Examples with Prior beast.math.distributions.Prior used on opensource projects

Example 1 with Prior

use of beast.math.distributions.Prior 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 Prior

use of beast.math.distributions.Prior in project beast2 by CompEvol.

the class PriorListInputEditor method init.

@Override
public void init(Input<?> input, BEASTInterface beastObject, int itemNr, ExpandOption isExpandOption, boolean addButtons) {
    List<?> list = (List<?>) input.get();
    Collections.sort(list, (Object o1, Object o2) -> {
        if (o1 instanceof BEASTInterface && o2 instanceof BEASTInterface) {
            String d1 = ((BEASTInterface) o1).getID();
            String id2 = ((BEASTInterface) o2).getID();
            // first the tree priors
            if (o1 instanceof TreeDistribution) {
                if (o2 instanceof TreeDistribution) {
                    TreeInterface tree1 = ((TreeDistribution) o1).treeInput.get();
                    if (tree1 == null) {
                        tree1 = ((TreeDistribution) o1).treeIntervalsInput.get().treeInput.get();
                    }
                    TreeInterface tree2 = ((TreeDistribution) o2).treeInput.get();
                    if (tree2 == null) {
                        tree2 = ((TreeDistribution) o2).treeIntervalsInput.get().treeInput.get();
                    }
                    return d1.compareTo(id2);
                } else {
                    return -1;
                }
            } else if (o1 instanceof MRCAPrior) {
                // last MRCA priors
                if (o2 instanceof MRCAPrior) {
                    return d1.compareTo(id2);
                } else {
                    return 1;
                }
            } else {
                if (o2 instanceof TreeDistribution) {
                    return 1;
                }
                if (o2 instanceof MRCAPrior) {
                    return -1;
                }
                if (o1 instanceof Prior) {
                    d1 = ((Prior) o1).getParameterName();
                }
                if (o2 instanceof Prior) {
                    id2 = ((Prior) o2).getParameterName();
                }
                return d1.compareTo(id2);
            }
        }
        return 0;
    });
    rangeButtons = new ArrayList<>();
    taxonButtons = new ArrayList<>();
    // m_buttonStatus = ButtonStatus.NONE;
    super.init(input, beastObject, itemNr, isExpandOption, addButtons);
    if (beastObject instanceof BeautiPanelConfig) {
        BeautiPanelConfig config = (BeautiPanelConfig) beastObject;
        if (config.parentBEASTObjects != null && config.parentBEASTObjects.size() > 0 && config.parentBEASTObjects.get(0).getID().equals("speciescoalescent")) {
            m_buttonStatus = ButtonStatus.NONE;
        }
    }
    if (m_buttonStatus == ButtonStatus.ALL || m_buttonStatus == ButtonStatus.ADD_ONLY) {
        addButton = new SmallButton("+ Add Prior", true);
        addButton.setName("addItem");
        addButton.setToolTipText("Add new prior (like an MRCA-prior) to the list of priors");
        addButton.addActionListener(e -> {
            addItem();
        });
        buttonBox.add(addButton);
        buttonBox.add(Box.createHorizontalGlue());
    }
}

Example 3 with Prior

use of beast.math.distributions.Prior in project beast2 by CompEvol.

the class PriorInputEditor method init.

