/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
-import jalview.gui.JvSwingUtils;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-import javax.swing.border.*;
-import javax.swing.event.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.GridLayout;
+import java.awt.Insets;
import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Arrays;
+import java.util.List;
+
+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.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.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.ListSelectionModel;
+import javax.swing.SpinnerModel;
+import javax.swing.SpinnerNumberModel;
+import javax.swing.SwingConstants;
+import javax.swing.border.Border;
+import javax.swing.border.EmptyBorder;
+import javax.swing.border.EtchedBorder;
+import javax.swing.border.TitledBorder;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
+import javax.swing.table.TableCellEditor;
+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.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;
/**
- * DOCUMENT ME!
+ * Base class for the Preferences panel.
*
* @author $author$
* @version $Revision$
*/
public class GPreferences extends JPanel
{
- JTabbedPane tabbedPane = new JTabbedPane();
+ private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
+
+ private static final Font LABEL_FONT_ITALIC = JvSwingUtils
+ .getLabelFont(false, true);
+
+ private static final Font LABEL_FONT_BOLD = JvSwingUtils
+ .getLabelFont(true, false);
+
+ /*
+ * Visual tab components
+ */
+ protected JCheckBox fullScreen = new JCheckBox();
+
+ protected JCheckBox openoverv = new JCheckBox();
- JButton ok = new JButton();
+ protected JCheckBox seqLimit = new JCheckBox();
- JButton cancel = new JButton();
+ protected JCheckBox rightAlign = new JCheckBox();
- JPanel okCancelPanel = new JPanel();
+ protected JComboBox<String> fontSizeCB = new JComboBox<>();
- BorderLayout borderLayout1 = new BorderLayout();
+ protected JComboBox<String> fontStyleCB = new JComboBox<>();
- protected JCheckBox quality = new JCheckBox();
+ protected JComboBox<String> fontNameCB = new JComboBox<>();
- JPanel visualTab = new JPanel();
- JPanel visual2Tab = new JPanel();
+ protected JCheckBox showOccupancy = new JCheckBox();
- protected JCheckBox fullScreen = new JCheckBox();
+ protected JCheckBox showUnconserved = new JCheckBox();
+
+ protected JCheckBox idItalics = new JCheckBox();
+
+ protected JCheckBox smoothFont = new JCheckBox();
+
+ protected JCheckBox scaleProteinToCdna = new JCheckBox();
+
+ protected JComboBox<String> gapSymbolCB = new JComboBox<>();
+
+ protected JCheckBox wrap = new JCheckBox();
+
+ protected JComboBox<String> sortby = new JComboBox<>();
+
+ protected JComboBox<String> sortAnnBy = new JComboBox<>();
+
+ protected JComboBox<String> sortAutocalc = new JComboBox<>();
+
+ protected JCheckBox startupCheckbox = new JCheckBox();
+
+ protected JTextField startupFileTextfield = new JTextField();
+
+ // below are in the 'second column'
+ protected JCheckBox annotations = new JCheckBox();
+
+ protected JCheckBox quality = new JCheckBox();
protected JCheckBox conservation = new JCheckBox();
protected JCheckBox identity = new JCheckBox();
- protected JCheckBox annotations = new JCheckBox();
+ protected JCheckBox showGroupConsensus = new JCheckBox();
- protected JPanel minColour = new JPanel();
- JLabel mincolourLabel = new JLabel();
+ protected JCheckBox showGroupConservation = new JCheckBox();
- protected JPanel maxColour = new JPanel();
- JLabel maxcolourLabel = new JLabel();
+ protected JCheckBox showConsensHistogram = new JCheckBox();
- JLabel gapLabel = new JLabel();
+ protected JCheckBox showConsensLogo = new JCheckBox();
- protected JComboBox colour = new JComboBox();
+ protected JCheckBox showDbRefTooltip = new JCheckBox();
- JLabel colourLabel = new JLabel();
+ protected JCheckBox showNpTooltip = new JCheckBox();
- JLabel fontLabel = new JLabel();
+ /*
+ * Structure tab and components
+ */
+ protected JPanel structureTab;
- protected JComboBox fontSizeCB = new JComboBox();
+ protected JCheckBox structFromPdb = new JCheckBox();
- protected JComboBox fontStyleCB = new JComboBox();
+ protected JCheckBox addSecondaryStructure = new JCheckBox();
- protected JComboBox fontNameCB = new JComboBox();
+ protected JCheckBox addTempFactor = new JCheckBox();
- protected JComboBox gapSymbolCB = new JComboBox();
+ protected JComboBox<String> structViewer = new JComboBox<>();
- protected JCheckBox startupCheckbox = new JCheckBox();
+ protected JLabel structureViewerPathLabel;
- protected JTextField startupFileTextfield = new JTextField();
+ protected JTextField structureViewerPath = new JTextField();
- JPanel connectTab = new JPanel();
+ protected ButtonGroup mappingMethod = new ButtonGroup();
- JLabel serverLabel = new JLabel();
+ protected JRadioButton siftsMapping = new JRadioButton();
- protected JList linkURLList = new JList();
+ protected JRadioButton nwMapping = new JRadioButton();
- protected JTextField proxyServerTB = new JTextField();
