public void testMerge2() {
    GeneralizedSuffixTree gst = new GeneralizedSuffixTree("12345 67890", "12345 sdfsd 67890");

    GeneralizedSuffixTree.CommonSubstr commonSubstr = gst.getLcs();
    assertNotNull(commonSubstr);
    assertEquals(0, commonSubstr.getBeginIndexes()[0]);
    assertEquals(5, commonSubstr.getEndIndexes()[0]);

    assertEquals("12345 ", gst.getLcsAsString());

    List<GeneralizedSuffixTree.CommonSubstr> list = gst.diff();
    assertEquals(2, list.size());

    for (GeneralizedSuffixTree.CommonSubstr cs : list)
      System.out.print(
          "12345 67890".substring(cs.getBeginIndexes()[0], cs.getEndIndexes()[0]) + " ");
    System.out.println();

    gst = new GeneralizedSuffixTree("12345 sdfsd 67890", "12345 67890");

    list = gst.diff();
    assertEquals(2, list.size());

    for (GeneralizedSuffixTree.CommonSubstr cs : list)
      System.out.print(
          "12345 sdfsd 67890".substring(cs.getBeginIndexes()[0], cs.getEndIndexes()[0]) + " ");
    System.out.println();
  }
 public void testAbabBaba2() {
   GeneralizedSuffixTree gst = new GeneralizedSuffixTree("abab", "baba", '#', '$');
   GeneralizedSuffixTree.CommonSubstr commonSubstr = gst.getLcs();
   assertNotNull(commonSubstr);
   assertEquals(0, commonSubstr.getBeginIndexes()[0]);
   assertEquals(2, commonSubstr.getEndIndexes()[0]);
 }
  public void testFailure() {
    GeneralizedSuffixTree gst = new GeneralizedSuffixTree("abba", "ccde", '#', '$');
    GeneralizedSuffixTree.CommonSubstr commonSubstr = gst.getLcs();
    assertNull(commonSubstr);

    gst = new GeneralizedSuffixTree("123456", "7890", '#', '$');
    List<GeneralizedSuffixTree.CommonSubstr> list = gst.diff();
    assertEquals(0, list.size());
  }
  public void testDiff() {
    GeneralizedSuffixTree gst = new GeneralizedSuffixTree("abcabeabg", "abdabfabh", '#', '$');

    GeneralizedSuffixTree.CommonSubstr commonSubstr = gst.getLcs();
    assertNotNull(commonSubstr);
    assertEquals(0, commonSubstr.getBeginIndexes()[0]);
    assertEquals(1, commonSubstr.getEndIndexes()[0]);
    assertEquals(10, commonSubstr.getBeginIndexes()[1]);
    assertEquals(11, commonSubstr.getEndIndexes()[1]);

    commonSubstr =
        gst.getLcs(gst.incIndexes(commonSubstr.getEndIndexes()), gst.getDefaultEndIndexes());
    assertNotNull(commonSubstr);
    assertEquals(3, commonSubstr.getBeginIndexes()[0]);
    assertEquals(4, commonSubstr.getEndIndexes()[0]);
    assertEquals(13, commonSubstr.getBeginIndexes()[1]);
    assertEquals(14, commonSubstr.getEndIndexes()[1]);

    commonSubstr =
        gst.getLcs(gst.incIndexes(commonSubstr.getEndIndexes()), gst.getDefaultEndIndexes());
    assertNotNull(commonSubstr);
    assertEquals(6, commonSubstr.getBeginIndexes()[0]);
    assertEquals(7, commonSubstr.getEndIndexes()[0]);
    assertEquals(16, commonSubstr.getBeginIndexes()[1]);
    assertEquals(17, commonSubstr.getEndIndexes()[1]);

    List<GeneralizedSuffixTree.CommonSubstr> list = gst.diff();
    assertEquals(3, list.size());

    for (GeneralizedSuffixTree.CommonSubstr cs : list) {
      System.out.print("abcabeabg".substring(cs.getBeginIndexes()[0], cs.getEndIndexes()[0]) + " ");
    }
    System.out.println();
  }
  public void testDiff4() {
    GeneralizedSuffixTree gst = new GeneralizedSuffixTree("abababcdde", "ddddddabc", '#', '$');
    List<GeneralizedSuffixTree.CommonSubstr> list = gst.diff();
    assertEquals(1, list.size());

    for (GeneralizedSuffixTree.CommonSubstr cs : list) {
      System.out.print(
          "ddddddddabc".substring(cs.getBeginIndexes()[0], cs.getEndIndexes()[0]) + " ");
    }
    System.out.println();
  }
  public void testDiff2() {
    GeneralizedSuffixTree gst = new GeneralizedSuffixTree("abababcdab", "abbbabceab", '#', '$');

