Examples with Taxa dr.evolution.util.Taxa used on opensource projects

Example 41 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class STARBEASTGenerator method writeSpeciesTreeLikelihood.

private void writeSpeciesTreeLikelihood(XMLWriter writer) {
    TreePriorType nodeHeightPrior = options.getPartitionTreePriors().get(0).getNodeHeightPrior();
    if (nodeHeightPrior == TreePriorType.SPECIES_BIRTH_DEATH) {
        writer.writeComment("Species Tree Likelihood: Birth Death Model");
        writer.writeOpenTag(SpeciationLikelihoodParser.SPECIATION_LIKELIHOOD, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, SPECIATION_LIKE) });
        writer.writeOpenTag(SpeciationLikelihoodParser.MODEL);
        writer.writeIDref(BirthDeathModelParser.BIRTH_DEATH_MODEL, BirthDeathModelParser.BIRTH_DEATH);
        writer.writeCloseTag(SpeciationLikelihoodParser.MODEL);
    } else if (nodeHeightPrior == TreePriorType.SPECIES_YULE || nodeHeightPrior == TreePriorType.SPECIES_YULE_CALIBRATION) {
        writer.writeComment("Species Tree Likelihood: Yule Model");
        writer.writeOpenTag(SpeciationLikelihoodParser.SPECIATION_LIKELIHOOD, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, SPECIATION_LIKE) });
        writer.writeOpenTag(SpeciationLikelihoodParser.MODEL);
        writer.writeIDref(YuleModelParser.YULE_MODEL, YuleModelParser.YULE);
        writer.writeCloseTag(SpeciationLikelihoodParser.MODEL);
        if (nodeHeightPrior == TreePriorType.SPECIES_YULE_CALIBRATION) {
            // should be only 1 calibrated node with monophyletic for species tree at moment
            if (options.speciesSets.size() == 1 && options.speciesSetsMono.size() == 1) {
                Taxa t = options.speciesSets.get(0);
                Parameter nodeCalib = options.getStatistic(t);
                writer.writeOpenTag(SpeciationLikelihoodParser.CALIBRATION, new Attribute[] { new Attribute.Default<String>(SpeciationLikelihoodParser.CORRECTION, CalibrationPoints.CorrectionType.EXACT.toString()) });
                writer.writeOpenTag(SpeciationLikelihoodParser.POINT);
                writer.writeIDref(TaxaParser.TAXA, t.getId());
                writeDistribution(nodeCalib, true, writer);
                writer.writeCloseTag(SpeciationLikelihoodParser.POINT);
                writer.writeCloseTag(SpeciationLikelihoodParser.CALIBRATION);
                if (!options.treeModelOptions.isNodeCalibrated(nodeCalib)) {
                }
            } else {
                throw new IllegalArgumentException("Calibrated Yule model is only applied to 1 calibrated node with monophyletic for species tree at moment !");
            }
        }
    } else {
        throw new IllegalArgumentException("Get wrong species tree prior using *BEAST : " + nodeHeightPrior.toString());
    }
    // <sp> tree
    writer.writeOpenTag(SpeciesTreeModelParser.SPECIES_TREE);
    writer.writeIDref(SpeciesTreeModelParser.SPECIES_TREE, SP_TREE);
    writer.writeCloseTag(SpeciesTreeModelParser.SPECIES_TREE);
    writer.writeCloseTag(SpeciationLikelihoodParser.SPECIATION_LIKELIHOOD);
}

Example 42 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class DataPanel method linkTrees.

public void linkTrees() {
    // keep previous PartitionTreePrior for reuse
    int[] selRows = dataTable.getSelectedRows();
    List<AbstractPartitionData> selectedPartitionData = new ArrayList<AbstractPartitionData>();
    for (int row : selRows) {
        AbstractPartitionData partition = options.dataPartitions.get(row);
        if (!selectedPartitionData.contains(partition))
            selectedPartitionData.add(partition);
    }
    if (selectedPartitionData.size() > 1) {
        if (!options.hasIdenticalTaxa(selectedPartitionData)) {
            String errMsg = "To share a tree, partitions need to have identical taxa.";
            if (selectedPartitionData.get(0).getDataType().getType() == DataType.MICRO_SAT)
                errMsg += "\nThe data must be all diploid or all haploid when you want to link the tree.";
            JOptionPane.showMessageDialog(this, errMsg, "Illegal Configuration", JOptionPane.ERROR_MESSAGE);
            return;
        }
    }
    Object[] treeArray = options.getPartitionTreeModels(selectedPartitionData).toArray();
    if (selectTreeDialog == null) {
        selectTreeDialog = new SelectTreeDialog(frame);
    }
    int result = selectTreeDialog.showDialog(treeArray);
    if (result != JOptionPane.CANCEL_OPTION) {
        PartitionTreeModel model = selectTreeDialog.getTree();
        if (selectTreeDialog.getMakeCopy()) {
            model.setName(selectTreeDialog.getName());
        }
        PartitionTreePrior prior = model.getPartitionTreePrior();
        options.linkTreePriors(prior);
        for (AbstractPartitionData partition : selectedPartitionData) {
            partition.setPartitionTreeModel(model);
        }
        for (Taxa taxa : options.taxonSets) {
            // Issue 454: all the taxon sets are deleted when link/unlink tree
            PartitionTreeModel prevModel = options.taxonSetsTreeModel.get(taxa);
            if (prevModel != model)
                options.taxonSetsTreeModel.put(taxa, model);
        }
    }
    modelsChanged();
    fireDataChanged();
    repaint();
}

