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

Example 16 with BEASTInterface

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

the class BeautiSubTemplate method createSubNet.

public BEASTInterface createSubNet(PartitionContext partition, List<BEASTInterface> list, int item, boolean init) {
    removeSubNet(list.get(item));
    if (xml == null) {
        // this is the NULL_TEMPLATE
        list.set(item, null);
        return null;
    }
    BEASTInterface o = createSubNet(partition, doc.pluginmap, init);
    list.set(item, o);
    return o;
}

Example 17 with BEASTInterface

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

the class BeautiSubTemplate method createSubNet.

private BEASTInterface createSubNet(PartitionContext context, /*BeautiDoc doc,*/
HashMap<String, BEASTInterface> idMap, boolean init) {
    subNetDepth++;
    if (subNetDepth > 10) {
        // looks like we cannot find what we are looking for
        throw new IllegalArgumentException("Potential programmer error: It looks like there is a required input that was not specified in the tenmplate");
    }
    // wrap in a beast element with appropriate name spaces
    String _sXML = "<beast version='2.0' \n" + "namespace='beast.app.beauti:beast.core:beast.evolution.branchratemodel:beast.evolution.speciation:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood:beast.evolution:beast.math.distributions'>\n" + xml + "</beast>\n";
    // resolve alignment references
    _sXML = _sXML.replaceAll("idref=[\"']data['\"]", "idref='" + context.partition + "'");
    _sXML = _sXML.replaceAll("[\"']@data['\"]", "'@" + context.partition + "'");
    // ensure uniqueness of IDs
    // _sXML.replaceAll("\\$\\(n\\)", partition);
    _sXML = BeautiDoc.translatePartitionNames(_sXML, context);
    XMLParser parser = new XMLParser();
    parser.setRequiredInputProvider(doc, context);
    List<BEASTInterface> beastObjects = null;
    try {
        beastObjects = parser.parseTemplate(_sXML, idMap, true);
        for (BEASTInterface beastObject : beastObjects) {
            doc.addPlugin(beastObject);
            try {
                Log.warning.println("Adding " + beastObject.getClass().getName() + " " + beastObject);
            } catch (Exception e) {
                Log.err.println("Adding " + beastObject.getClass().getName());
            }
        }
        for (BeautiConnector connector : connectors) {
            if (init && connector.atInitialisationOnly()) {
                // ||
                doc.connect(connector, context);
            }
            // System.out.println(connector.sourceID + " == " + connector.targetID);
            if (connector.targetID != null && connector.targetID.equals("prior")) {
                Log.warning.println(">>> No description for connector " + connector.sourceID + " == " + connector.targetID);
            }
            if (connector.getTipText() != null) {
                String ID = BeautiDoc.translatePartitionNames(connector.sourceID, context);
                String tipText = BeautiDoc.translatePartitionNames(connector.getTipText(), context).trim().replaceAll("\\s+", " ");
                // System.out.println(ID + " -> " + tipText);
                doc.tipTextMap.put(ID, tipText);
            }
        }
        if (suppressedInputs.get() != null) {
            String[] inputs = suppressedInputs.get().split(",");
            for (String input : inputs) {
                input = input.trim();
                doc.beautiConfig.suppressBEASTObjects.add(input);
            }
        }
        if (inlineInput.get() != null) {
            String[] inputs = inlineInput.get().split(",");
            for (String input : inputs) {
                input = input.trim();
                doc.beautiConfig.inlineBEASTObject.add(input);
            }
        }
        if (collapsedInput.get() != null) {
            String[] inputs = collapsedInput.get().split(",");
            for (String input : inputs) {
                input = input.trim();
                doc.beautiConfig.collapsedBEASTObjects.add(input);
            }
        }
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    if (mainID.equals("[top]")) {
        subNetDepth--;
        return beastObjects.get(0);
    }
    String id = mainID;
    // id.replaceAll("\\$\\(n\\)", partition);
    id = BeautiDoc.translatePartitionNames(id, context);
    BEASTInterface beastObject = doc.pluginmap.get(id);
    if (this == doc.beautiConfig.partitionTemplate.get()) {
        // HACK: need to make sure the subst model is of the correct type
        BEASTInterface treeLikelihood = doc.pluginmap.get("treeLikelihood." + context.partition);
        if (treeLikelihood != null && ((GenericTreeLikelihood) treeLikelihood).siteModelInput.get() instanceof SiteModel.Base) {
            SiteModel.Base siteModel = (SiteModel.Base) ((GenericTreeLikelihood) treeLikelihood).siteModelInput.get();
            SubstitutionModel substModel = siteModel.substModelInput.get();
            try {
                if (!siteModel.canSetSubstModel(substModel)) {
                    setUpSubstModel(siteModel, context);
                }
            } catch (Exception e) {
                setUpSubstModel(siteModel, context);
            }
        }
        // HACK2: rename file name for trace log if it has the default value
        Logger logger = (Logger) doc.pluginmap.get("tracelog");
        if (logger != null) {
            String fileName = logger.fileNameInput.get();
            if (fileName.startsWith("beast.") && treeLikelihood != null) {
                Alignment data = ((GenericTreeLikelihood) treeLikelihood).dataInput.get();
                while (data instanceof FilteredAlignment) {
                    data = ((FilteredAlignment) data).alignmentInput.get();
                }
                fileName = data.getID() + fileName.substring(5);
                try {
                    logger.fileNameInput.setValue(fileName, logger);
                } catch (Exception e) {
                    e.printStackTrace();
                }
            }
        }
    }
    subNetDepth--;
    // System.err.println(new XMLProducer().toXML(beastObject));
    return beastObject;
}

Example 18 with BEASTInterface

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

the class BeautiSubTemplate method removeSubNet.