    GeneralizedSuffixTree.CommonSubstr commonSubstr = gst.getLcs();
    assertNotNull(commonSubstr);
    assertEquals(3, commonSubstr.getBeginIndexes()[0]);
    assertEquals(6, commonSubstr.getEndIndexes()[0]);
    assertEquals(14, commonSubstr.getBeginIndexes()[1]);
    assertEquals(17, commonSubstr.getEndIndexes()[1]);

    int[] beginIndexes = gst.incIndexes(commonSubstr.getEndIndexes());
    commonSubstr = gst.getLcs(gst.getDefaultBeginIndexes(), commonSubstr.getBeginIndexes());
    assertNotNull(commonSubstr);
    assertEquals(0, commonSubstr.getBeginIndexes()[0]);
    assertEquals(1, commonSubstr.getEndIndexes()[0]);
    assertEquals(11, commonSubstr.getBeginIndexes()[1]);
    assertEquals(12, commonSubstr.getEndIndexes()[1]);

    commonSubstr = gst.getLcs(beginIndexes, gst.getDefaultEndIndexes());
    assertNotNull(commonSubstr);
    assertEquals(8, commonSubstr.getBeginIndexes()[0]);
    assertEquals(9, commonSubstr.getEndIndexes()[0]);
    assertEquals(19, commonSubstr.getBeginIndexes()[1]);
    assertEquals(20, commonSubstr.getEndIndexes()[1]);

    List<GeneralizedSuffixTree.CommonSubstr> list = gst.diff();
    assertEquals(3, list.size());

    for (GeneralizedSuffixTree.CommonSubstr cs : list) {
      System.out.print(
          "abababcdab".substring(cs.getBeginIndexes()[0], cs.getEndIndexes()[0]) + " ");
    }
    System.out.println();
  }
  public void testAlive3() {
    GeneralizedSuffixTree gst =
        new GeneralizedSuffixTree(
            new String[] {"superiorcalifornialives", "sealivers", "szalivefrerds"},
            new char[] {'#', '$', '%'});
    assertEquals("alive", gst.getLcsAsString());

    List<GeneralizedSuffixTree.CommonSubstr> list = gst.diff();
    assertEquals(3, list.size());

    for (GeneralizedSuffixTree.CommonSubstr cs : list)
      System.out.print(
          "superiorcalifornialives".substring(cs.getBeginIndexes()[0], cs.getEndIndexes()[0])
              + " ");
    System.out.println();
  }
  public void testLcs() {
    GeneralizedSuffixTree gst = new GeneralizedSuffixTree("abababcdab", "abbbabceab", '#', '$');
    GeneralizedSuffixTree.CommonSubstr commonSubstr = gst.getLcs();

    int beginIndexes[] = commonSubstr.getBeginIndexes();
    int endIndexes[] = commonSubstr.getEndIndexes();
    assertEquals(3, beginIndexes[0]);
    assertEquals(6, endIndexes[0]);
    assertEquals(14, beginIndexes[1]);
    assertEquals(17, endIndexes[1]);

    int leftEndIndexes[] = new int[] {3, 14};
    int rightBeginIndexes[] = new int[] {7, 18};

    commonSubstr = gst.getLcs(gst.getDefaultBeginIndexes(), leftEndIndexes);
    beginIndexes = commonSubstr.getBeginIndexes();
    endIndexes = commonSubstr.getEndIndexes();
    assertEquals(0, beginIndexes[0]);
    assertEquals(1, endIndexes[0]);
    assertEquals(11, beginIndexes[1]);
    assertEquals(12, endIndexes[1]);

    commonSubstr = gst.getLcs(rightBeginIndexes, gst.getDefaultEndIndexes());
    beginIndexes = commonSubstr.getBeginIndexes();
    endIndexes = commonSubstr.getEndIndexes();
    assertEquals(8, beginIndexes[0]);
    assertEquals(9, endIndexes[0]);
    assertEquals(19, beginIndexes[1]);
    assertEquals(20, endIndexes[1]);
  }
  public void testAbababcAbbbabc() {
    GeneralizedSuffixTree gst = new GeneralizedSuffixTree("abababc", "abbbabc", '#', '$');
    assertEquals("babc", gst.getLcsAsString());
    assertEquals(3, gst.getSuffixTree().indexOf("babc"));
    assertEquals(5, gst.getSuffixTree().indexOf("bc"));

