*/
package jalview.jbgui;
+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.gui.Desktop;
+import jalview.gui.JalviewBooleanRadioButtons;
+import jalview.gui.JvOptionPane;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.BackupFilenameParts;
+import jalview.io.BackupFiles;
+import jalview.io.BackupFilesPresetEntry;
+import jalview.io.IntKeyStringValueEntry;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.StringUtils;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.util.Arrays;
import java.util.List;
+import javax.swing.AbstractButton;
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.JCheckBox;
import javax.swing.JComboBox;
+import javax.swing.JComponent;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
import javax.swing.JPanel;
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.TableCellEditor;
import javax.swing.table.TableCellRenderer;
-import jalview.bin.Cache;
-import jalview.fts.core.FTSDataColumnPreferences;
-import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
-import jalview.fts.service.pdb.PDBFTSRestClient;
-import jalview.gui.Desktop;
-import jalview.gui.JalviewBooleanRadioButtons;
-import jalview.gui.JvOptionPane;
-import jalview.gui.JvSwingUtils;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.BackupFilenameParts;
-import jalview.io.BackupFiles;
-import jalview.io.BackupFilesPresetEntry;
-import jalview.io.IntKeyStringValueEntry;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
+import net.miginfocom.swing.MigLayout;
/**
* Base class for the Preferences panel.
protected JCheckBox showConsensLogo = new JCheckBox();
+ protected JCheckBox showInformationHistogram = new JCheckBox();
+
+ protected JCheckBox showHMMLogo = new JCheckBox();
protected JCheckBox showDbRefTooltip = new JCheckBox();
protected JCheckBox showNpTooltip = new JCheckBox();
protected JCheckBox structFromPdb = new JCheckBox();
- protected JCheckBox useRnaView = new JCheckBox();
-
protected JCheckBox addSecondaryStructure = new JCheckBox();
protected JCheckBox addTempFactor = new JCheckBox();
protected JCheckBox sortByTree = new JCheckBox();
/*
+ * hmmer tab and components
+ */
+ protected JPanel hmmerTab;
+
+ protected JCheckBox hmmrTrimTermini;
+
+ protected AbstractButton hmmerBackgroundUniprot;
+
+ protected AbstractButton hmmerBackgroundAlignment;
+
+ protected JTextField hmmerSequenceCount;
+
+ protected JTextField hmmerPath;
+
+ protected JTextField cygwinPath;
+
+ /*
* Web Services tab
*/
protected JPanel wsTab = new JPanel();
+ protected JPanel slivkaTab = new JPanel();
/*
* Backups tab components
* a lot of these are member variables instead of local variables only so that they
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(initConnectionsTab(),
MessageManager.getString("label.connections"));
- if (!Platform.isJS())
- {
- tabbedPane.add(initBackupsTab(),
- MessageManager.getString("label.backups"));
- }
+ if (!Platform.isJS())
+ {
+ tabbedPane.add(initBackupsTab(),
+ MessageManager.getString("label.backups"));
+ }
tabbedPane.add(initLinksTab(),
MessageManager.getString("label.urllinks"));
*/
if (!Platform.isJS())
{
+ tabbedPane.add(initHMMERTab(), MessageManager.getString("label.hmmer"));
+ tabbedPane.add(initStartupTab(),
+ MessageManager.getString("label.startup"));
wsTab.setLayout(new BorderLayout());
tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
}
+
+ slivkaTab.setLayout(new BorderLayout());
+ tabbedPane.add(slivkaTab, "Slivka Services");
/*
* Handler to validate a tab before leaving it - currently only for
}
}
- 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:
}
}
}
/**
- * Initialises the Output tab
+ * Initialises the hmmer tabbed panel
+ *
+ * @return
+ */
