예제 #1
0
  public PartitionModelPanel(final PartitionSubstitutionModel partitionModel) {

    super(12, (OSType.isMac() ? 6 : 24));

    this.model = partitionModel;

    initCodonPartitionComponents();

    PanelUtils.setupComponent(nucSubstCombo);
    nucSubstCombo.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {
            model.setNucSubstitutionModel((NucModelType) nucSubstCombo.getSelectedItem());
          }
        });
    nucSubstCombo.setToolTipText("<html>Select the type of nucleotide substitution model.</html>");

    PanelUtils.setupComponent(aaSubstCombo);
    aaSubstCombo.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {
            AminoAcidModelType type = (AminoAcidModelType) aaSubstCombo.getSelectedItem();
            model.setAaSubstitutionModel(type);
            citationText.setText(type.getCitation().toString());
          }
        });
    aaSubstCombo.setToolTipText("<html>Select the type of amino acid substitution model.</html>");

    PanelUtils.setupComponent(binarySubstCombo);
    binarySubstCombo.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {
            model.setBinarySubstitutionModel((BinaryModelType) binarySubstCombo.getSelectedItem());
            useAmbiguitiesTreeLikelihoodCheck.setSelected(
                binarySubstCombo.getSelectedItem() == BinaryModelType.BIN_COVARION);
            useAmbiguitiesTreeLikelihoodCheck.setEnabled(
                binarySubstCombo.getSelectedItem() != BinaryModelType.BIN_COVARION);
          }
        });
    binarySubstCombo.setToolTipText("<html>Select the type of binary substitution model.</html>");

    PanelUtils.setupComponent(useAmbiguitiesTreeLikelihoodCheck);
    useAmbiguitiesTreeLikelihoodCheck.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {
            model.setUseAmbiguitiesTreeLikelihood(useAmbiguitiesTreeLikelihoodCheck.isSelected());
          }
        });
    useAmbiguitiesTreeLikelihoodCheck.setToolTipText(
        "<html>Detemine useAmbiguities in &lt treeLikelihood &gt .</html>");

    PanelUtils.setupComponent(frequencyCombo);
    frequencyCombo.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {
            model.setFrequencyPolicy((FrequencyPolicyType) frequencyCombo.getSelectedItem());
          }
        });
    frequencyCombo.setToolTipText(
        "<html>Select the policy for determining the base frequencies.</html>");

    PanelUtils.setupComponent(heteroCombo);
    heteroCombo.setToolTipText(
        "<html>Select the type of site-specific rate<br>heterogeneity model.</html>");
    heteroCombo.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {

            boolean gammaHetero =
                heteroCombo.getSelectedIndex() == 1 || heteroCombo.getSelectedIndex() == 3;

            model.setGammaHetero(gammaHetero);
            model.setInvarHetero(
                heteroCombo.getSelectedIndex() == 2 || heteroCombo.getSelectedIndex() == 3);

            if (gammaHetero) {
              gammaCatLabel.setEnabled(true);
              gammaCatCombo.setEnabled(true);
            } else {
              gammaCatLabel.setEnabled(false);
              gammaCatCombo.setEnabled(false);
            }

            if (codingCombo.getSelectedIndex() != 0) {
              heteroUnlinkCheck.setEnabled(heteroCombo.getSelectedIndex() != 0);
              heteroUnlinkCheck.setSelected(heteroCombo.getSelectedIndex() != 0);
            }
          }
        });

