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package com.aliasi.test.unit.cluster;
import com.aliasi.cluster.Dendrogram;
import com.aliasi.cluster.LeafDendrogram;
import com.aliasi.cluster.LinkDendrogram;
import org.junit.Test;
import static junit.framework.Assert.assertEquals;
import static junit.framework.Assert.assertFalse;
import static junit.framework.Assert.assertTrue;
import static junit.framework.Assert.assertNull;
import static junit.framework.Assert.assertNotNull;
import static com.aliasi.test.unit.Asserts.assertNotEquals;
import static com.aliasi.util.CollectionUtils.asSet;
import com.aliasi.util.SmallSet;
import java.util.HashSet;
import java.util.Set;
public class DendrogramTest {
@Test
public void testEquivalence() {
Dendrogram leaf1 = new LeafDendrogram("1");
Dendrogram leaf2 = new LeafDendrogram("2");
Dendrogram link1_2 = new LinkDendrogram(leaf1,leaf2,1.0);
Dendrogram leaf3 = new LeafDendrogram("3");
Dendrogram link12_3 = new LinkDendrogram(leaf3,link1_2,2.0);
Dendrogram leaf4 = new LeafDendrogram("4");
Dendrogram leaf5 = new LeafDendrogram("5");
Dendrogram link4_5 = new LinkDendrogram(leaf4,leaf5,1.5);
Dendrogram leaf6 = new LeafDendrogram("6");
Dendrogram link45_6 = new LinkDendrogram(leaf6,link4_5,3.0);
Dendrogram link123_456 = new LinkDendrogram(link12_3,link45_6,4.0);
Dendrogram leaf1_B = new LeafDendrogram("1");
Dendrogram leaf2_B = new LeafDendrogram("2");
Dendrogram link1_2_B = new LinkDendrogram(leaf2_B,leaf1_B,1.0);
Dendrogram leaf3_B = new LeafDendrogram("3");
Dendrogram link12_3_B = new LinkDendrogram(leaf3_B,link1_2_B,2.0);
Dendrogram leaf4_B = new LeafDendrogram("4");
Dendrogram leaf5_B = new LeafDendrogram("5");
Dendrogram link4_5_B = new LinkDendrogram(leaf5_B,leaf4_B,1.5);
Dendrogram leaf6_B = new LeafDendrogram("6");
Dendrogram link45_6_B = new LinkDendrogram(leaf6_B,link4_5_B,3.0);
Dendrogram link123_456_B = new LinkDendrogram(link45_6_B,link12_3_B, 4.0);
assertTrue(Dendrogram.structurallyEquivalent(leaf1,leaf1));
assertTrue(Dendrogram.structurallyEquivalent(leaf1,leaf1_B));
assertFalse(Dendrogram.structurallyEquivalent(leaf1,leaf2_B));
assertFalse(Dendrogram.structurallyEquivalent(leaf1,link1_2_B));
assertTrue(Dendrogram.structurallyEquivalent(link1_2,link1_2));
assertTrue(Dendrogram.structurallyEquivalent(link1_2,link1_2_B));
assertFalse(Dendrogram.structurallyEquivalent(link1_2,leaf1_B));
assertFalse(Dendrogram.structurallyEquivalent(link1_2,link12_3));
assertFalse(Dendrogram.structurallyEquivalent(link1_2,link12_3_B));
assertTrue(Dendrogram.structurallyEquivalent(link123_456,link123_456));
assertTrue(Dendrogram.structurallyEquivalent(link123_456,link123_456_B));
assertFalse(Dendrogram.structurallyEquivalent(link123_456,leaf1_B));
assertFalse(Dendrogram.structurallyEquivalent(link123_456,link1_2));
}
@Test
public void testPartition() {
Dendrogram leaf1 = new LeafDendrogram("1");
Dendrogram leaf2 = new LeafDendrogram("2");
Dendrogram link1_2 = new LinkDendrogram(leaf1,leaf2,1.0);
