import javax.swing.AbstractCellEditor;
import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.DefaultListCellRenderer;
import javax.swing.JButton;
import javax.swing.JPasswordField;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
+import javax.swing.JSlider;
import javax.swing.JSpinner;
import javax.swing.JTabbedPane;
import javax.swing.JTable;
import javax.swing.table.TableCellRenderer;
import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.bin.MemorySetting;
import jalview.fts.core.FTSDataColumnPreferences;
import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.io.IntKeyStringValueEntry;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.StringUtils;
/**
* Base class for the Preferences panel.
protected JCheckBox structFromPdb = new JCheckBox();
- protected JCheckBox useRnaView = new JCheckBox();
-
protected JCheckBox addSecondaryStructure = new JCheckBox();
protected JCheckBox addTempFactor = new JCheckBox();
private JLabel messageLabel = new JLabel("", JLabel.CENTER);
+ /*
+ * Startup tab components
+ */
+
+ protected JCheckBox customiseMemorySetting = new JCheckBox();
+
+ protected JLabel exampleMemoryLabel = new JLabel();
+
+ protected JTextArea exampleMemoryMessageTextArea = new JTextArea();
+
+ protected JLabel maxMemoryLabel = new JLabel();
+
+ protected JLabel jvmMemoryPercentLabel = new JLabel();
+
+ protected JSlider jvmMemoryPercentSlider = new JSlider();
+
+ protected JLabel jvmMemoryPercentDisplay = new JLabel();
+
+ protected JLabel jvmMemoryMaxLabel = new JLabel();
+
+ protected JTextField jvmMemoryMaxTextField = new JTextField(null, 8);
+
+ protected JComboBox<Object> lafCombo = new JComboBox<>();
+
/**
* Creates a new GPreferences object.
*/
tabbedPane.add(initEditingTab(),
MessageManager.getString("label.editing"));
+ tabbedPane.add(initStartupTab(),
+ MessageManager.getString("label.startup"));
+
/*
* See WsPreferences for the real work of configuring this tab.
*/
}
}
- public final static int CONNECTIONS_TAB = 5;
+ public static enum TabRef
+ {
+ CONNECTIONS_TAB, STRUCTURE_TAB
+ };
- public void selectTab(int selectTab)
+ public void selectTab(TabRef selectTab)
{
// select a given tab - currently only for Connections
switch (selectTab)
case CONNECTIONS_TAB:
tabbedPane.setSelectedComponent(connectTab);
break;
+ case STRUCTURE_TAB:
+ tabbedPane.setSelectedComponent(structureTab);
+ break;
default:
}
}
{
boolean selected = structFromPdb.isSelected();
// enable other options only when the first is checked
- useRnaView.setEnabled(selected);
addSecondaryStructure.setEnabled(selected);
addTempFactor.setEnabled(selected);
}
// indent checkboxes that are conditional on the first one
ypos += lineSpacing;
- useRnaView.setFont(LABEL_FONT);
- useRnaView.setText(MessageManager.getString("label.use_rnaview"));
- useRnaView.setBounds(new Rectangle(25, ypos, width, height));
- structureTab.add(useRnaView);
-
- ypos += lineSpacing;
addSecondaryStructure.setFont(LABEL_FONT);
addSecondaryStructure
.setText(MessageManager.getString("label.autoadd_secstr"));
}
/**
- * Show a dialog for the user to choose a file. Returns the chosen path, or
- * null on Cancel.
+ * Show a dialog for the user to choose a file. Returns the chosen path, or null
+ * on Cancel.
