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

Example 1 with MCMC

use of beast.core.MCMC 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 2 with MCMC

use of beast.core.MCMC 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 3 with MCMC

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

the class BeautiBase method operatorsAsString.

String operatorsAsString() {
    MCMC mcmc = (MCMC) doc.mcmc.get();
    List<Operator> operators = mcmc.operatorsInput.get();
    return "assertOperatorsEqual" + pluginListAsString(operators);
}

Example 4 with MCMC

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

the class AlignmentListInputEditor method updateModel.

/**
 * set partition of type columnNr to partition model nr rowNr *
 */
void updateModel(int columnNr, int rowNr) {
    Log.warning.println("updateModel: " + rowNr + " " + columnNr + " " + table.getSelectedRow() + " " + table.getSelectedColumn());
    for (int i = 0; i < partitionCount; i++) {
        Log.warning.println(i + " " + tableData[i][0] + " " + tableData[i][SITEMODEL_COLUMN] + " " + tableData[i][CLOCKMODEL_COLUMN] + " " + tableData[i][TREE_COLUMN]);
    }
    getDoc();
    String partition = (String) tableData[rowNr][columnNr];
    // check if partition needs renaming
    String oldName = null;
    boolean isRenaming = false;
    try {
        switch(columnNr) {
            case SITEMODEL_COLUMN:
                if (!doc.pluginmap.containsKey("SiteModel.s:" + partition)) {
                    String id = ((BEASTInterface) likelihoods[rowNr].siteModelInput.get()).getID();
                    oldName = BeautiDoc.parsePartition(id);
                    doc.renamePartition(BeautiDoc.SITEMODEL_PARTITION, oldName, partition);
                    isRenaming = true;
                }
                break;
            case CLOCKMODEL_COLUMN:
                {
                    String id = likelihoods[rowNr].branchRateModelInput.get().getID();
                    String clockModelName = id.substring(0, id.indexOf('.')) + ".c:" + partition;
                    if (!doc.pluginmap.containsKey(clockModelName)) {
                        oldName = BeautiDoc.parsePartition(id);
                        doc.renamePartition(BeautiDoc.CLOCKMODEL_PARTITION, oldName, partition);
                        isRenaming = true;
                    }
                }
                break;
            case TREE_COLUMN:
                if (!doc.pluginmap.containsKey("Tree.t:" + partition)) {
                    String id = likelihoods[rowNr].treeInput.get().getID();
                    oldName = BeautiDoc.parsePartition(id);
                    doc.renamePartition(BeautiDoc.TREEMODEL_PARTITION, oldName, partition);
                    isRenaming = true;
                }
                break;
        }
    } catch (Exception e) {
        JOptionPane.showMessageDialog(this, "Cannot rename item: " + e.getMessage());
        tableData[rowNr][columnNr] = oldName;
        return;
    }
    if (isRenaming) {
        doc.determinePartitions();
        initTableData();
        setUpComboBoxes();
        table.repaint();
        return;
    }
    int partitionID = BeautiDoc.ALIGNMENT_PARTITION;
    switch(columnNr) {
        case SITEMODEL_COLUMN:
            partitionID = BeautiDoc.SITEMODEL_PARTITION;
            break;
        case CLOCKMODEL_COLUMN:
            partitionID = BeautiDoc.CLOCKMODEL_PARTITION;
            break;
        case TREE_COLUMN:
            partitionID = BeautiDoc.TREEMODEL_PARTITION;
            break;
    }
    int partitionNr = doc.getPartitionNr(partition, partitionID);
    GenericTreeLikelihood treeLikelihood = null;
    if (partitionNr >= 0) {
        // we ar linking
        treeLikelihood = likelihoods[partitionNr];
    }
    // (TreeLikelihood) doc.pluginmap.get("treeLikelihood." +
    // tableData[rowNr][NAME_COLUMN]);
    boolean needsRePartition = false;
    PartitionContext oldContext = new PartitionContext(this.likelihoods[rowNr]);
    switch(columnNr) {
        case SITEMODEL_COLUMN:
            {
                SiteModelInterface siteModel = null;
                if (treeLikelihood != null) {
                    // getDoc().getPartitionNr(partition,
                    // BeautiDoc.SITEMODEL_PARTITION) !=
                    // rowNr) {
                    siteModel = treeLikelihood.siteModelInput.get();
                } else {
                    siteModel = (SiteModel) doc.pluginmap.get("SiteModel.s:" + partition);
                    if (siteModel != likelihoods[rowNr].siteModelInput.get()) {
                        PartitionContext context = getPartitionContext(rowNr);
                        try {
                            siteModel = (SiteModel.Base) BeautiDoc.deepCopyPlugin((BEASTInterface) likelihoods[rowNr].siteModelInput.get(), likelihoods[rowNr], (MCMC) doc.mcmc.get(), oldContext, context, doc, null);
                        } catch (RuntimeException e) {
                            JOptionPane.showMessageDialog(this, "Could not clone site model: " + e.getMessage());
                            return;
                        }
                    }
                }
                SiteModelInterface target = this.likelihoods[rowNr].siteModelInput.get();
                if (target instanceof SiteModel.Base && siteModel instanceof SiteModel.Base) {
                    if (!((SiteModel.Base) target).substModelInput.canSetValue(((SiteModel.Base) siteModel).substModelInput.get(), (SiteModel.Base) target)) {
                        throw new IllegalArgumentException("Cannot link site model: substitution models (" + ((SiteModel.Base) target).substModelInput.get().getClass().toString() + " and " + ((SiteModel.Base) siteModel).substModelInput.get().getClass().toString() + ") are incompatible");
                    }
                } else {
                    throw new IllegalArgumentException("Don't know how to link this site model");
                }
                needsRePartition = (this.likelihoods[rowNr].siteModelInput.get() != siteModel);
                this.likelihoods[rowNr].siteModelInput.setValue(siteModel, this.likelihoods[rowNr]);
                partition = ((BEASTInterface) likelihoods[rowNr].siteModelInput.get()).getID();
                partition = BeautiDoc.parsePartition(partition);
                getDoc().setCurrentPartition(BeautiDoc.SITEMODEL_PARTITION, rowNr, partition);
            }
            break;
        case CLOCKMODEL_COLUMN:
            {
                BranchRateModel clockModel = null;
                if (treeLikelihood != null) {
                    // getDoc().getPartitionNr(partition,
                    // BeautiDoc.CLOCKMODEL_PARTITION)
                    // != rowNr) {
                    clockModel = treeLikelihood.branchRateModelInput.get();
                } else {
                    clockModel = getDoc().getClockModel(partition);
                    if (clockModel != likelihoods[rowNr].branchRateModelInput.get()) {
                        PartitionContext context = getPartitionContext(rowNr);
                        try {
                            clockModel = (BranchRateModel) BeautiDoc.deepCopyPlugin(likelihoods[rowNr].branchRateModelInput.get(), likelihoods[rowNr], (MCMC) doc.mcmc.get(), oldContext, context, doc, null);
                        } catch (RuntimeException e) {
                            JOptionPane.showMessageDialog(this, "Could not clone clock model: " + e.getMessage());
                            return;
                        }
                    }
                }