Dendrogram leaf3 = new LeafDendrogram("3");
Dendrogram link12_3 = new LinkDendrogram(leaf3,link1_2,2.0);
Dendrogram leaf4 = new LeafDendrogram("4");
Dendrogram leaf5 = new LeafDendrogram("5");
Dendrogram link4_5 = new LinkDendrogram(leaf4,leaf5,1.5);
Dendrogram leaf6 = new LeafDendrogram("6");
Dendrogram link45_6 = new LinkDendrogram(leaf6,link4_5,3.0);
Dendrogram link123_456 = new LinkDendrogram(link12_3,link45_6,4.0);
assertEquals(6,link123_456.size());
assertEqualPartition(new Dendrogram[] { link12_3, link45_6},
link123_456.partitionK(2));
assertEqualPartition(new Dendrogram[] { link12_3, link4_5, leaf6},
link123_456.partitionK(3));
assertEqualPartition(new Dendrogram[] { link1_2, leaf3, link4_5, leaf6},
link123_456.partitionK(4));
assertEqualPartition(new Dendrogram[] { link1_2, leaf3, leaf4, leaf5, leaf6},
link123_456.partitionK(5));
assertEqualPartition(new Dendrogram[] { leaf1, leaf2, leaf3, leaf4, leaf5, leaf6},
link123_456.partitionK(6));
}
@Test(expected=IllegalArgumentException.class)
public void testPartitionExc1() {
Dendrogram leaf1 = new LeafDendrogram("1");
Dendrogram leaf2 = new LeafDendrogram("2");
Dendrogram link1_2 = new LinkDendrogram(leaf1,leaf2,1.0);
Dendrogram leaf3 = new LeafDendrogram("3");
Dendrogram link12_3 = new LinkDendrogram(leaf3,link1_2,2.0);
Dendrogram leaf4 = new LeafDendrogram("4");
Dendrogram leaf5 = new LeafDendrogram("5");
Dendrogram link4_5 = new LinkDendrogram(leaf4,leaf5,1.5);
Dendrogram leaf6 = new LeafDendrogram("6");
Dendrogram link45_6 = new LinkDendrogram(leaf6,link4_5,3.0);
Dendrogram link123_456 = new LinkDendrogram(link12_3,link45_6,4.0);
link123_456.partitionK(7);
}
@Test(expected=IllegalArgumentException.class)
public void testPartitionExc2() {
Dendrogram leaf1 = new LeafDendrogram("1");
Dendrogram leaf2 = new LeafDendrogram("2");
Dendrogram link1_2 = new LinkDendrogram(leaf1,leaf2,1.0);
Dendrogram leaf3 = new LeafDendrogram("3");
Dendrogram link12_3 = new LinkDendrogram(leaf3,link1_2,2.0);
Dendrogram leaf4 = new LeafDendrogram("4");
Dendrogram leaf5 = new LeafDendrogram("5");
Dendrogram link4_5 = new LinkDendrogram(leaf4,leaf5,1.5);
Dendrogram leaf6 = new LeafDendrogram("6");
Dendrogram link45_6 = new LinkDendrogram(leaf6,link4_5,3.0);
Dendrogram link123_456 = new LinkDendrogram(link12_3,link45_6,4.0);
link123_456.partitionK(0);
}
@Test(expected=IllegalArgumentException.class)
public void testPartitionExc3() {
Dendrogram leaf1 = new LeafDendrogram("1");
Dendrogram leaf2 = new LeafDendrogram("2");
Dendrogram link1_2 = new LinkDendrogram(leaf1,leaf2,1.0);
Dendrogram leaf3 = new LeafDendrogram("3");
Dendrogram link12_3 = new LinkDendrogram(leaf3,link1_2,2.0);
Dendrogram leaf4 = new LeafDendrogram("4");
Dendrogram leaf5 = new LeafDendrogram("5");
Dendrogram link4_5 = new LinkDendrogram(leaf4,leaf5,1.5);
Dendrogram leaf6 = new LeafDendrogram("6");
Dendrogram link45_6 = new LinkDendrogram(leaf6,link4_5,3.0);
Dendrogram link123_456 = new LinkDendrogram(link12_3,link45_6,4.0);
link123_456.partitionK(-10);
}
