Examples with Tree beast.evolution.tree.Tree used on opensource projects

Example 1 with Tree

use of beast.evolution.tree.Tree in project beast2 by CompEvol.

the class BeautiDoc method deepCopyPlugin.

/**
 * Create a deep copy of a beastObject, but in a different partition context
 * First, find all beastObjects that are predecessors of the beastObject to be copied
 * that are ancestors of StateNodes
 *
 * @param beastObject
 * @param parent
 * @return
 */
public static BEASTInterface deepCopyPlugin(BEASTInterface beastObject, BEASTInterface parent, MCMC mcmc, PartitionContext oldContext, PartitionContext newContext, BeautiDoc doc, List<BEASTInterface> tabooList) {
    /**
     * taboo = list of beastObjects that should not be copied *
     */
    Set<BEASTInterface> taboo = new HashSet<>();
    taboo.add(parent);
    // add state
    taboo.add(mcmc.startStateInput.get());
    // add likelihood and prior
    if (mcmc.posteriorInput.get() instanceof CompoundDistribution) {
        for (Distribution distr : ((CompoundDistribution) mcmc.posteriorInput.get()).pDistributions.get()) {
            if (distr instanceof CompoundDistribution) {
                taboo.add(distr);
            }
        }
    }
    // add posterior
    taboo.add(mcmc.posteriorInput.get());
    // parent of operators
    taboo.add(mcmc);
    // add loggers
    taboo.addAll(mcmc.loggersInput.get());
    // add exception for *BEAST logger (perhaps need to be generalised?)
    if (doc.pluginmap.containsKey("SpeciesTreeLoggerX")) {
        taboo.add(doc.pluginmap.get("SpeciesTreeLoggerX"));
    }
    // add trees
    for (StateNode node : mcmc.startStateInput.get().stateNodeInput.get()) {
        if (node instanceof Tree) {
            taboo.add(node);
        }
    }
    // add MRCAPriors
    for (String id : doc.pluginmap.keySet()) {
        BEASTInterface o = doc.pluginmap.get(id);
        if (o instanceof MRCAPrior) {
            taboo.add(o);
        }
    }
    if (tabooList != null) {
        taboo.addAll(tabooList);
    }
    // find predecessors of beastObject to be copied
    List<BEASTInterface> predecessors = new ArrayList<>();
    collectPredecessors(beastObject, predecessors);
    // find ancestors of StateNodes that are predecessors + the beastObject
    // itself
    Set<BEASTInterface> ancestors = new HashSet<>();
    collectAncestors(beastObject, ancestors, taboo);
    Log.info.print(Arrays.toString(ancestors.toArray()));
    for (BEASTInterface beastObject2 : predecessors) {
        if (beastObject2 instanceof StateNode) {
            Set<BEASTInterface> ancestors2 = new HashSet<>();
            collectAncestors(beastObject2, ancestors2, taboo);
            ancestors.addAll(ancestors2);
        } else if (beastObject2 instanceof Alignment || beastObject2 instanceof FilteredAlignment) {
            for (Object output : beastObject2.getOutputs()) {
                if (!taboo.contains(output)) {
                    Set<BEASTInterface> ancestors2 = new HashSet<>();
                    collectAncestors((BEASTInterface) output, ancestors2, taboo);
                    ancestors.addAll(ancestors2);
                }
            }
        }
    }
    // collect priors
    predecessors.addAll(ancestors);
    for (BEASTInterface o : predecessors) {
        if (o instanceof Prior) {
            List<BEASTInterface> priorPredecessors = new ArrayList<>();
            collectPredecessors(o, priorPredecessors);
            ancestors.addAll(priorPredecessors);
        }
    }
    Log.info.print(Arrays.toString(predecessors.toArray()));
    for (BEASTInterface p : ancestors) {
        Log.info.print("(");
        try {
            for (BEASTInterface p2 : p.listActiveBEASTObjects()) {
                if (ancestors.contains(p2)) {
                    Log.info.print(p2.getID() + " ");
                }
            }
        } catch (IllegalArgumentException e) {
            e.printStackTrace();
        }
        Log.info.print(") ");
        Log.info.println(p.getID());
    }
    // now the ancestors contain all beastObjects to be copied
    // make a copy of all individual BEASTObjects, before connecting them up
    Map<String, BEASTInterface> copySet = new HashMap<>();
    for (BEASTInterface beastObject2 : ancestors) {
        String id = beastObject2.getID();
        if (id == null) {
            id = beastObject.getClass().getName().replaceAll(".*\\.", "");
            int i = 0;
            while (doc.pluginmap.containsKey(id + "." + i)) {
                i++;
            }
            id = id + "." + i;
            beastObject2.setID(id);
        }
        String copyID = renameId(id, oldContext, newContext);
        if (!id.equals(copyID)) {
            if (doc.pluginmap.containsKey(copyID)) {
                BEASTInterface org = doc.pluginmap.get(copyID);
                copySet.put(id, org);
            } else {
                BEASTInterface copy;
                try {
                    copy = beastObject2.getClass().newInstance();
                    copy.setID(copyID);
                    copySet.put(id, copy);
                } catch (InstantiationException | IllegalAccessException e) {
                    e.printStackTrace();
                    throw new RuntimeException("Programmer error: every object in the model should have a default constructor that is publicly accessible");
                }
            }
        }
        Log.warning.println("Copy: " + id + " -> " + copyID);
    }
    // set all inputs of copied beastObjects + outputs to taboo
    for (BEASTInterface beastObject2 : ancestors) {
        String id = beastObject2.getID();
        BEASTInterface copy = copySet.get(id);
        if (copy != null) {
            Log.warning.println("Processing: " + id + " -> " + copy.getID());