                // make sure that *if* the clock model has a tree as input, it is
                // the same as
                // for the likelihood
                TreeInterface tree = null;
                for (Input<?> input : ((BEASTInterface) clockModel).listInputs()) {
                    if (input.getName().equals("tree")) {
                        tree = (TreeInterface) input.get();
                    }
                }
                if (tree != null && tree != this.likelihoods[rowNr].treeInput.get()) {
                    JOptionPane.showMessageDialog(this, "Cannot link clock model with different trees");
                    throw new IllegalArgumentException("Cannot link clock model with different trees");
                }
                needsRePartition = (this.likelihoods[rowNr].branchRateModelInput.get() != clockModel);
                this.likelihoods[rowNr].branchRateModelInput.setValue(clockModel, this.likelihoods[rowNr]);
                partition = likelihoods[rowNr].branchRateModelInput.get().getID();
                partition = BeautiDoc.parsePartition(partition);
                getDoc().setCurrentPartition(BeautiDoc.CLOCKMODEL_PARTITION, rowNr, partition);
            }
            break;
        case TREE_COLUMN:
            {
                TreeInterface tree = null;
                if (treeLikelihood != null) {
                    // getDoc().getPartitionNr(partition,
                    // BeautiDoc.TREEMODEL_PARTITION) !=
                    // rowNr) {
                    tree = treeLikelihood.treeInput.get();
                } else {
                    tree = (TreeInterface) doc.pluginmap.get("Tree.t:" + partition);
                    if (tree != likelihoods[rowNr].treeInput.get()) {
                        PartitionContext context = getPartitionContext(rowNr);
                        try {
                            tree = (TreeInterface) BeautiDoc.deepCopyPlugin((BEASTInterface) likelihoods[rowNr].treeInput.get(), likelihoods[rowNr], (MCMC) doc.mcmc.get(), oldContext, context, doc, null);
                        } catch (RuntimeException e) {
                            JOptionPane.showMessageDialog(this, "Could not clone tree model: " + e.getMessage());
                            return;
                        }
                        State state = ((MCMC) doc.mcmc.get()).startStateInput.get();
                        List<StateNode> stateNodes = new ArrayList<>();
                        stateNodes.addAll(state.stateNodeInput.get());
                        for (StateNode s : stateNodes) {
                            if (s.getID().endsWith(".t:" + oldContext.tree) && !(s instanceof TreeInterface)) {
                                try {
                                    @SuppressWarnings("unused") StateNode copy = (StateNode) BeautiDoc.deepCopyPlugin(s, likelihoods[rowNr], (MCMC) doc.mcmc.get(), oldContext, context, doc, null);
                                } catch (RuntimeException e) {
                                    JOptionPane.showMessageDialog(this, "Could not clone tree model: " + e.getMessage());
                                    return;
                                }
                            }
                        }
                    }
                }
                // sanity check: make sure taxon sets are compatible
                Taxon.assertSameTaxa(tree.getID(), tree.getTaxonset().getTaxaNames(), likelihoods[rowNr].dataInput.get().getID(), likelihoods[rowNr].dataInput.get().getTaxaNames());
                needsRePartition = (this.likelihoods[rowNr].treeInput.get() != tree);
                Log.warning.println("needsRePartition = " + needsRePartition);
                if (needsRePartition) {
                    TreeInterface oldTree = this.likelihoods[rowNr].treeInput.get();
                    List<TreeInterface> tModels = new ArrayList<>();
                    for (GenericTreeLikelihood likelihood : likelihoods) {
                        if (likelihood.treeInput.get() == oldTree) {
                            tModels.add(likelihood.treeInput.get());
                        }
                    }
                    if (tModels.size() == 1) {
                        // remove old tree from model
                        ((BEASTInterface) oldTree).setInputValue("estimate", false);
                        // use toArray to prevent ConcurrentModificationException
                        for (Object beastObject : BEASTInterface.getOutputs(oldTree).toArray()) {
                            // .toArray(new BEASTInterface[0])) {
                            for (Input<?> input : ((BEASTInterface) beastObject).listInputs()) {
                                try {
                                    if (input.get() == oldTree) {
                                        if (input.getRule() != Input.Validate.REQUIRED) {
                                            input.setValue(tree, /*null*/
                                            (BEASTInterface) beastObject);
                                        // } else {
                                        // input.setValue(tree, (BEASTInterface) beastObject);
                                        }
                                    } else if (input.get() instanceof List) {
                                        @SuppressWarnings("unchecked") List<TreeInterface> list = (List<TreeInterface>) input.get();
                                        if (list.contains(oldTree)) {
                                            // && input.getRule() != Validate.REQUIRED) {
                                            list.remove(oldTree);
                                            if (!list.contains(tree)) {
                                                list.add(tree);
                                            }
                                        }
                                    }
                                } catch (Exception e) {
                                    e.printStackTrace();
                                }
                            }
                        }
                    }
                }
                likelihoods[rowNr].treeInput.setValue(tree, likelihoods[rowNr]);
                // TreeDistribution d = getDoc().getTreePrior(partition);
                // CompoundDistribution prior = (CompoundDistribution)
                // doc.pluginmap.get("prior");
                // if (!getDoc().posteriorPredecessors.contains(d)) {
                // prior.pDistributions.setValue(d, prior);
                // }
                partition = likelihoods[rowNr].treeInput.get().getID();
                partition = BeautiDoc.parsePartition(partition);
                getDoc().setCurrentPartition(BeautiDoc.TREEMODEL_PARTITION, rowNr, partition);
            }
    }
    tableData[rowNr][columnNr] = partition;
    if (needsRePartition) {
        List<BeautiSubTemplate> templates = new ArrayList<>();
        templates.add(doc.beautiConfig.partitionTemplate.get());
        templates.addAll(doc.beautiConfig.subTemplates);
        // keep applying rules till model does not change
        doc.setUpActivePlugins();
        int n;
        do {
            n = doc.posteriorPredecessors.size();
            doc.applyBeautiRules(templates, false, oldContext);
            doc.setUpActivePlugins();
        } while (n != doc.posteriorPredecessors.size());
        doc.determinePartitions();
    }
    if (treeLikelihood == null) {
        initTableData();
        setUpComboBoxes();
    }
    updateStatus();
}