    PanelUtils.setupComponent(gammaCatCombo);
    gammaCatCombo.setToolTipText(
        "<html>Select the number of categories to use for<br>the discrete gamma rate heterogeneity model.</html>");
    gammaCatCombo.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {

            model.setGammaCategories(gammaCatCombo.getSelectedIndex() + 4);
          }
        });

    setYang96Button = new JButton("Use Yang96 model");
    setYang96Button.addActionListener(
        new ActionListener() {
          public void actionPerformed(ActionEvent ev) {
            setYang96Model();
          }
        });
    PanelUtils.setupComponent(setYang96Button);
    setYang96Button.setToolTipText(
        "<html>Sets a 3 codon-position model with independent GTR and Gamma as described in<br>"
            + "Yang (1996) <i>J Mol Evol</i> <b>42</b>: 587–596. This model is named 3' in this paper.</html>");

    setSRD06Button = new JButton("Use SRD06 model");
    setSRD06Button.addActionListener(
        new ActionListener() {
          public void actionPerformed(ActionEvent ev) {
            setSRD06Model();
          }
        });
    PanelUtils.setupComponent(setSRD06Button);
    setSRD06Button.setToolTipText(
        "<html>Sets the SRD06 model as described in<br>"
            + "Shapiro, Rambaut & Drummond (2006) <i>MBE</i> <b>23</b>: 7-9.</html>");

    citationText = new JTextArea(1, 40);
    citationText.setLineWrap(true);
    citationText.setWrapStyleWord(true);
    citationText.setEditable(false);
    citationText.setFont(this.getFont());
    citationText.setOpaque(false);
    AminoAcidModelType type = (AminoAcidModelType) aaSubstCombo.getSelectedItem();
    citationText.setText(type.getCitation().toString());

    dolloCheck.addActionListener(
        new ActionListener() {
          public void actionPerformed(ActionEvent actionEvent) {
            if (dolloCheck.isSelected()) {
              binarySubstCombo.setSelectedIndex(0);
              binarySubstCombo.setEnabled(false);
              useAmbiguitiesTreeLikelihoodCheck.setSelected(true);
              useAmbiguitiesTreeLikelihoodCheck.setEnabled(false);
              frequencyCombo.setEnabled(false);
              frequencyCombo.setSelectedItem(FrequencyPolicyType.EMPIRICAL);
              heteroCombo.setSelectedIndex(0);
              heteroCombo.setEnabled(false);
              model.setBinarySubstitutionModel(BinaryModelType.BIN_DOLLO);
              model.setDolloModel(true);
              DolloComponentOptions comp =
                  (DolloComponentOptions)
                      model.getOptions().getComponentOptions(DolloComponentOptions.class);
              comp.createParameters(model.getOptions());
              comp.setActive(true);

            } else {
              binarySubstCombo.setEnabled(true);
              useAmbiguitiesTreeLikelihoodCheck.setEnabled(true);
              frequencyCombo.setEnabled(true);
              heteroCombo.setEnabled(true);
              model.setBinarySubstitutionModel(
                  (BinaryModelType) binarySubstCombo.getSelectedItem());
              model.setDolloModel(false);
            }
          }
        });

    PanelUtils.setupComponent(dolloCheck);
    //        dolloCheck.addChangeListener(new ChangeListener() {
    //            public void stateChanged(ChangeEvent e) {
    //                model.setDolloModel(true);
    //            }
    //        });
    dolloCheck.setEnabled(true);
    dolloCheck.setToolTipText(
        "<html>Activates a Stochastic Dollo model as described in<br>"
            + "Alekseyenko, Lee & Suchard (2008) <i>Syst Biol</i> <b>57</b>: 772-784.</html>");

    PanelUtils.setupComponent(discreteTraitSiteModelCombo);
    discreteTraitSiteModelCombo.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {
            model.setDiscreteSubstType(
                (DiscreteSubstModelType) discreteTraitSiteModelCombo.getSelectedItem());
          }
        });

    PanelUtils.setupComponent(continuousTraitSiteModelCombo);
    continuousTraitSiteModelCombo.setToolTipText(
        "<html>Select the model of continuous random walk, either homogenous<br>"
            + "or relaxed random walk (RRW) with a choice of distributions.</html>");
    continuousTraitSiteModelCombo.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {
            model.setContinuousSubstModelType(
                (ContinuousSubstModelType) continuousTraitSiteModelCombo.getSelectedItem());
          }
        });

