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

Example 71 with Taxon

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

the class Partition method traverse.

// END: simulatePartition
private //
void traverse(//
NodeRef node, //
int[] parentSequence, //
int[] category) {
    if (DEBUG) {
        synchronized (this) {
            System.out.println();
            System.out.println("I'm at: " + node.toString());
            System.out.println();
        }
    }
    for (int iChild = 0; iChild < treeModel.getChildCount(node); iChild++) {
        NodeRef child = treeModel.getChild(node, iChild);
        int[] partitionSequence = new int[partitionSiteCount];
        double[] cProb = new double[stateCount];
        double[][] probabilities = getTransitionProbabilities(child);
        if (DEBUG) {
            synchronized (this) {
                System.out.println("Going to child " + iChild + ": " + child.toString());
                System.out.println("Child finite transition probs matrix:");
                Utils.print2DArray(probabilities, stateCount);
                System.out.println();
            }
        }
        for (int i = 0; i < partitionSiteCount; i++) {
            System.arraycopy(probabilities[category[i]], parentSequence[i] * stateCount, cProb, 0, stateCount);
            if (DEBUG) {
                synchronized (this) {
                    System.out.println("site:" + i);
                    System.out.println("site probs:");
                    Utils.printArray(cProb);
                }
            }
            // END: DEBUG
            partitionSequence[i] = randomChoicePDF(cProb, partitionNumber, "seq");
        }
        if (DEBUG) {
            synchronized (this) {
                //					partitionSequence = new int[]{1, 3, 2, 3, 0, 1, 0, 1, 0, 2, 2, 0, 1, 3, 3, 3, 0, 1, 2, 1, 3, 1, 1, 1, 1, 3, 0, 0, 3, 2, 3, 2, 3, 2, 1, 2, 1, 3, 2, 3, 3, 0, 2, 2, 3, 2, 3, 2, 3, 1, 2, 0, 2, 1, 3, 2, 3, 1, 1, 1, 1, 0, 2, 3, 1, 0, 2, 1, 2, 1, 3, 0, 0, 0, 0, 0, 2, 0, 2, 3, 1, 0, 1, 3, 0, 2, 1, 2, 1, 3, 0, 0, 3, 2, 2, 0, 1, 0, 0, 3  };
                System.out.println("Simulated sequence:");
                Utils.printArray(partitionSequence);
            }
        }
        if (treeModel.getChildCount(child) == 0) {
            Taxon taxon = treeModel.getNodeTaxon(child);
            alignmentMap.put(taxon, partitionSequence);
            if (DEBUG) {
                synchronized (this) {
                    System.out.println("Simulated sequence (translated):");
                    System.out.println(Utils.intArray2Sequence(taxon, partitionSequence, BeagleSequenceSimulator.gapFlag, dataType).getSequenceString());
                }
            }
        // END: DEBUG
        } else {
            if (outputAncestralSequences) {
                alignmentMap.put(new Taxon("internalNodeHeight" + treeModel.getNodeHeight(child)), partitionSequence);
            }
        }
        // END: tip node check
        traverse(treeModel.getChild(node, iChild), partitionSequence, category);
    }
// END: child nodes loop
}

Example 72 with Taxon

use of dr.evolution.util.Taxon 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);
    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(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 73 with Taxon

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

the class TreeUtils method setHeightsFromDates.

/**
     * Sets the tip heights from the tip dates
     */
public static void setHeightsFromDates(MutableTree tree) {
    dr.evolution.util.Date mostRecent = null;
    for (int i = 0; i < tree.getExternalNodeCount(); i++) {
        Taxon taxon = tree.getNodeTaxon(tree.getExternalNode(i));
        dr.evolution.util.Date date = (dr.evolution.util.Date) taxon.getAttribute("date");
        if (date != null) {
            if ((mostRecent == null) || date.after(mostRecent)) {
                mostRecent = date;
            }
        }
    }
    TimeScale timeScale = new TimeScale(mostRecent.getUnits(), true, mostRecent.getAbsoluteTimeValue());
    for (int i = 0; i < tree.getExternalNodeCount(); i++) {
        NodeRef node = tree.getExternalNode(i);
        Taxon taxon = tree.getNodeTaxon(node);
        dr.evolution.util.Date date = (dr.evolution.util.Date) taxon.getAttribute("date");
        if (date != null) {
            double height = timeScale.convertTime(date.getTimeValue(), date);
            tree.setNodeHeight(node, height);
        } else {
            tree.setNodeHeight(node, 0.0);
        }
    }
    adjustInternalHeights(tree, tree.getRoot());
    if (mostRecent != null) {
        tree.setUnits(mostRecent.getUnits());
    }
}

Example 74 with Taxon

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

the class TreeUtils method getTipDates.

/**
     * Gets the tip dates from a tree.
     */
public static void getTipDates(Tree tree, Variate dates) {
    for (int i = 0; i < tree.getExternalNodeCount(); i++) {
        Taxon taxon = tree.getNodeTaxon(tree.getExternalNode(i));
        Object date = taxon.getAttribute("date");
        if (date != null) {
            if (date instanceof Date) {
                dates.add(((Date) date).getTimeValue());
            } else {
                try {
                    dates.add(Double.parseDouble(date.toString()));
                } catch (NumberFormatException nfe) {
                    dates.add(0.0);
                }
            }
        } else {
            dates.add(0.0);
        }
    }
}

Example 75 with Taxon

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

the class TraitsPanel method guessTrait.

public void guessTrait() {
    if (options.taxonList == null) {
        // validation of check empty taxonList
        return;
    }
    if (currentTrait == null) {
        if (!addTrait()) {
            // if addTrait() cancel then false
            return;
        }
    }
    int result;
    do {
        TraitGuesser currentTraitGuesser = new TraitGuesser(currentTrait);
        if (guessTraitDialog == null) {
            guessTraitDialog = new GuessTraitDialog(frame);
        }
        guessTraitDialog.setDescription("Extract values for trait '" + currentTrait + "' from taxa labels");
        result = guessTraitDialog.showDialog();
        if (result == -1 || result == JOptionPane.CANCEL_OPTION) {
            return;
        }
        guessTraitDialog.setupGuesserFromDialog(currentTraitGuesser);
        try {
            int[] selRows = dataTable.getSelectedRows();
            if (selRows.length > 0) {
                Taxa selectedTaxa = new Taxa();
                for (int row : selRows) {
                    Taxon taxon = (Taxon) dataTable.getValueAt(row, 0);
                    selectedTaxa.addTaxon(taxon);
                }
                currentTraitGuesser.guessTrait(selectedTaxa);
            } else {
                currentTraitGuesser.guessTrait(options.taxonList);
            }
        } catch (IllegalArgumentException iae) {
            JOptionPane.showMessageDialog(this, iae.getMessage(), "Unable to guess trait value", JOptionPane.ERROR_MESSAGE);
            result = -1;
        }
        dataTableModel.fireTableDataChanged();
    } while (result < 0);
}