+ /*
+ * Colours tab components
+ */
+ protected JPanel minColour = new JPanel();
+
+ protected JPanel maxColour = new JPanel();
+
+ protected JComboBox<String> protColour = new JComboBox<>();
+
+ protected JComboBox<String> nucColour = new JComboBox<>();
+
+ /*
+ * Overview tab components
+ */
+ protected JPanel gapColour = new JPanel();
- protected JTextField proxyPortTB = new JTextField();
+ protected JPanel hiddenColour = new JPanel();
- JLabel portLabel = new JLabel();
+ protected JCheckBox useLegacyGap;
- JLabel browserLabel = new JLabel();
+ protected JCheckBox showHiddenAtStart;
- protected JTextField defaultBrowser = new JTextField();
+ protected JLabel gapLabel;
- JButton newLink = new JButton();
+ /*
+ * Connections tab components
+ */
+ protected JPanel connectTab;
+
+ protected JTable linkUrlTable = new JTable();
+
+ protected JButton editLink = new JButton();
+
+ protected JButton deleteLink = new JButton();
- JButton editLink = new JButton();
+ protected JTextField filterTB = new JTextField();
- JButton deleteLink = new JButton();
+ protected JButton doReset = new JButton();
- JScrollPane linkScrollPane = new JScrollPane();
+ protected JButton userOnly = new JButton();
- JPanel linkPanel = new JPanel();
+ protected JLabel httpLabel = new JLabel();
- BorderLayout borderLayout2 = new BorderLayout();
+ protected JLabel httpsLabel = new JLabel();
- JPanel editLinkButtons = new JPanel();
+ protected JLabel portLabel = new JLabel();
- GridLayout gridLayout1 = new GridLayout();
+ protected JLabel serverLabel = new JLabel();
- protected JList linkNameList = new JList();
+ protected JLabel portLabel2 = new JLabel();
- JPanel linkPanel2 = new JPanel();
+ protected JLabel serverLabel2 = new JLabel();
- BorderLayout borderLayout3 = new BorderLayout();
+ protected JLabel proxyAuthUsernameLabel = new JLabel();
- protected JCheckBox useProxy = new JCheckBox();
+ protected JLabel proxyAuthPasswordLabel = new JLabel();
- JPanel jPanel1 = new JPanel();
+ protected JLabel passwordNotStoredLabel = new JLabel();
- TitledBorder titledBorder1 = new TitledBorder("Proxy Server");
+ protected JTextField proxyServerHttpTB = new JTextField();
- TitledBorder titledBorder2 = new TitledBorder("File Output");
+ protected JTextField proxyPortHttpTB = new JTextField();
- GridBagLayout gridBagLayout2 = new GridBagLayout();
+ protected JTextField proxyServerHttpsTB = new JTextField();
- GridBagLayout gridBagLayout1 = new GridBagLayout();
+ protected JTextField proxyPortHttpsTB = new JTextField();
- GridBagLayout gridBagLayout3 = new GridBagLayout();
+ protected JCheckBox proxyAuth = new JCheckBox();
- protected JComboBox sortby = new JComboBox();
+ protected JTextField proxyAuthUsernameTB = new JTextField();
- JLabel sortLabel = new JLabel();
+ protected JPasswordField proxyAuthPasswordPB = new JPasswordField();
- JPanel jPanel2 = new JPanel();
- JPanel visual2panel = new JPanel();
+ protected ButtonGroup proxyType = new ButtonGroup();
- GridLayout gridLayout2 = new GridLayout();
+ protected JRadioButton noProxy = new JRadioButton();
- GridLayout gridLayout4 = new GridLayout();
+ protected JRadioButton systemProxy = new JRadioButton();
- JPanel annsettingsPanel = new JPanel();
+ protected JRadioButton customProxy = new JRadioButton();
- JPanel autoAnnotSettings1 = new JPanel();
+ protected JButton applyProxyButton = new JButton();
+
+ protected JCheckBox usagestats = new JCheckBox();
+
+ protected JCheckBox questionnaire = new JCheckBox();
- JPanel autoAnnotSettings2 = new JPanel();
+ protected JCheckBox versioncheck = new JCheckBox();
- JPanel autoAnnotSettings3 = new JPanel();
+ /*
+ * Output tab components
+ */
+ protected JComboBox<Object> epsRendering = new JComboBox<>();
- JPanel exportTab = new JPanel();
+ protected JComboBox<Object> htmlRendering = new JComboBox<>();
- JLabel epsLabel = new JLabel();
+ protected JComboBox<Object> svgRendering = new JComboBox<>();
- protected JComboBox epsRendering = new JComboBox();
-
protected JLabel userIdWidthlabel = new JLabel();
- protected JCheckBox autoIdWidth = new JCheckBox();
- protected JTextField userIdWidth = new JTextField();
+ protected JCheckBox autoIdWidth = new JCheckBox();
- JLabel jLabel1 = new JLabel();
+ protected JTextField userIdWidth = new JTextField();
protected JCheckBox blcjv = new JCheckBox();
protected JCheckBox pfamjv = new JCheckBox();
- FlowLayout flowLayout1 = new FlowLayout();
-
protected JCheckBox pirjv = new JCheckBox();
- JPanel jPanel11 = new JPanel();
+ protected JCheckBox modellerOutput = new JCheckBox();
- Font verdana11 = JvSwingUtils.getLabelFont();
+ protected JCheckBox embbedBioJSON = new JCheckBox();
- protected JCheckBox seqLimit = new JCheckBox();
+ /*
+ * Editing tab components
+ */
+ protected JCheckBox autoCalculateConsCheck = new JCheckBox();
- GridLayout gridLayout3 = new GridLayout();
+ protected JCheckBox padGaps = new JCheckBox();
- protected JCheckBox smoothFont = new JCheckBox();
+ protected JCheckBox sortByTree = new JCheckBox();