    PanelUtils.setupComponent(latLongCheck);
    latLongCheck.setToolTipText(
        "<html>Specify whether this is a geographical trait representing <br>"
            + "latitude and longitude. Provides appropriate statistics to log file.</html>");

    latLongCheck.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {
            model.setIsLatitudeLongitude(latLongCheck.isSelected());
          }
        });
    latLongCheck.setEnabled(false);

    PanelUtils.setupComponent(useLambdaCheck);
    useLambdaCheck.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {
            ContinuousComponentOptions component =
                (ContinuousComponentOptions)
                    model.getOptions().getComponentOptions(ContinuousComponentOptions.class);
            component.setUseLambda(model, useLambdaCheck.isSelected());
          }
        });
    useLambdaCheck.setToolTipText(
        "<html>Estimate degree of phylogenetic correlation in continuous traits using <br>"
            + "a tree transform. Inspired by Pagel (1999), described in Lemey et al (2013) <i>in prep</i></html>");

    PanelUtils.setupComponent(activateBSSVS);
    activateBSSVS.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {
            model.setActivateBSSVS(activateBSSVS.isSelected());
          }
        });
    activateBSSVS.setToolTipText(
        "<html>Activates Bayesian stochastic search variable selection on the rates as described in<br>"
            + "Lemey, Rambaut, Drummond & Suchard (2009) <i>PLoS Computational Biology</i> <b>5</b>: e1000520</html>");

    // ============ micro-sat ================
    microsatName.setColumns(30);
    microsatName.addKeyListener(
        new java.awt.event.KeyListener() {
          public void keyTyped(KeyEvent e) {}

          public void keyPressed(KeyEvent e) {}

          public void keyReleased(KeyEvent e) {
            model.getMicrosatellite().setName(microsatName.getText());
          }
        });
    microsatMax.setColumns(10);
    microsatMax.addKeyListener(
        new java.awt.event.KeyListener() {
          public void keyTyped(KeyEvent e) {}

          public void keyPressed(KeyEvent e) {}

          public void keyReleased(KeyEvent e) {
            model.getMicrosatellite().setMax(Integer.parseInt(microsatMax.getText()));
          }
        });
    microsatMin.setColumns(10);
    microsatMin.addKeyListener(
        new java.awt.event.KeyListener() {
          public void keyTyped(KeyEvent e) {}

          public void keyPressed(KeyEvent e) {}

          public void keyReleased(KeyEvent e) {
            model.getMicrosatellite().setMin(Integer.parseInt(microsatMin.getText()));
          }
        });

    PanelUtils.setupComponent(shareMicroSatCheck);
    shareMicroSatCheck.addActionListener(
        new ActionListener() {
          public void actionPerformed(ActionEvent e) {
            model.getOptions().shareMicroSat = shareMicroSatCheck.isSelected();
            if (shareMicroSatCheck.isSelected()) {
              model.getOptions().shareMicroSat();
            } else {
              model.getOptions().unshareMicroSat();
            }
            setOptions();
          }
        });

    PanelUtils.setupComponent(rateProportionCombo);
    rateProportionCombo.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {
            model.setRatePorportion(
                (MicroSatModelType.RateProportionality) rateProportionCombo.getSelectedItem());
          }
        });
    // rateProportionCombo.setToolTipText("<html>Select the type of microsatellite substitution
    // model.</html>");
    PanelUtils.setupComponent(mutationBiasCombo);
    mutationBiasCombo.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {
            model.setMutationBias(
                (MicroSatModelType.MutationalBias) mutationBiasCombo.getSelectedItem());
          }
        });
    PanelUtils.setupComponent(phaseCombo);
    phaseCombo.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {
            model.setPhase((MicroSatModelType.Phase) phaseCombo.getSelectedItem());
          }
        });

    setupPanel();
    setOpaque(false);
  }
예제 #2
0
  /** Initializes and binds the components related to modeling codon positions. */
  private void initCodonPartitionComponents() {