            // set inputs
            for (Input<?> input : beastObject2.listInputs()) {
                if (input.get() != null) {
                    if (input.get() instanceof List) {
                        // ((List)copy.getInput(input.getName())).clear();
                        for (Object o : (List<?>) input.get()) {
                            if (o instanceof BEASTInterface) {
                                BEASTInterface value = getCopyValue((BEASTInterface) o, copySet, oldContext, newContext, doc);
                                // make sure it is not already in the list
                                Object o2 = copy.getInput(input.getName()).get();
                                boolean alreadyInList = false;
                                if (o2 instanceof List) {
                                    List<?> currentList = (List<?>) o2;
                                    for (Object v : currentList) {
                                        if (v == value) {
                                            alreadyInList = true;
                                            break;
                                        }
                                    }
                                }
                                if (!alreadyInList) {
                                    // add to the list
                                    copy.setInputValue(input.getName(), value);
                                }
                            } else {
                                // it is a primitive value
                                if (copy instanceof Parameter.Base && input.getName().equals("value")) {
                                    // // prevent appending to parameter values
                                    Parameter.Base<?> p = ((Parameter.Base<?>) copy);
                                    ((List<?>) p.valuesInput.get()).clear();
                                }
                                copy.setInputValue(input.getName(), input.get());
                            }
                        }
                    } else if (input.get() instanceof BEASTInterface) {
                        // handle BEASTObject
                        BEASTInterface value = getCopyValue((BEASTInterface) input.get(), copySet, oldContext, newContext, doc);
                        copy.setInputValue(input.getName(), value);
                    } else if (input.get() instanceof String) {
                        // may need to replace partition info
                        String s = (String) input.get();
                        s = s.replaceAll("\\.c:[a-zA-Z0-9_]*", ".c:" + newContext.clockModel);
                        s = s.replaceAll("\\.s:[a-zA-Z0-9_]*", ".s:" + newContext.siteModel);
                        s = s.replaceAll("\\.t:[a-zA-Z0-9_]*", ".t:" + newContext.tree);
                        copy.setInputValue(input.getName(), s);
                    } else {
                        // it is a primitive value
                        copy.setInputValue(input.getName(), input.get());
                    }
                }
            }
            // set outputs
            for (Object output : beastObject2.getOutputs()) {
                if (taboo.contains(output) && output != parent) {
                    BEASTInterface output2 = getCopyValue((BEASTInterface) output, copySet, oldContext, newContext, doc);
                    for (Input<?> input : ((BEASTInterface) output).listInputs()) {
                        // do not add state node initialisers automatically
                        if (input.get() instanceof List && // do not update state node initialisers
                        !(taboo.contains(output2) && input.getName().equals("init"))) {
                            List<?> list = (List<?>) input.get();
                            if (list.contains(beastObject2)) {
                                List<?> list2 = (List<?>) output2.getInput(input.getName()).get();
                                if (!list2.contains(copy)) {
                                    output2.setInputValue(input.getName(), copy);
                                }
                            }
                        }
                    }
                }
            }
            copySet.put(id, copy);
        // Log.warning.println(base.operatorsAsString());
        }
    }
    // deep copy must be obtained from copyset, before sorting
    // since the sorting changes (deletes items) from the copySet map
    BEASTInterface deepCopy = copySet.get(beastObject.getID());
    // first need to sort copySet by topology, before we can initAndValidate
    // them
    List<BEASTInterface> sorted = new ArrayList<>();
    Collection<BEASTInterface> values = copySet.values();
    while (values.size() > 0) {
        for (BEASTInterface copy : values) {
            boolean found = false;
            for (BEASTInterface beastObject2 : copy.listActiveBEASTObjects()) {
                if (values.contains(beastObject2)) {
                    found = true;
                    break;
                }
            }
            if (!found) {
                sorted.add(copy);
            }
        }
        values.remove(sorted.get(sorted.size() - 1));
    }
    // initialise copied beastObjects
    Set<BEASTInterface> done = new HashSet<>();
    for (BEASTInterface copy : sorted) {
        try {
            if (!done.contains(copy)) {
                copy.initAndValidate();
                done.add(copy);
            }
        } catch (Exception e) {
            // ignore
            Log.warning.print(e.getMessage());
        }
        if (doc != null) {
            doc.addPlugin(copy);
        }
    }
    doc.scrubAll(true, false);
    return deepCopy;
}