*
* @return
*/
String choice = null;
JFileChooser chooser = new JFileChooser();
+ // Enable appBundleIsTraversable in macOS FileChooser to allow selecting
+ // hidden executables within .app dirs
+ if (Platform.isMac())
+ {
+ chooser.putClientProperty("JFileChooser.appBundleIsTraversable",
+ true);
+ }
+
// chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.open_local_file"));
updateBackupFilesExampleLabel();
}
+ /*
+ * Load the saved Memory settings
+ */
+ protected void loadLastSavedMemorySettings()
+ {
+ customiseMemorySetting.setSelected(
+ Cache.getDefault(MemorySetting.CUSTOMISED_SETTINGS, false));
+ jvmMemoryPercentSlider
+ .setValue(Cache.getDefault(MemorySetting.MEMORY_JVMMEMPC, 90));
+ jvmMemoryMaxTextField.setText(
+ Cache.getDefault(MemorySetting.MEMORY_JVMMEMMAX, "32g"));
+ }
+
private boolean warnAboutSuffixReverseChange()
{
BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
&& nowSuffixTemplate.equals(savedSuffixTemplate);
}
+ /* Initialises the Startup tabbed panel.
+ *
+ * @return
+ * */
+
+ private JPanel initStartupTab()
+ {
+ JPanel startupTab = new JPanel();
+ startupTab.setBorder(
+ new TitledBorder(MessageManager.getString("label.memory")));
+ startupTab.setLayout(new GridBagLayout());
+
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.weightx = 0.0;
+ gbc.weighty = 0.0;
+ gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+ gbc.fill = GridBagConstraints.NONE;
+
+ initMemoryPanel();
+
+ gbc.gridheight = 1;
+ gbc.gridwidth = 3;
+
+ gbc.gridy = 0; // row 1
+ gbc.gridx = 0;
+ JLabel memoryText = new JLabel();
+ memoryText.setFont(LABEL_FONT_ITALIC);
+ memoryText
+ .setText(MessageManager.getString("label.memory_setting_text"));
+ startupTab.add(memoryText, gbc);
+
+ gbc.gridy++; // row 2
+ gbc.gridx = 0;
+ JPanel exampleMemoryPanel = new JPanel();
+ exampleMemoryPanel
+ .setLayout(new BoxLayout(exampleMemoryPanel, BoxLayout.Y_AXIS));
+ exampleMemoryPanel.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.memory_example_tooltip")));
+ JLabel exampleTextLabel = new JLabel();
+ exampleTextLabel
+ .setText(MessageManager.getString("label.memory_example_text"));
+ exampleTextLabel.setForeground(Color.GRAY);
+ exampleTextLabel.setFont(LABEL_FONT);
+ exampleMemoryPanel.add(exampleTextLabel);
+ exampleMemoryPanel.add(exampleMemoryLabel);
+ exampleMemoryPanel.setBackground(Color.WHITE);
+ exampleMemoryPanel.setBorder(BorderFactory.createEtchedBorder());
+ startupTab.add(exampleMemoryPanel, gbc);
+
+ gbc.gridy++; // row 3
+ gbc.gridx = 0;
+ startupTab.add(customiseMemorySetting, gbc);
+
+ gbc.gridy += 2; // row 4 with a gap
+ gbc.gridx = 0;
+ startupTab.add(maxMemoryLabel, gbc);
+
+ gbc.gridy += 2; // row 5
+ gbc.gridx = 0;
+ gbc.gridwidth = 1;
+ startupTab.add(jvmMemoryPercentLabel, gbc);
+ gbc.gridx++;
+ startupTab.add(jvmMemoryPercentSlider, gbc);
+ gbc.gridx++;
+ // gbc.weightx = 0.1;
+ startupTab.add(jvmMemoryPercentDisplay, gbc);
+ // gbc.weightx = 1.0;
+ gbc.gridwidth = 3;
+
+ gbc.gridy++; // row 6
+ gbc.gridx = 0;
+ startupTab.add(jvmMemoryMaxLabel, gbc);
+ gbc.gridx++;
+ startupTab.add(jvmMemoryMaxTextField, gbc);
+
+ gbc.gridy++; // row 7
+ gbc.gridx = 0;
+ gbc.gridwidth = 4;
+ exampleMemoryMessageTextArea.setBackground(startupTab.getBackground());
