Examples with CladeNodeModel dr.evomodel.bigfasttree.constrainedtree.CladeNodeModel used on opensource projects

Search in sources :

Example 6 with CladeNodeModel

use of dr.evomodel.bigfasttree.constrainedtree.CladeNodeModel in project beast-mcmc by beast-dev.

the class CladeAwareSubtreeLeapTest method setUp.

public void setUp() throws Exception {
    super.setUp();
    MathUtils.setSeed(112432);
    NewickImporter importer = new NewickImporter("(((0:1.0,(1:1.0,2:1.0)n6:1.0)n7:1.0,3:2.0)n8:1.0,(4:3.0,5:1.0)n9:1.0)n10;");
    NewickImporter constraintsImporter = new NewickImporter("((0:1.0,1:1.0,2:1.0,3:1.0):1.0,4:1.0,5:0.1);");
    Tree rawTree = importer.importTree(null);
    Tree constraintsTree = constraintsImporter.importTree(null);
    tree = new BigFastTreeModel(rawTree);
    cladeNodeModel = new CladeNodeModel(constraintsTree, tree);
    operator = new CladeAwareSubtreeLeap(cladeNodeModel, 100);
}
Also used : CladeAwareSubtreeLeap(dr.evomodel.bigfasttree.constrainedtree.CladeAwareSubtreeLeap) NewickImporter(dr.evolution.io.NewickImporter) Tree(dr.evolution.tree.Tree) CladeNodeModel(dr.evomodel.bigfasttree.constrainedtree.CladeNodeModel)

Example 7 with CladeNodeModel

use of dr.evomodel.bigfasttree.constrainedtree.CladeNodeModel in project beast-mcmc by beast-dev.

the class CladeAwareSubtreePruneRegraftParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    CladeNodeModel cladeModel = (CladeNodeModel) xo.getChild(CladeNodeModel.class);
    final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    return new CladeAwareSubtreePruneRegraft(cladeModel, weight);
}
Also used : CladeNodeModel(dr.evomodel.bigfasttree.constrainedtree.CladeNodeModel) CladeAwareSubtreePruneRegraft(dr.evomodel.bigfasttree.constrainedtree.CladeAwareSubtreePruneRegraft)

Example 8 with CladeNodeModel

use of dr.evomodel.bigfasttree.constrainedtree.CladeNodeModel in project beast-mcmc by beast-dev.

the class CladeNodeModelTest method testCladeCount.