private void assertEqualPartition(Dendrogram[] ds1, Set ds2) {
HashSet expected = new HashSet();
for (int i = 0; i < ds1.length; ++i)
expected.add(ds1[i].memberSet());
assertEquals(expected,ds2);
}
@Test
public void testPartitionByMax() {
Dendrogram leafaa = new LeafDendrogram("aa");
Dendrogram leafaaa = new LeafDendrogram("aaa");
Dendrogram leafaaaaa = new LeafDendrogram("aaaaa");
Dendrogram leafbbb = new LeafDendrogram("bbb");
Dendrogram leafbbbb = new LeafDendrogram("bbbb");
Dendrogram link_bs = new LinkDendrogram(leafbbb,leafbbbb,
1.0);
Dendrogram link_aa_aaa = new LinkDendrogram(leafaa,leafaaa,
1.0);
Dendrogram link_as = new LinkDendrogram(leafaaaaa,link_aa_aaa,
2.0);
Dendrogram dendro = new LinkDendrogram(link_as,link_bs,
3.0);
Set> part0 = dendro.partitionDistance(0.0);
Set> part1 = dendro.partitionDistance(1.0);
Set> part2 = dendro.partitionDistance(2.0);
Set> part3 = dendro.partitionDistance(3.0);
Set> part4 = dendro.partitionDistance(4.0);
Set> eqClasses0 = new HashSet>();
eqClasses0.add(leafaa.memberSet());
eqClasses0.add(leafaaa.memberSet());
eqClasses0.add(leafaaaaa.memberSet());
eqClasses0.add(leafbbb.memberSet());
eqClasses0.add(leafbbbb.memberSet());
assertEquals(eqClasses0,part0);
Set> eqClasses1 = new HashSet>();
eqClasses1.add(link_aa_aaa.memberSet());
eqClasses1.add(link_bs.memberSet());
eqClasses1.add(leafaaaaa.memberSet());
assertEquals(eqClasses1,part1);
Set> eqClasses2 = new HashSet>();
eqClasses2.add(link_bs.memberSet());
eqClasses2.add(link_as.memberSet());
assertEquals(eqClasses2,part2);
Set> eqClasses3 = new HashSet>();
eqClasses3.add(dendro.memberSet());
assertEquals(eqClasses3,part3);
assertEquals(eqClasses3,part4);
}
@Test
public void testOne() {
Dendrogram leaf1 = new LeafDendrogram("foo");
assertEquals(0.0,leaf1.score(),0.0001);
assertEquals(leaf1,leaf1.dereference());
assertNull(leaf1.parent());
// set behavior
assertEquals(1,leaf1.size());
assertTrue(leaf1.contains("foo"));
assertEquals(leaf1.memberSet(),SmallSet.create("foo"));
}
@Test
public void testTwo() {
Dendrogram leaf1 = new LeafDendrogram("foo");
Dendrogram leaf2 = new LeafDendrogram("bar");
Dendrogram link1 = new LinkDendrogram(leaf1,leaf2,1.0);
assertEquals(1.0,link1.score(),0.0001);
assertEquals(link1,link1.dereference());
assertEquals(link1,leaf1.dereference());
assertEquals(link1,leaf2.dereference());
assertEquals(link1,leaf1.parent());
assertEquals(link1,leaf2.parent());
// set behavior
assertEquals(2,link1.size());
assertTrue(link1.memberSet().contains("foo"));
assertTrue(link1.memberSet().contains("bar"));
assertEquals(SmallSet.create("foo","bar"),link1.memberSet());
Dendrogram leaf3 = new LeafDendrogram("baz");
Dendrogram link2 = new LinkDendrogram(leaf3,link1,2.0);
assertEquals(link2,link1.parent());
assertEquals(link2,link1.dereference());
assertEquals(link2,link1.dereference());
assertEquals(link2,link2.dereference());
assertEquals(link2,link2.dereference());
assertEquals(link2,leaf1.dereference());
assertEquals(link2,leaf1.dereference());