Example 5 with MCMC

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

the class ExampleJSONParsingTest method test_ThatJSONExamplesRun.

public void test_ThatJSONExamplesRun(String dir) {
    try {
        Logger.FILE_MODE = Logger.LogFileMode.overwrite;
        System.out.println("Test that JSON Examples run in " + dir);
        File exampleDir = new File(dir);
        String[] exampleFiles = exampleDir.list(new FilenameFilter() {

            @Override
            public boolean accept(File dir, String name) {
                return name.endsWith(".json");
            }
        });
        List<String> failedFiles = new ArrayList<String>();
        int seed = 127;
        for (String fileName : exampleFiles) {
            Randomizer.setSeed(seed);
            // need more than one to prevent trouble with multiMCMC logs
            seed += 10;
            System.out.println("Processing " + fileName);
            JSONParser parser = new JSONParser();
            try {
                beast.core.Runnable runable = parser.parseFile(new File(dir + "/" + fileName));
                if (runable instanceof MCMC) {
                    MCMC mcmc = (MCMC) runable;
                    mcmc.setInputValue("preBurnin", 0);
                    mcmc.setInputValue("chainLength", 1000l);
                    mcmc.run();
                }
            } catch (Exception e) {
                System.out.println("ExampleJSONParsing::Failed for " + fileName + ": " + e.getMessage());
                failedFiles.add(fileName);
            }
            System.out.println("Done " + fileName);
        }
        if (failedFiles.size() > 0) {
            System.out.println("\ntest_ThatJSONExamplesRun::Failed for : " + failedFiles.toString());
        } else {
            System.out.println("SUCCESS!!!");
        }
        assertTrue(failedFiles.toString(), failedFiles.size() == 0);
    } catch (Exception e) {
        System.out.println("exception thrown ");
        System.out.println(e.getMessage());
        ;
    }
}