public void testCladeCount() throws IOException, Importer.ImportException, TreeUtils.MissingTaxonException {
    NewickImporter importer = new NewickImporter("(Lishui/LS557/2020:0,((Netherlands/Utrecht_10015/2020:0.00006795400000000001,USA/IL-NM073/2020:0.00006799599999999999):0.000033976,England/LOND-D604F/2020:0.000101963):0.000033968,Guangdong/2020XN4459-P0041/2020:0.000000005,(Portugal/PT0063/2020:0,(Spain/Zaragoza2486/2020:0.000102605,Scotland/CVR746/2020:0.000000005,Spain/COV000882/2020:0.000067956,Colombia/INS-79253/2020:0.000101944,Uruguay/UY-4/2020:0.000031515):0.000033979,(Spain/CastillaLaMancha201329/2020:0.000000005,Netherlands/NoordHolland_10011/2020:0.000033987):0.00006799,England/LIVE-9CE87/2020:0.00013727299999999998,Spain/Granada-COV002916/2020:0.000033979999999999997):0.000033968,((USA/VI-CDC-3705/2020:0.000000005,Australia/VIC229/2020:0,USA/MA-MGH-00063/2020:0,(USA/WA-S41/2020:0.000068895,USA/WA-UW114/2020:0.000067978,USA/WA-UW17/2020:0.000000005,(USA/WA-S582/2020:0,USA/WA-UW-1682/2020:0.000000005,USA/WA-S994/2020:0.000101934):0.000033955,USA/WA-S121/2020:0.000000005,USA/WA-S154/2020:0.000067982,USA/WA-UW37/2020:0,USA/WA-S321/2020:0,USA/WA-S445/2020:0,USA/WA-S512/2020:0,USA/WA-S33/2020:0.000033979,Canada/BC_6981299/2020:0.000033972,USA/WA-UW-1294/2020:0.000033972,USA/WA-UW-2247/2020:0.000033988,Australia/VIC140/2020:0.000033984,USA/WA-UW61/2020:0.000033972,Canada/BC_8606204/2020:0.000166157,(USA/WA-S734/2020:0,USA/WA-S844/2020:0.000033983):0.000067965,(USA/WA-S1191/2020:0.000067947,USA/WA-S951/2020:0.000101914):0.000095803,Australia/NSW99/2020:0.000101953,(USA/WA-S317/2020:0.000000005,USA/WA-S721/2020:0.00003397):0.00010195700000000001,USA/WA-UW139/2020:0.000135916,USA/WA-S572/2020:0.000033979999999999997,USA/WA-S279/2020:0.000033972,USA/WA-UW28/2020:0.000034002,USA/WA-S114/2020:0.000033969,(USA/WA-S852/2020:0.000203899,(USA/WA-S568/2020:0,USA/WA-S791/2020:0.00006794599999999999):0.000033983):0.000101964,USA/WA-S842/2020:0.000067951):0.000033986,Singapore/302/2020:0.000101947):0.00016677,(((USA/IL-NM0112/2020:0.00003397,USA/IL-NM053/2020:0.000034229,USA/IL-NM059/2020:0.000101967):0.00003397,USA/WI-UW-218/2020:0.000033995):0.000030539,(USA/UT-QDX-63/2020:0,USA/CA-QDX-111/2020:0,USA/TX-HMH0427/2020:0.000203861):0.000101955):0.00023787300000000002):0.000033959,(((Scotland/CVR3203/2020:0.000000005,Scotland/CVR2246/2020:0.000000005,Scotland/GCVR-1714B2/2020:0.000033975999999999995,Scotland/CVR3514/2020:0.000068628):0.000067954,Australia/NT08/2020:0.000034000999999999995):0.00003397,Spain/COV001440/2020:0,Spain/Alcaniz2449/2020:0.000068985,Spain/COV001548/2020:0,USA/WI-WSLH-200057/2020:0.000000005,Spain/Valencia6/2020:0.0000343,Spain/Granada-COV002944/2020:0.000