void removeSubNet(Object o) {
    if (o == null) {
        // nothing to do
        return;
    }
    BEASTInterface beastObject = null;
    if (o instanceof BEASTInterface) {
        beastObject = (BEASTInterface) o;
    }
    // find template that created this beastObject
    String id = beastObject.getID();
    // String partition = BeautiDoc.parsePartition(id);
    if (id.indexOf(".") > 0) {
        id = id.substring(0, id.indexOf("."));
    }
    BeautiSubTemplate template = null;
    for (BeautiSubTemplate template2 : doc.beautiConfig.subTemplatesInput.get()) {
        if (template2.matchesName(id)) {
            template = template2;
            break;
        }
    }
    if (template == null) {
        throw new RuntimeException("Cannot find template for removing " + beastObject.getID());
    }
    PartitionContext context = doc.getContextFor(beastObject);
    removeSubNet(template, context);
}

Example 19 with BEASTInterface

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

the class GeneTreeForSpeciesTreeDistributionInputEditor method createPloidyEditor.

public InputEditor createPloidyEditor() {
    InputEditor editor = new InputEditor.Base(doc) {

        private static final long serialVersionUID = 1L;

        @Override
        public Class<?> type() {
            return null;
        }

        @Override
        public void init(Input<?> input, BEASTInterface beastObject, int itemNr, ExpandOption isExpandOption, boolean addButtons) {
            m_beastObject = beastObject;
            m_input = input;
            m_bAddButtons = addButtons;
            this.itemNr = itemNr;
            addInputLabel();
            m_selectBeastObjectBox = new JComboBox<>(valuesString);
            setSelection();
            String selectString = input.get().toString();
            m_selectBeastObjectBox.setSelectedItem(selectString);
            m_selectBeastObjectBox.addActionListener(e -> {
                int i = m_selectBeastObjectBox.getSelectedIndex();
                if (i == OTHER) {
                    setSelection();
                    return;
                }
                try {
                    setValue(_values[i]);
                // lm_input.setValue(selected, m_beastObject);
                } catch (Exception e1) {
                    e1.printStackTrace();
                }
            });
            m_selectBeastObjectBox.setToolTipText(input.getHTMLTipText());
            add(m_selectBeastObjectBox);
            add(Box.createGlue());
        }

        private void setSelection() {
            Double value = (Double) m_input.get();
            m_selectBeastObjectBox.setSelectedIndex(OTHER);
            for (int i = 0; i < _values.length; i++) {
                if (value.equals(_values[i])) {
                    m_selectBeastObjectBox.setSelectedIndex(i);
                }
            }
        }
    };
    editor.init(((GeneTreeForSpeciesTreeDistribution) m_beastObject).ploidyInput, m_beastObject, -1, ExpandOption.FALSE, true);
    return editor;
}

Example 20 with BEASTInterface

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

the class XMLParser method useAnnotatedConstructor.

@SuppressWarnings({ "rawtypes", "unchecked" })
private BEASTInterface useAnnotatedConstructor(Node node, String _id, String clazzName, List<NameValuePair> inputInfo) throws XMLParserException {
    Class<?> clazz = null;
    try {
        clazz = Class.forName(clazzName);
    } catch (ClassNotFoundException e) {
        // cannot get here, since we checked the class existed before
        e.printStackTrace();
    }
    Constructor<?>[] allConstructors = clazz.getDeclaredConstructors();
    for (Constructor<?> ctor : allConstructors) {
        Annotation[][] annotations = ctor.getParameterAnnotations();
        List<Param> paramAnnotations = new ArrayList<>();
        for (Annotation[] a0 : annotations) {
            for (Annotation a : a0) {
                if (a instanceof Param) {
                    paramAnnotations.add((Param) a);
                }
            }
        }
        for (NameValuePair pair : inputInfo) {
            pair.processed = false;
        }
        Class<?>[] types = ctor.getParameterTypes();
        // Type[] gtypes = ctor.getGenericParameterTypes();
        if (types.length > 0 && paramAnnotations.size() == types.length) {
            try {
                Object[] args = new Object[types.length];
                for (int i = 0; i < types.length; i++) {
                    Param param = paramAnnotations.get(i);
                    Type type = types[i];
                    if (type.getTypeName().equals("java.util.List")) {
                        if (args[i] == null) {
                            // no need to parameterise list due to type erasure
                            args[i] = new ArrayList();
                        }
                        List<Object> values = getListOfValues(param, inputInfo);
                        ((List) args[i]).addAll(values);
                    } else {
                        args[i] = getValue(param, types[i], inputInfo);
                        // and the args[i] is a String -- we need to invoke the String constructor
                        if (args[i].getClass().equals(String.class) && types[i] != String.class) {
                            for (Constructor<?> argctor : types[i].getDeclaredConstructors()) {
                                Class<?>[] argtypes = argctor.getParameterTypes();
                                if (argtypes.length == 1 && argtypes[0] == String.class) {
                                    Object o = argctor.newInstance(args[i]);
                                    args[i] = o;
                                    break;
                                }
                            }
                        }
                    }
                }
                // ensure all inputs are used
                boolean allUsed = true;
                for (NameValuePair pair : inputInfo) {
                    if (!pair.processed) {
                        allUsed = false;
                    }
                }
                if (allUsed) {
                    try {
                        Object o = ctor.newInstance(args);
                        BEASTInterface beastObject = (BEASTInterface) o;
                        register(node, beastObject);
                        return beastObject;
                    } catch (InstantiationException | IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
                        throw new XMLParserException(node, "Could not create object: " + e.getMessage(), 1012);
                    }
                }
            } catch (NoSuchMethodException | SecurityException | InstantiationException | IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
            // we get here when a param value cannot be constructed from a default value
            // let's try the next constructor (if any)
            }
        }
    }
    return null;
}