    GeneralizedSuffixTree.CommonSubstr commonSubstr = gst.getLcs();
    assertNotNull(commonSubstr);
    assertEquals(3, commonSubstr.getBeginIndexes()[0]);
    assertEquals(6, commonSubstr.getEndIndexes()[0]);

    commonSubstr = gst.getLcs(gst.getDefaultBeginIndexes(), commonSubstr.getBeginIndexes());
    assertNotNull(commonSubstr);
    assertEquals(0, commonSubstr.getBeginIndexes()[0]);
    assertEquals(1, commonSubstr.getEndIndexes()[0]);
  }
  public void testAlive() {
    GeneralizedSuffixTree gst =
        new GeneralizedSuffixTree("superriorcalifoernialives", "sealiver", '#', '$');
    assertEquals("alive", gst.getLcsAsString());

    List<GeneralizedSuffixTree.CommonSubstr> list = gst.diff();
    assertEquals(3, list.size());

    for (GeneralizedSuffixTree.CommonSubstr cs : list)
      System.out.print(
          "superriorcalifoernialives".substring(cs.getBeginIndexes()[0], cs.getEndIndexes()[0])
              + " ");
    System.out.println();

    gst = new GeneralizedSuffixTree("aaasuperriorcalifoernialives", "aaasealiver", '#', '$');
    assertEquals("alive", gst.getLcsAsString());

    list = gst.diff();
    assertEquals(3, list.size());

    for (GeneralizedSuffixTree.CommonSubstr cs : list)
      System.out.print(
          "aaasuperriorcalifoernialives".substring(cs.getBeginIndexes()[0], cs.getEndIndexes()[0])
              + " ");
    System.out.println();

    gst = new GeneralizedSuffixTree("aaasealiver", "aaasuperriorcalifoernialives", '#', '$');
    assertEquals("alive", gst.getLcsAsString());

    list = gst.diff();
    assertEquals(3, list.size());

    for (GeneralizedSuffixTree.CommonSubstr cs : list)
      System.out.print(
          "aaasealiver".substring(cs.getBeginIndexes()[0], cs.getEndIndexes()[0]) + " ");
    System.out.println();
  }
  public void testLcs2() {
    GeneralizedSuffixTree gst = new GeneralizedSuffixTree("ddddddddabc", "abababc", '#', '$');
    GeneralizedSuffixTree.CommonSubstr commonSubstr = gst.getLcs();

    int beginIndexes[] = commonSubstr.getBeginIndexes();
    int endIndexes[] = commonSubstr.getEndIndexes();
    assertEquals(8, beginIndexes[0]);
    assertEquals(10, endIndexes[0]);
    assertEquals(16, beginIndexes[1]);
    assertEquals(18, endIndexes[1]);

    int leftEndIndexes[] = new int[] {8, 16};
    int rightBeginIndexes[] = new int[] {11, 19};

    commonSubstr = gst.getLcs(gst.getDefaultBeginIndexes(), leftEndIndexes);
    assertNull(commonSubstr);

    commonSubstr = gst.getLcs(rightBeginIndexes, gst.getDefaultEndIndexes());
    assertNull(commonSubstr);
  }
 public void testAbabBabaBa() {
   GeneralizedSuffixTree gst =
       new GeneralizedSuffixTree(new String[] {"abab", "baba", "ba"}, new char[] {'#', '$', '%'});
   TestHelper.dumpEdges(gst.getSuffixTree());
   assertEquals("ba", gst.getLcsAsString());
 }
  public void testMerge() {
    GeneralizedSuffixTree gst =
        new GeneralizedSuffixTree(
            "djfhsdajkzzsdfajkhasdjfghhshafjhsrtyuidfsj",
            "djfhsdajkfasdfajkhasdjfadjshafjhsadjhsadfsj");
    assertEquals("sdfajkhasdjf", gst.getLcsAsString());

    List<GeneralizedSuffixTree.CommonSubstr> list = gst.diff();
    assertEquals(4, list.size());

    for (GeneralizedSuffixTree.CommonSubstr cs : list)
      System.out.print(
          "djfhsdajkzzsdfajkhasdjfghhshafjhsrtyuidfsj"
                  .substring(cs.getBeginIndexes()[0], cs.getEndIndexes()[0])
              + " ");
    System.out.println();

    gst =
        new GeneralizedSuffixTree(
            "djfhsdajkfasdfajkhasdjfadjshafjhsadjhsadfsj",
            "djfhsdajkzzsdfajkhasdjfghhshafjhsrtyuidfsj");
    assertEquals("sdfajkhasdjf", gst.getLcsAsString());

    list = gst.diff();
    assertEquals(4, list.size());

