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

Example 81 with BEASTInterface

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

the class BeautiDoc method determinePartitions.

public void determinePartitions() {
    CompoundDistribution likelihood = (CompoundDistribution) pluginmap.get("likelihood");
    if (likelihood == null) {
        return;
    }
    partitionNames.clear();
    possibleContexts.clear();
    for (Distribution distr : likelihood.pDistributions.get()) {
        if (distr instanceof GenericTreeLikelihood) {
            GenericTreeLikelihood treeLikelihood = (GenericTreeLikelihood) distr;
            alignments.add(treeLikelihood.dataInput.get());
            PartitionContext context = new PartitionContext(treeLikelihood);
            partitionNames.add(context);
            boolean found = false;
            for (PartitionContext context2 : possibleContexts) {
                if (context.equals(context2)) {
                    found = true;
                }
            }
            if (!found) {
                possibleContexts.add(context);
            }
        }
    }
    alignments.clear();
    for (int i = 0; i < 3; i++) {
        pPartitionByAlignments[i].clear();
        pPartition[i].clear();
        currentPartitions[i].clear();
    }
    List<GenericTreeLikelihood> treeLikelihoods = new ArrayList<>();
    for (Distribution distr : likelihood.pDistributions.get()) {
        if (distr instanceof GenericTreeLikelihood) {
            GenericTreeLikelihood treeLikelihood = (GenericTreeLikelihood) distr;
            alignments.add(treeLikelihood.dataInput.get());
            treeLikelihoods.add(treeLikelihood);
        }
    }
    for (Distribution distr : likelihood.pDistributions.get()) {
        if (distr instanceof GenericTreeLikelihood) {
            GenericTreeLikelihood treeLikelihood = (GenericTreeLikelihood) distr;
            try {
                // sync SiteModel, ClockModel and Tree to any changes that
                // may have occurred
                // this should only affect the clock model in practice
                int partition = getPartitionNr((BEASTInterface) treeLikelihood.siteModelInput.get());
                GenericTreeLikelihood treeLikelihood2 = treeLikelihoods.get(partition);
                treeLikelihood.siteModelInput.setValue(treeLikelihood2.siteModelInput.get(), treeLikelihood);
                currentPartitions[0].add(partition);
                BranchRateModel rateModel = treeLikelihood.branchRateModelInput.get();
                if (rateModel != null) {
                    partition = getPartitionNr((BEASTInterface) rateModel);
                    treeLikelihood2 = treeLikelihoods.get(partition);
                    treeLikelihood.branchRateModelInput.setValue(treeLikelihood2.branchRateModelInput.get(), treeLikelihood);
                    currentPartitions[1].add(partition);
                } else {
                    currentPartitions[1].add(0);
                }
                partition = getPartitionNr((BEASTInterface) treeLikelihood.treeInput.get());
                treeLikelihood2 = treeLikelihoods.get(partition);
                treeLikelihood.treeInput.setValue(treeLikelihood2.treeInput.get(), treeLikelihood);
                currentPartitions[2].add(partition);
            } catch (Exception e) {
                e.printStackTrace();
            }
            pPartitionByAlignments[0].add(treeLikelihood);
            pPartitionByAlignments[1].add(treeLikelihood);
            pPartitionByAlignments[2].add(treeLikelihood);
        }
    }
    int partitionCount = partitionNames.size();
    for (int i = 0; i < 3; i++) {
        boolean[] usedPartition = new boolean[partitionCount];
        for (int j = 0; j < partitionCount; j++) {
            // getPartitionNr(m_pPartitionByAlignments[i].get(j));
            int partitionIndex = currentPartitions[i].get(j);
            usedPartition[partitionIndex] = true;
        }
        for (int j = 0; j < partitionCount; j++) {
            if (usedPartition[j]) {
                pPartition[i].add(pPartitionByAlignments[i].get(j));
            }
        }
    }
    Log.warning.println("PARTITIONS0:\n");
    Log.warning.println(Arrays.toString(currentPartitions));
}

Example 82 with BEASTInterface

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

the class BeautiDoc method connect.