- JPanel calcTab = new JPanel();
+ /*
+ * Web Services tab
+ */
+ protected JPanel wsTab = new JPanel();
- protected JCheckBox autoCalculateConsCheck = new JCheckBox();
+ /*
+ * Backups tab components
+ * a lot of these are member variables instead of local variables only so that they
+ * can be enabled/disabled easily in one go
+ */
- protected JCheckBox padGaps = new JCheckBox();
+ protected JCheckBox enableBackupFiles = new JCheckBox();
- protected JCheckBox modellerOutput = new JCheckBox();
+ protected JPanel presetsPanel = new JPanel();
- protected JPanel dasPanel = new JPanel();
+ protected JLabel presetsComboLabel = new JLabel();
- BorderLayout borderLayout4 = new BorderLayout();
+ protected JCheckBox customiseCheckbox = new JCheckBox();
- protected JPanel wsPanel = new JPanel();
+ protected JButton revertButton = new JButton();
- BorderLayout borderLayout5 = new BorderLayout();
+ protected JComboBox<Object> backupfilesPresetsCombo = new JComboBox<>();
- protected JCheckBox wrap = new JCheckBox();
+ private int backupfilesPresetsComboLastSelected = 0;
- protected JCheckBox rightAlign = new JCheckBox();
+ protected JPanel suffixPanel = new JPanel();
- protected JCheckBox showUnconserved = new JCheckBox();
+ protected JPanel keepfilesPanel = new JPanel();
- protected JCheckBox showDbRefTooltip = new JCheckBox();
+ protected JPanel exampleFilesPanel = new JPanel();
- protected JCheckBox showNpTooltip = new JCheckBox();
+ protected JTextField suffixTemplate = new JTextField(null, 8);
- protected JCheckBox idItalics = new JCheckBox();
+ protected JLabel suffixTemplateLabel = new JLabel();
- protected JCheckBox openoverv = new JCheckBox();
+ protected JLabel suffixDigitsLabel = new JLabel();
- protected JCheckBox usagestats = new JCheckBox();
+ protected JSpinner suffixDigitsSpinner = new JSpinner();
- protected JCheckBox questionnaire = new JCheckBox();
+ protected JalviewBooleanRadioButtons suffixReverse = new JalviewBooleanRadioButtons();
- protected JCheckBox versioncheck = new JCheckBox();
+ protected JalviewBooleanRadioButtons backupfilesKeepAll = new JalviewBooleanRadioButtons();
- protected JLabel showGroupbits = new JLabel();
+ public JSpinner backupfilesRollMaxSpinner = new JSpinner();
- protected JLabel showConsensbits = new JLabel();
+ protected JLabel oldBackupFilesLabel = new JLabel();
- protected JCheckBox showConsensLogo = new JCheckBox();
+ protected JalviewBooleanRadioButtons backupfilesConfirmDelete = new JalviewBooleanRadioButtons();
- protected JCheckBox showConsensHistogram = new JCheckBox();
+ protected JTextArea backupfilesExampleLabel = new JTextArea();
- protected JCheckBox showGroupConsensus = new JCheckBox();
+ private final JTabbedPane tabbedPane = new JTabbedPane();
- protected JCheckBox showGroupConservation = new JCheckBox();
+ private JLabel messageLabel = new JLabel("", JLabel.CENTER);
- protected JCheckBox shareSelections = new JCheckBox();
+ /*
+ * 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 JCheckBox followHighlight = new JCheckBox();
+ protected JLabel jvmMemoryMaxLabel = new JLabel();
- protected JCheckBox sortByTree= new JCheckBox();
+ protected JTextField jvmMemoryMaxTextField = new JTextField(null, 8);
+
+ protected JComboBox<Object> lafCombo = new JComboBox<>();
/**
* Creates a new GPreferences object.
}
/**
- * DOCUMENT ME!
+ * Construct the panel and its tabbed sub-panels.
*
* @throws Exception
- * DOCUMENT ME!
*/
private void jbInit() throws Exception
{
- this.setLayout(borderLayout1);
- ok.setText("OK");
- ok.addActionListener(new ActionListener()
+ // final JTabbedPane tabbedPane = new JTabbedPane();
+ this.setLayout(new BorderLayout());
+
+ // message label at top
+ this.add(messageLabel, BorderLayout.NORTH);
+
+ JPanel okCancelPanel = initOkCancelPanel();
+ this.add(tabbedPane, BorderLayout.CENTER);
+ this.add(okCancelPanel, BorderLayout.SOUTH);
+
+ tabbedPane.add(initVisualTab(),
+ MessageManager.getString("label.visual"));
+
+ tabbedPane.add(initColoursTab(),
+ MessageManager.getString("label.colours"));
+
+ tabbedPane.add(initOverviewTab(),
+ MessageManager.getString("label.overview"));
+
+ tabbedPane.add(initStructureTab(),
+ MessageManager.getString("label.structure"));
+
+ tabbedPane.add(initConnectionsTab(),
+ MessageManager.getString("label.connections"));
+
+ if (!Platform.isJS())
{
- public void actionPerformed(ActionEvent e)
- {
- ok_actionPerformed(e);
- }
- });
- cancel.setText("Cancel");
- cancel.addActionListener(new ActionListener()
+ tabbedPane.add(initBackupsTab(),
+ MessageManager.getString("label.backups"));
+ }
+
+ tabbedPane.add(initLinksTab(),
+ MessageManager.getString("label.urllinks"));
+
+ tabbedPane.add(initOutputTab(),
+ MessageManager.getString("label.output"));
+
+ tabbedPane.add(initEditingTab(),
+ MessageManager.getString("label.editing"));
+
+ tabbedPane.add(initStartupTab(),
+ MessageManager.getString("label.startup"));
+
+ /*
+ * See WsPreferences for the real work of configuring this tab.
