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

Example 66 with BEASTInterface

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

the class BeautiConfig method selectAlignments.

/**
 * if fileArray == null, then use getAlignments(doc)
 * @param doc
 * @param parent
 * @param fileArray
 * @return a list of alignments based on the user selected alignment provider
 */
public List<BEASTInterface> selectAlignments(BeautiDoc doc, JComponent parent, File[] fileArray) {
    List<BeautiAlignmentProvider> providers = alignmentProvider;
    BeautiAlignmentProvider selectedProvider = null;
    if (providers.size() == 1) {
        selectedProvider = providers.get(0);
    } else {
        selectedProvider = (BeautiAlignmentProvider) JOptionPane.showInputDialog(parent, "Select what to add", "Add partition", JOptionPane.QUESTION_MESSAGE, null, providers.toArray(), providers.get(0));
        if (selectedProvider == null) {
            return null;
        }
    }
    List<BEASTInterface> beastObjects = selectedProvider.getAlignments(doc, fileArray);
    // create taxon sets, if any
    if (beastObjects != null) {
        for (BEASTInterface o : beastObjects) {
            if (o instanceof Alignment) {
                try {
                    BeautiDoc.createTaxonSet((Alignment) o, doc);
                } catch (Exception e) {
                    e.printStackTrace();
                }
            }
        }
    }
    doc.connectModel();
    if (beastObjects != null) {
        for (BEASTInterface o : beastObjects) {
            if (o instanceof MRCAPrior) {
                doc.addMRCAPrior((MRCAPrior) o);
            }
        }
    }
    return beastObjects;
}

Example 67 with BEASTInterface

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

the class BeautiPanel method updateList.

public void updateList() {
    if (listModel == null) {
        return;
    }
    listModel.clear();
    if (listModel.size() > 0) {
        // this is a weird bit of code, since listModel.clear should ensure that size()==0, but it doesn't
        return;
    }
    String type = config.hasPartitionsInput.get().toString();
    for (BEASTInterface partition : doc.getPartitions(type)) {
        if (type.equals("SiteModel")) {
            partition = (BEASTInterface) ((GenericTreeLikelihood) partition).siteModelInput.get();
        } else if (type.equals("ClockModel")) {
            partition = ((GenericTreeLikelihood) partition).branchRateModelInput.get();
        } else if (type.equals("Tree")) {
            partition = (BEASTInterface) ((GenericTreeLikelihood) partition).treeInput.get();
        }
        String partitionID = partition.getID();
        partitionID = partitionID.substring(partitionID.lastIndexOf('.') + 1);
        if (partitionID.length() > 1 && partitionID.charAt(1) == ':') {
            partitionID = partitionID.substring(2);
        }
        listModel.addElement(partitionID);
    }
    if (partitionIndex >= 0 && listModel.size() > 0)
        listOfPartitions.setSelectedIndex(partitionIndex);
}

Example 68 with BEASTInterface

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

the class BeautiPanel method cloneFrom.

/**
 * Clones partition identified by sourceID to targetID and type (Site/Clock/Tree model)
 * as stored in config.
 * @param sourceID
 * @param targetID
 */
public void cloneFrom(String sourceID, String targetID) {
    if (sourceID.equals(targetID)) {
        return;
    }
    String type = config.hasPartitionsInput.get().toString();
    java.util.List<BEASTInterface> list = doc.getPartitions(type);
    int source = -1, target = -1;
    for (int i = 0; i < list.size(); i++) {
        BEASTInterface partition = list.get(i);
        if (type.equals("SiteModel")) {
            partition = (BEASTInterface) ((GenericTreeLikelihood) partition).siteModelInput.get();
        } else if (type.equals("ClockModel")) {
            partition = ((GenericTreeLikelihood) partition).branchRateModelInput.get();
        } else if (type.equals("Tree")) {
            partition = (BEASTInterface) ((GenericTreeLikelihood) partition).treeInput.get();
        }
        String partitionID = partition.getID();
        partitionID = partitionID.substring(partitionID.lastIndexOf('.') + 1);
        if (partitionID.length() > 1 && partitionID.charAt(1) == ':') {
            partitionID = partitionID.substring(2);
        }
        if (partitionID.equals(sourceID)) {
            source = i;
        }
        if (partitionID.equals(targetID)) {
            target = i;
        }
    }
    if (target == -1) {
        throw new RuntimeException("Programmer error: sourceID and targetID should be in list");
    }
    CompoundDistribution likelihoods = (CompoundDistribution) doc.pluginmap.get("likelihood");
    GenericTreeLikelihood likelihoodSource = (GenericTreeLikelihood) likelihoods.pDistributions.get().get(source);
    GenericTreeLikelihood likelihood = (GenericTreeLikelihood) likelihoods.pDistributions.get().get(target);
    PartitionContext oldContext = doc.getContextFor(likelihoodSource);
    PartitionContext newContext = doc.getContextFor(likelihood);
    // this ensures the config.sync does not set any input value
    config._input.setValue(null, config);
    if (type.equals("SiteModel")) {
        SiteModelInterface siteModelSource = likelihoodSource.siteModelInput.get();
        SiteModelInterface siteModel = null;
        try {
            siteModel = (SiteModel.Base) BeautiDoc.deepCopyPlugin((BEASTInterface) siteModelSource, likelihood, (MCMC) doc.mcmc.get(), oldContext, newContext, doc, null);
        } catch (RuntimeException e) {
            JOptionPane.showMessageDialog(this, "Could not clone " + sourceID + " to " + targetID + " " + e.getMessage());
            return;
        }
        likelihood.siteModelInput.setValue(siteModel, likelihood);
        return;
    } else if (type.equals("ClockModel")) {
        BranchRateModel clockModelSource = likelihoodSource.branchRateModelInput.get();
        BranchRateModel clockModel = null;
        try {
            clockModel = (BranchRateModel) BeautiDoc.deepCopyPlugin((BEASTInterface) clockModelSource, likelihood, (MCMC) doc.mcmc.get(), oldContext, newContext, doc, null);
        } catch (Exception e) {
            JOptionPane.showMessageDialog(this, "Could not clone " + sourceID + " to " + targetID + " " + e.getMessage());
            return;
        }
        // make sure that *if* the clock model has a tree as input, it is
        // the same as for the likelihood
        TreeInterface tree = null;
        try {
            for (Input<?> input : ((BEASTInterface) clockModel).listInputs()) {
                if (input.getName().equals("tree")) {
                    tree = (TreeInterface) input.get();
                }
            }
        } catch (IllegalArgumentException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        if (tree != null && tree != likelihood.treeInput.get()) {
            // likelihood.treeInput.setValue(tree, likelihood);
            JOptionPane.showMessageDialog(null, "Cannot clone clock model with different trees");
            return;
        }
        likelihood.branchRateModelInput.setValue(clockModel, likelihood);
        return;
    } else if (type.equals("Tree")) {
        TreeInterface tree = null;
        TreeInterface treeSource = likelihoodSource.treeInput.get();
        try {
            tree = (TreeInterface) BeautiDoc.deepCopyPlugin((BEASTInterface) treeSource, likelihood, (MCMC) doc.mcmc.get(), oldContext, newContext, doc, null);
        } catch (Exception e) {
            JOptionPane.showMessageDialog(this, "Could not clone " + sourceID + " to " + targetID + " " + e.getMessage());
            return;
        }
        // sanity check: make sure taxon sets are compatible
        Taxon.assertSameTaxa(tree.getID(), tree.getTaxonset().getTaxaNames(), likelihood.dataInput.get().getID(), likelihood.dataInput.get().getTaxaNames());
        likelihood.treeInput.setValue(tree, likelihood);
        return;
    } else {
        throw new RuntimeException("Programmer error calling cloneFrom: Should only clone Site/Clock/Tree model");
    }
}