000005,Spain/COV001929/2020:0.000000005,Spain/COV002049/2020:0.000000005,(Spain/Valencia59/2020:0,Spain/Valencia306/2020:0.000000005):0.000033996,(Spain/COV001117/2020:0.00010265,Spain/COV002055/2020:0.000000005,England/20126000104/2020:0.00006758400000000001):0.000033997,Spain/COV001576/2020:0.000000005,Chile/Santiago-1/2020:0.000000005,Spain/COV000721/2020:0.000000005,(Spain/COV001575/2020:0,Spain/COV001505/2020:0):0.000067968,Spain/Madrid_H12_28/2020:0.000067957,Spain/COV001568/2020:0.000033975,England/CAMB-83357/2020:0.000068619,(Spain/Almeria-COV002842/2020:0.000000005,Spain/Malaga-COV002841/2020:0.000000005):0.000067851):0.000169854,Spain/Madrid_LP16_6193/2020:0.00006795299999999999,Singapore/51/2020:0.000044697,(Thailand/Nonthaburi_193/2020:0,Thailand/Bangkok_237/2020:0,Thailand/Bangkok_238/2020:0,((Thailand/Bangkok-0034/2020:0.000000005,Thailand/Bangkok_2295/2020:0,Thailand/Bangkok-0065/2020:0.000047826,Thailand/Bangkok-CONI-0147/2020:0.000033997):0.000033983,Thailand/SI202769-NT/2020:0.000203899):0.000101951):0.00006797500000000001,Shenzhen/SZTH-002/2020:0.000033999);");
    NewickImporter constraintsImporter = new NewickImporter("(Lishui/LS557/2020:0,((Netherlands/Utrecht_10015/2020:0.00006795400000000001,USA/IL-NM073/2020:0.00006799599999999999):0.000033976,England/LOND-D604F/2020:0.000101963):0.000033968,Guangdong/2020XN4459-P0041/2020:0.000000005,(Portugal/PT0063/2020:0,(Spain/Zaragoza2486/2020:0.000102605,Scotland/CVR746/2020:0.000000005,Spain/COV000882/2020:0.000067956,Colombia/INS-79253/2020:0.000101944,Uruguay/UY-4/2020:0.000031515):0.000033979,(Spain/CastillaLaMancha201329/2020:0.000000005,Netherlands/NoordHolland_10011/2020:0.000033987):0.00006799,England/LIVE-9CE87/2020:0.00013727299999999998,Spain/Granada-COV002916/2020:0.000033979999999999997):0.000033968,((USA/VI-CDC-3705/2020:0.000000005,Australia/VIC229/2020:0,USA/MA-MGH-00063/2020:0,(USA/WA-S41/2020:0.000068895,USA/WA-UW114/2020:0.000067978,USA/WA-UW17/2020:0.000000005,(USA/WA-S582/2020:0,USA/WA-UW-1682/2020:0.000000005,USA/WA-S994/2020:0.000101934):0.000033955,USA/WA-S121/2020:0.000000005,USA/WA-S154/2020:0.000067982,USA/WA-UW37/2020:0,USA/WA-S321/2020:0,USA/WA-S445/2020:0,USA/WA-S512/2020:0,USA/WA-S33/2020:0.000033979,Canada/BC_6981299/2020:0.000033972,USA/WA-UW-1294/2020:0.000033972,USA/WA-UW-2247/2020:0.000033988,Australia/VIC140/2020:0.000033984,USA/WA-UW61/2020:0.000033972,Canada/BC_8606204/2020:0.000166157,(USA/WA-S734/2020:0,USA/WA-S844/2020:0.000033983):0.000067965,(USA/WA-S1191/2020:0.000067947,USA/WA-S951/2020:0.000101914):0.000095803,Australia/NSW99/2020:0.000101953,(USA/WA-S317/2020:0.000000005,USA/WA-S721/2020:0.00003397):0.00010195700000000001,USA/WA-UW139/2020:0.000135916,USA/WA-S