@Override
public void init(Input<?> input, BEASTInterface beastObject, int listItemNr, ExpandOption isExpandOption, boolean addButtons) {
    m_bAddButtons = addButtons;
    m_input = input;
    m_beastObject = beastObject;
    this.itemNr = listItemNr;
    Box itemBox = Box.createHorizontalBox();
    Prior prior = (Prior) beastObject;
    String text = prior.getParameterName();
    JLabel label = new JLabel(text);
    Font font = label.getFont();
    Dimension size = new Dimension(font.getSize() * 200 / 13, font.getSize() * 25 / 13);
    label.setMinimumSize(size);
    label.setPreferredSize(size);
    itemBox.add(label);
    List<BeautiSubTemplate> availableBEASTObjects = doc.getInputEditorFactory().getAvailableTemplates(prior.distInput, prior, null, doc);
    JComboBox<BeautiSubTemplate> comboBox = new JComboBox<BeautiSubTemplate>(availableBEASTObjects.toArray(new BeautiSubTemplate[] {}));
    comboBox.setName(text + ".distr");
    String id = prior.distInput.get().getID();
    // Log.warning.println("id=" + id);
    id = id.substring(0, id.indexOf('.'));
    for (BeautiSubTemplate template : availableBEASTObjects) {
        if (template.classInput.get() != null && template.shortClassName.equals(id)) {
            comboBox.setSelectedItem(template);
        }
    }
    comboBox.addActionListener(e -> {
        @SuppressWarnings("unchecked") JComboBox<BeautiSubTemplate> comboBox1 = (JComboBox<BeautiSubTemplate>) e.getSource();
        List<?> list = (List<?>) m_input.get();
        BeautiSubTemplate template = (BeautiSubTemplate) comboBox1.getSelectedItem();
        // String id = ((BEASTObject) list.get(item)).getID();
        // String partition = BeautiDoc.parsePartition(id);
        PartitionContext context = doc.getContextFor((BEASTInterface) list.get(itemNr));
        Prior prior1 = (Prior) list.get(itemNr);
        try {
            template.createSubNet(context, prior1, prior1.distInput, true);
        } catch (Exception e1) {
            e1.printStackTrace();
        }
        sync();
        refreshPanel();
    });
    JPanel panel = new JPanel();
    panel.add(comboBox);
    panel.setMaximumSize(size);
    itemBox.add(panel);
    if (prior.m_x.get() instanceof RealParameter) {
        // add range button for real parameters
        RealParameter p = (RealParameter) prior.m_x.get();
        JButton rangeButton = new JButton(paramToString(p));
        rangeButton.addActionListener(e -> {
            JButton rangeButton1 = (JButton) e.getSource();
            List<?> list = (List<?>) m_input.get();
            Prior prior1 = (Prior) list.get(itemNr);
            RealParameter p1 = (RealParameter) prior1.m_x.get();
            BEASTObjectDialog dlg = new BEASTObjectDialog(p1, RealParameter.class, doc);
            if (dlg.showDialog()) {
                dlg.accept(p1, doc);
                rangeButton1.setText(paramToString(p1));
                refreshPanel();
            }
        });
        itemBox.add(Box.createHorizontalStrut(10));
        itemBox.add(rangeButton);
    } else if (prior.m_x.get() instanceof IntegerParameter) {
        // add range button for real parameters
        IntegerParameter p = (IntegerParameter) prior.m_x.get();
        JButton rangeButton = new JButton(paramToString(p));
        rangeButton.addActionListener(e -> {
            JButton rangeButton1 = (JButton) e.getSource();
            List<?> list = (List<?>) m_input.get();
            Prior prior1 = (Prior) list.get(itemNr);
            IntegerParameter p1 = (IntegerParameter) prior1.m_x.get();
            BEASTObjectDialog dlg = new BEASTObjectDialog(p1, IntegerParameter.class, doc);
            if (dlg.showDialog()) {
                dlg.accept(p1, doc);
                rangeButton1.setText(paramToString(p1));
                refreshPanel();
            }
        });
        itemBox.add(Box.createHorizontalStrut(10));
        itemBox.add(rangeButton);
    }
    int fontsize = comboBox.getFont().getSize();
    comboBox.setMaximumSize(new Dimension(1024 * fontsize / 13, 24 * fontsize / 13));
    String tipText = getDoc().tipTextMap.get(beastObject.getID());
    // System.out.println(beastObject.getID());
    if (tipText != null) {
        JLabel tipTextLabel = new JLabel(" " + tipText);
        itemBox.add(tipTextLabel);
    }
    itemBox.add(Box.createGlue());
    add(itemBox);
}

Example 4 with Prior

use of beast.math.distributions.Prior in project beast2 by CompEvol.

the class BeautiBase method assertParameterCountInPriorIs.

void assertParameterCountInPriorIs(int i) {
    // count nr of parameters in Prior objects in prior
    // including those for prior distributions (Normal, etc)
    // useful to make sure they do (or do not) get linked
    Set<Function> parameters = new LinkedHashSet<>();
    CompoundDistribution prior = (CompoundDistribution) doc.pluginmap.get("prior");
    for (Distribution p : prior.pDistributions.get()) {
        if (p instanceof Prior) {
            Prior p2 = (Prior) p;
            parameters.add(p2.m_x.get());
            for (BEASTInterface o : p2.distInput.get().listActiveBEASTObjects()) {
                if (o instanceof Parameter) {
                    parameters.add((Parameter<?>) o);
                }
            }
        }
    }
    System.err.println("Number of parameters in prior = " + parameters.size());
    if (i >= 0) {
        assertThat(parameters.size()).as("Expected " + i + " parameters in prior").isEqualTo(i);
    }
}