Examples with Distribution beast.core.Distribution used on opensource projects

Example 1 with Distribution

use of beast.core.Distribution 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 Distribution

use of beast.core.Distribution 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 Distribution

use of beast.core.Distribution 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 Distribution

use of beast.core.Distribution in project beast2 by CompEvol.

the class BeautiDoc method extractSequences.

void extractSequences(String xml) throws XMLParserException, SAXException, IOException, ParserConfigurationException {
    // parse the XML fragment into a DOM document
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    Document doc = factory.newDocumentBuilder().parse(new InputSource(new StringReader(xml)));
    doc.normalize();
    // find top level beast element
    NodeList nodes = doc.getElementsByTagName("*");
    Node topNode = nodes.item(0);
    String beautiTemplate = XMLParser.getAttribute(topNode, "beautitemplate");
    if (beautiTemplate == null) {
        int choice = JOptionPane.showConfirmDialog(getFrame(), "This file does not appear to be generated by BEAUti. If you load it, unexpected behaviour may follow");
        if (choice != JOptionPane.OK_OPTION) {
            return;
        }
        // load standard template
        if (beautiConfig == null) {
            String templateXML = processTemplate(STANDARD_TEMPLATE);
            loadTemplate(templateXML);
        }
    } else {
        String templateXML = processTemplate(beautiTemplate + ".xml");
        loadTemplate(templateXML);
    }
    String beautiStatus = XMLParser.getAttribute(topNode, "beautistatus");
    if (beautiStatus == null) {
        beautiStatus = "";
    }
    autoSetClockRate = !beautiStatus.contains("noAutoSetClockRate");
    beauti.autoSetClockRate.setSelected(autoSetClockRate);
    allowLinking = beautiStatus.contains("allowLinking");
    beauti.allowLinking.setSelected(allowLinking);
    autoUpdateFixMeanSubstRate = !beautiStatus.contains("noAutoUpdateFixMeanSubstRate");
    beauti.autoUpdateFixMeanSubstRate.setSelected(autoUpdateFixMeanSubstRate);
    // parse file
    XMLParser parser = new XMLParser();
    BEASTInterface MCMC = parser.parseFragment(xml, true);
    mcmc.setValue(MCMC, this);
    BEASTObjectPanel.addPluginToMap(MCMC, this);
    // reconstruct all objects from templates
    try {
        CompoundDistribution posterior = (CompoundDistribution) ((beast.core.MCMC) mcmc.get()).posteriorInput.get();
        for (Distribution distr : posterior.pDistributions.get()) {
            if (distr.getID().equals("likelihood")) {
                for (Distribution likelihood : ((CompoundDistribution) distr).pDistributions.get()) {
                    if (likelihood instanceof GenericTreeLikelihood) {
                        GenericTreeLikelihood treeLikelihood = (GenericTreeLikelihood) likelihood;
                        PartitionContext context = new PartitionContext(treeLikelihood);
                        try {
                            beautiConfig.partitionTemplate.get().createSubNet(context, false);
                        } catch (Exception e) {
                        // e.printStackTrace();
                        }
                        for (BeautiSubTemplate subTemplate : beautiConfig.subTemplates) {
                            try {
                                subTemplate.createSubNet(context, false);
                            } catch (Exception e) {
                            // e.printStackTrace();
                            }
                        }
                    }
                }
            }
        }
    } catch (Exception e) {
    // e.printStackTrace();
    }
    // MCMC = parser.parseFragment(xml, true);
    // mcmc.setValue(MCMC, this);
    // PluginPanel.addPluginToMap(MCMC, this);
    // if (xml.indexOf(XMLProducer.DO_NOT_EDIT_WARNING) > 0) {
    // int start = xml.indexOf(XMLProducer.DO_NOT_EDIT_WARNING);
    // int end = xml.lastIndexOf("-->");
    // xml = xml.substring(start, end);
    // xml = xml.replaceAll(XMLProducer.DO_NOT_EDIT_WARNING, "");
    // xml = "<beast namespace='" + XMLProducer.DEFAULT_NAMESPACE + "'>" + xml + "</beast>";
    // List<BEASTObject> beastObjects = parser.parseBareFragments(xml, true);
    // for (BEASTObject beastObject : beastObjects) {
    // PluginPanel.addPluginToMap(beastObject, this);
    // }
    // }
    // extract alignments
    determinePartitions();
}

Example 5 with Distribution

use of beast.core.Distribution in project beast2 by CompEvol.

the class BeautiBase method priorsAsString.

String priorsAsString() {
    CompoundDistribution prior = (CompoundDistribution) doc.pluginmap.get("prior");
    List<Distribution> priors = prior.pDistributions.get();
    return "assertPriorsEqual" + pluginListAsString(priors);
}