public void setOptions(BeautiOptions options) { this.options = options; chainLengthField.setValue(options.chainLength); echoEveryField.setValue(options.echoEvery); logEveryField.setValue(options.logEvery); if (options.fileNameStem != null) { fileNameStemField.setText(options.fileNameStem); } else { fileNameStemField.setText(DEFAULT_FILE_NAME_STEM); fileNameStemField.setEnabled(false); } operatorAnalaysisCheck.setSelected(options.operatorAnalysis); updateOtherFileNames(options); if (options.contains(Microsatellite.INSTANCE)) { samplePriorCheckBox.setSelected(false); samplePriorCheckBox.setVisible(false); } else { samplePriorCheckBox.setVisible(true); samplePriorCheckBox.setSelected(options.samplePriorOnly); } optionsPanel.validate(); optionsPanel.repaint(); }
@SuppressWarnings({"unchecked"}) public SimulationPanel(final MainFrame frame, final PartitionDataList dataList) { this.frame = frame; this.dataList = dataList; optionPanel = new OptionsPanel(12, 12, SwingConstants.CENTER); simulationsNumberField = new WholeNumberField(1, Integer.MAX_VALUE); simulationsNumberField.setColumns(10); simulationsNumberField.setValue(dataList.simulationsCount); optionPanel.addComponentWithLabel("Number of simulations:", simulationsNumberField); setSeed = new JCheckBox(); setSeed.addItemListener(new SetSeedCheckBoxListener()); setSeed.setSelected(dataList.setSeed); optionPanel.addComponentWithLabel("Set seed:", setSeed); startingSeedNumberField = new WholeNumberField(1, Long.MAX_VALUE); startingSeedNumberField.setColumns(10); startingSeedNumberField.setValue(dataList.startingSeed); startingSeedNumberField.setEnabled(dataList.setSeed); optionPanel.addComponentWithLabel("Starting seed:", startingSeedNumberField); outputFormat = new JComboBox(); optionPanel.addComponentWithLabel("Output format:", outputFormat); outputFormatModel = new DefaultComboBoxModel(SimpleAlignment.OutputType.values()); outputFormat.setModel(outputFormatModel); outputAncestralSequences = new JCheckBox(); outputAncestralSequences.addItemListener(new outputAncestralSequencesCheckBoxListener()); outputAncestralSequences.setSelected(dataList.useParallel); optionPanel.addComponentWithLabel("Output ancestral sequences:", outputAncestralSequences); useParallel = new JCheckBox(); useParallel.addItemListener(new UseParallelCheckBoxListener()); useParallel.setSelected(dataList.useParallel); optionPanel.addComponentWithLabel("Use parallel implementation:", useParallel); // Buttons holder JPanel buttonsHolder = new JPanel(); buttonsHolder.setOpaque(false); // simulate button simulate = new JButton("Simulate", Utils.createImageIcon(Utils.BIOHAZARD_ICON)); simulate.addActionListener(new ListenSimulate()); buttonsHolder.add(simulate); generateXML = new JButton("Generate XML", Utils.createImageIcon(Utils.HAMMER_ICON)); generateXML.addActionListener(new ListenGenerateXML()); buttonsHolder.add(generateXML); setOpaque(false); setLayout(new BorderLayout()); add(optionPanel, BorderLayout.NORTH); add(buttonsHolder, BorderLayout.SOUTH); } // END: SimulationPanel
public MCMCPanel(BeautiFrame parent) { setLayout(new BorderLayout()); // Mac OS X components have more spacing round them already optionsPanel = new OptionsPanel(12, (OSType.isMac() ? 6 : 24)); this.frame = parent; setOpaque(false); optionsPanel.setOpaque(false); chainLengthField.setValue(100000); chainLengthField.setColumns(10); optionsPanel.addComponentWithLabel("Length of chain:", chainLengthField); chainLengthField.addKeyListener( new java.awt.event.KeyListener() { public void keyTyped(KeyEvent e) {} public void keyPressed(KeyEvent e) {} public void keyReleased(KeyEvent e) { options.chainLength = chainLengthField.getValue(); frame.setDirty(); } }); optionsPanel.addSeparator(); echoEveryField.setValue(1000); echoEveryField.setColumns(10); optionsPanel.addComponentWithLabel("Echo state to screen every:", echoEveryField); echoEveryField.addKeyListener( new java.awt.event.KeyListener() { public void keyTyped(KeyEvent e) {} public void keyPressed(KeyEvent e) {} public void keyReleased(KeyEvent e) { options.echoEvery = echoEveryField.getValue(); frame.setDirty(); } }); logEveryField.setValue(100); logEveryField.setColumns(10); optionsPanel.addComponentWithLabel("Log