+ */
+ if (!Platform.isJS())
{
- public void actionPerformed(ActionEvent e)
- {
- cancel_actionPerformed(e);
- }
- });
- quality.setEnabled(false);
- quality.setFont(verdana11);
- quality.setHorizontalAlignment(SwingConstants.RIGHT);
- quality.setHorizontalTextPosition(SwingConstants.LEFT);
- quality.setSelected(true);
- quality.setText("Quality");
- visualTab.setBorder(new TitledBorder("Open new alignment"));
- visualTab.setLayout(null);
- visual2Tab.setBorder(new TitledBorder("Open new alignment"));
- visual2Tab.setLayout(new FlowLayout());
- fullScreen.setFont(verdana11);
- fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
- fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
- fullScreen.setText("Maximise Window");
- conservation.setEnabled(false);
- conservation.setFont(verdana11);
- conservation.setHorizontalAlignment(SwingConstants.RIGHT);
- conservation.setHorizontalTextPosition(SwingConstants.LEFT);
- conservation.setSelected(true);
- conservation.setText("Conservation");
- identity.setEnabled(false);
- identity.setFont(verdana11);
- identity.setHorizontalAlignment(SwingConstants.RIGHT);
- identity.setHorizontalTextPosition(SwingConstants.LEFT);
- identity.setSelected(true);
- identity.setText("Consensus");
- showGroupbits.setFont(verdana11);
- showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
- showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupbits.setText("Show group:");
- showConsensbits.setFont(verdana11);
- showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
- showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showConsensbits.setText("Consensus:");
- showConsensHistogram.setEnabled(false);
- showConsensHistogram.setFont(verdana11);
- showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
- showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
- showConsensHistogram.setSelected(true);
- showConsensHistogram.setText("Histogram");
- showConsensLogo.setEnabled(false);
- showConsensLogo.setFont(verdana11);
- showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
- showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
- showConsensLogo.setSelected(true);
- showConsensLogo.setText("Logo");
- showGroupConsensus.setEnabled(false);
- showGroupConsensus.setFont(verdana11);
- showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
- showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupConsensus.setSelected(true);
- showGroupConsensus.setText("Consensus");
- showGroupConservation.setEnabled(false);
- showGroupConservation.setFont(verdana11);
- showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
- showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupConservation.setSelected(true);
- showGroupConservation.setText("Conservation");
- showNpTooltip.setEnabled(true);
- showNpTooltip.setFont(verdana11);
- showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
- showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
- showNpTooltip.setSelected(true);
- showNpTooltip.setText("Non-positional Features");
- showDbRefTooltip.setEnabled(true);
- showDbRefTooltip.setFont(verdana11);
- showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
- showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
- showDbRefTooltip.setSelected(true);
- showDbRefTooltip.setText("Database References");
- annotations.setFont(verdana11);
- annotations.setHorizontalAlignment(SwingConstants.RIGHT);
- annotations.setHorizontalTextPosition(SwingConstants.LEADING);
- annotations.setSelected(true);
- annotations.setText("Show Annotations");
- annotations.setBounds(new Rectangle(169, 12, 200, 23));
- annotations.addActionListener(new ActionListener()
+ wsTab.setLayout(new BorderLayout());
+ tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
+ }
+
+ /*
+ * Handler to validate a tab before leaving it - currently only for
+ * Structure.
+ * Adding a clearMessage() so messages are cleared when changing tabs.
+ */
+ tabbedPane.addChangeListener(new ChangeListener()
{
- public void actionPerformed(ActionEvent e)
+ private Component lastTab;
+
+ @Override
+ public void stateChanged(ChangeEvent e)
{
- annotations_actionPerformed(e);
+ if (lastTab == structureTab
+ && tabbedPane.getSelectedComponent() != structureTab)
+ {
+ if (!validateStructure())
+ {
+ tabbedPane.setSelectedComponent(structureTab);
+ return;
+ }
+ }
+ lastTab = tabbedPane.getSelectedComponent();
+
+ clearMessage();
}
+
});
- identity.addActionListener(new ActionListener()
+ }
+
+ public void setMessage(String message)
+ {
+ if (message != null)
{
- public void actionPerformed(ActionEvent e)
- {
- annotations_actionPerformed(e);
- }
- });
- showGroupConsensus.addActionListener(new ActionListener()
+ messageLabel.setText(message);
+ messageLabel.setFont(LABEL_FONT_BOLD);
+ messageLabel.setForeground(Color.RED.darker());
+ messageLabel.revalidate();
+ messageLabel.repaint();
+ }
+ // note message not cleared if message is null. call clearMessage()
+ // directly.
