Examples with BigFastTreeIntervals dr.evomodel.bigfasttree.BigFastTreeIntervals used on opensource projects

Example 1 with BigFastTreeIntervals

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

the class BigFastTreeTreeIntervalsTest method testHandelHeightChange.

public void testHandelHeightChange() throws TreeUtils.MissingTaxonException {
    IntervalList bigFastIntervals = new BigFastTreeIntervals(tree);
    bigFastIntervals.calculateIntervals();
    double[] intervals = { 0, 0.5, 0.49, 0.01, 0.5, 0, 0.5, 0.5, 0.5, 1.5 };
    // node             1-2, 4  , 5  , 6  , 0  , 3, 7  , 9  , 8  , 10
    boolean pass = true;
    tree.beginTreeEdit();
    tree.setNodeHeight(tree.getNode(10), 4.5);
    tree.endTreeEdit();
    bigFastIntervals.calculateIntervals();
    for (int j = 0; j < bigFastIntervals.getIntervalCount(); j++) {
        if (Math.abs(bigFastIntervals.getInterval(j) - intervals[j]) > 1E-3) {
            System.out.println(bigFastIntervals.getInterval(j) - intervals[j]);
            System.out.println("expected: " + intervals[j] + " got: " + bigFastIntervals.getInterval(j));
            pass = false;
            break;
        }
    }
    assertTrue(pass);
}

Example 2 with BigFastTreeIntervals

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

the class BigFastTreeTreeIntervalsTest method testOrderChange.

// 0.5
// 1.0           +------ 0 * [1.5]
// +----------------------- |(7) *  [2]
// 1.0           |                        |                                             +-- 1 * [0]
// +----------------------- |(8) *  [3]              +---------------------------------------------|(6) [0.1]
// |                        |                                                                      +--- 2 * [0]
// |                        |                1.5
// |(10) &  [4]             +-------------------------------- 3 * [1.5]
// |                                                       2.0
// |        1.5                   +----------------------------------------------------- 4 & [0.5]
// +-----------------------------|(9) & [2.5]     1.51
// +-------------------------------------------- 5 & [0.99]
public void testOrderChange() throws TreeUtils.MissingTaxonException, IOException, Importer.ImportException {
    NewickImporter importer = new NewickImporter("(((0:0.5,(1:1.0,2:1.0)n6:1.0)n7:1.0,3:1.5)n8:1.0,(4:2.0,5:1.51)n9:1.5)n10;");
    tree = new BigFastTreeModel(importer.importTree(null));
    IntervalList bigFastIntervals = new BigFastTreeIntervals(tree);
    IntervalList intervals = new TreeIntervals(tree, null, null);
    bigFastIntervals.calculateIntervals();
    // node             1-2,6,  4  , 5  ,  0  ,  3, 7  , 9  , 8  , 10
    boolean pass = true;
    NodeRef parent = tree.getNode(6);
    NodeRef sibling = tree.getNode(2);
    NodeRef grandParent = tree.getParent(parent);
    NodeRef j = tree.getNode(2);
    tree.beginTreeEdit();
    tree.removeChild(grandParent, parent);
    tree.removeChild(parent, sibling);
    tree.addChild(grandParent, sibling);
    NodeRef jParent = tree.getParent(j);
    tree.removeChild(jParent, j);
    tree.addChild(jParent, parent);
    tree.addChild(parent, j);
    tree.setNodeHeight(parent, 0.1);
    tree.endTreeEdit();
    bigFastIntervals.calculateIntervals();
    List<Integer> missed = new ArrayList<>();
    for (int i = 0; i < bigFastIntervals.getIntervalCount(); i++) {
        if (bigFastIntervals.getInterval(i) != intervals.getInterval(i)) {
            System.out.println("expected: " + intervals.getInterval(i) + " got: " + bigFastIntervals.getInterval(i));
            missed.add(i);
        }
    }
    System.out.println(missed);
    assertEquals(0, missed.size());
}

Example 3 with BigFastTreeIntervals

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

the class BigFastTreeTreeIntervalsTest method testsmallTree.

// clade * 0-3 root 8
// clade & 4-5 root 10
// 0.5
// 1.0           +------ 0 * [1.5]
// +----------------------- |(7) *  [2]                          1.0
// 1.0           |                        |        1.0             +----------------------- 1 * [0]
// +----------------------- |(8) *  [3]              +----------------------- |(6) [1]    1.0
// |                        |                                                 +----------------------- 2 * [0]
// |                        |                1.5
// |(10) &  [4]             +-------------------------------- 3 * [1.5]
// |                                                       2.0
// |        1.5                   +----------------------------------------------------- 4 & [0.5]
// +-----------------------------|(9) & [2.5]     1.51
// +-------------------------------------------- 5 & [0.99]
public void testsmallTree() throws TreeUtils.MissingTaxonException {
    IntervalList bigFastIntervals = new BigFastTreeIntervals(tree);
    bigFastIntervals.calculateIntervals();
    double[] intervals = { 0, 0.5, 0.49, 0.01, 0.5, 0, 0.5, 0.5, 0.5, 1.0 };
    // node             1-2, 4  , 5  , 6  , 0  , 3, 7  , 9  , 8  , 10
    boolean pass = true;
    for (int j = 0; j < bigFastIntervals.getIntervalCount(); j++) {
        if (Math.abs(bigFastIntervals.getInterval(j) - intervals[j]) > 1E-3) {
            System.out.println(bigFastIntervals.getInterval(j) - intervals[j]);
            System.out.println("expected: " + intervals[j] + " got: " + bigFastIntervals.getInterval(j));
            pass = false;
            break;
        }
    }
    assertTrue(pass);
}