parameters every:", logEveryField); logEveryField.addKeyListener( new java.awt.event.KeyListener() { public void keyTyped(KeyEvent e) {} public void keyPressed(KeyEvent e) {} public void keyReleased(KeyEvent e) { options.logEvery = logEveryField.getValue(); frame.setDirty(); } }); optionsPanel.addSeparator(); fileNameStemField.setColumns(32); optionsPanel.addComponentWithLabel("File name stem:", fileNameStemField); fileNameStemField.setEditable(true); fileNameStemField.addKeyListener( new java.awt.event.KeyListener() { public void keyTyped(KeyEvent e) {} public void keyPressed(KeyEvent e) {} public void keyReleased(KeyEvent e) { options.fileNameStem = fileNameStemField.getText(); updateOtherFileNames(options); frame.setDirty(); } }); optionsPanel.addComponent(addTxt); if (OSType.isWindows()) { addTxt.setSelected(true); } else { addTxt.setSelected(false); } addTxt.addChangeListener( new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { setOptions(options); frame.setDirty(); } }); optionsPanel.addSeparator(); logFileNameField.setColumns(32); optionsPanel.addComponentWithLabel("Log file name:", logFileNameField); logFileNameField.setEditable(false); // optionsPanel.addComponent(allowOverwriteLogCheck); // allowOverwriteLogCheck.setSelected(false); // allowOverwriteLogCheck.addChangeListener(new ChangeListener() { // public void stateChanged(ChangeEvent changeEvent) { // options.allowOverwriteLog = allowOverwriteLogCheck.isSelected(); // } // }); treeFileNameField.setColumns(32); optionsPanel.addComponentWithLabel("Trees file name:", treeFileNameField); treeFileNameField.setEditable(false); // addComponent(mapTreeLogCheck); // mapTreeLogCheck.setOpaque(false); // mapTreeLogCheck.addActionListener(new java.awt.event.ActionListener() { // public void actionPerformed(ActionEvent e) { // mapTreeFileNameField.setEnabled(mapTreeLogCheck.isSelected()); // } // }); // // mapTreeFileNameField.setColumns(32); // addComponentWithLabel("MAP tree file name:", mapTreeFileNameField); optionsPanel.addComponent(substTreeLogCheck); substTreeLogCheck.setOpaque(false); substTreeLogCheck.addActionListener( new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { options.substTreeLog = substTreeLogCheck.isSelected(); updateTreeFileNameList(); substTreeFileNameField.setEnabled(substTreeLogCheck.isSelected()); if (substTreeLogCheck.isSelected()) { substTreeFileNameField.setText(displayTreeList(options.substTreeFileName)); } else { substTreeFileNameField.setText(""); } frame.setDirty(); } }); substTreeFileNameField.setColumns(32); substTreeFileNameField.setEditable(false); substTreeFileNameField.setEnabled(false); optionsPanel.addComponentWithLabel("Substitutions trees file name:", substTreeFileNameField); optionsPanel.addComponent(operatorAnalaysisCheck); operatorAnalaysisCheck.addActionListener( new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { options.operatorAnalysis = operatorAnalaysisCheck.isSelected(); updateOtherFileNames(options); frame.setDirty(); } }); operatorAnalaysisFileNameField.setColumns(32); operatorAnalaysisFileNameField.setEditable(false); operatorAnalaysisFileNameField.setEnabled(false); optionsPanel.addComponentWithLabel( "Operator analysis file name:", operatorAnalaysisFileNameField); optionsPanel.addSeparator(); optionsPanel.addComponent(samplePriorCheckBox); samplePriorCheckBox.setOpaque(false); samplePriorCheckBox.addChangeListener( new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { frame.setDirty(); } }); // logFileNameField.addKeyListener(listener); // treeFileNameField.addKeyListener(listener); // mapTreeFileNameField.addKeyListener(listener); // substTreeFileNameField.addKeyListener(listener); // optionsPanel.setPreferredSize(new java.awt.Dimension(500, 600)); JPanel panel = new JPanel(new FlowLayout(FlowLayout.CENTER)); panel.add(optionsPanel, BorderLayout.CENTER); panel.setOpaque(false); JScrollPane scrollPane = new JScrollPane( panel, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); scrollPane.setOpaque(false); scrollPane.setBorder(null); scrollPane.getViewport().setOpaque(false); add(scrollPane, BorderLayout.CENTER); }
public void setSeed(long seed) { seedText.setValue(seed); }