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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,127 @@ | ||
| package bdmm.core.util; | ||
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| import master.BeastTreeFromMaster; | ||
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| import java.util.ArrayList; | ||
| import java.util.List; | ||
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| import beast.base.core.Description; | ||
| import beast.base.core.Input; | ||
| import beast.base.evolution.alignment.Alignment; | ||
| import beast.base.evolution.alignment.TaxonSet; | ||
| import beast.base.evolution.tree.Node; | ||
| import beast.base.evolution.tree.TraitSet; | ||
| import beast.base.evolution.tree.coalescent.RandomTree; | ||
| import beast.base.inference.StateNode; | ||
| import beast.base.inference.StateNodeInitialiser; | ||
| import beast.base.inference.parameter.IntegerParameter; | ||
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| /** | ||
| * User: [email protected] | ||
| * Date: 07.03.17 | ||
| */ | ||
| @Description("Make a random tree with tip dates and states obtained from MASTER simulation") | ||
| public class RandomCoalescentTreeFromMaster extends RandomTree implements StateNodeInitialiser { | ||
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| public Input<BeastTreeFromMaster> masterTreeInput = new Input<BeastTreeFromMaster>( | ||
| "masterTree", | ||
| "The tree from which traits should be inherited", Input.Validate.REQUIRED); | ||
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| public Input<Double> popSize = new Input<Double>("popSize", "popSize for tree initialization",1.); | ||
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| public Input<Boolean> typesKnown = new Input<Boolean>("typesKnown", "Set to false if the tree should not known the leave types. Default true.", true); | ||
| public Input<Boolean> printTypes = new Input<Boolean>("printTypes", "print the tip types of simulated tree (default false)",false); | ||
| public Input<List<IntegerParameter>> changeType = new Input<>("changeType", "Change the type of tip tip with type changeType at index 0 to the changeType at index 1.", new ArrayList<>(), Input.Validate.OPTIONAL); | ||
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| StateNode tree; | ||
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| @Override | ||
| public void initAndValidate() { | ||
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| init(); | ||
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| super.initAndValidate(); | ||
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| } | ||
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| public void init() { | ||
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| BeastTreeFromMaster masterTree = masterTreeInput.get(); | ||
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| int taxonCount = masterTree.getLeafNodeCount(); | ||
| System.out.println("taxonCount: " + taxonCount); | ||
| nodeCount = masterTree.getNodeCount(); | ||
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| tree = new RandomTree(); | ||
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| TraitSet typeTrait = new TraitSet(); | ||
| TraitSet dateTrait = new TraitSet(); | ||
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| Alignment taxa = taxaInput.get(); | ||
| TaxonSet taxonset = new TaxonSet(); | ||
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| Alignment actualTaxa = new Alignment(); | ||
| for (int i=0; i<taxonCount; i++) { | ||
| actualTaxa.setInputValue("sequence", taxa.sequenceInput.get().get(i)); | ||
| } | ||
| actualTaxa.initAndValidate(); | ||
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| taxonset.initByName("alignment", actualTaxa); | ||
| setInputValue("taxa",actualTaxa); | ||
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| String types = ""; | ||
| String dates = ""; | ||
| Boolean changeTypes = (changeType.get()!=null); | ||
| int[] changeTypeArray = new int[2*changeType.get().size()]; | ||
| boolean changed; | ||
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| if (changeTypes){ | ||
| for (int i=0; i<changeType.get().size(); i++) { | ||
| changeTypeArray[i*2] = changeType.get().get(i).getValue(0); | ||
| changeTypeArray[i*2+1] = changeType.get().get(i).getValue(1); | ||
| } | ||
| } | ||
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| if (printTypes.get()) | ||
| System.out.println("Tip types of simulated tree:"); | ||
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| for (Node beastNode : masterTree.getExternalNodes()){ | ||
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| dates += beastNode.getID() + "=" + beastNode.getHeight() +","; | ||
| if (typesKnown.get()) { | ||
| if (changeTypes){ | ||
| changed = false; | ||
| for (int i=0; i<changeType.get().size() && !changed; i++) { | ||
| if (changeTypeArray[i*2] == (Integer) beastNode.getMetaData("location")) { | ||
| beastNode.setMetaData("location", changeTypeArray[i*2+1]); | ||
| changed=true; | ||
| }}} | ||
| types += beastNode.getID() + "=" + (beastNode.getMetaData("location")) + ","; | ||
| } | ||
| else | ||
| types += beastNode.getID() + "= -1,"; // -1 refers to unknown type in bdmm | ||
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| if (printTypes.get()) | ||