+ JScrollPane sp = new JScrollPane(exampleMemoryMessageTextArea);
+ sp.setBorder(BorderFactory.createEmptyBorder());
+ sp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+ sp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_NEVER);
+ startupTab.add(sp, gbc);
+
+ // fill empty space to push widget to top left
+ gbc.gridy++;
+ gbc.weighty = 1.0;
+ gbc.gridx = 100;
+ gbc.gridwidth = 1;
+ gbc.weightx = 1.0;
+ startupTab.add(new JPanel(), gbc);
+
+ setMemoryPercentDisplay();
+ memoryOptionsSetEnabled();
+ return startupTab;
+ }
+
+ private void initMemoryPanel()
+ {
+ // Enable memory settings checkbox
+ customiseMemorySetting.setFont(LABEL_FONT_BOLD);
+ customiseMemorySetting.setText(
+ MessageManager.getString("label.customise_memory_settings"));
+ customiseMemorySetting.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ memoryOptionsSetEnabled();
+ }
+ });
+
+ loadLastSavedMemorySettings();
+
+ exampleMemoryLabel.setFont(LABEL_FONT_BOLD);
+ exampleMemoryLabel.setBackground(Color.WHITE);
+
+ maxMemoryLabel = new JLabel(
+ MessageManager.getString("label.maximum_memory_used"));
+ maxMemoryLabel.setFont(LABEL_FONT_BOLD);
+
+ // Maximum memory percentage slider
+ jvmMemoryPercentLabel.setFont(LABEL_FONT);
+ jvmMemoryPercentLabel.setText(
+ MessageManager.getString("label.percent_of_physical_memory"));
+ jvmMemoryPercentSlider.setPaintLabels(true);
+ jvmMemoryPercentSlider.setPaintTicks(true);
+ jvmMemoryPercentSlider.setPaintTrack(true);
+ jvmMemoryPercentSlider.setMajorTickSpacing(50);
+ jvmMemoryPercentSlider.setMinorTickSpacing(10);
+ jvmMemoryPercentSlider.addChangeListener(new ChangeListener()
+ {
+ @Override
+ public void stateChanged(ChangeEvent e)
+ {
+ setMemoryPercentDisplay();
+ }
+ });
+ jvmMemoryPercentDisplay.setFont(LABEL_FONT);
+ setMemoryPercentDisplay();
+
+ // Maximum memory cap textbox
+ jvmMemoryMaxLabel.setFont(LABEL_FONT);
+ jvmMemoryMaxLabel
+ .setText(MessageManager.getString("label.maximum_memory"));
+ initMemoryMaxTextField();
+
+ exampleMemoryMessageTextArea.setFont(LABEL_FONT_ITALIC);
+ exampleMemoryMessageTextArea.setForeground(Color.GRAY);
+ exampleMemoryMessageTextArea.setEditable(false);
+ exampleMemoryMessageTextArea.setLineWrap(true);
+ exampleMemoryMessageTextArea.setWrapStyleWord(true);
+ exampleMemoryMessageTextArea.setText(" ");
+ exampleMemoryMessageTextArea.setRows(2);
+ exampleMemoryMessageTextArea.setColumns(40);
+
+ setExampleMemoryLabel();
+ }
+
+ private void initMemoryMaxTextField()
+ {
+ jvmMemoryMaxTextField.setToolTipText(
+ MessageManager.getString("label.maximum_memory_tooltip"));
+ jvmMemoryMaxTextField.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ validateMemoryMaxTextField();
+ setExampleMemoryLabel();
+ }
+ });
+
+ jvmMemoryMaxTextField.addKeyListener(new KeyListener()
+ {
+ @Override
+ public void keyReleased(KeyEvent e)
+ {
+ validateMemoryMaxTextField();
+ setExampleMemoryLabel();
+ }
+
+ @Override
+ public void keyPressed(KeyEvent e)
+ {
+ }
+
+ // try and stop invalid typing
+ @Override
+ public void keyTyped(KeyEvent e)
+ {
+ char c = Character.toLowerCase(e.getKeyChar());
+ String text = jvmMemoryMaxTextField.getText();
+ String suffixes = "tgmkb";
+ int pos = jvmMemoryMaxTextField.getCaretPosition();
