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

Example 1 with BEASTInterface

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

the class BeautiDoc method toXML.

public String toXML() {
    Set<BEASTInterface> beastObjects = new HashSet<>();
    // for (BEASTObject beastObject : pluginmap.values()) {
    // String name = beastObject.getClass().getName();
    // if (!name.startsWith("beast.app.beauti")) {
    // beastObjects.add(beastObject);
    // }
    // }
    String xml = new XMLProducer().toXML(mcmc.get(), beastObjects);
    xml = xml.replaceFirst("<beast ", "<beast beautitemplate='" + templateName + "' beautistatus='" + getBeautiStatus() + "' ");
    return xml + "\n";
}

Example 2 with BEASTInterface

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

the class BeautiDoc method disconnect.

public void disconnect(BEASTInterface srcBEASTObject, String targetID, String inputName) {
    try {
        BEASTInterface target = pluginmap.get(targetID);
        if (target == null) {
            return;
        }
        final Input<?> input = target.getInput(inputName);
        Object o = input.get();
        if (o instanceof List) {
            List<?> list = (List<?>) o;
            // System.err.println("   " + ((List)o).size());
            for (int i = 0; i < list.size(); i++) {
                if (list.get(i) == srcBEASTObject) {
                    warning("  DEL " + targetID + "/" + inputName + " contains " + (srcBEASTObject == null ? "null" : srcBEASTObject.getID()) + "\n");
                    list.remove(i);
                }
            }
            if (srcBEASTObject != null && srcBEASTObject.getOutputs() != null) {
                srcBEASTObject.getOutputs().remove(target);
            }
        } else {
            if (input.get() != null && input.get() instanceof BEASTInterface && input.get() == srcBEASTObject) {
                // ((BEASTInterface) input.get()).getID().equals(targetID)) {
                input.setValue(null, target);
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 3 with BEASTInterface

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

the class BeautiDoc method getUnlinkCandidate.

public BEASTInterface getUnlinkCandidate(Input<?> input, BEASTInterface parent) {
    PartitionContext oldContext = getContextFor((BEASTInterface) input.get());
    PartitionContext newContext = getContextFor(parent);
    BEASTInterface beastObject = deepCopyPlugin((BEASTInterface) input.get(), parent, (MCMC) mcmc.get(), oldContext, newContext, this, null);
    return beastObject;
}

Example 4 with BEASTInterface

use of beast.core.BEASTInterface 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 5 with BEASTInterface

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

the class BeautiDoc method renamePartition.

public void renamePartition(int partitionID, String oldName, String newName) {
    Log.warning.println("renamePartition: " + partitionID + " " + oldName + " " + newName);
    // sanity check: make sure newName is not already in use by another partition
    String newsuffix = null;
    switch(partitionID) {
        case ALIGNMENT_PARTITION:
            newsuffix = "." + newName;
            break;
        case SITEMODEL_PARTITION:
            newsuffix = ".s:" + newName;
            break;
        case CLOCKMODEL_PARTITION:
            newsuffix = ".c:" + newName;
            break;
        case TREEMODEL_PARTITION:
            newsuffix = ".t:" + newName;
            break;
        default:
            throw new IllegalArgumentException();
    }
    for (BEASTInterface beastObject : pluginmap.values()) {
        if (beastObject.getID().endsWith(newsuffix)) {
            throw new IllegalArgumentException("Name " + newName + " is already in use");
        }
    }
    // do the renaming
    String oldsuffix = null;
    switch(partitionID) {
        case ALIGNMENT_PARTITION:
            oldsuffix = "." + oldName;
            break;
        case SITEMODEL_PARTITION:
            oldsuffix = ".s:" + oldName;
            break;
        case CLOCKMODEL_PARTITION:
            oldsuffix = ".c:" + oldName;
            break;
        case TREEMODEL_PARTITION:
            oldsuffix = ".t:" + oldName;
            break;
        default:
            throw new IllegalArgumentException();
    }
    for (BEASTInterface beastObject : pluginmap.values()) {
        if (beastObject.getID().endsWith(oldsuffix)) {
            String id = beastObject.getID();
            id = id.substring(0, id.indexOf(oldsuffix)) + newsuffix;
            beastObject.setID(id);
        }
    }
    if (partitionID == ALIGNMENT_PARTITION) {
        // make exception for renaming alignment: its ID does not contain a dot
        for (BEASTInterface beastObject : pluginmap.values()) {
            if (beastObject.getID().equals(oldName)) {
                beastObject.setID(newName);
            }
        }
    }
    // update beastObject map
    String[] keyset = pluginmap.keySet().toArray(new String[0]);
    for (String key : keyset) {
        if (key.endsWith(oldsuffix)) {
            BEASTInterface beastObject = pluginmap.remove(key);
            key = key.substring(0, key.indexOf(oldsuffix)) + newsuffix;
            pluginmap.put(key, beastObject);
        }
    }
    // update tip text map
    keyset = tipTextMap.keySet().toArray(new String[0]);
    for (String key : keyset) {
        if (key.endsWith(oldsuffix)) {
            String tip = tipTextMap.remove(key);
            key = key.substring(0, key.indexOf(oldsuffix)) + newsuffix;
            tip = tip.replaceAll(oldsuffix, newsuffix);
            tipTextMap.put(key, tip);
        }
    }
    // update partition name table
    determinePartitions();
}