Example 2 with Tree

use of beast.evolution.tree.Tree in project beast2 by CompEvol.

the class BeautiDoc method addTraitSet.

/**
 * assigns trait to first available tree *
 */
void addTraitSet(TraitSet trait) {
    if (trait != null) {
        CompoundDistribution likelihood = (CompoundDistribution) pluginmap.get("likelihood");
        for (Distribution d : likelihood.pDistributions.get()) {
            if (d instanceof GenericTreeLikelihood) {
                try {
                    // TODO: this might not be a valid type conversion from TreeInterface to Tree
                    Tree tree = (Tree) ((GenericTreeLikelihood) d).treeInput.get();
                    tree.m_traitList.setValue(trait, tree);
                } catch (Exception e) {
                    e.printStackTrace();
                }
                scrubAll(true, false);
                return;
            }
        }
    }
}

Example 3 with Tree

use of beast.evolution.tree.Tree in project beast2 by CompEvol.

the class BeautiDoc method setClockRate.

void setClockRate() {
    boolean needsEstimationBySPTree = false;
    if (pluginmap.containsKey("Tree.t:Species")) {
        Tree sptree = (Tree) pluginmap.get("Tree.t:Species");
        // check whether there is a calibration
        for (Object beastObject : sptree.getOutputs()) {
            if (beastObject instanceof MRCAPrior) {
                MRCAPrior prior = (MRCAPrior) beastObject;
                if (prior.distInput.get() != null) {
                    needsEstimationBySPTree = true;
                }
            }
        }
    }
    BEASTInterface likelihood = pluginmap.get("likelihood");
    if (likelihood instanceof CompoundDistribution) {
        int i = 0;
        RealParameter firstClock = null;
        for (Distribution distr : ((CompoundDistribution) likelihood).pDistributions.get()) {
            if (distr instanceof GenericTreeLikelihood) {
                GenericTreeLikelihood treeLikelihood = (GenericTreeLikelihood) distr;
                boolean needsEstimation = needsEstimationBySPTree;
                if (i > 0) {
                    BranchRateModel.Base model = treeLikelihood.branchRateModelInput.get();
                    needsEstimation = (model.meanRateInput.get() != firstClock) || firstClock.isEstimatedInput.get();
                } else {
                    // TODO: this might not be a valid type conversion from TreeInterface to Tree
                    Tree tree = (Tree) treeLikelihood.treeInput.get();
                    // check whether there are tip dates
                    if (tree.hasDateTrait()) {
                        needsEstimation = true;
                    }
                    // check whether there is a calibration
                    for (Object beastObject : tree.getOutputs()) {
                        if (beastObject instanceof MRCAPrior) {
                            MRCAPrior prior = (MRCAPrior) beastObject;
                            if (prior.distInput.get() != null) {
                                needsEstimation = true;
                            }
                        }
                    }
                }
                BranchRateModel.Base model = treeLikelihood.branchRateModelInput.get();
                if (model != null) {
                    RealParameter clockRate = model.meanRateInput.get();
                    clockRate.isEstimatedInput.setValue(needsEstimation, clockRate);
                    if (firstClock == null) {
                        firstClock = clockRate;
                    }
                }
                i++;
            }
        }
    }
}

Example 4 with Tree

use of beast.evolution.tree.Tree in project beast2 by CompEvol.

the class BeautiDoc method scrubAll.

// TreeDistribution getTreePrior(String partition) {
// int k = 0;