Example 43 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class TaxaParser method parseXMLObject.

/** @return an instance of Node created from a DOM element */
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Taxa taxonList = new Taxa();
    for (int i = 0; i < xo.getChildCount(); i++) {
        Object child = xo.getChild(i);
        if (child instanceof Taxon) {
            Taxon taxon = (Taxon) child;
            taxonList.addTaxon(taxon);
        } else if (child instanceof TaxonList) {
            TaxonList taxonList1 = (TaxonList) child;
            for (int j = 0; j < taxonList1.getTaxonCount(); j++) {
                taxonList.addTaxon(taxonList1.getTaxon(j));
            }
        } else {
            throwUnrecognizedElement(xo);
        }
    }
    return taxonList;
}

Example 44 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class TaxonSetPanel method initPanel.

protected void initPanel(Action addTaxonSetAction, Action removeTaxonSetAction) {
    JScrollPane scrollPane1 = new JScrollPane(taxonSetsTable, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
    JToolBar toolBar1 = new JToolBar();
    toolBar1.setFloatable(false);
    toolBar1.setOpaque(false);
    toolBar1.setBorder(BorderFactory.createEmptyBorder());
    toolBar1.setLayout(new FlowLayout(java.awt.FlowLayout.LEFT, 0, 0));
    JButton button = new JButton(importTaxonSetsAction);
    PanelUtils.setupComponent(button);
    toolBar1.add(button);
    ActionPanel actionPanel1 = new ActionPanel(false);
    actionPanel1.setAddAction(addTaxonSetAction);
    actionPanel1.setRemoveAction(removeTaxonSetAction);
    addTaxonSetAction.setEnabled(false);
    removeTaxonSetAction.setEnabled(false);
    JPanel controlPanel1 = new JPanel(new FlowLayout(FlowLayout.LEFT));
    controlPanel1.add(actionPanel1);
    // Excluded Taxon List
    excludedTaxaTableModel = new TaxaTableModel(false);
    excludedTaxaTable = new JTable(excludedTaxaTableModel);
    excludedTaxaTable.getColumnModel().getColumn(0).setCellRenderer(new TableRenderer(SwingConstants.LEFT, new Insets(0, 4, 0, 4)));
    excludedTaxaTable.getColumnModel().getColumn(0).setMinWidth(20);
    excludedTaxaTable.getSelectionModel().addListSelectionListener(new ListSelectionListener() {

        public void valueChanged(ListSelectionEvent evt) {
            excludedTaxaTableSelectionChanged();
        }
    });
    JScrollPane scrollPane2 = new JScrollPane(excludedTaxaTable, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
    includedTaxonSetsComboBox = new JComboBox(new String[] { TAXON.toLowerCase() + "..." });
    excludedTaxonSetsComboBox = new JComboBox(new String[] { TAXON.toLowerCase() + "..." });
    includedTaxaLabel.setText("");
    excludedTaxaLabel.setText("");
    Box panel1 = new Box(BoxLayout.X_AXIS);
    panel1.add(new JLabel("Select: "));
    panel1.setOpaque(false);
    excludedTaxonSetsComboBox.setOpaque(false);
    panel1.add(excludedTaxonSetsComboBox);
    // Included Taxon List
    includedTaxaTableModel = new TaxaTableModel(true);
    includedTaxaTable = new JTable(includedTaxaTableModel);
    includedTaxaTable.getColumnModel().getColumn(0).setCellRenderer(new TableRenderer(SwingConstants.LEFT, new Insets(0, 4, 0, 4)));
    includedTaxaTable.getColumnModel().getColumn(0).setMinWidth(20);
    includedTaxaTable.getSelectionModel().addListSelectionListener(new ListSelectionListener() {