+ private JPanel initHMMERTab()
+ {
+ hmmerTab = new JPanel();
+ hmmerTab.setLayout(new BoxLayout(hmmerTab, BoxLayout.Y_AXIS));
+ hmmerTab.setLayout(new MigLayout("flowy"));
+
+ /*
+ * path to hmmer binaries folder
+ */
+ JPanel installationPanel = new JPanel(new MigLayout("flowy"));
+ // new FlowLayout(FlowLayout.LEFT));
+ JvSwingUtils.createTitledBorder(installationPanel,
+ MessageManager.getString("label.installation"), true);
+ hmmerTab.add(installationPanel);
+ JLabel hmmerLocation = new JLabel(
+ MessageManager.getString("label.hmmer_location"));
+ hmmerLocation.setFont(LABEL_FONT);
+ final int pathFieldLength = 40;
+ hmmerPath = new JTextField(pathFieldLength);
+ hmmerPath.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser(true);
+ if (chosen != null)
+ {
+ hmmerPath.setText(chosen);
+ validateHmmerPath();
+ }
+ }
+ }
+ });
+ installationPanel.add(hmmerLocation);
+ installationPanel.add(hmmerPath);
+
+ /*
+ * path to Cygwin binaries folder (for Windows)
+ */
+ if (Platform.isWindowsAndNotJS())
+ {
+ JLabel cygwinLocation = new JLabel(
+ MessageManager.getString("label.cygwin_location"));
+ cygwinLocation.setFont(LABEL_FONT);
+ cygwinPath = new JTextField(pathFieldLength);
+ cygwinPath.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser(true);
+ if (chosen != null)
+ {
+ cygwinPath.setText(chosen);
+ validateCygwinPath();
+ }
+ }
+ }
+ });
+ installationPanel.add(cygwinLocation);
+ installationPanel.add(cygwinPath);
+ }
+
+ /*
+ * preferences for hmmalign
+ */
+ JPanel alignOptionsPanel = new JPanel(new MigLayout());
+ // new FlowLayout(FlowLayout.LEFT));
+ JvSwingUtils.createTitledBorder(alignOptionsPanel,
+ MessageManager.getString("label.hmmalign_options"), true);
+ hmmerTab.add(alignOptionsPanel);
+ hmmrTrimTermini = new JCheckBox();
+ hmmrTrimTermini.setFont(LABEL_FONT);
+ hmmrTrimTermini.setText(MessageManager.getString("label.trim_termini"));
+ alignOptionsPanel.add(hmmrTrimTermini);
+
+ /*
+ * preferences for hmmsearch
+ */
+ JPanel searchOptions = new JPanel(new MigLayout());
+ // FlowLayout(FlowLayout.LEFT));
+ JvSwingUtils.createTitledBorder(searchOptions,
+ MessageManager.getString("label.hmmsearch_options"), true);
+ hmmerTab.add(searchOptions);
+ JLabel sequencesToKeep = new JLabel(
+ MessageManager.getString("label.no_of_sequences"));
+ sequencesToKeep.setFont(LABEL_FONT);
+ searchOptions.add(sequencesToKeep);
+ hmmerSequenceCount = new JTextField(5);
+ searchOptions.add(hmmerSequenceCount);
+
+ /*
+ * preferences for Information Content annotation
+ */
+ // JPanel dummy = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ JPanel annotationOptions = new JPanel(new MigLayout("left"));
+ JvSwingUtils.createTitledBorder(annotationOptions,
+ MessageManager.getString("label.information_annotation"), true);
+ // dummy.add(annotationOptions);
+ hmmerTab.add(annotationOptions);
+ ButtonGroup backgroundOptions = new ButtonGroup();
+ hmmerBackgroundUniprot = new JRadioButton(
+ MessageManager.getString("label.freq_uniprot"));
+ hmmerBackgroundUniprot.setFont(LABEL_FONT);
+ hmmerBackgroundAlignment = new JRadioButton(
+ MessageManager.getString("label.freq_alignment"));
+ hmmerBackgroundAlignment.setFont(LABEL_FONT);
+ backgroundOptions.add(hmmerBackgroundUniprot);
+ backgroundOptions.add(hmmerBackgroundAlignment);
+ backgroundOptions.setSelected(hmmerBackgroundUniprot.getModel(), true);
+ // disable buttons for now as annotation only uses Uniprot background
+ hmmerBackgroundAlignment.setEnabled(false);
+ hmmerBackgroundUniprot.setEnabled(false);
+ annotationOptions.add(hmmerBackgroundUniprot, "wrap");
+ annotationOptions.add(hmmerBackgroundAlignment);
+
+ return hmmerTab;
+ }
+
+ /**
+ * Initialises the Output tabbed panel.