+ this.revalidate();
+ this.repaint();
+ }
+
+ public void clearMessage()
+ {
+ // only repaint if message exists
+ if (messageLabel.getText() != null
+ && messageLabel.getText().length() > 0)
+ {
+ messageLabel.setText("");
+ messageLabel.revalidate();
+ messageLabel.repaint();
+ this.revalidate();
+ this.repaint();
+ }
+ }
+
+ public static enum TabRef
+ {
+ CONNECTIONS_TAB, STRUCTURE_TAB
+ };
+
+ 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 Editing tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initEditingTab()
+ {
+ JPanel editingTab = new JPanel();
+ editingTab.setLayout(null);
+ autoCalculateConsCheck.setFont(LABEL_FONT);
+ autoCalculateConsCheck.setText(
+ MessageManager.getString("label.autocalculate_consensus"));
+ autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
+ padGaps.setFont(LABEL_FONT);
+ padGaps.setText(
+ MessageManager.getString("label.pad_gaps_when_editing"));
+ padGaps.setBounds(new Rectangle(22, 94, 168, 23));
+ sortByTree.setFont(LABEL_FONT);
+ sortByTree
+ .setText(MessageManager.getString("label.sort_with_new_tree"));
+ sortByTree.setToolTipText(MessageManager.getString(
+ "label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
+ sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
+ editingTab.add(autoCalculateConsCheck);
+ editingTab.add(padGaps);
+ editingTab.add(sortByTree);
+ return editingTab;
+ }
+
+ /**
+ * Initialises the Output tab
+ *
+ * @return
+ */
+ private JPanel initOutputTab()
+ {
+ JPanel outputTab = new JPanel();
+ outputTab.setLayout(null);
+
+ JLabel epsLabel = new JLabel(
+ MessageManager.formatMessage("label.rendering_style", "EPS"));
+ epsLabel.setFont(LABEL_FONT);
+ epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ epsLabel.setBounds(new Rectangle(9, 31, 160, 24));
+ epsRendering.setFont(LABEL_FONT);
+ epsRendering.setBounds(new Rectangle(174, 34, 187, 21));
+ JLabel htmlLabel = new JLabel(
+ MessageManager.formatMessage("label.rendering_style", "HTML"));
+ htmlLabel.setFont(LABEL_FONT);
+ htmlLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ htmlLabel.setBounds(new Rectangle(9, 55, 160, 24));
+ htmlRendering.setFont(LABEL_FONT);
+ htmlRendering.setBounds(new Rectangle(174, 58, 187, 21));
+ JLabel svgLabel = new JLabel(
+ MessageManager.formatMessage("label.rendering_style", "SVG"));
+ svgLabel.setFont(LABEL_FONT);
+ svgLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ svgLabel.setBounds(new Rectangle(9, 79, 160, 24));
+ svgRendering.setFont(LABEL_FONT);
+ svgRendering.setBounds(new Rectangle(174, 82, 187, 21));
+
+ JLabel jLabel1 = new JLabel();
+ jLabel1.setFont(LABEL_FONT);
+ jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
+ jLabel1.setText(MessageManager.getString("label.append_start_end"));
+ jLabel1.setFont(LABEL_FONT);
+
+ fastajv.setFont(LABEL_FONT);
+ fastajv.setHorizontalAlignment(SwingConstants.LEFT);
+ clustaljv.setText(MessageManager.getString("label.clustal") + " ");
+ blcjv.setText(MessageManager.getString("label.blc") + " ");
+ fastajv.setText(MessageManager.getString("label.fasta") + " ");
+ msfjv.setText(MessageManager.getString("label.msf") + " ");
+ pfamjv.setText(MessageManager.getString("label.pfam") + " ");
+ pileupjv.setText(MessageManager.getString("label.pileup") + " ");
+ msfjv.setFont(LABEL_FONT);
+ msfjv.setHorizontalAlignment(SwingConstants.LEFT);
+ pirjv.setText(MessageManager.getString("label.pir") + " ");
+ JPanel jPanel11 = new JPanel();
+ jPanel11.setFont(LABEL_FONT);
+ TitledBorder titledBorder2 = new TitledBorder(
+ MessageManager.getString("label.file_output"));
+ jPanel11.setBorder(titledBorder2);
+ jPanel11.setBounds(new Rectangle(30, 120, 196, 182));
+ GridLayout gridLayout3 = new GridLayout();
+ jPanel11.setLayout(gridLayout3);
+ gridLayout3.setRows(8);
+ blcjv.setFont(LABEL_FONT);
+ blcjv.setHorizontalAlignment(SwingConstants.LEFT);
+ clustaljv.setFont(LABEL_FONT);
+ clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
+ pfamjv.setFont(LABEL_FONT);
+ pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
+ pileupjv.setFont(LABEL_FONT);
+ pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
+ pirjv.setFont(LABEL_FONT);
+ pirjv.setHorizontalAlignment(SwingConstants.LEFT);
+ autoIdWidth.setFont(LABEL_FONT);
+ autoIdWidth.setText(
+ MessageManager.getString("label.automatically_set_id_width"));
+ autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.adjusts_width_generated_eps_png")));
+ autoIdWidth.setBounds(new Rectangle(228, 144, 320, 23));
+ autoIdWidth.addActionListener(new ActionListener()
{
+
+ @Override
public void actionPerformed(ActionEvent e)
{
- annotations_actionPerformed(e);
+ autoIdWidth_actionPerformed();
}
});
- showUnconserved.setFont(verdana11);
- showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
- showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
- showUnconserved.setSelected(true);
- showUnconserved.setText("Show Unconserved");
- showUnconserved.addActionListener(new ActionListener()
+ userIdWidthlabel.setFont(LABEL_FONT);
+ userIdWidthlabel.setText(
+ MessageManager.getString("label.figure_id_column_width"));
+ userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.manually_specify_width_left_column")));
+ userIdWidthlabel.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, MessageManager.getString(
+ "label.manually_specify_width_left_column")));
+ userIdWidthlabel.setBounds(new Rectangle(236, 168, 320, 23));
+ userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
+ userIdWidth.setText("");
+ userIdWidth.setBounds(new Rectangle(232, 192, 84, 23));
+ userIdWidth.addActionListener(new ActionListener()
{
+
+ @Override
public void actionPerformed(ActionEvent e)
{
- showunconserved_actionPerformed(e);
+ userIdWidth_actionPerformed();
}
});
- // / TODO: fit these in to preferences panel!!!!!