        public void valueChanged(ListSelectionEvent evt) {
            includedTaxaTableSelectionChanged();
        }
    });
    includedTaxaTable.doLayout();
    JScrollPane scrollPane3 = new JScrollPane(includedTaxaTable, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
    Box panel2 = new Box(BoxLayout.X_AXIS);
    panel2.add(new JLabel("Select: "));
    panel2.setOpaque(false);
    includedTaxonSetsComboBox.setOpaque(false);
    panel2.add(includedTaxonSetsComboBox);
    Icon includeIcon = null, excludeIcon = null;
    try {
        includeIcon = new ImageIcon(IconUtils.getImage(BeautiApp.class, "images/include.png"));
        excludeIcon = new ImageIcon(IconUtils.getImage(BeautiApp.class, "images/exclude.png"));
    } catch (Exception e) {
    // do nothing
    }
    JPanel buttonPanel = createAddRemoveButtonPanel(includeTaxonAction, includeIcon, "Include selected " + TAXA.toLowerCase() + " in the " + TAXON.toLowerCase(), excludeTaxonAction, excludeIcon, "Exclude selected " + TAXA.toLowerCase() + " from the " + TAXON.toLowerCase(), BoxLayout.Y_AXIS);
    taxonSetEditingPanel = new JPanel();
    taxonSetEditingPanel.setBorder(BorderFactory.createTitledBorder(""));
    taxonSetEditingPanel.setOpaque(false);
    taxonSetEditingPanel.setLayout(new GridBagLayout());
    excludedTaxaSearchField.setColumns(12);
    // excludedTaxaSearchField.putClientProperty("JTextField.variant", "search");
    excludedTaxaSearchField.putClientProperty("Quaqua.TextField.style", "search");
    excludedTaxaSearchField.putClientProperty("Quaqua.TextField.sizeVariant", "small");
    includedTaxaSearchField.setColumns(12);
    // includedTaxaSearchField.putClientProperty("JTextField.variant", "search");
    includedTaxaSearchField.putClientProperty("Quaqua.TextField.style", "search");
    includedTaxaSearchField.putClientProperty("Quaqua.TextField.sizeVariant", "small");
    GridBagConstraints c = new GridBagConstraints();
    c.gridx = 0;
    c.gridy = 0;
    c.weightx = 0.5;
    c.weighty = 0;
    c.fill = GridBagConstraints.HORIZONTAL;
    c.anchor = GridBagConstraints.CENTER;
    c.insets = new Insets(3, 6, 3, 0);
    taxonSetEditingPanel.add(excludedTaxaSearchField, c);
    c.gridx = 0;
    c.gridy = 1;
    c.weightx = 0.5;
    c.weighty = 1;
    c.fill = GridBagConstraints.BOTH;
    c.anchor = GridBagConstraints.CENTER;
    c.insets = new Insets(0, 6, 0, 0);
    taxonSetEditingPanel.add(scrollPane2, c);
    c.gridx = 0;
    c.gridy = 2;
    c.weightx = 0.5;
    c.weighty = 0;
    c.fill = GridBagConstraints.HORIZONTAL;
    c.anchor = GridBagConstraints.CENTER;
    c.insets = new Insets(0, 6, 3, 0);
    taxonSetEditingPanel.add(excludedTaxaLabel, c);
    c.gridx = 0;
    c.gridy = 3;
    c.weightx = 0.5;
    c.weighty = 0;
    c.fill = GridBagConstraints.HORIZONTAL;
    c.anchor = GridBagConstraints.CENTER;
    c.insets = new Insets(0, 6, 3, 0);
    taxonSetEditingPanel.add(panel1, c);
    c.gridx = 1;
    c.gridy = 0;
    c.weightx = 0;
    c.weighty = 1;
    c.gridheight = 4;
    c.fill = GridBagConstraints.NONE;
    c.anchor = GridBagConstraints.CENTER;
    c.insets = new Insets(12, 2, 12, 4);
    taxonSetEditingPanel.add(buttonPanel, c);
    c.gridx = 2;
    c.gridy = 0;
    c.weightx = 0.5;
    c.weighty = 0;
    c.gridheight = 1;
    c.fill = GridBagConstraints.HORIZONTAL;
    c.anchor = GridBagConstraints.CENTER;
    c.insets = new Insets(3, 0, 3, 6);
    taxonSetEditingPanel.add(includedTaxaSearchField, c);
    c.gridx = 2;
    c.gridy = 1;
    c.weightx = 0.5;
    c.weighty = 1;
    c.fill = GridBagConstraints.BOTH;
    c.anchor = GridBagConstraints.CENTER;
    c.insets = new Insets(0, 0, 0, 6);
    taxonSetEditingPanel.add(scrollPane3, c);
    c.gridx = 2;
    c.gridy = 2;
    c.weightx = 0.5;
    c.weighty = 0;
    c.fill = GridBagConstraints.HORIZONTAL;
    c.anchor = GridBagConstraints.CENTER;
    c.insets = new Insets(0, 0, 3, 6);
    taxonSetEditingPanel.add(includedTaxaLabel, c);
    c.gridx = 2;
    c.gridy = 3;
    c.weightx = 0.5;
    c.weighty = 0;
    c.fill = GridBagConstraints.HORIZONTAL;
    c.anchor = GridBagConstraints.CENTER;
    c.insets = new Insets(0, 0, 3, 6);
    taxonSetEditingPanel.add(panel2, c);
    JPanel panel3 = new JPanel();
    panel3.setOpaque(false);
    panel3.setLayout(new GridBagLayout());
    c = new GridBagConstraints();
    c.gridx = 0;
    c.gridy = 0;
    c.weightx = 0.5;
    c.weighty = 1;
    c.fill = GridBagConstraints.BOTH;
    c.anchor = GridBagConstraints.CENTER;
    c.insets = new Insets(0, 0, 2, 12);
    panel3.add(scrollPane1, c);
    c.gridx = 0;
    c.gridy = 1;
    c.weightx = 0;
    c.weighty = 0;
    c.fill = GridBagConstraints.NONE;
    c.anchor = GridBagConstraints.WEST;
    c.insets = new Insets(2, 0, 0, 12);
    panel3.add(actionPanel1, c);
    c.gridx = 1;
    c.gridy = 0;
    c.weightx = 0.5;
    c.weighty = 1;
    c.fill = GridBagConstraints.BOTH;
    c.anchor = GridBagConstraints.CENTER;
    c.insets = new Insets(0, 0, 0, 0);
    panel3.add(taxonSetEditingPanel, c);
    setOpaque(false);
    setBorder(new BorderUIResource.EmptyBorderUIResource(new Insets(12, 12, 12, 12)));
    setLayout(new BorderLayout(0, 0));
    add(toolBar1, BorderLayout.NORTH);
    add(panel3, BorderLayout.CENTER);
    // taxonSetsTable.addMouseListener(new MouseAdapter() {
    // public void mouseClicked(MouseEvent e) {
    // if (e.getClickCount() == 2) {
    // JTable target = (JTable)e.getSource();
    // int row = target.getSelectedRow();
    // taxonSetsTableDoubleClicked(row);
    // }
    // }
    // });
    includedTaxaSearchField.getDocument().addDocumentListener(new DocumentListener() {

