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

Example 6 with BEASTInterface

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

the class BeautiDoc method loadTemplate.

void loadTemplate(String xml) throws XMLParserException, SAXException, IOException, ParserConfigurationException {
    // load the template and its beauti configuration parts
    XMLParser parser = new XMLParser();
    BEASTObjectPanel.init();
    List<BEASTInterface> beastObjects = parser.parseTemplate(xml, new HashMap<>(), true);
    for (BEASTInterface beastObject : beastObjects) {
        if (beastObject instanceof beast.core.Runnable) {
            mcmc.setValue(beastObject, this);
        } else if (beastObject instanceof BeautiConfig) {
            beautiConfig = (BeautiConfig) beastObject;
            beautiConfig.setDoc(this);
        } else {
            Log.warning.println("template item " + beastObject.getID() + " is ignored");
        }
        BEASTObjectPanel.addPluginToMap(beastObject, this);
    }
}

Example 7 with BEASTInterface

use of beast.core.BEASTInterface 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 8 with BEASTInterface

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

the class BeautiDoc method mergeSequences.

/**
 * Merge sequence data with xml specification.
 * @throws ParserConfigurationException
 * @throws IOException
 * @throws SAXException
 * @throws XMLParserException
 */
void mergeSequences(String xml) throws XMLParserException, SAXException, IOException, ParserConfigurationException {
    if (xml == null) {
        xml = processTemplate(STANDARD_TEMPLATE);
    }
    loadTemplate(xml);
    // create XML for alignments
    if (beautiConfig != null) {
        for (Alignment alignment : alignments) {
            beautiConfig.partitionTemplate.get().createSubNet(alignment, this, true);
        }
    } else {
        // replace alignment
        for (BEASTInterface beastObject : pluginmap.values()) {
            if (beastObject instanceof Alignment) {
                // use toArray to prevent ConcurrentModificationException
                for (Object output : beastObject.getOutputs().toArray()) {
                    replaceInputs((BEASTInterface) output, beastObject, alignments.get(0));
                }
            }
        }
        return;
    }
    determinePartitions();
}

Example 9 with BEASTInterface

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

the class BeautiDoc method suggestedLinks.

/**
 * return all RealParameters that have
 * the same ID in another partition, or
 * the same partition with the same substitution model as output
 *
 * @param beastObject
 * @return
 */
public List<BEASTInterface> suggestedLinks(BEASTInterface beastObject) {
    String id = beastObject.getID();
    List<BEASTInterface> list = new ArrayList<>();
    String partitionID = null;
    if (id.indexOf('.') >= 0) {
        partitionID = id.substring(id.indexOf('.') + 1);
        id = id.substring(0, id.indexOf('.'));
    } else {
        return list;
    }
    for (BEASTInterface candidate : posteriorPredecessors) {
        String id2 = candidate.getID();
        if (id2.indexOf('.') >= 0) {
            String partitionID2 = id2.substring(id2.indexOf('.') + 1);
            id2 = id2.substring(0, id2.indexOf('.'));
            if (id2.equals(id)) {
                list.add(candidate);
            }
            if (beastObject instanceof Parameter<?> && partitionID2.equals(partitionID) && candidate.getClass().equals(beastObject.getClass())) {
                boolean dimensionMatches = true;
                if (((Parameter<?>) beastObject).getDimension() != ((Parameter<?>) candidate).getDimension()) {
                    dimensionMatches = false;
                }
                // ensure they share an output
                boolean foundCommonOutput = false;
                for (Object out1 : beastObject.getOutputs()) {
                    for (Object out2 : candidate.getOutputs()) {
                        if (out1 == out2 && out1 instanceof SubstitutionModel) {
                            foundCommonOutput = true;
                            break;
                        }
                    }
                }
                if (dimensionMatches && foundCommonOutput) {
                    list.add(candidate);
                }
            }
        }
    }
    list.remove(beastObject);
    return list;
}

Example 10 with BEASTInterface

use of beast.core.BEASTInterface 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());
    }
}