Example 69 with BEASTInterface

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

the class BeautiPanel method refreshInputPanel.

void refreshInputPanel() throws NoSuchMethodException, SecurityException, ClassNotFoundException, InstantiationException, IllegalAccessException, IllegalArgumentException, InvocationTargetException {
    doc.currentInputEditors.clear();
    InputEditor.Base.g_nLabelWidth = config.labelWidthInput.get();
    BEASTInterface beastObject = config;
    final Input<?> input = config.resolveInput(doc, partitionIndex);
    boolean addButtons = config.addButtons();
    ExpandOption forceExpansion = config.forceExpansion();
    refreshInputPanel(beastObject, input, addButtons, forceExpansion);
}

Example 70 with BEASTInterface

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

the class XMLParser method createBeastObject.

// createObject
/**
 * create BEASTInterface either using Inputs, or using annotated constructor *
 */
private BEASTInterface createBeastObject(Node node, String ID, String clazzName, List<NameValuePair> inputInfo) throws XMLParserException {
    BEASTInterface beastObject = useAnnotatedConstructor(node, ID, clazzName, inputInfo);
    if (beastObject != null) {
        return beastObject;
    }
    // create new instance using class name
    Object o = null;
    try {
        Class<?> c = Class.forName(clazzName);
        o = c.newInstance();
    } catch (InstantiationException e) {
        // created for instance because it is abstract
        throw new XMLParserException(node, "Cannot instantiate class. Please check the spec attribute.", 1006);
    } catch (ClassNotFoundException e) {
    // ignore -- class was found in beastObjectNames before
    } catch (IllegalAccessException e) {
        // T O D O Auto-generated catch block
        e.printStackTrace();
        throw new XMLParserException(node, "Cannot access class. Please check the spec attribute.", 1011);
    }
    // set id
    beastObject = (BEASTInterface) o;
    beastObject.setID(ID);
    // hack required to make log-parsing easier
    if (o instanceof State) {
        m_state = (State) o;
    }
    // process inputs for annotated constructors
    for (NameValuePair pair : inputInfo) {
        if (pair.value instanceof BEASTInterface) {
            setInput(node, beastObject, pair.name, (BEASTInterface) pair.value);
        } else if (pair.value instanceof String) {
            setInput(node, beastObject, pair.name, (String) pair.value);
        } else {
            throw new RuntimeException("Programmer error: value should be String or BEASTInterface");
        }
    }
    // fill in missing inputs, if an input provider is available
    try {
        if (requiredInputProvider != null) {
            for (Input<?> input : beastObject.listInputs()) {
                if (input.get() == null && input.getRule() == Validate.REQUIRED) {
                    Object o2 = requiredInputProvider.createInput(beastObject, input, partitionContext);
                    if (o2 != null) {
                        input.setValue(o2, beastObject);
                    }
                }
            }
        }
    } catch (Exception e) {
        throw new XMLParserException(node, e.getMessage(), 1008);
    }
    // sanity check: all attributes should be valid input names
    if (!(beastObject instanceof Map)) {
        for (NameValuePair pair : inputInfo) {
            String name = pair.name;
            if (!(name.equals("id") || name.equals("idref") || name.equals("spec") || name.equals("name"))) {
                try {
                    beastObject.getInput(name);
                } catch (Exception e) {
                    throw new XMLParserException(node, e.getMessage(), 1009);
                }
            }
        }
    }
    // make sure object o is in outputs of inputs
    for (NameValuePair pair : inputInfo) {
        if (pair.value instanceof BEASTInterface) {
            ((BEASTInterface) pair.value).getOutputs().add((BEASTInterface) o);
        }
    }
    register(node, beastObject);
    return beastObject;
}