        public void changedUpdate(DocumentEvent e) {
            selectIncludedTaxa(includedTaxaSearchField.getText());
        }

        public void removeUpdate(DocumentEvent e) {
            selectIncludedTaxa(includedTaxaSearchField.getText());
        }

        public void insertUpdate(DocumentEvent e) {
            selectIncludedTaxa(includedTaxaSearchField.getText());
        }
    });
    excludedTaxaSearchField.getDocument().addDocumentListener(new DocumentListener() {

        public void changedUpdate(DocumentEvent e) {
            selectExcludedTaxa(excludedTaxaSearchField.getText());
        }

        public void removeUpdate(DocumentEvent e) {
            selectExcludedTaxa(excludedTaxaSearchField.getText());
        }

        public void insertUpdate(DocumentEvent e) {
            selectExcludedTaxa(excludedTaxaSearchField.getText());
        }
    });
    includedTaxaTable.addMouseListener(new MouseAdapter() {

        public void mouseClicked(MouseEvent e) {
            if (e.getClickCount() == 2) {
                includeSelectedTaxa();
            }
        }
    });
    excludedTaxaTable.addMouseListener(new MouseAdapter() {

        public void mouseClicked(MouseEvent e) {
            if (e.getClickCount() == 2) {
                excludeSelectedTaxa();
            }
        }
    });
    includedTaxaTable.addFocusListener(new FocusAdapter() {

        public void focusGained(FocusEvent focusEvent) {
            excludedTaxaTable.clearSelection();
        }
    });
    excludedTaxaTable.addFocusListener(new FocusAdapter() {

