Examples with TreeModel dr.evomodel.tree.TreeModel used on opensource projects

Example 51 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class TraceCorrelationAssert method createPrimateTreeModel.

//************************** data ****************************
protected TreeModel createPrimateTreeModel() {
    SimpleNode[] nodes = new SimpleNode[10];
    for (int n = 0; n < 10; n++) {
        nodes[n] = new SimpleNode();
    }
    //        nodes[0].setHeight(0);
    // human
    nodes[0].setTaxon(taxa[0]);
    // chimp
    nodes[1].setTaxon(taxa[1]);
    // bonobo
    nodes[2].setTaxon(taxa[2]);
    nodes[3].setHeight(0.010772);
    nodes[3].addChild(nodes[1]);
    nodes[3].addChild(nodes[2]);
    nodes[4].setHeight(0.024003);
    nodes[4].addChild(nodes[0]);
    nodes[4].addChild(nodes[3]);
    // gorilla
    nodes[5].setTaxon(taxa[3]);
    nodes[6].setHeight(0.036038);
    nodes[6].addChild(nodes[4]);
    nodes[6].addChild(nodes[5]);
    // orangutan
    nodes[7].setTaxon(taxa[4]);
    nodes[8].setHeight(0.069125);
    nodes[8].addChild(nodes[6]);
    nodes[8].addChild(nodes[7]);
    // siamang
    nodes[9].setTaxon(taxa[5]);
    SimpleNode root = new SimpleNode();
    root.setHeight(0.099582);
    root.addChild(nodes[8]);
    root.addChild(nodes[9]);
    Tree tree = new SimpleTree(root);
    tree.setUnits(Units.Type.YEARS);
    //treeModel
    return new TreeModel(tree);
}

Example 52 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class MainFrame method generateNumberOfSimulations.

// END: doExport
// threading, UI, exceptions handling
private void generateNumberOfSimulations(final File outFile) {
    setBusy();
    SwingWorker<Void, Void> worker = new SwingWorker<Void, Void>() {

        ArrayList<TreeModel> simulatedTreeModelList = new ArrayList<TreeModel>();

        // Executed in background thread
        public Void doInBackground() {
            try {
                if (BeagleSequenceSimulatorApp.VERBOSE) {
                    Utils.printPartitionDataList(dataList);
                    System.out.println();
                }
                long startingSeed = dataList.startingSeed;
                for (int i = 0; i < dataList.simulationsCount; i++) {
                    String fullPath = Utils.getMultipleWritePath(outFile, dataList.outputFormat.toString().toLowerCase(), i);
                    PrintWriter writer = new PrintWriter(new FileWriter(fullPath));
                    ArrayList<Partition> partitionsList = new ArrayList<Partition>();
                    for (PartitionData data : dataList) {
                        if (data.record == null) {
                            writer.close();
                            throw new RuntimeException("Set data in Partitions tab for " + (partitionsList.size() + 1) + " partition.");
                        } else {
                            TreeModel treeModel = data.createTreeModel();
                            simulatedTreeModelList.add(treeModel);
                            // create partition
                            Partition partition = new Partition(//
                            treeModel, //
                            data.createBranchModel(), //
                            data.createSiteRateModel(), //
                            data.createClockRateModel(), //
                            data.createFrequencyModel(), // from
                            data.from - 1, // to
                            data.to - 1, // every
                            data.every);
                            if (data.ancestralSequenceString != null) {
                                partition.setRootSequence(data.createAncestralSequence());
                            }
                            partitionsList.add(partition);
                        }
                    }
                    if (dataList.setSeed) {
                        MathUtils.setSeed(startingSeed);
                        startingSeed += 1;
                    }
                    beagleSequenceSimulator = new BeagleSequenceSimulator(partitionsList);
                    SimpleAlignment alignment = beagleSequenceSimulator.simulate(dataList.useParallel, dataList.outputAncestralSequences);
                    alignment.setOutputType(dataList.outputFormat);
                    //                        if (dataList.outputFormat == SimpleAlignment.OutputType.NEXUS) {
                    //                            alignment.setOutputType(dataList.outputFormat);
                    //                        } else if(dataList.outputFormat == SimpleAlignment.OutputType.XML) {
                    //                        	alignment.setOutputType(dataList.outputFormat);
                    //                        }else {
                    //                        	//
                    //                        }
                    writer.println(alignment.toString());
                    writer.close();
                }
            // END: simulationsCount loop
            } catch (Exception e) {
                Utils.handleException(e);
                setStatus("Exception occured.");
                setIdle();
            }
            return null;
        }

        // END: doInBackground
        // Executed in event dispatch thread
        public void done() {
            //            	LinkedHashMap<Integer, LinkedHashMap<NodeRef, int[]>> partitionSequencesMap = beagleSequenceSimulator.getPartitionSequencesMap();
            terminalPanel.setText(Utils.partitionDataListToString(dataList, simulatedTreeModelList));
            setStatus("Generated " + Utils.getSiteCount(dataList) + " sites.");
            setIdle();
        }
    };
    worker.execute();
}

Example 53 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class TransmissionWilsonBaldingB method proposeTree.