    PanelUtils.setupComponent(substUnlinkCheck);

    substUnlinkCheck.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {
            model.setUnlinkedSubstitutionModel(substUnlinkCheck.isSelected());
          }
        });
    substUnlinkCheck.setEnabled(false);
    substUnlinkCheck.setToolTipText(
        ""
            + "<html>Gives each codon position partition different<br>"
            + "substitution model parameters.</html>");

    PanelUtils.setupComponent(heteroUnlinkCheck);
    heteroUnlinkCheck.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {
            model.setUnlinkedHeterogeneityModel(heteroUnlinkCheck.isSelected());
          }
        });
    heteroUnlinkCheck.setEnabled(heteroCombo.getSelectedIndex() != 0);
    heteroUnlinkCheck.setToolTipText(
        "<html>Gives each codon position partition different<br>rate heterogeneity model parameters.</html>");

    PanelUtils.setupComponent(freqsUnlinkCheck);
    freqsUnlinkCheck.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {
            model.setUnlinkedFrequencyModel(freqsUnlinkCheck.isSelected());
          }
        });
    freqsUnlinkCheck.setEnabled(false);
    freqsUnlinkCheck.setToolTipText(
        "<html>Gives each codon position partition different<br>nucleotide frequency parameters.</html>");

    PanelUtils.setupComponent(codingCombo);
    codingCombo.setToolTipText("<html>Select how to partition the codon positions.</html>");
    codingCombo.addItemListener(
        new ItemListener() {
          public void itemStateChanged(ItemEvent ev) {

            switch (codingCombo.getSelectedIndex()) {
              case 0:
                model.setCodonHeteroPattern(null);
                break;
              case 1:
                model.setCodonHeteroPattern("112");
                break;
              default:
                model.setCodonHeteroPattern("123");
                break;
            }

            if (codingCombo.getSelectedIndex() != 0) {
              // codon position partitioning
              substUnlinkCheck.setEnabled(true);
              heteroUnlinkCheck.setEnabled(heteroCombo.getSelectedIndex() != 3);
              freqsUnlinkCheck.setEnabled(true);
              substUnlinkCheck.setSelected(true);
              heteroUnlinkCheck.setSelected(heteroCombo.getSelectedIndex() != 0);
              freqsUnlinkCheck.setSelected(true);

            } else {
              substUnlinkCheck.setEnabled(false);
              substUnlinkCheck.setSelected(false);
              heteroUnlinkCheck.setEnabled(false);
              heteroUnlinkCheck.setSelected(false);
              freqsUnlinkCheck.setEnabled(false);
              freqsUnlinkCheck.setSelected(false);
            }
          }
        });
  }
예제 #3
0
  public DataPanel(
      BeautiFrame parent,
      Action importDataAction,
      Action removeDataAction /*, Action importTraitsAction*/) {

    this.frame = parent;

    dataTableModel = new DataTableModel();
    dataTable = new JTable(dataTableModel);

    dataTable.getTableHeader().setReorderingAllowed(false);
    dataTable
        .getTableHeader()
        .setDefaultRenderer(new HeaderRenderer(SwingConstants.LEFT, new Insets(0, 4, 0, 4)));

    TableColumn col = dataTable.getColumnModel().getColumn(5);
    ComboBoxRenderer comboBoxRenderer = new ComboBoxRenderer();
    comboBoxRenderer.putClientProperty("JComboBox.isTableCellEditor", Boolean.TRUE);
    col.setCellRenderer(comboBoxRenderer);

    //        col = dataTable.getColumnModel().getColumn(5);
    //        comboBoxRenderer = new ComboBoxRenderer();
    //        comboBoxRenderer.putClientProperty("JComboBox.isTableCellEditor", Boolean.TRUE);
    //        col.setCellRenderer(comboBoxRenderer);

    col = dataTable.getColumnModel().getColumn(6);
    comboBoxRenderer = new ComboBoxRenderer();
    comboBoxRenderer.putClientProperty("JComboBox.isTableCellEditor", Boolean.TRUE);
    col.setCellRenderer(comboBoxRenderer);

    col = dataTable.getColumnModel().getColumn(7);
    comboBoxRenderer = new ComboBoxRenderer();
    comboBoxRenderer.putClientProperty("JComboBox.isTableCellEditor", Boolean.TRUE);
    col.setCellRenderer(comboBoxRenderer);