// for (Alignment data : alignments) {
// if (data.getID().equals(partition)) {
// return treePriors.get(k);
// }
// k++;
// }
// return null;
// }
public synchronized void scrubAll(boolean useNotEstimatedStateNodes, boolean isInitial) {
    try {
        if (autoSetClockRate) {
            setClockRate();
        }
        if (autoUpdateFixMeanSubstRate) {
            SiteModelInputEditor.customConnector(this);
        }
        // }
        if (pluginmap.containsKey("Tree.t:Species")) {
            Tree tree = (Tree) pluginmap.get("Tree.t:Species");
            tree.isEstimatedInput.setValue(true, tree);
        }
        // go through all templates, and process connectors in relevant ones
        boolean progress = true;
        while (progress) {
            warning("============================ start scrubbing ===========================");
            progress = false;
            setUpActivePlugins();
            // process MRCA priors
            for (String id : pluginmap.keySet()) {
                if (id != null && id.endsWith(".prior")) {
                    BEASTInterface beastObject = pluginmap.get(id);
                    if (beastObject instanceof MRCAPrior) {
                        MRCAPrior prior = (MRCAPrior) beastObject;
                        if (prior.treeInput.get().isEstimatedInput.get() == false) {
                            // disconnect
                            disconnect(beastObject, "prior", "distribution");
                        } else {
                            // connect
                            connect(beastObject, "prior", "distribution");
                        }
                    }
                }
            }
            List<BeautiSubTemplate> templates = new ArrayList<>();
            templates.add(beautiConfig.partitionTemplate.get());
            templates.addAll(beautiConfig.subTemplates);
            for (PartitionContext context : possibleContexts) {
                applyBeautiRules(templates, isInitial, context);
            }
            // add 'Species' as special partition name
            applyBeautiRules(templates, isInitial, new PartitionContext("Species"));
            // if the model changed, some rules that use inposterior() may
            // not have been triggered properly
            // so we need to check that the model changed, and if so,
            // revisit the BeautiConnectors
            List<BEASTInterface> posteriorPredecessors2 = new ArrayList<>();
            collectPredecessors(((MCMC) mcmc.get()).posteriorInput.get(), posteriorPredecessors2);
            if (posteriorPredecessors.size() != posteriorPredecessors2.size()) {
                progress = true;
            } else {
                for (BEASTInterface beastObject : posteriorPredecessors2) {
                    if (!posteriorPredecessors.contains(beastObject)) {
                        progress = true;
                        break;
                    }
                }
            }
        }
        List<BeautiSubTemplate> templates = new ArrayList<>();
        templates.add(beautiConfig.hyperPriorTemplate);
        for (BEASTInterface beastObject : pluginmap.values()) {
            if (beastObject instanceof RealParameter) {
                if (beastObject.getID() != null && beastObject.getID().startsWith("parameter.")) {
                    PartitionContext context = new PartitionContext(beastObject.getID().substring("parameter.".length()));
                    applyBeautiRules(templates, isInitial, context);
                }
            }
        }
        collectClockModels();
        // collectTreePriors();
        Log.warning.println("PARTITIONS:\n");
        Log.warning.println(Arrays.toString(currentPartitions));
        determineLinks();
    } catch (Exception e) {
        Log.err.println(e.getMessage());
    }
}