| System.out.println(beastNode.getID() + "=" + (beastNode.getMetaData("location")) +","); | ||
| } | ||
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| dates = dates.substring(0,dates.length()-1); | ||
| types = types.substring(0,types.length()-1); | ||
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| typeTrait.initByName("value", types, "taxa", taxonset, "traitname", "type"); | ||
| dateTrait.initByName("value", dates, "taxa", taxonset, "traitname", "date-backward"); | ||
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| setInputValue("trait",dateTrait); | ||
| setInputValue("trait",typeTrait); | ||
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| } | ||
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| public void getInitialisedStateNodes(List<StateNode> stateNodes){ | ||
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| stateNodes.add(this); | ||
| } | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,91 @@ | ||
| package bdmm.core.util; | ||
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| import master.BeastTreeFromMaster; | ||
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| import java.util.List; | ||
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| import beast.base.core.Description; | ||
| import beast.base.core.Input; | ||
| import beast.base.evolution.alignment.Alignment; | ||
| import beast.base.evolution.alignment.TaxonSet; | ||
| import beast.base.evolution.tree.Node; | ||
| import beast.base.evolution.tree.TraitSet; | ||
| import beast.base.evolution.tree.Tree; | ||
| import beast.base.evolution.tree.coalescent.RandomTree; | ||
| import beast.base.inference.StateNode; | ||
| import beast.base.inference.StateNodeInitialiser; | ||
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| /** | ||
| * User: Denise | ||
| * Date: 06.06.14 | ||
| * Time: 16:34 | ||
| */ | ||
| @Description("Make a random tree with tip dates and states obtained from MASTER simulation") | ||
| public class RandomTreeFromMaster extends Tree implements StateNodeInitialiser { | ||
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| public Input<BeastTreeFromMaster> masterTreeInput = new Input<BeastTreeFromMaster>( | ||
| "masterTree", | ||
| "The tree from which traits should be inherited", Input.Validate.REQUIRED); | ||
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| public Input<StateNode> treeInput = new Input<StateNode>( | ||
| "tree", | ||
| "The initial tree which is to inherited traits from masterTree", Input.Validate.REQUIRED); | ||
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| public Input<Alignment> taxaInput = new Input<Alignment>("taxa", "set of taxa to initialise tree specified by alignment"); | ||
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| StateNode tree; | ||
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| @Override | ||
| public void initAndValidate() { | ||
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| super.initAndValidate(); | ||
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| initStateNodes(); | ||
| } | ||
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| public void initStateNodes() { | ||
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| BeastTreeFromMaster masterTree = masterTreeInput.get(); | ||
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| tree = new RandomTree(); | ||
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| TraitSet typeTrait = new TraitSet(); | ||
| TraitSet dateTrait = new TraitSet(); | ||
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| Alignment taxa = taxaInput.get(); | ||
| TaxonSet taxonset = new TaxonSet(); | ||
| taxonset.initByName("alignment", taxa); | ||
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| String types = ""; | ||
| String dates = ""; | ||
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| for (Node beastNode : masterTree.getExternalNodes()){ | ||
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| dates += beastNode.getID() + "=" + beastNode.getHeight() +","; | ||
| types += beastNode.getID() + "=" + (beastNode.getMetaData("location")) +","; | ||
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| } | ||
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| dates = dates.substring(0,dates.length()-1); | ||
| types = types.substring(0,types.length()-1); | ||
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| typeTrait.initByName("value", types, "taxa", taxonset, "traitname", "type"); | ||
| dateTrait.initByName("value", dates, "taxa", taxonset, "traitname", "date-backward"); | ||
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| tree.initByName("trait",dateTrait,"trait",typeTrait, "taxa", taxa, "populationModel", ((RandomTree)treeInput.get()).populationFunctionInput.get()); | ||
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| treeInput.get().setInputValue("trait",dateTrait); | ||
| treeInput.get().setInputValue("trait",typeTrait); | ||
| treeInput.get().assignFromWithoutID(tree); | ||
| } | ||
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| public void getInitialisedStateNodes(List<StateNode> stateNodes){ | ||
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| stateNodes.add(treeInput.get()); | ||
| } | ||
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| } |
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