Example 4 with BigFastTreeIntervals

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

the class BigFastTreeTreeIntervalsTest method testCompareIntervals.

public void testCompareIntervals() throws TreeUtils.MissingTaxonException, IOException, Importer.ImportException {
    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 importer = new NewickImporter("(((0:0.5,(1:1.0,2:1.0)n6:1.0)n7:1.0,3:1.5)n8:1.0,(4:2.0,5:1.51)n9:1.5)n10;");
    // NewickImporter constraintsImporter = new NewickImporter("(((0:0.5,(1:1.0,2:1.0)n6:1.0)n7:1.0,3:1.5)n8:1.0,(4:2.0,5:1.51)n9:1.5)n10;");
    tree = new DefaultTreeModel(importer.importTree(null));
    IntervalList intervals = new TreeIntervals(tree, null, null);
    BigFastTreeIntervals bigFastTreeIntervals = new BigFastTreeIntervals(tree);
    SubtreeLeapOperator op = new SubtreeLeapOperator(tree, 1, 0.0001, SubtreeLeapOperator.DistanceKernelType.NORMAL, AdaptationMode.ADAPTATION_OFF, 0.2);
    NodeHeightOperator nh = new NodeHeightOperator(tree, 1, 1, NodeHeightOperator.OperatorType.UNIFORM, AdaptationMode.ADAPTATION_OFF, 0.25);
    NodeHeightOperator root = new NodeHeightOperator(tree, 1, 0.75, NodeHeightOperator.OperatorType.SCALEROOT, AdaptationMode.ADAPTATION_OFF, 0.25);
    boolean pass = true;
    MathUtils.setSeed(2);
    for (int i = 0; i < 100000; i++) {
        op.doOperation();
        intervals.calculateIntervals();
        // bigFastIntervals.makeDirty();
        bigFastTreeIntervals.calculateIntervals();
        for (int j = 0; j < bigFastTreeIntervals.getIntervalCount(); j++) {
            if (intervals.getInterval(j) != bigFastTreeIntervals.getInterval(j)) {
                System.out.println(i);
                System.out.println("interval wrong");
                pass = false;
                break;
            }
        }
        for (int j = 0; j < bigFastTreeIntervals.getIntervalCount(); j++) {
            if (intervals.getLineageCount(j) != bigFastTreeIntervals.getLineageCount(j)) {
                System.out.println(i);
                System.out.println("lineage Counts wrong: " + j);
                System.out.println("expected: " + intervals.getLineageCount(j));
                System.out.println("got " + bigFastTreeIntervals.getLineageCount(j));
                pass = false;
                break;
            }
        }
        for (int j = 0; j < bigFastTreeIntervals.getIntervalCount(); j++) {
            if (intervals.getIntervalTime(j) != bigFastTreeIntervals.getIntervalTime(j)) {
                System.out.println(i);
                System.out.println("times wrong");
                pass = false;
                break;
            }
        }
        if (!pass) {
            break;
        }
    }
    assertTrue(pass);
}

Example 5 with BigFastTreeIntervals

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

the class SmoothSkygridLikelihoodParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    List<IntervalList> intervalList = new ArrayList<>();
    List<TreeIntervals> debugIntervalList = new ArrayList<>();
    if (xo.hasChildNamed(INTERVALS)) {
        XMLObject cxo = xo.getChild(INTERVALS);
        for (int i = 0; i < cxo.getChildCount(); ++i) {
            intervalList.add((IntervalList) cxo.getChild(i));
        }
    } else {
        XMLObject cxo = xo.getChild(POPULATION_TREE);
        for (int i = 0; i < cxo.getChildCount(); ++i) {
            TreeModel tree = (TreeModel) cxo.getChild(i);
            intervalList.add(new BigFastTreeIntervals(tree));
            debugIntervalList.add(new TreeIntervals(tree));
        }
    }
    Parameter logPopSizes = (Parameter) xo.getElementFirstChild(POPULATION_PARAMETER);
    Parameter gridPoints = (Parameter) xo.getElementFirstChild(GRID_POINTS);
    if (!SmoothSkygridLikelihood.checkValidParameters(logPopSizes, gridPoints)) {
        throw new XMLParseException("Invalid initial parameters");
    }
    SmoothSkygridLikelihood likelihood = new SmoothSkygridLikelihood(xo.getId(), intervalList, logPopSizes, gridPoints);
    likelihood.setDebugIntervalList(debugIntervalList);
    return likelihood;
}