- shareSelections.setFont(verdana11);
- shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
- shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
- shareSelections.setSelected(true);
- shareSelections.setText("Share selection across views");
- followHighlight.setFont(verdana11);
- followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
- followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
- // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
- followHighlight.setSelected(true);
- followHighlight.setText("Scroll to highlighted regions");
-
- gapLabel.setFont(verdana11);
- gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- gapLabel.setText("Gap Symbol ");
- colour.setFont(verdana11);
- colour.setBounds(new Rectangle(172, 225, 155, 21));
- colourLabel.setFont(verdana11);
- colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- colourLabel.setText("Alignment Colour ");
- fontLabel.setFont(verdana11);
- fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- fontLabel.setText("Font ");
- fontSizeCB.setFont(verdana11);
- fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
- fontStyleCB.setFont(verdana11);
- fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
- fontNameCB.setFont(verdana11);
- fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
- gapSymbolCB.setFont(verdana11);
- gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
- mincolourLabel.setFont(verdana11);
+ modellerOutput.setFont(LABEL_FONT);
+ modellerOutput
+ .setText(MessageManager.getString("label.use_modeller_output"));
+ modellerOutput.setBounds(new Rectangle(228, 274, 320, 23));
+ embbedBioJSON.setFont(LABEL_FONT);
+ embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
+ embbedBioJSON.setBounds(new Rectangle(228, 248, 250, 23));
+
+ jPanel11.add(jLabel1);
+ jPanel11.add(blcjv);
+ jPanel11.add(clustaljv);
+ jPanel11.add(fastajv);
+ jPanel11.add(msfjv);
+ jPanel11.add(pfamjv);
+ jPanel11.add(pileupjv);
+ jPanel11.add(pirjv);
+ outputTab.add(autoIdWidth);
+ outputTab.add(userIdWidth);
+ outputTab.add(userIdWidthlabel);
+ outputTab.add(modellerOutput);
+ if (!Platform.isJS())
+ {
+ /*
+ * JalviewJS doesn't support Lineart option or SVG output
+ */
+ outputTab.add(embbedBioJSON);
+ outputTab.add(epsLabel);
+ outputTab.add(epsRendering);
+ outputTab.add(htmlLabel);
+ outputTab.add(htmlRendering);
+ outputTab.add(svgLabel);
+ outputTab.add(svgRendering);
+ }
+ outputTab.add(jPanel11);
+ return outputTab;
+ }
+
+ /**
+ * Initialises the Connections tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initConnectionsTab()
+ {
+ connectTab = new JPanel();
+ connectTab.setLayout(new GridBagLayout());
+
+ JPanel proxyPanel = initConnTabProxyPanel();
+ initConnTabCheckboxes();
+
+ // Add proxy server panel
+ connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
+ GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
+ new Insets(10, 0, 5, 12), 4, 10));
+
+ // Add usage stats, version check and questionnaire checkboxes
+ connectTab.add(usagestats,
+ new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 5, 5), 70, 1));
+ connectTab.add(questionnaire,
+ new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 5, 10), 70, 1));
+ connectTab.add(versioncheck,
+ new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 5, 5), 70, 1));
+
+ versioncheck.setVisible(false);
+
+ // Add padding so the panel doesn't look ridiculous
+ JPanel spacePanel = new JPanel();
+ connectTab.add(spacePanel,
+ new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
+ GridBagConstraints.WEST, GridBagConstraints.BOTH,
+ new Insets(0, 0, 0, 5), 70, 1));
+
+ return connectTab;
+ }
+
+ /**
+ * Initialises the Links tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initLinksTab()
+ {
+ JPanel linkTab = new JPanel();
+ linkTab.setLayout(new GridBagLayout());
+
+ // Set up table for Url links
+ linkUrlTable.getTableHeader().setReorderingAllowed(false);
+ linkUrlTable.setFillsViewportHeight(true);
+ linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
+ linkUrlTable.setAutoCreateRowSorter(true);
+ linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+
+ // adjust row height so radio buttons actually fit
+ // don't do this in the renderer, it causes the awt thread to activate
+ // constantly
+ JRadioButton temp = new JRadioButton();
+ linkUrlTable.setRowHeight(temp.getMinimumSize().height);
+
+ // Table in scrollpane so that the table is given a scrollbar
+ JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
+ linkScrollPane.setBorder(null);
+
+ // Panel for links functionality
+ JPanel linkPanel = new JPanel(new GridBagLayout());
+ linkPanel.setBorder(new TitledBorder(
+ MessageManager.getString("label.url_linkfrom_sequence_id")));
+
+ // Put the Url links panel together
+
+ // Buttons go at top right, resizing only resizes the blank space vertically
+ JPanel buttonPanel = initLinkTabUrlButtons();
+ GridBagConstraints linkConstraints1 = new GridBagConstraints();
+ linkConstraints1.insets = new Insets(0, 0, 5, 0);
+ linkConstraints1.gridx = 0;
+ linkConstraints1.gridy = 0;
