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lphy-base/src/test/java/lphy/base/evolution/likelihood/PhyloCTMCTest.java
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| package lphy.base.evolution.likelihood; | ||
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| import lphy.base.evolution.branchrate.LocalClock; | ||
| import lphy.base.evolution.tree.TimeTree; | ||
| import lphy.base.evolution.tree.TimeTreeNode; | ||
| import lphy.base.function.tree.Newick; | ||
| import lphy.core.model.Value; | ||
| import org.junit.jupiter.api.BeforeEach; | ||
| import org.junit.jupiter.api.Test; | ||
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| import java.util.List; | ||
| import java.util.Objects; | ||
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| import static org.junit.jupiter.api.Assertions.assertEquals; | ||
| import static org.junit.jupiter.api.Assertions.assertNotNull; | ||
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| public class PhyloCTMCTest { | ||
| String newickTree; | ||
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| @BeforeEach | ||
| void setUp() { | ||
| newickTree = "((1:2.0, (2:1.0, 3:1.0):1.0):2.0, 4:4.0)"; | ||
| } | ||
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| @Test | ||
| void apply() { | ||
| // generate a tree with local clock | ||
| TimeTree tree = Newick.parseNewick(newickTree); | ||
| TimeTreeNode node1 = null; | ||
| TimeTreeNode node2 = null; | ||
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| for (int i = 0; i<tree.getNodes().size(); i++){ | ||
| if (Objects.equals(tree.getNodes().get(i).getId(), "4")){ //node2 is the leaf node 4 | ||
| node2 = tree.getNodes().get(i); | ||
| } else if (tree.getNodes().get(i).getAllLeafNodes().size() == 2){ //node1 is the parent of (2,3) | ||
| node1 = tree.getNodes().get(i); | ||
| } | ||
| } | ||
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| assertNotNull(node1); | ||
| assertNotNull(node2); | ||
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| TimeTreeNode[] clades = {node1, node2}; | ||
| Double[] cladeRates = {0.4, 0.3}; | ||
| double rootRate = 0.2; | ||
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| Value<TimeTree> treeValue = new Value<>("tree", tree); | ||
| Value<Object[]> cladesValue = new Value<>("clades", clades); | ||
| Value<Double[]> cladeRatesValue = new Value<>("cladeRates", cladeRates); | ||
| Value<Double> rootRateValue = new Value<>("rootRate" , rootRate); | ||
| Value<Boolean> includeStemValue = new Value<>("includeStem" , Boolean.TRUE); | ||
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| LocalClock localClockInstance = new LocalClock(treeValue, cladesValue, cladeRatesValue, rootRateValue, includeStemValue); | ||
| TimeTree newTree = localClockInstance.apply().value(); | ||
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| // test PhyloCTMC | ||
| Double[][] Q = { | ||
| { -1.0, 0.5, 0.3, 0.2 }, | ||
| { 0.4, -1.0, 0.1, 0.5 }, | ||
| { 0.3, 0.2, -1.0, 0.5 }, | ||
| { 0.2, 0.3, 0.5, -1.0 } | ||
| }; | ||
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| Value<TimeTree> newTreeValue = new Value<>("newTree", newTree); | ||
| Value<Double[][]> QValue = new Value<>("Q", Q); | ||
| Value<Double[]> siteRatesValue = new Value<Double[]>("siteRates", new Double[]{0.1, 0.1, 0.1, 0.1, 0.1}); | ||
| Value<Integer> LValue = new Value<Integer>("L", 5); | ||
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| PhyloCTMC phyloCTMCInstance = new PhyloCTMC( | ||
| newTreeValue,null,null, | ||
| QValue,siteRatesValue,null, | ||
| LValue,null, null); | ||
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| phyloCTMCInstance.sample(); | ||
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| Double[] branchRates = phyloCTMCInstance.getBranchRates().value(); | ||
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| List<TimeTreeNode> allNodes = newTree.getNodes(); | ||
| assertEquals(allNodes.size(), branchRates.length); | ||
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| // index 0 : node 2 | ||
| assertEquals(allNodes.get(0).getBranchRate(), branchRates[0]); | ||
| // index 1 : node 3 | ||
| assertEquals(allNodes.get(1).getBranchRate(), branchRates[1]); | ||
| // index 2 : node 1 | ||
| assertEquals(allNodes.get(2).getBranchRate(), branchRates[2]); | ||
| // index 3 : node 4 | ||
| assertEquals("4" , allNodes.get(3).getId()); | ||
| assertEquals(0.3, allNodes.get(3).getBranchRate()); | ||
| assertEquals(allNodes.get(3).getBranchRate(), branchRates[3]); | ||
| // index 4 : node (2,3) | ||
| assertEquals(allNodes.get(4).getBranchRate(), branchRates[4]); | ||
| // index 5 : node ((2,3),1) | ||
| assertEquals(allNodes.get(5).getBranchRate(), branchRates[5]); | ||
| // index 6 : node (((2,3),1),4) | ||
| assertEquals(allNodes.get(6).getBranchRate(), branchRates[6]); | ||
| } | ||
| } |