public void proposeTree() {
    TreeModel tree = c2cLikelihood.getTreeModel();
    BranchMapModel branchMap = c2cLikelihood.getBranchMap();
    NodeRef i;
    double oldMinAge, newMinAge, newRange, oldRange, newAge, q;
    // choose a random eligible node
    final int nodeCount = tree.getNodeCount();
    do {
        i = tree.getNode(MathUtils.nextInt(nodeCount));
    } while (!eligibleForMove(i, tree, branchMap));
    final NodeRef iP = tree.getParent(i);
    //this one can go anywhere
    NodeRef j = tree.getNode(MathUtils.nextInt(tree.getNodeCount()));
    NodeRef jP = tree.getParent(j);
    while ((jP != null && tree.getNodeHeight(jP) <= tree.getNodeHeight(i)) || (i == j)) {
        j = tree.getNode(MathUtils.nextInt(tree.getNodeCount()));
        jP = tree.getParent(j);
    }
    if (iP == tree.getRoot() || j == tree.getRoot()) {
        throw new RuntimeException("Root changes not allowed!");
    }
    if (jP == iP || j == iP || jP == i)
        throw new RuntimeException("move failed");
    final NodeRef CiP = getOtherChild(tree, iP, i);
    NodeRef PiP = tree.getParent(iP);
    if (resampleInfectionTimes) {
        AbstractCase iCase = branchMap.get(i.getNumber());
        AbstractCase iPCase = branchMap.get(iP.getNumber());
        AbstractCase CiPCase = branchMap.get(CiP.getNumber());
        AbstractCase PiPCase = null;
        if (PiP != null) {
            PiPCase = branchMap.get(PiP.getNumber());
        }
        if (iCase != iPCase) {
            iCase.setInfectionBranchPosition(MathUtils.nextDouble());
        }
        // what happens between PiP and CiP
        if (PiPCase == null || CiPCase != PiPCase) {
            CiPCase.setInfectionBranchPosition(MathUtils.nextDouble());
        }
        // what happens between k and j
        AbstractCase jCase = branchMap.get(j.getNumber());
        jCase.setInfectionBranchPosition(MathUtils.nextDouble());
    }
    newMinAge = Math.max(tree.getNodeHeight(i), tree.getNodeHeight(j));
    newRange = tree.getNodeHeight(jP) - newMinAge;
    newAge = newMinAge + (MathUtils.nextDouble() * newRange);
    oldMinAge = Math.max(tree.getNodeHeight(i), tree.getNodeHeight(CiP));
    oldRange = tree.getNodeHeight(PiP) - oldMinAge;
    q = newRange / Math.abs(oldRange);
    if (branchMap.get(PiP.getNumber()) != branchMap.get(CiP.getNumber())) {
        q *= 0.5;
    }
    if (branchMap.get(jP.getNumber()) != branchMap.get(j.getNumber())) {
        q *= 2;
    }
    tree.beginTreeEdit();
    if (j == tree.getRoot()) {
        // 1. remove edges <iP, CiP>
        tree.removeChild(iP, CiP);
        tree.removeChild(PiP, iP);
        // 2. add edges <k, iP>, <iP, j>, <PiP, CiP>
        tree.addChild(iP, j);
        tree.addChild(PiP, CiP);
        // iP is the new root
        tree.setRoot(iP);
    } else if (iP == tree.getRoot()) {
        // 1. remove edges <k, j>, <iP, CiP>, <PiP, iP>
        tree.removeChild(jP, j);
        tree.removeChild(iP, CiP);
        // 2. add edges <k, iP>, <iP, j>, <PiP, CiP>
        tree.addChild(iP, j);
        tree.addChild(jP, iP);
        //CiP is the new root
        tree.setRoot(CiP);
    } else {
        // 1. remove edges <k, j>, <iP, CiP>, <PiP, iP>
        tree.removeChild(jP, j);
        tree.removeChild(iP, CiP);
        tree.removeChild(PiP, iP);
        // 2. add edges <k, iP>, <iP, j>, <PiP, CiP>
        tree.addChild(iP, j);
        tree.addChild(jP, iP);
        tree.addChild(PiP, CiP);
    }
    tree.setNodeHeight(iP, newAge);
    tree.endTreeEdit();
    //
    logq = Math.log(q);
    if (MathUtils.nextInt(2) == 0) {
        branchMap.set(iP.getNumber(), branchMap.get(jP.getNumber()), true);
    } else {
        branchMap.set(iP.getNumber(), branchMap.get(j.getNumber()), true);
    }
    if (DEBUG) {
        c2cLikelihood.getTreeModel().checkPartitions();
    }
}

Example 54 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class TransmissionExchangeOperatorB method doOperation.

public double doOperation() {
    TreeModel tree = c2cLikelihood.getTreeModel();
    double hr = exchange();
    final int tipCount = tree.getExternalNodeCount();
    assert tree.getExternalNodeCount() == tipCount : "Lost some tips";
    return hr;
}

Example 55 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class TransmissionExchangeOperatorA method doOperation.

public double doOperation() {
    TreeModel tree = c2cLikelihood.getTreeModel();
    double hr = exchange();
    final int tipCount = tree.getExternalNodeCount();
    assert tree.getExternalNodeCount() == tipCount : "Lost some tips";
    return hr;
}