*
* @return
*/
connectTab = new JPanel();
connectTab.setLayout(new GridBagLayout());
- // Label for browser text box
- JLabel browserLabel = new JLabel();
- browserLabel.setFont(LABEL_FONT);
- browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
- browserLabel.setText(
- MessageManager.getString("label.default_browser_unix"));
- defaultBrowser.setFont(LABEL_FONT);
- defaultBrowser.setText("");
- final String tooltip = JvSwingUtils.wrapTooltip(true,
- MessageManager.getString("label.double_click_to_browse"));
- defaultBrowser.setToolTipText(tooltip);
- defaultBrowser.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mouseClicked(MouseEvent e)
- {
- if (e.getClickCount() > 1)
- {
- defaultBrowser_mouseClicked(e);
- }
- }
- });
JPanel proxyPanel = initConnTabProxyPanel();
initConnTabCheckboxes();
- // Add default Browser text box
- connectTab.add(browserLabel,
- new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE,
- new Insets(10, 0, 5, 5), 5, 1));
- defaultBrowser.setFont(LABEL_FONT);
- defaultBrowser.setText("");
-
- connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
- 0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
- new Insets(10, 0, 5, 10), 30, 1));
-
// Add proxy server panel
connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
proxyPortHttpsTB.setColumns(4);
proxyAuthUsernameTB.setFont(LABEL_FONT);
proxyAuthUsernameTB.setColumns(30);
+
+ // check for any change to enable applyProxyButton
+ DocumentListener d = new DocumentListener()
+ {
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ applyProxyButtonEnabled(true);
+ }
+
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ applyProxyButtonEnabled(true);
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ applyProxyButtonEnabled(true);
+ }
+ };
+ proxyServerHttpTB.getDocument().addDocumentListener(d);
+ proxyPortHttpTB.getDocument().addDocumentListener(d);
+ proxyServerHttpsTB.getDocument().addDocumentListener(d);
+ proxyPortHttpsTB.getDocument().addDocumentListener(d);
+ proxyAuthUsernameTB.getDocument().addDocumentListener(d);
proxyAuthPasswordPB.setFont(LABEL_FONT);
proxyAuthPasswordPB.setColumns(30);
proxyAuthPasswordPB.getDocument()
@Override
public void changedUpdate(DocumentEvent e)
{
- proxyAuthPasswordHighlight(true);
+ proxyAuthPasswordCheckHighlight(true);
+ applyProxyButtonEnabled(true);
}
@Override
public void insertUpdate(DocumentEvent e)
{
- proxyAuthPasswordHighlight(true);
+ proxyAuthPasswordCheckHighlight(true);
+ applyProxyButtonEnabled(true);
}
@Override
public void removeUpdate(DocumentEvent e)
{
- proxyAuthPasswordHighlight(true);
+ proxyAuthPasswordCheckHighlight(true);
+ applyProxyButtonEnabled(true);
}
});
gbc.gridy++;
proxyPanel.add(hpPanel, gbc);
- // Require authentication checkbox
- gbc.gridy++;
- proxyPanel.add(proxyAuth, gbc);
-
- // username and password
- JPanel upPanel = new JPanel();
- upPanel.setLayout(new GridBagLayout());
- // username row
- c.gridy = 0;
- c.gridx = 0;
- c.gridwidth = 1;
- c.weightx = 0.4;
- c.anchor = GridBagConstraints.LINE_END;
- upPanel.add(proxyAuthUsernameLabel, c);
-
- c.gridx++;
- c.weightx = 1.0;
- c.anchor = GridBagConstraints.LINE_START;
- upPanel.add(proxyAuthUsernameTB, c);
-
- // password row
- c.gridy++;
- c.gridx = 0;
- c.weightx = 0.4;
- c.anchor = GridBagConstraints.LINE_END;
- upPanel.add(proxyAuthPasswordLabel, c);
-
- c.gridx++;
- c.weightx = 1.0;
- c.anchor = GridBagConstraints.LINE_START;
- upPanel.add(proxyAuthPasswordPB, c);
-
- c.gridx++;
- c.weightx = 0.4;
- c.anchor = GridBagConstraints.LINE_START;
- upPanel.add(passwordNotStoredLabel, c);
-
- gbc.gridy++;
- proxyPanel.add(upPanel, gbc);
+ if (!Platform.isJS())
+ /**
+ * java.net.Authenticator is not implemented in SwingJS. Not displaying the
+ * Authentication options in Preferences.