assertEquals(link2,leaf2.dereference());
assertEquals(link2,leaf2.dereference());
assertEquals(link2,leaf3.dereference());
assertEquals(link2,leaf3.dereference());
HashSet set = new HashSet();
set.add("foo");
set.add("bar");
set.add("baz");
assertEquals(set,link2.memberSet());
assertNotNull(new LinkDendrogram(leaf1,leaf2,Double.POSITIVE_INFINITY));
}
@Test
public void testEquals() {
assertNotEquals(new LeafDendrogram("foo"),
new LeafDendrogram("foo"));
}
@Test(expected=IllegalArgumentException.class)
public void testConstruxEx1() {
LeafDendrogram leaf1 = new LeafDendrogram("foo");
LeafDendrogram leaf2 = new LeafDendrogram("bar");
new LinkDendrogram(leaf1,leaf2,-3.0);
}
@Test(expected=IllegalArgumentException.class)
public void testConstruxEx2() {
LeafDendrogram leaf1 = new LeafDendrogram("foo");
LeafDendrogram leaf2 = new LeafDendrogram("bar");
new LinkDendrogram(leaf1,leaf2,Double.NaN);
}
@Test(expected=IllegalArgumentException.class)
public void testConstruxEx3() {
LeafDendrogram leaf1 = new LeafDendrogram("foo");
LeafDendrogram leaf2 = new LeafDendrogram("bar");
new LinkDendrogram(leaf1,leaf2,Double.NEGATIVE_INFINITY );
}
@Test
public void testPartitionDistanceLeaf() {
Dendrogram leaf1 = new LeafDendrogram("foo");
assertEquals(asSet(asSet("foo")),
leaf1.partitionDistance(1.0));
}
@Test
public void testPartitionDistanceLink() {
Dendrogram leaf1 = new LeafDendrogram("foo");
Dendrogram leaf2 = new LeafDendrogram("bar");
Dendrogram link12 = new LinkDendrogram(leaf1,leaf2,2.0);
assertEquals(asSet(asSet("foo"),asSet("bar")),
link12.partitionDistance(1.0));
assertEquals(asSet(asSet("foo","bar")),
link12.partitionDistance(20.0));
}
/*
@Test(expected=IllegalArgumentException.class)
public void testScatterExc1() {
Object[] labels = new Object[] { "a", "b", "c" };
ProximityMatrix matrix = new ProximityMatrix(3);
matrix.setValue(0,1,5.0);
matrix.setValue(0,2,3.0);
matrix.setValue(1,2,2.0);
Dendrogram leafA = new LeafDendrogram("a");
Dendrogram leafB = new LeafDendrogram("b");
Dendrogram leafC = new LeafDendrogram("c");
Dendrogram linkB_C = new LinkDendrogram(leafB,leafC,2.0);
Dendrogram linkA__B_C = new LinkDendrogram(linkB_C,leafA,5.0);
linkA__B_C.withinClusterScatter(0,matrix);
}
@Test(expected=IllegalArgumentException.class)
public void testScatterExc2() {
Object[] labels = new Object[] { "a", "b", "c" };
ProximityMatrix matrix = new ProximityMatrix(3);
matrix.setValue(0,1,5.0);
matrix.setValue(0,2,3.0);
matrix.setValue(1,2,2.0);
Dendrogram leafA = new LeafDendrogram("a");
Dendrogram leafB = new LeafDendrogram("b");
Dendrogram leafC = new LeafDendrogram("c");
Dendrogram linkB_C = new LinkDendrogram(leafB,leafC,2.0);
Dendrogram linkA__B_C = new LinkDendrogram(linkB_C,leafA,5.0);
linkA__B_C.withinClusterScatter(4,matrix);
}
@Test
public void testScatter() {
Object[] labels = new Object[] { "a", "b", "c" };
ProximityMatrix matrix = new ProximityMatrix(labels);
matrix.setValue(0,1,5.0);
matrix.setValue(0,2,3.0);
matrix.setValue(1,2,2.0);
