

    @Before
    public void setUp() throws Exception {

        IntSequence sequence = new ArraySequence(text);
        lst = new LinearizedSuffixTreeImpl(sequence, alphabet.length - 1);
        lpt = new LinearizedSuffixTreeImpl(sequence.reverse(), alphabet.length - 1);
    }

    @Test
    public void testGetExtendedLcpTable() {
        assertArrayEquals(sExtendedLcpTable, lst.getExtendedLcpTable());
        assertArrayEquals(pExtendedLcpTable, lpt.getExtendedLcpTable());
    }

    @Test
    public void testGetNewChildTable() {
        assertArrayEquals(sNewChildTable, lst.getChildTable());
        assertArrayEquals(pNewChildTable, lpt.getChildTable());
    }

    @Test
    public void testGetTop() {
        Interval top = lst.top();
        assertTrue(top.left() == 0);
        assertTrue(top.right() == text.length - 1);
        assertTrue(top.lcp() == 0);
    }

    @Test
    public void testGetSuffixTable() {
        assertArrayEquals(suffixTable, lst.getSuffixTable());
        assertArrayEquals(prefixTable, lpt.getSuffixTable());
    }

    @Test
    public void testGetLcpTable() {
        assertArrayEquals(sLcpTable, lst.getLcpTable());
        assertArrayEquals(pLcpTable, lpt.getLcpTable());
    }

    @Test
    public void testAlpabetSize() {
        assertTrue(lst.alphabetSize() == alphabet.length - 1);
    }

    @Test
    public void testTraversePreOrder() {
        Iterator<BinaryInterval> iterator = lst.preorderIterator();
        int i = 0;
        while (iterator.hasNext()) {
            Interval node = iterator.next();
            IntervalImpl ref = preOrder[i++];
            if (!ref.equals(node)) {
                System.err.println(ref + " != " + node);
                fail("node mismatch");
            } else {
                System.out.println(ref + " == " + node);
            }
        }
        assertTrue(i == preOrder.length);
    }

    @Test
    public void testSearch() {
        IntSequence pattern;
        Interval interval;
        pattern = new ArraySequence(new int[] { 3, 4 });
        interval = lst.search(pattern);
        System.out.printf("%s\t->%s\n", interval, interval.label());
        assertTrue(seqEquals(interval.label(), pattern));
        pattern = new ArraySequence(new int[] { 3, 4, 2, 1 });
        interval = lst.search(pattern);
        System.out.printf("%s\t->%s\n", interval, interval.label());
        assertTrue(seqEquals(interval.label(), pattern));
        pattern = new ArraySequence(new int[] { 3, 4, 1 });
        interval = lst.search(pattern);
        assertNull(interval);
    }
   
    @Test
    public void testLongestSearch() {
        int[] patternToFind = { 2, 1, 4 };
        int[] expectedArray = {2, 1};
        IntSequence pattern = new ArraySequence(patternToFind);
        IntSequence expected = new ArraySequence(expectedArray);
        System.out.println("Looking for : " + pattern);
        System.out.println("Expected: " + expected);
        Interval result = lst.longestSearch(pattern);
        System.out.println("Longest found: " + result.label());
        assertEquals(expected, result.label());
    }

    private boolean seqEquals(IntSequence sequence, IntSequence other) {
        if (sequence.size() != other.size())
            return false;
        for (int i = 0; i < sequence.size(); i++) {
            if (sequence.get(i) != other.get(i))
                return false;
        }
        return true;
    }

}
TOP

Related Classes of com.googlecode.gaal.suffix.impl.LinearizedSuffixTreeImplTest

TOP
Copyright © 2018 www.massapi.com. All rights reserved.
All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.