+ *
+ * @j2sIgnore
+ *
+ */
+ {
+ // Require authentication checkbox
+ gbc.gridy++;
+ proxyPanel.add(proxyAuth, gbc);
+
+ // username and password
+ JPanel upPanel = new JPanel();
+ upPanel.setLayout(new GridBagLayout());
+ // username row
+ c.gridy = 0;
+ c.gridx = 0;
+ c.gridwidth = 1;
+ c.weightx = 0.4;
+ c.anchor = GridBagConstraints.LINE_END;
+ upPanel.add(proxyAuthUsernameLabel, c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ c.anchor = GridBagConstraints.LINE_START;
+ upPanel.add(proxyAuthUsernameTB, c);
+
+ // password row
+ c.gridy++;
+ c.gridx = 0;
+ c.weightx = 0.4;
+ c.anchor = GridBagConstraints.LINE_END;
+ upPanel.add(proxyAuthPasswordLabel, c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ c.anchor = GridBagConstraints.LINE_START;
+ upPanel.add(proxyAuthPasswordPB, c);
+
+ c.gridx++;
+ c.weightx = 0.4;
+ c.anchor = GridBagConstraints.LINE_START;
+ upPanel.add(passwordNotStoredLabel, c);
+
+ gbc.gridy++;
+ proxyPanel.add(upPanel, gbc);
+
+ } // end j2sIgnore
applyProxyButton.setText(MessageManager.getString("action.apply"));
applyProxyButton.addActionListener(new ActionListener()
public void actionPerformed(ActionEvent e)
{
saveProxySettings();
+ applyProxyButton.setEnabled(false);
}
});
gbc.gridy++;
return proxyPanel;
}
- public void proxyAuthPasswordHighlight(boolean enabled)
+ public void proxyAuthPasswordCheckHighlight(boolean enabled)
+ {
+ proxyAuthPasswordCheckHighlight(enabled, false);
+ }
+
+ public void proxyAuthPasswordCheckHighlight(boolean enabled,
+ boolean grabFocus)
{
if (enabled && proxyType.isSelected(customProxy.getModel())
&& proxyAuth.isSelected()
&& !proxyAuthUsernameTB.getText().isEmpty()
&& proxyAuthPasswordPB.getDocument().getLength() == 0)
{
-
- proxyAuthPasswordPB.grabFocus();
+ if (grabFocus)
+ proxyAuthPasswordPB.grabFocus();
proxyAuthPasswordPB.setBackground(Color.PINK);
}
else
}
}
+ public void applyProxyButtonEnabled(boolean enabled)
+ {
+ applyProxyButton.setEnabled(enabled);
+ }
+
public void saveProxySettings()
{
// overridden in Preferences
protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
protColourLabel.setText(
MessageManager.getString("label.prot_alignment_colour") + " ");
- JvSwingUtils.addtoLayout(coloursTab,
+ GPreferences.addtoLayout(coloursTab,
MessageManager
.getString("label.default_colour_scheme_for_alignment"),
protColourLabel, protColour);
nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
nucColourLabel.setText(
MessageManager.getString("label.nuc_alignment_colour") + " ");
- JvSwingUtils.addtoLayout(coloursTab,
+ GPreferences.addtoLayout(coloursTab,
MessageManager
.getString("label.default_colour_scheme_for_alignment"),
nucColourLabel, nucColour);
annotationShding.setBorder(new TitledBorder(
MessageManager.getString("label.annotation_shading_default")));
annotationShding.setLayout(new GridLayout(1, 2));
- JvSwingUtils.addtoLayout(annotationShding,
+ GPreferences.addtoLayout(annotationShding,
MessageManager.getString(
"label.default_minimum_colour_annotation_shading"),
mincolourLabel, minColour);
- JvSwingUtils.addtoLayout(annotationShding,
+ GPreferences.addtoLayout(annotationShding,
MessageManager.getString(
"label.default_maximum_colour_annotation_shading"),
maxcolourLabel, maxColour);
{
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"));
ypos += lineSpacing;
structureViewerPathLabel = new JLabel();
- structureViewerPathLabel.setFont(LABEL_FONT);// new Font("SansSerif", 0, 11));
+ structureViewerPathLabel.setFont(LABEL_FONT);// new Font("SansSerif", 0,
+ // 11));
structureViewerPathLabel.setHorizontalAlignment(SwingConstants.LEFT);