572/2020:0.000033979999999999997,USA/WA-S279/2020:0.000033972,USA/WA-UW28/2020:0.000034002,USA/WA-S114/2020:0.000033969,(USA/WA-S852/2020:0.000203899,(USA/WA-S568/2020:0,USA/WA-S791/2020:0.00006794599999999999):0.000033983):0.000101964,USA/WA-S842/2020:0.000067951):0.000033986,Singapore/302/2020:0.000101947):0.00016677,(((USA/IL-NM0112/2020:0.00003397,USA/IL-NM053/2020:0.000034229,USA/IL-NM059/2020:0.000101967):0.00003397,USA/WI-UW-218/2020:0.000033995):0.000030539,(USA/UT-QDX-63/2020:0,USA/CA-QDX-111/2020:0,USA/TX-HMH0427/2020:0.000203861):0.000101955):0.00023787300000000002):0.000033959,(((Scotland/CVR3203/2020:0.000000005,Scotland/CVR2246/2020:0.000000005,Scotland/GCVR-1714B2/2020:0.000033975999999999995,Scotland/CVR3514/2020:0.000068628):0.000067954,Australia/NT08/2020:0.000034000999999999995):0.00003397,Spain/COV001440/2020:0,Spain/Alcaniz2449/2020:0.000068985,Spain/COV001548/2020:0,USA/WI-WSLH-200057/2020:0.000000005,Spain/Valencia6/2020:0.0000343,Spain/Granada-COV002944/2020:0.000000005,Spain/COV001929/2020:0.000000005,Spain/COV002049/2020:0.000000005,(Spain/Valencia59/2020:0,Spain/Valencia306/2020:0.000000005):0.000033996,(Spain/COV001117/2020:0.00010265,Spain/COV002055/2020:0.000000005,England/20126000104/2020:0.00006758400000000001):0.000033997,Spain/COV001576/2020:0.000000005,Chile/Santiago-1/2020:0.000000005,Spain/COV000721/2020:0.000000005,(Spain/COV001575/2020:0,Spain/COV001505/2020:0):0.000067968,Spain/Madrid_H12_28/2020:0.000067957,Spain/COV001568/2020:0.000033975,England/CAMB-83357/2020:0.000068619,(Spain/Almeria-COV002842/2020:0.000000005,Spain/Malaga-COV002841/2020:0.000000005):0.000067851):0.000169854,Spain/Madrid_LP16_6193/2020:0.00006795299999999999,Singapore/51/2020:0.000044697,(Thailand/Nonthaburi_193/2020:0,Thailand/Bangkok_237/2020:0,Thailand/Bangkok_238/2020:0,((Thailand/Bangkok-0034/2020:0.000000005,Thailand/Bangkok_2295/2020:0,Thailand/Bangkok-0065/2020:0.000047826,Thailand/Bangkok-CONI-0147/2020:0.000033997):0.000033983,Thailand/SI202769-NT/2020:0.000203899):0.000101951):0.00006797500000000001,Shenzhen/SZTH-002/2020:0.000033999);");
    TreeModel tree = new BigFastTreeModel(importer.importTree(null));
    Tree constraintsTree = constraintsImporter.importTree(null);
    CladeNodeModel cladeNodeModel = new CladeNodeModel(constraintsTree, tree);
    assertEquals(constraintsTree.getInternalNodeCount(), cladeNodeModel.getCladeCount());
}
Also used : TreeModel(dr.evomodel.tree.TreeModel) BigFastTreeModel(dr.evomodel.bigfasttree.BigFastTreeModel) NewickImporter(dr.evolution.io.NewickImporter) BigFastTreeModel(dr.evomodel.bigfasttree.BigFastTreeModel) Tree(dr.evolution.tree.Tree) CladeNodeModel(dr.evomodel.bigfasttree.constrainedtree.CladeNodeModel)

