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lphy-base/src/main/java/lphy/base/evolution/tree/LabelClade.java
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| package lphy.base.evolution.tree; | ||
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| import lphy.core.model.DeterministicFunction; | ||
| import lphy.core.model.Value; | ||
| import lphy.core.model.annotation.GeneratorInfo; | ||
| import lphy.core.model.annotation.ParameterInfo; | ||
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| public class LabelClade extends DeterministicFunction<TimeTree> { | ||
| public static final String treeParamName = "tree"; | ||
| public static final String taxaParamName = "taxa"; | ||
| public static final String labelParamName = "label"; | ||
| public LabelClade(@ParameterInfo(name = treeParamName, description = "the tree to label")Value<TimeTree> tree, | ||
| @ParameterInfo(name = taxaParamName, description = "the root of the taxa names would be labelled") Value<String[]> taxa, | ||
| @ParameterInfo(name = labelParamName, description = "the label") Value<String> label){ | ||
| if (tree == null) throw new IllegalArgumentException("The tree cannot be null!"); | ||
| if (taxa == null) throw new IllegalArgumentException("The taxa name cannot be null!"); | ||
| if (label == null) throw new IllegalArgumentException("Please label the mrca of the taxa!"); | ||
| setParam(treeParamName, tree); | ||
| setParam(taxaParamName, taxa); | ||
| setParam(labelParamName, label); | ||
| } | ||
| @GeneratorInfo(name = "labelClade", description = "Find the most recent common ancestor of given taxa names in the tree and give it a label.") | ||
| @Override | ||
| public Value<TimeTree> apply() { | ||
| // make a deep copy of the tree | ||
| TimeTree tree = getTree().value(); | ||
| TimeTree newTree = new TimeTree(tree); | ||
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| // find mrca node | ||
| Value<TimeTree> treeValue = new Value<>("newTree", newTree); | ||
| MRCA mrcaInstance = new MRCA(treeValue, getTaxa()); | ||
| TimeTreeNode mrca = mrcaInstance.apply().value(); | ||
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| // set label metadata | ||
| String label = getLabel().value(); | ||
| mrca.setMetaData("label", label); | ||
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| return new Value<>(null, newTree,this); | ||
| } | ||
| public Value<TimeTree> getTree(){ | ||
| return getParams().get(treeParamName); | ||
| } | ||
| public Value<String[]> getTaxa(){ | ||
| return getParams().get(taxaParamName); | ||
| } | ||
| public Value<String> getLabel(){ | ||
| return getParams().get(labelParamName); | ||
| } | ||
| } |
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66
lphy-base/src/test/java/lphy/base/evolution/tree/LabelCladeTest.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,66 @@ | ||
| package lphy.base.evolution.tree; | ||
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| 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 static org.junit.jupiter.api.Assertions.assertEquals; | ||
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| public class LabelCladeTest { | ||
| String newickTree; | ||
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| @BeforeEach | ||
| void setUp() { | ||
| newickTree = "(((((1:2.0, (2:1.0, 3:1.0):1.0):2.0, (5:2.0, 6:2.0):2.0):2.0):0.0,4:6.0):6.0, 7:12.0)"; | ||
| } | ||
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| @Test | ||
| void applyTest1() { | ||
| TimeTree tree = Newick.parseNewick(newickTree); | ||
| String[] taxa = {"4", "7"}; | ||
| String label = "label"; | ||
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| Value<TimeTree> treeValue = new Value<>("tree", tree); | ||
| Value<String[]> taxaValue = new Value<>("taxa", taxa); | ||
| Value<String> labelValue = new Value<>("label", label); | ||
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| LabelClade labelCladeInstance = new LabelClade(treeValue, taxaValue, labelValue); | ||
| MRCA mrcaInstance = new MRCA(treeValue,taxaValue); | ||
| TimeTree observe = labelCladeInstance.apply().value(); | ||
| TimeTreeNode mrcaNode = mrcaInstance.apply().value(); | ||
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| // only index should be same for mrca | ||
| assertEquals(mrcaNode.getIndex(), observe.getRoot().getIndex()); | ||
| // check label | ||
| assertEquals(label, observe.getRoot().getMetaData("label")); | ||
| assertEquals(observe.getRoot(), observe.getLabeledNode(label)); | ||
| } | ||
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| @Test | ||
| void applyTest2() { | ||
| TimeTree tree = Newick.parseNewick(newickTree); | ||
| String[] taxa = {"3", "5"}; | ||
| String label = "label"; | ||
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| Value<TimeTree> treeValue = new Value<>("tree", tree); | ||
| Value<String[]> taxaValue = new Value<>("taxa", taxa); | ||
| Value<String> labelValue = new Value<>("label", label); | ||
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| LabelClade labelCladeInstance = new LabelClade(treeValue, taxaValue, labelValue); | ||
| MRCA mrcaInstance = new MRCA(treeValue,taxaValue); | ||
| TimeTree observe = labelCladeInstance.apply().value(); | ||
| TimeTreeNode mrcaNode = mrcaInstance.apply().value(); | ||
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| boolean found = false; | ||
| for (TimeTreeNode node: observe.getInternalNodes()){ | ||
| if (node.getAllLeafNodes().size() == 5 && node.age == 4){ | ||
| assertEquals(node.getIndex(), mrcaNode.getIndex()); | ||
| assertEquals(label, node.getMetaData("label")); | ||
| assertEquals(node, observe.getLabeledNode(label)); | ||
| found = true; | ||
| } | ||
| } | ||
| assert(found); | ||
| } | ||
| } |