        public void focusGained(FocusEvent focusEvent) {
            includedTaxaTable.clearSelection();
        }
    });
    includedTaxaTable.getSelectionModel().addListSelectionListener(new ListSelectionListener() {

        public void valueChanged(ListSelectionEvent e) {
            if (!includedSelectionChanging) {
                if (includedTaxonSetsComboBox.getSelectedIndex() != 0) {
                    includedTaxonSetsComboBox.setSelectedIndex(0);
                }
                includedTaxaSearchField.setText("");
            }
        }
    });
    includedTaxonSetsComboBox.addItemListener(new ItemListener() {

        public void itemStateChanged(ItemEvent e) {
            includedSelectionChanging = true;
            includedTaxaTable.clearSelection();
            if (includedTaxonSetsComboBox.getSelectedIndex() > 0) {
                String taxaName = includedTaxonSetsComboBox.getSelectedItem().toString();
                if (!taxaName.endsWith("...")) {
                    Taxa taxa = options.getTaxa(taxaName);
                    if (taxa != null) {
                        for (int i = 0; i < taxa.getTaxonCount(); i++) {
                            Taxon taxon = taxa.getTaxon(i);
                            int index = includedTaxa.indexOf(taxon);
                            includedTaxaTable.getSelectionModel().addSelectionInterval(index, index);
                        }
                    }
                }
            }
            includedSelectionChanging = false;
        }
    });
    excludedTaxaTable.getSelectionModel().addListSelectionListener(new ListSelectionListener() {

        public void valueChanged(ListSelectionEvent e) {
            if (!excludedSelectionChanging) {
                if (excludedTaxonSetsComboBox.getSelectedIndex() != 0) {
                    excludedTaxonSetsComboBox.setSelectedIndex(0);
                }
                excludedTaxaSearchField.setText("");
            }
        }
    });
    excludedTaxonSetsComboBox.addItemListener(new ItemListener() {

        public void itemStateChanged(ItemEvent e) {
            excludedSelectionChanging = true;
            excludedTaxaTable.clearSelection();
            if (excludedTaxonSetsComboBox.getSelectedIndex() > 0) {
                String taxaName = excludedTaxonSetsComboBox.getSelectedItem().toString();
                if (!taxaName.endsWith("...")) {
                    Taxa taxa = options.getTaxa(taxaName);
                    if (taxa != null) {
                        for (int i = 0; i < taxa.getTaxonCount(); i++) {
                            Taxon taxon = taxa.getTaxon(i);
                            int index = excludedTaxa.indexOf(taxon);
                            excludedTaxaTable.getSelectionModel().addSelectionInterval(index, index);
                        }
                    }
                }
            }
            excludedSelectionChanging = false;
        }
    });
    includedTaxaTable.doLayout();
    excludedTaxaTable.doLayout();
}

Example 45 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class BEAUTiImporter method importBEASTFile.

// xml
private void importBEASTFile(File file) throws IOException, ImportException, JDOMException {
    try {
        FileReader reader = new FileReader(file);
        BeastImporter importer = new BeastImporter(reader);
        List<TaxonList> taxonLists = new ArrayList<TaxonList>();
        List<Alignment> alignments = new ArrayList<Alignment>();
        importer.importBEAST(taxonLists, alignments);
        TaxonList taxa = taxonLists.get(0);
        int count = 1;
        for (Alignment alignment : alignments) {
            String name = file.getName();
            if (alignment.getId() != null && alignment.getId().length() > 0) {
                name = alignment.getId();
            } else {
                if (alignments.size() > 1) {
                    name += count;
                }
            }
            setData(name, taxa, alignment, null, null, null, null, null);
            count++;
        }
        // assume that any additional taxon lists are taxon sets...
        for (int i = 1; i < taxonLists.size(); i++) {
            Taxa taxonSet = (Taxa) taxonLists.get(i);
            options.taxonSets.add(taxonSet);
            options.taxonSetsMono.put(taxonSet, false);
            options.taxonSetsIncludeStem.put(taxonSet, false);
            options.taxonSetsTreeModel.put(taxonSet, options.getPartitionTreeModels().get(0));
            // force the creation of a tmrca statistic
            options.updateTMRCAStatistic(taxonSet);
        }
        Collections.sort(options.taxonSets);
        reader.close();
    } catch (JDOMException e) {
        throw new JDOMException(e.getMessage());
    } catch (ImportException e) {
        throw new ImportException(e.getMessage());
    } catch (IOException e) {
        throw new IOException(e.getMessage());
    }
}