Example 9 with CladeNodeModel

use of dr.evomodel.bigfasttree.constrainedtree.CladeNodeModel in project beast-mcmc by beast-dev.

the class ApproximatePoissonTreeLikelihoodTest method testOtherChildUpdates.

public void testOtherChildUpdates() throws IOException, Importer.ImportException, TreeUtils.MissingTaxonException {
    branchRateModel = new StrictClockBranchRates(new Parameter.Default(1.0));
    NewickImporter importer = new NewickImporter("((1:1.0,2:0.5,3:2.0):0.1,4:0.3,(7:0.2,8:0.1,9:0.3):0.2,6:0.01)");
    NewickImporter importer2 = new NewickImporter("((6:1,(4:1,((9:1,7:1):2,8:2):3.0):6):4,(1:1,(3:3,2:2):1):1);");
    tree = importer.importTree(null);
    treeModel = new BigFastTreeModel(importer2.importTree(null));
    CladeNodeModel cladeModel = new CladeNodeModel(tree, treeModel);
    BranchLengthProvider constrainedBranchLengthProvider = new ConstrainedTreeBranchLengthProvider(cladeModel);
    approximatePoissonTreeLikelihood = new ApproximatePoissonTreeLikelihood("approximateTreeLikelihood", 1, treeModel, branchRateModel, constrainedBranchLengthProvider);
    approximatePoissonTreeLikelihood.getLogLikelihood();
    NodeRef node = treeModel.getNode(1);
    NodeRef sibling = treeModel.getNode(9);
    NodeRef parent = treeModel.getParent(node);
    NodeRef grandparent = treeModel.getParent(parent);
    NodeRef root = treeModel.getRoot();
    CladeRef clade = cladeModel.getClade(parent);
    treeModel.beginTreeEdit();
    treeModel.removeChild(grandparent, parent);
    treeModel.removeChild(parent, sibling);
    treeModel.setNodeHeight(parent, treeModel.getNodeHeight(root) + 1);
    treeModel.setRoot(parent);
    // cladeModel.setRootNode(clade, parent);
    treeModel.addChild(parent, root);
    treeModel.addChild(grandparent, sibling);
    treeModel.endTreeEdit();
    double LL = approximatePoissonTreeLikelihood.getLogLikelihood();
    approximatePoissonTreeLikelihood.makeDirty();
    double newLL = approximatePoissonTreeLikelihood.getLogLikelihood();
    assertEquals(LL, newLL);
}
Also used : NodeRef(dr.evolution.tree.NodeRef) NewickImporter(dr.evolution.io.NewickImporter) ConstrainedTreeBranchLengthProvider(dr.evomodel.bigfasttree.constrainedtree.ConstrainedTreeBranchLengthProvider) CladeNodeModel(dr.evomodel.bigfasttree.constrainedtree.CladeNodeModel) ConstrainedTreeBranchLengthProvider(dr.evomodel.bigfasttree.constrainedtree.ConstrainedTreeBranchLengthProvider) CladeRef(dr.evomodel.bigfasttree.constrainedtree.CladeRef) StrictClockBranchRates(dr.evomodel.branchratemodel.StrictClockBranchRates)

Example 10 with CladeNodeModel

use of dr.evomodel.bigfasttree.constrainedtree.CladeNodeModel in project beast-mcmc by beast-dev.

the class ApproximatePoissonTreeLikelihoodTest method testRootAndRootChildUpdates.

// This tests updating when the root and rootchild2  change
// +- 6
// |
// +------| gp       +- 4 *
// |      |          |
// |      +----------| p       + 9
// |                 |     +---|
// |                 +-----|   + 7
// | r                     |
// |                       +--- 8
// |
// |+- 1
// +|
// | +----- 3
// +-|
// +--- 2
// To
// +-------------------- 4 *
// |
// |       +- 6
// |p      |
// |+------| gp                + 9
// ||      |               +---|
// ||      +---------------|   + 7
// +|                      |
// | r                    +--- 8
// |
// | +- 1
// +-|
// | +---- 3
// +-|
// +-- 2
// 
// 
public void testRootAndRootChildUpdates() throws IOException, Importer.ImportException, TreeUtils.MissingTaxonException {
    branchRateModel = new StrictClockBranchRates(new Parameter.Default(1.0));
    NewickImporter importer = new NewickImporter("((1:1.0,2:0.5,3:2.0):0.1,4:0.3,(7:0.2,8:0.1,9:0.3):0.2,6:0.01)");
    NewickImporter importer2 = new NewickImporter("((6:1,(4:1,((9:1,7:1):2,8:2):3.0):6):4,(1:1,(3:3,2:2):1):1);");
    tree = importer.importTree(null);
    treeModel = new BigFastTreeModel(importer2.importTree(null));
    CladeNodeModel cladeModel = new CladeNodeModel(tree, treeModel);
    BranchLengthProvider constrainedBranchLengthProvider = new ConstrainedTreeBranchLengthProvider(cladeModel);
    approximatePoissonTreeLikelihood = new ApproximatePoissonTreeLikelihood("approximateTreeLikelihood", 1, treeModel, branchRateModel, constrainedBranchLengthProvider);
    approximatePoissonTreeLikelihood.getLogLikelihood();
    NodeRef node = treeModel.getNode(9);
    NodeRef sibling = treeModel.getNode(1);
    NodeRef parent = treeModel.getParent(node);
    NodeRef grandparent = treeModel.getParent(parent);
    NodeRef root = treeModel.getRoot();
    CladeRef clade = cladeModel.getClade(node);
    treeModel.beginTreeEdit();
    treeModel.removeChild(grandparent, parent);
    treeModel.removeChild(parent, sibling);
    treeModel.setNodeHeight(parent, treeModel.getNodeHeight(root) + 1);
    treeModel.setRoot(parent);
    // cladeModel.setRootNode(clade, parent);
    treeModel.addChild(parent, root);
    treeModel.addChild(grandparent, sibling);
    treeModel.endTreeEdit();
    double LL = approximatePoissonTreeLikelihood.getLogLikelihood();
    approximatePoissonTreeLikelihood.makeDirty();
    double newLL = approximatePoissonTreeLikelihood.getLogLikelihood();
    assertEquals(LL, newLL);
}
Also used : NodeRef(dr.evolution.tree.NodeRef) NewickImporter(dr.evolution.io.NewickImporter) ConstrainedTreeBranchLengthProvider(dr.evomodel.bigfasttree.constrainedtree.ConstrainedTreeBranchLengthProvider) CladeNodeModel(dr.evomodel.bigfasttree.constrainedtree.CladeNodeModel) ConstrainedTreeBranchLengthProvider(dr.evomodel.bigfasttree.constrainedtree.ConstrainedTreeBranchLengthProvider) CladeRef(dr.evomodel.bigfasttree.constrainedtree.CladeRef) StrictClockBranchRates(dr.evomodel.branchratemodel.StrictClockBranchRates)