structureViewerPathLabel.setText(MessageManager
.formatMessage("label.viewer_path", "Chimera(X)"));
- structureViewerPathLabel.setBounds(new Rectangle(10, ypos, 170, height));
+ structureViewerPathLabel
+ .setBounds(new Rectangle(10, ypos, 170, height));
structureViewerPathLabel.setEnabled(false);
structureTab.add(structureViewerPathLabel);
{
if (structureViewerPath.isEnabled() && e.getClickCount() == 2)
{
- String chosen = openFileChooser();
+ String chosen = openFileChooser(false);
if (chosen != null)
{
structureViewerPath.setText(chosen);
/*
* hide Chimera options in JalviewJS
*/
- if (Platform.isJS())
+ if (Platform.isJS())
{
structureViewerPathLabel.setVisible(false);
structureViewerPath.setVisible(false);
viewerLabel.setVisible(false);
structViewer.setVisible(false);
}
-
+
return structureTab;
}
}
/**
- * 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
*/
- protected String openFileChooser()
+ protected String openFileChooser(boolean forFolder)
{
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);
+ }
+
+ if (forFolder)
+ {
+ chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ }
// chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.open_local_file"));
visualTab.add(fontNameCB);
visualTab.add(fontSizeCB);
visualTab.add(fontStyleCB);
+
if (Platform.isJS())
{
startupCheckbox.setVisible(false);
startupFileTextfield.setVisible(false);
}
+
return visualTab;
}
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.
*
}
});
-
// enable checkbox 1 col
gbc.gridwidth = 1;
gbc.gridheight = 1;
exampleFilesPanel.setBorder(tb);
exampleFilesPanel.setLayout(new GridBagLayout());
-
backupfilesExampleLabel.setEditable(false);
backupfilesExampleLabel
.setBackground(exampleFilesPanel.getBackground());
}
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;
}
boolean ret = false;
String warningMessage = MessageManager
.getString("label.warning_confirm_change_reverse");
- int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
+ int confirm = JvOptionPane.showConfirmDialog(Desktop.getDesktopPane(),
warningMessage,
MessageManager.getString("label.change_increment_decrement"),
JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
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;
}
public void proxyType_actionPerformed()
{
setCustomProxyEnabled();
- proxyAuthPasswordHighlight(true);
+ proxyAuthPasswordCheckHighlight(true);
+ applyProxyButtonEnabled(true);
}
public void proxyAuth_actionPerformed()
{
setProxyAuthEnabled();
- proxyAuthPasswordHighlight(true);
+ proxyAuthPasswordCheckHighlight(true);
+ applyProxyButtonEnabled(true);
}
/**
}
}
-}
+ protected void validateHmmerPath()
+ {
+ }
+
+ protected void validateCygwinPath()
+ {
+ }
+
+ /**
+ * A helper method to add a panel containing a label and a component to a
+ * panel
+ *
+ * @param panel
+ * @param tooltip
+ * @param label
+ * @param valBox
+ */
+ protected static void addtoLayout(JPanel panel, String tooltip,
+ JComponent label, JComponent valBox)
+ {
+ JPanel laypanel = new JPanel(new GridLayout(1, 2));
+ JPanel labPanel = new JPanel(new BorderLayout());
+ JPanel valPanel = new JPanel();
+ labPanel.setBounds(new Rectangle(7, 7, 158, 23));
+ valPanel.setBounds(new Rectangle(172, 7, 270, 23));
+ labPanel.add(label, BorderLayout.WEST);
+ valPanel.add(valBox);
+ laypanel.add(labPanel);
+ laypanel.add(valPanel);
+ valPanel.setToolTipText(tooltip);
+ labPanel.setToolTipText(tooltip);
+ valBox.setToolTipText(tooltip);
+ panel.add(laypanel);
+ panel.validate();
+ }
+}
git://source.jalview.org / jalview.git / blobdiff