+ int suffixPos = StringUtils.firstCharPosIgnoreCase(text, suffixes);
+ if (!((('0' <= c && c <= '9')
+ && (suffixPos == -1 || pos <= suffixPos)) // digits only allowed
+ // before suffix
+ || (suffixes.indexOf(Character.toLowerCase(c)) >= 0 // valid
+ // suffix
+ && pos == text.length() // at end of text and
+ && suffixPos == -1) // there isn't already one
+ ))
+ {
+ // don't process
+ e.consume();
+ }
+ }
+ });
+ }
+
+ private boolean isMemoryMaxTextFieldValid()
+ {
+ return MemorySetting
+ .isValidMemoryString(jvmMemoryMaxTextField.getText());
+ }
+
+ private void validateMemoryMaxTextField()
+ {
+ if (isMemoryMaxTextFieldValid())
+ {
+ jvmMemoryMaxTextField.setBackground(Color.WHITE);
+ }
+ else
+ {
+ jvmMemoryMaxTextField.setBackground(Color.PINK);
+ }
+ }
+
+ private void setMemoryPercentDisplay()
+ {
+ jvmMemoryPercentDisplay
+ .setText(jvmMemoryPercentSlider.getValue() + "%");
+ setExampleMemoryLabel();
+ }
+
+ private void setExampleMemoryLabel()
+ {
+ boolean selected = customiseMemorySetting.isSelected();
+ int jvmmempc = jvmMemoryPercentSlider.getValue();
+ String jvmmemmax = jvmMemoryMaxTextField.getText();
+
+ long mem;
+ if (selected && (0 <= jvmmempc && jvmmempc <= 100)
+ && MemorySetting.isValidMemoryString(jvmmemmax))
+ {
+ mem = MemorySetting.getMemorySetting(jvmmemmax,
+ String.valueOf(jvmmempc), false, true);
+ }
+ else
+ {
+ mem = MemorySetting.getMemorySetting(null, null, false, true);
+ }
+ exampleMemoryLabel.setText(MemorySetting.memoryLongToString(mem));
+ String message = MemorySetting.getAdjustmentMessage();
+ exampleMemoryMessageTextArea.setText(
+ MessageManager.getString("label.adjustments_for_this_computer")
+ + ": "
+ + (message == null
+ ? MessageManager.getString("label.none")
+ : message));
+ }
+
+ private void memoryOptionsSetEnabled()
+ {
+ boolean enabled = customiseMemorySetting.isSelected();
+ // leave exampleMemoryLabel enabled always
+ maxMemoryLabel.setEnabled(enabled);
+ jvmMemoryPercentLabel.setEnabled(enabled);
+ jvmMemoryPercentSlider.setEnabled(enabled);
+ jvmMemoryPercentDisplay.setEnabled(enabled);
+ jvmMemoryMaxLabel.setEnabled(enabled);
+ jvmMemoryMaxTextField.setEnabled(enabled);
+ exampleMemoryMessageTextArea.setEnabled(enabled);
+ setExampleMemoryLabel();
+ }
+
/**
* Initialises the Backups tabbed panel.
*
}
else
{
- Cache.log.error(
+ Console.error(
"Preset '" + value + "' [key:" + key + "] not implemented");
}
.getSelectedItem();
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Problem casting Combo entry to IntKeyStringValueEntry.");
e = null;
}
e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
continue;
}
i = ((Integer) s.getValue()).intValue();
} catch (Exception e)
{
- Cache.log.error(
+ Console.error(
"Exception casting the initial value of s.getValue()");
}
}
i = (Integer) s.getValue();
} catch (Exception e)
{
- Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
+ Console.error("Failed casting (Integer) JSpinner s.getValue()");
}
return i;
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void ok_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void cancel_actionPerformed(ActionEvent e)
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void annotations_actionPerformed(ActionEvent e)
{