Aggregations

CladeNodeModel (dr.evomodel.bigfasttree.constrainedtree.CladeNodeModel)12 NewickImporter (dr.evolution.io.NewickImporter)8 ConstrainedTreeBranchLengthProvider (dr.evomodel.bigfasttree.constrainedtree.ConstrainedTreeBranchLengthProvider)6 Tree (dr.evolution.tree.Tree)5 StrictClockBranchRates (dr.evomodel.branchratemodel.StrictClockBranchRates)5 NodeRef (dr.evolution.tree.NodeRef)4 TreeModel (dr.evomodel.tree.TreeModel)4 CladeAwareSubtreeLeap (dr.evomodel.bigfasttree.constrainedtree.CladeAwareSubtreeLeap)3 CladeRef (dr.evomodel.bigfasttree.constrainedtree.CladeRef)3 PoissonDistribution (dr.math.distributions.PoissonDistribution)3 TreeUtils (dr.evolution.tree.TreeUtils)2 DistanceMatrix (dr.evolution.distance.DistanceMatrix)1 BigFastTreeModel (dr.evomodel.bigfasttree.BigFastTreeModel)1 CladeAwareSubtreePruneRegraft (dr.evomodel.bigfasttree.constrainedtree.CladeAwareSubtreePruneRegraft)1 ConstraintsTreeLikelihood (dr.evomodel.bigfasttree.constrainedtree.ConstraintsTreeLikelihood)1 BranchRateModel (dr.evomodel.branchratemodel.BranchRateModel)1 AdaptationMode (dr.inference.operators.AdaptationMode)1
About Me
UseOf

Java Tutorials :

Simple Java RabbitMQ Example with Spring
Simple Springboot JPA Eclipeslink Example
Simple SpringBoot JPA Hibernate Example
Jackson JSON @JsonIgnore and @JsonIgnoreProperties Examples
Java Infinite recursion (StackOverflowError) Jackson solutions
Simple Java Jackson Serialize Objects to JSON and convert them back To Object
ElasticSearch 5 - Upload files using Java API in binary field Example
Java JAXB marshall unmarshall Examples from String and Stream
Java 8 forEach List and Map examples
ElasticSearch 5 Java API SearchRequestBuilder examples
Java ElasticSearch 5 examples with node index and mapping - running local
Convert String to int or Integer Java 8
Java 9 in action - JShell - Ubuntu
Java - removing invalid characters from a file name
Hello world!? or Hello Tutorial