public void testAbabBaba2() {
GeneralizedSuffixTree gst = new GeneralizedSuffixTree("abab", "baba", '#', '$');
GeneralizedSuffixTree.CommonSubstr commonSubstr = gst.getLcs();
assertNotNull(commonSubstr);
assertEquals(0, commonSubstr.getBeginIndexes()[0]);
assertEquals(2, commonSubstr.getEndIndexes()[0]);
}
public void testMerge2() {
GeneralizedSuffixTree gst = new GeneralizedSuffixTree("12345 67890", "12345 sdfsd 67890");
GeneralizedSuffixTree.CommonSubstr commonSubstr = gst.getLcs();
assertNotNull(commonSubstr);
assertEquals(0, commonSubstr.getBeginIndexes()[0]);
assertEquals(5, commonSubstr.getEndIndexes()[0]);
assertEquals("12345 ", gst.getLcsAsString());
List<GeneralizedSuffixTree.CommonSubstr> list = gst.diff();
assertEquals(2, list.size());
for (GeneralizedSuffixTree.CommonSubstr cs : list)
System.out.print(
"12345 67890".substring(cs.getBeginIndexes()[0], cs.getEndIndexes()[0]) + " ");
System.out.println();
gst = new GeneralizedSuffixTree("12345 sdfsd 67890", "12345 67890");
list = gst.diff();
assertEquals(2, list.size());
for (GeneralizedSuffixTree.CommonSubstr cs : list)
System.out.print(
"12345 sdfsd 67890".substring(cs.getBeginIndexes()[0], cs.getEndIndexes()[0]) + " ");
System.out.println();
}
public void testDiff4() {
GeneralizedSuffixTree gst = new GeneralizedSuffixTree("abababcdde", "ddddddabc", '#', '$');
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 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 testLcs2() {
GeneralizedSuffixTree gst = new GeneralizedSuffixTree("ddddddddabc", "abababc", '#', '$');
GeneralizedSuffixTree.CommonSubstr commonSubstr = gst.getLcs();
int beginIndexes[] = commonSubstr.getBeginIndexes();
int endIndexes[] = commonSubstr.getEndIndexes();
assertEquals(8, beginIndexes[0]);
assertEquals(10, endIndexes[0]);
assertEquals(16, beginIndexes[1]);
assertEquals(18, endIndexes[1]);
int leftEndIndexes[] = new int[] {8, 16};
int rightBeginIndexes[] = new int[] {11, 19};
commonSubstr = gst.getLcs(gst.getDefaultBeginIndexes(), leftEndIndexes);
assertNull(commonSubstr);
commonSubstr = gst.getLcs(rightBeginIndexes, gst.getDefaultEndIndexes());
assertNull(commonSubstr);
}
public void testAlive() {
GeneralizedSuffixTree gst =
new GeneralizedSuffixTree("superriorcalifoernialives", "sealiver", '#', '$');
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 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 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 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 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();
}