    TableEditorStopper.ensureEditingStopWhenTableLosesFocus(dataTable);

    dataTable
        .getSelectionModel()
        .addListSelectionListener(
            new ListSelectionListener() {
              public void valueChanged(ListSelectionEvent evt) {
                selectionChanged();
              }
            });

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

    scrollPane =
        new JScrollPane(
            dataTable,
            JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,
            JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
    scrollPane.setOpaque(false);

    JToolBar toolBar1 = new JToolBar();
    toolBar1.setFloatable(false);
    toolBar1.setOpaque(false);
    toolBar1.setLayout(new BoxLayout(toolBar1, BoxLayout.X_AXIS));

    JButton button = new JButton(unlinkModelsAction);
    unlinkModelsAction.setEnabled(false);
    PanelUtils.setupComponent(button);
    toolBar1.add(button);

    button = new JButton(linkModelsAction);
    linkModelsAction.setEnabled(false);
    PanelUtils.setupComponent(button);
    toolBar1.add(button);

    toolBar1.addSeparator();

    button = new JButton(unlinkClocksAction);
    unlinkClocksAction.setEnabled(false);
    PanelUtils.setupComponent(button);
    toolBar1.add(button);

    button = new JButton(linkClocksAction);
    linkClocksAction.setEnabled(false);
    PanelUtils.setupComponent(button);
    toolBar1.add(button);

    toolBar1.addSeparator();

    button = new JButton(unlinkTreesAction);
    unlinkTreesAction.setEnabled(false);
    PanelUtils.setupComponent(button);
    toolBar1.add(button);

    button = new JButton(linkTreesAction);
    linkTreesAction.setEnabled(false);
    PanelUtils.setupComponent(button);
    toolBar1.add(button);

    // too crowded on the toolbar  - just double click to show
    //            button = new JButton(showAction);
    //            showAction.setEnabled(false);
    //            PanelUtils.setupComponent(button);
    //            toolBar1.add(button);

    ActionPanel actionPanel1 = new ActionPanel(false);
    actionPanel1.setAddAction(importDataAction);
    actionPanel1.setRemoveAction(removeDataAction);
    removeDataAction.setEnabled(false);

    JPanel controlPanel1 = new JPanel(new FlowLayout(FlowLayout.LEFT));
    controlPanel1.setOpaque(false);
    controlPanel1.add(actionPanel1);

    controlPanel1.add(new JLabel("   "));
    PanelUtils.setupComponent(createImportTraitButton);
    controlPanel1.add(createImportTraitButton);

    //        controlPanel1.add(new JLabel(" or "));
    //
    //        button = new JButton(importTraitsAction);
    //        PanelUtils.setupComponent(button);
    //        controlPanel1.add(button);

    JPanel panel1 = new JPanel(new BorderLayout());
    panel1.setOpaque(false);
    panel1.add(useStarBEASTCheck, BorderLayout.NORTH);
    panel1.add(toolBar1, BorderLayout.SOUTH);

    setOpaque(false);
    setBorder(new BorderUIResource.EmptyBorderUIResource(new Insets(12, 12, 12, 12)));
    setLayout(new BorderLayout(0, 0));
    add(panel1, BorderLayout.NORTH);
    add(scrollPane, BorderLayout.CENTER);
    add(controlPanel1, BorderLayout.SOUTH);

    useStarBEASTCheck.setEnabled(false);
    useStarBEASTCheck.setToolTipText(STARBEASTOptions.CITATION);
    useStarBEASTCheck.addActionListener(
        new java.awt.event.ActionListener() {
          public void actionPerformed(
              ActionEvent e) { // wrong listener Issue 397: *BEAST in BEAUti is broken
            frame.setupStarBEAST(useStarBEASTCheck.isSelected());
            dataTableModel.fireTableDataChanged();
          }
        });
  }