Example 5 with Tree

use of beast.evolution.tree.Tree in project beast2 by CompEvol.

the class WilsonBaldingTest method topologyDistribution.

/**
 * Test topology distribution.
 * @throws Exception
 */
@Test
public void topologyDistribution() throws Exception {
    // Fix seed: will hopefully ensure success of test unless something
    // goes terribly wrong.
    Randomizer.setSeed(42);
    // Assemble model:
    ConstantPopulation constantPop = new ConstantPopulation();
    constantPop.initByName("popSize", new RealParameter("10000.0"));
    List<Object> alignmentInitArgs = new ArrayList<Object>();
    for (int i = 0; i < 4; i++) {
        Sequence thisSeq = new Sequence();
        thisSeq.initByName("taxon", String.valueOf(i), "value", "?");
        alignmentInitArgs.add("sequence");
        alignmentInitArgs.add(thisSeq);
    }
    Alignment alignment = new Alignment();
    alignment.initByName(alignmentInitArgs.toArray());
    Tree tree = new RandomTree();
    tree.initByName("taxa", alignment, "populationModel", constantPop);
    TreeIntervals treeIntervals = new TreeIntervals();
    treeIntervals.initByName("tree", tree);
    Coalescent coalescentDistrib = new Coalescent();
    coalescentDistrib.initByName("treeIntervals", treeIntervals, "populationModel", constantPop);
    // Set up state:
    State state = new State();
    state.initByName("stateNode", tree);
    // Set up operator:
    WilsonBalding wilsonBalding = new WilsonBalding();
    wilsonBalding.initByName("weight", "1", "tree", tree);
    // Set up logger:
    TreeReport treeReport = new TreeReport();
    treeReport.initByName("logEvery", "100", "burnin", "200000", "credibleSetPercentage", "95.0", "log", tree, "silent", true);
    // Set up MCMC:
    MCMC mcmc = new MCMC();
    mcmc.initByName("chainLength", "2000000", "state", state, "distribution", coalescentDistrib, "operator", wilsonBalding, "logger", treeReport);
    // Run MCMC:
    mcmc.run();
    // Obtain analysis results:
    TreeTraceAnalysis analysis = treeReport.getAnalysis();
    Map<String, Integer> topologyCounts = analysis.getTopologyCounts();
    int totalTreesUsed = analysis.getNTrees();
    // Test topology distribution against ideal:
    double tol = 0.005;
    for (int i = 0; i < topologies.length; i++) {
        double thisProb = topologyCounts.get(topologies[i]) / (double) totalTreesUsed;
        boolean withinTol = (thisProb > probs[i] - tol && thisProb < probs[i] + tol);
        Assert.assertTrue(withinTol);
        System.err.format("Topology %s rel. freq. %.3f", topologies[i], thisProb);
        if (withinTol)
            System.err.println(" (Within tolerance " + tol + " of " + String.valueOf(probs[i]) + ")");
        else
            System.err.println(" (FAILURE: outside tolerance " + tol + " of " + String.valueOf(probs[i]) + ")");
    }
}