Dendrogram leafA = new LeafDendrogram("a",1);
Dendrogram leafB = new LeafDendrogram("b",2);
Dendrogram leafC = new LeafDendrogram("c",3);
Dendrogram linkB_C = new LinkDendrogram(leafB,leafC,2.0);
Dendrogram linkA__B_C = new LinkDendrogram(linkB_C,leafA,5.0);
assertEquals(0.0,leafA.totalScatter(matrix),0.0001);
assertEquals(0.0,leafB.totalScatter(matrix),0.0001);
assertEquals(0.0,leafC.totalScatter(matrix),0.0001);
assertEquals(2.0,linkB_C.totalScatter(matrix),0.0001);
assertEquals(10.0,linkA__B_C.totalScatter(matrix),0.0001);
assertEquals(10.0,linkA__B_C.withinClusterScatter(1,matrix),0.0001);
assertEquals(2.0,linkA__B_C.withinClusterScatter(2,matrix),0.0001);
assertEquals(0.0,linkA__B_C.withinClusterScatter(3,matrix),0.0001);
Dendrogram linkA_B = new LinkDendrogram(leafA,leafB,5.0);
assertEquals(5.0,linkA_B.totalScatter(matrix),0.0001);
}
@Test
public void testCophenetic() {
Dendrogram leafA = new LeafDendrogram("a",1);
Matrix cmA = leafA.copheneticMatrix(new Object[] { "a" });
assertEquals(1,cmA.numRows());
assertEquals(1,cmA.numColumns());
assertEquals(0.0,cmA.value(0,0),0.0001);
Dendrogram leafB = new LeafDendrogram("b",2);
Dendrogram linkA_B = new LinkDendrogram(leafA,leafB,1.0);
Dendrogram leafC = new LeafDendrogram("c",3);
Dendrogram leafD = new LeafDendrogram("d",4);
Dendrogram linkC_D = new LinkDendrogram(leafC,leafD,2.0);
Dendrogram linkC_D__A_B = new LinkDendrogram(linkA_B,linkC_D,5.0);
Dendrogram leafE = new LeafDendrogram("e",5);
Dendrogram top = new LinkDendrogram(linkC_D__A_B,leafE,7.0);
assertEquals(5,top.size());
Object[] labels = new Object[] { "a", "b", "c", "d", "e" };
Matrix cm = top.copheneticMatrix(labels);
assertEquals(0.0,cm.value(0,0),0.0001);
assertEquals(1.0,cm.value(0,1),0.0001);
assertEquals(5.0,cm.value(0,2),0.0001);
assertEquals(5.0,cm.value(0,3),0.0001);
assertEquals(7.0,cm.value(0,4),0.0001);
assertEquals(0.0,cm.value(1,1),0.0001);
assertEquals(5.0,cm.value(1,2),0.0001);
assertEquals(5.0,cm.value(1,3),0.0001);
assertEquals(7.0,cm.value(1,4),0.0001);
assertEquals(0.0,cm.value(2,2),0.0001);
assertEquals(2.0,cm.value(2,3),0.0001);
assertEquals(7.0,cm.value(2,4),0.0001);
assertEquals(0.0,cm.value(3,3),0.0001);
assertEquals(7.0,cm.value(3,4),0.0001);
assertEquals(0.0,cm.value(4,4),0.0001);
ProximityMatrix pm = new ProximityMatrix(labels);
pm.setValue(0,1,1);
pm.setValue(0,2,5);
pm.setValue(0,3,7);
pm.setValue(0,4,9);
pm.setValue(1,2,7);
pm.setValue(1,3,5);
pm.setValue(1,4,9);
pm.setValue(2,3,2);
pm.setValue(2,4,7);
pm.setValue(3,4,11);
double[] xs = new double[] { cm.value(0,1),
cm.value(0,2),
cm.value(0,3),
cm.value(0,4),
cm.value(1,2),
cm.value(1,3),
cm.value(1,4),
cm.value(2,3),
cm.value(2,4),
cm.value(3,4) };
double[] ys = new double[] { pm.value(0,1),
pm.value(0,2),
pm.value(0,3),
pm.value(0,4),
pm.value(1,2),
pm.value(1,3),
pm.value(1,4),
pm.value(2,3),
pm.value(2,4),
pm.value(3,4) };
assertEquals(Statistics.correlation(xs,ys),
top.copheneticCorrelation(pm),
0.0001);
}
*/
}
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