+ linkConstraints1.weightx = 1.0;
+ linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
+ linkTab.add(buttonPanel, linkConstraints1);
+
+ // Links table goes at top left, resizing resizes the table
+ GridBagConstraints linkConstraints2 = new GridBagConstraints();
+ linkConstraints2.insets = new Insets(0, 0, 5, 5);
+ linkConstraints2.gridx = 0;
+ linkConstraints2.gridy = 1;
+ linkConstraints2.weightx = 1.0;
+ linkConstraints2.weighty = 1.0;
+ linkConstraints2.fill = GridBagConstraints.BOTH;
+ linkTab.add(linkScrollPane, linkConstraints2);
+
+ // Filter box and buttons goes at bottom left, resizing resizes the text box
+ JPanel filterPanel = initLinkTabFilterPanel();
+ GridBagConstraints linkConstraints3 = new GridBagConstraints();
+ linkConstraints3.insets = new Insets(0, 0, 0, 5);
+ linkConstraints3.gridx = 0;
+ linkConstraints3.gridy = 2;
+ linkConstraints3.weightx = 1.0;
+ linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
+ linkTab.add(filterPanel, linkConstraints3);
+
+ return linkTab;
+ }
+
+ private JPanel initLinkTabFilterPanel()
+ {
+ // Filter textbox and reset button
+ JLabel filterLabel = new JLabel(
+ MessageManager.getString("label.filter"));
+ filterLabel.setFont(LABEL_FONT);
+ filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
+
+ filterTB.setFont(LABEL_FONT);
+ filterTB.setText("");
+
+ doReset.setText(MessageManager.getString("action.showall"));
+ userOnly.setText(MessageManager.getString("action.customfilter"));
+
+ // Panel for filter functionality
+ JPanel filterPanel = new JPanel(new GridBagLayout());
+ filterPanel.setBorder(new TitledBorder("Filter"));
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.WEST;
+
+ filterPanel.add(filterLabel, gbc);
+
+ GridBagConstraints gbc1 = new GridBagConstraints();
+ gbc1.gridx = 1;
+ gbc1.gridwidth = 2;
+ gbc1.fill = GridBagConstraints.HORIZONTAL;
+ gbc1.anchor = GridBagConstraints.WEST;
+ gbc1.weightx = 1.0;
+ filterPanel.add(filterTB, gbc1);
+
+ GridBagConstraints gbc2 = new GridBagConstraints();
+ gbc2.gridx = 3;
+ gbc2.fill = GridBagConstraints.NONE;
+ gbc2.anchor = GridBagConstraints.WEST;
+ filterPanel.add(doReset, gbc2);
+
+ GridBagConstraints gbc3 = new GridBagConstraints();
+ gbc3.gridx = 4;
+ gbc3.fill = GridBagConstraints.NONE;
+ gbc3.anchor = GridBagConstraints.WEST;
+ filterPanel.add(userOnly, gbc3);
+
+ return filterPanel;
+ }
+
+ private JPanel initLinkTabUrlButtons()
+ {
+ // Buttons for new / edit / delete Url links
+ JButton newLink = new JButton();
+ newLink.setText(MessageManager.getString("action.new"));
+
+ editLink.setText(MessageManager.getString("action.edit"));
+
+ deleteLink.setText(MessageManager.getString("action.delete"));
+
+ // no current selection, so initially disable delete/edit buttons
+ editLink.setEnabled(false);
+ deleteLink.setEnabled(false);
+
+ newLink.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ newLink_actionPerformed(e);
+ }
+ });
+
+ editLink.setText(MessageManager.getString("action.edit"));
+ editLink.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ editLink_actionPerformed(e);
+ }
+ });
+
+ deleteLink.setText(MessageManager.getString("action.delete"));
+ deleteLink.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ deleteLink_actionPerformed(e);
+ }
+ });
+
+ JPanel buttonPanel = new JPanel(new GridBagLayout());
+ buttonPanel.setBorder(new TitledBorder("Edit links"));
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+ gbc.fill = GridBagConstraints.NONE;
+ buttonPanel.add(newLink, gbc);
+
+ GridBagConstraints gbc1 = new GridBagConstraints();
+ gbc1.gridx = 1;
+ gbc1.gridy = 0;
+ gbc1.fill = GridBagConstraints.NONE;
+ buttonPanel.add(editLink, gbc1);
+
+ GridBagConstraints gbc2 = new GridBagConstraints();
+ gbc2.gridx = 2;
+ gbc2.gridy = 0;
+ gbc2.fill = GridBagConstraints.NONE;
+ buttonPanel.add(deleteLink, gbc2);
+
+ GridBagConstraints gbc3 = new GridBagConstraints();
+ gbc3.gridx = 3;
+ gbc3.gridy = 0;
+ gbc3.fill = GridBagConstraints.HORIZONTAL;
+ gbc3.weightx = 1.0;
+ JPanel spacePanel = new JPanel();
+ spacePanel.setBorder(null);
+ buttonPanel.add(spacePanel, gbc3);
+
+ return buttonPanel;
+ }
+
+ /**
+ * Initialises the proxy server panel in the Connections tab
+ *
+ * @return the proxy server panel
+ */
+ private JPanel initConnTabProxyPanel()
+ {
+ // Label for server text box
+ serverLabel.setText(MessageManager.getString("label.host") + ": ");
+ serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ serverLabel.setFont(LABEL_FONT);
+ serverLabel2.setText(MessageManager.getString("label.host") + ": ");
+ serverLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
+ serverLabel2.setFont(LABEL_FONT);
+
+ // Proxy server and port text boxes
+ proxyServerHttpTB.setFont(LABEL_FONT);
+ proxyServerHttpTB.setColumns(40);
+ proxyPortHttpTB.setFont(LABEL_FONT);
+ proxyPortHttpTB.setColumns(4);
+ proxyServerHttpsTB.setFont(LABEL_FONT);
+ proxyServerHttpsTB.setColumns(40);
+ proxyPortHttpsTB.setFont(LABEL_FONT);
+ 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()