/**
 * connect source beastObject with target beastObject
 *
 * @ *
 */
public void connect(BeautiConnector connector, PartitionContext context) {
    if (!connector.isRegularConnector) {
        return;
    }
    String srcID = translatePartitionNames(connector.sourceID, context);
    BEASTInterface srcBEASTObject = pluginmap.get(srcID);
    if (srcBEASTObject == null) {
        throw new IllegalArgumentException("Could not find beastObject with id " + srcID + ". Typo in template perhaps?\n");
    }
    String targetID = translatePartitionNames(connector.targetID, context);
    connect(srcBEASTObject, targetID, connector.targetInput);
}

Example 83 with BEASTInterface

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

the class BeautiDoc method collectClockModels.

private void collectClockModels() {
    // collect branch rate models from model
    CompoundDistribution likelihood = (CompoundDistribution) pluginmap.get("likelihood");
    while (clockModels.size() < partitionNames.size()) {
        try {
            GenericTreeLikelihood treelikelihood = new GenericTreeLikelihood();
            treelikelihood.branchRateModelInput.setValue(new StrictClockModel(), treelikelihood);
            List<BeautiSubTemplate> availableBEASTObjects = inputEditorFactory.getAvailableTemplates(treelikelihood.branchRateModelInput, treelikelihood, null, this);
            BEASTInterface beastObject = availableBEASTObjects.get(0).createSubNet(partitionNames.get(clockModels.size()), true);
            clockModels.add((BranchRateModel.Base) beastObject);
        } catch (Exception e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    int k = 0;
    for (Distribution d : likelihood.pDistributions.get()) {
        BranchRateModel clockModel = ((GenericTreeLikelihood) d).branchRateModelInput.get();
        // sanity check
        Tree tree = null;
        try {
            for (Input<?> input : ((BEASTInterface) clockModel).listInputs()) {
                if (input.getName().equals("tree")) {
                    tree = (Tree) input.get();
                }
            }
            if (tree != null && tree != ((GenericTreeLikelihood) d).treeInput.get()) {
                clockModel = clockModels.get(k);
                Log.warning.println("WARNING: unlinking clock model for " + d.getID());
                // TODO #557: this should move to the event of clock model drop box
                // JOptionPane.showMessageDialog(beauti.getSelectedComponent(),
                // "Cannot link all clock model(s) except strict clock with different trees !");
                ((GenericTreeLikelihood) d).branchRateModelInput.setValue(clockModel, d);
            }
        } catch (Exception e) {
        // ignore
        }
        if (clockModel != null) {
            String id = ((BEASTInterface) clockModel).getID();
            id = parsePartition(id);
            String partition = alignments.get(k).getID();
            if (id.equals(partition)) {
                clockModels.set(k, clockModel);
            }
            k++;
        }
    }
}

Example 84 with BEASTInterface

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

the class BeautiDoc method toJSON.

// save
private String toJSON() {
    Set<BEASTInterface> beastObjects = new HashSet<>();
    String json = new JSONProducer().toJSON(mcmc.get(), beastObjects);
    json = json.replaceFirst("\\{", "{ beautitemplate:\"" + templateName + "\", beautistatus:\"" + getBeautiStatus() + "\", ");
    return json + "\n";
}

Example 85 with BEASTInterface

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

the class BeautiDoc method setUpActivePlugins.

// scrubAll
protected void setUpActivePlugins() {
    posteriorPredecessors = new ArrayList<>();
    collectPredecessors(((MCMC) mcmc.get()).posteriorInput.get(), posteriorPredecessors);
    likelihoodPredecessors = new ArrayList<>();
    if (pluginmap.containsKey("likelihood")) {
        collectPredecessors(pluginmap.get("likelihood"), likelihoodPredecessors);
    }
    Log.trace.print("InPosterior=");
    for (BEASTInterface o : posteriorPredecessors) {
        pluginmap.put(o.getID(), o);
        Log.trace.print(o.getID() + " ");
    // if (!pluginmap.containsKey(o)) {
    // System.err.println("MISSING: " + o.getID());
    // }
    }
    Log.trace.println();
}