    for (GeneralizedSuffixTree.CommonSubstr cs : list)
      System.out.print(
          "djfhsdajkfasdfajkhasdjfadjshafjhsadjhsadfsj"
                  .substring(cs.getBeginIndexes()[0], cs.getEndIndexes()[0])
              + " ");
    System.out.println();

    gst =
        new GeneralizedSuffixTree(
            "djfhsdajkzzsdfaaaaaaaaaaaaaafjhsrtyuidfsj",
            "djfhsdajkfasdfaaaaaaaaaaajshafjhsadjhsadfsj");
    assertEquals("sdfaaaaaaaaaaa", gst.getLcsAsString());

    list = gst.diff();
    assertEquals(4, list.size());

    for (GeneralizedSuffixTree.CommonSubstr cs : list)
      System.out.print(
          "djfhsdajkzzsdfaaaaaaaaaaaaaafjhsrtyuidfsj"
                  .substring(cs.getBeginIndexes()[0], cs.getEndIndexes()[0])
              + " ");
    System.out.println();

    gst =
        new GeneralizedSuffixTree(
            "djfhsdajkfasdfaaaaaaaaaaajshafjhsadjhsadfsj",
            "djfhsdajkzzsdfaaaaaaaaaaaaaafjhsrtyuidfsj");
    assertEquals("sdfaaaaaaaaaaa", gst.getLcsAsString());

    list = gst.diff();
    assertEquals(4, list.size());

    for (GeneralizedSuffixTree.CommonSubstr cs : list)
      System.out.print(
          "djfhsdajkfasdfaaaaaaaaaaajshafjhsadjhsadfsj"
                  .substring(cs.getBeginIndexes()[0], cs.getEndIndexes()[0])
              + " ");
    System.out.println();
  }
  public void testDefaultTerminators() {
    char[] terminators = GeneralizedSuffixTree.getDefaultTerminators(2);
    assertEquals(2, terminators.length);
    assertEquals('\ud800', terminators[0]);
    assertEquals('\ud801', terminators[1]);

    GeneralizedSuffixTree gst = new GeneralizedSuffixTree(new String[] {"abab", "baba"});
    TestHelper.dumpEdges(gst.getSuffixTree());
    assertEquals("aba", gst.getLcsAsString());

    gst = new GeneralizedSuffixTree(new String[] {"abababcdab", "abbbabceab"});

    GeneralizedSuffixTree.CommonSubstr commonSubstr = gst.getLcs();
    assertNotNull(commonSubstr);
    assertEquals(3, commonSubstr.getBeginIndexes()[0]);
    assertEquals(6, commonSubstr.getEndIndexes()[0]);
    assertEquals(14, commonSubstr.getBeginIndexes()[1]);
    assertEquals(17, commonSubstr.getEndIndexes()[1]);

    int[] beginIndexes = gst.incIndexes(commonSubstr.getEndIndexes());
    commonSubstr = gst.getLcs(gst.getDefaultBeginIndexes(), commonSubstr.getBeginIndexes());
    assertNotNull(commonSubstr);
    assertEquals(0, commonSubstr.getBeginIndexes()[0]);
    assertEquals(1, commonSubstr.getEndIndexes()[0]);
    assertEquals(11, commonSubstr.getBeginIndexes()[1]);
    assertEquals(12, commonSubstr.getEndIndexes()[1]);

    commonSubstr = gst.getLcs(beginIndexes, gst.getDefaultEndIndexes());
    assertNotNull(commonSubstr);
    assertEquals(8, commonSubstr.getBeginIndexes()[0]);
    assertEquals(9, commonSubstr.getEndIndexes()[0]);
    assertEquals(19, commonSubstr.getBeginIndexes()[1]);
    assertEquals(20, commonSubstr.getEndIndexes()[1]);

    List<GeneralizedSuffixTree.CommonSubstr> list = gst.diff();
    assertEquals(3, list.size());

    for (GeneralizedSuffixTree.CommonSubstr cs : list) {
      System.out.print(
          "abababcdab".substring(cs.getBeginIndexes()[0], cs.getEndIndexes()[0]) + " ");
    }
    System.out.println();
  }
 public void testXabxaBabxba() {
   GeneralizedSuffixTree gst = new GeneralizedSuffixTree("xabxa", "babxba", '#', '$');
   TestHelper.dumpEdges(gst.getSuffixTree());
   assertEquals("abx", gst.getLcsAsString());
 }
 public void testAbababcDdddddddabc() {
   GeneralizedSuffixTree gst = new GeneralizedSuffixTree("abababc", "ddddddddabc", '#', '$');
   assertEquals("abc", gst.getLcsAsString());
 }