+ .addDocumentListener(new DocumentListener()
+ {
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ proxyAuthPasswordCheckHighlight(true);
+ applyProxyButtonEnabled(true);
+ }
+
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ proxyAuthPasswordCheckHighlight(true);
+ applyProxyButtonEnabled(true);
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ proxyAuthPasswordCheckHighlight(true);
+ applyProxyButtonEnabled(true);
+ }
+
+ });
+
+ // Label for Port text box
+ portLabel.setFont(LABEL_FONT);
+ portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ portLabel.setText(MessageManager.getString("label.port") + ": ");
+ portLabel2.setFont(LABEL_FONT);
+ portLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
+ portLabel2.setText(MessageManager.getString("label.port") + ": ");
+
+ httpLabel.setText("HTTP");
+ httpLabel.setFont(LABEL_FONT_BOLD);
+ httpLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ httpsLabel.setText("HTTPS");
+ httpsLabel.setFont(LABEL_FONT_BOLD);
+ httpsLabel.setHorizontalAlignment(SwingConstants.LEFT);
+
+ proxyAuthUsernameLabel
+ .setText(MessageManager.getString("label.username") + ": ");
+ proxyAuthUsernameLabel.setFont(LABEL_FONT);
+ proxyAuthUsernameLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ proxyAuthPasswordLabel
+ .setText(MessageManager.getString("label.password") + ": ");
+ proxyAuthPasswordLabel.setFont(LABEL_FONT);
+ proxyAuthPasswordLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ passwordNotStoredLabel.setText(
+ "(" + MessageManager.getString("label.not_stored") + ")");
+ passwordNotStoredLabel.setFont(LABEL_FONT_ITALIC);
+ passwordNotStoredLabel.setHorizontalAlignment(SwingConstants.LEFT);
+
+ // Proxy type radio buttons
+ noProxy.setFont(LABEL_FONT);
+ noProxy.setHorizontalAlignment(SwingConstants.LEFT);
+ noProxy.setText(MessageManager.getString("label.no_proxy"));
+ systemProxy.setFont(LABEL_FONT);
+ systemProxy.setHorizontalAlignment(SwingConstants.LEFT);
+ systemProxy.setText(MessageManager.formatMessage("label.system_proxy",
+ displayUserHostPort(Cache.startupProxyProperties[4],
+ Cache.startupProxyProperties[0],
+ Cache.startupProxyProperties[1]),
+ displayUserHostPort(Cache.startupProxyProperties[6],
+ Cache.startupProxyProperties[2],
+ Cache.startupProxyProperties[3])));
+ customProxy.setFont(LABEL_FONT);
+ customProxy.setHorizontalAlignment(SwingConstants.LEFT);
+ customProxy.setText(
+ MessageManager.getString("label.use_proxy_server") + ":");
+ ActionListener al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ proxyType_actionPerformed();
+ }
+ };
+ noProxy.addActionListener(al);
+ systemProxy.addActionListener(al);
+ customProxy.addActionListener(al);
+ proxyType.add(noProxy);
+ proxyType.add(systemProxy);
+ proxyType.add(customProxy);
+
+ proxyAuth.setFont(LABEL_FONT);
+ proxyAuth.setHorizontalAlignment(SwingConstants.LEFT);
+ proxyAuth.setText(MessageManager.getString("label.auth_required"));
+ proxyAuth.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ proxyAuth_actionPerformed();
+ }
+ });
+
+ setCustomProxyEnabled();
+
+ // Make proxy server panel
+ JPanel proxyPanel = new JPanel();
+ TitledBorder titledBorder1 = new TitledBorder(
+ MessageManager.getString("label.proxy_servers"));
+ proxyPanel.setBorder(titledBorder1);
+ proxyPanel.setLayout(new GridBagLayout());
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ gbc.weightx = 1.0;
+
+ GridBagConstraints c = new GridBagConstraints();
+ // Proxy type radio buttons (3)
+ JPanel ptPanel = new JPanel();
+ ptPanel.setLayout(new GridBagLayout());
+ c.weightx = 1.0;
+ c.gridy = 0;
+ c.gridx = 0;
+ c.gridwidth = 1;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ ptPanel.add(noProxy, c);
+ c.gridy++;
+ ptPanel.add(systemProxy, c);
+ c.gridy++;
+ ptPanel.add(customProxy, c);
+
+ gbc.gridy = 0;
+ proxyPanel.add(ptPanel, gbc);
+
+ // host and port text boxes
+ JPanel hpPanel = new JPanel();
+ hpPanel.setLayout(new GridBagLayout());
+ // HTTP host port row
+ c.gridy = 0;
+ c.gridx = 0;
+
+ c.weightx = 0.1;
+ c.anchor = GridBagConstraints.LINE_START;
+ hpPanel.add(httpLabel, c);
+
+ c.gridx++;
+ c.weightx = 0.1;
+ c.anchor = GridBagConstraints.LINE_END;
+ hpPanel.add(serverLabel, c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ c.anchor = GridBagConstraints.LINE_START;
+ hpPanel.add(proxyServerHttpTB, c);
+
+ c.gridx++;
+ c.weightx = 0.1;
+ c.anchor = GridBagConstraints.LINE_END;
+ hpPanel.add(portLabel, c);
+
+ c.gridx++;
+ c.weightx = 0.2;
+ c.anchor = GridBagConstraints.LINE_START;
+ hpPanel.add(proxyPortHttpTB, c);
+
+ // HTTPS host port row
+ c.gridy++;
+ c.gridx = 0;
+ c.gridwidth = 1;
+
+ c.anchor = GridBagConstraints.LINE_START;
+ hpPanel.add(httpsLabel, c);
+
+ c.gridx++;
+ c.anchor = GridBagConstraints.LINE_END;
+ hpPanel.add(serverLabel2, c);
+
+ c.gridx++;
+ c.anchor = GridBagConstraints.LINE_START;
+ hpPanel.add(proxyServerHttpsTB, c);
+
+ c.gridx++;
+ c.anchor = GridBagConstraints.LINE_END;
+ hpPanel.add(portLabel2, c);
+
+ c.gridx++;
+ c.anchor = GridBagConstraints.LINE_START;
+ hpPanel.add(proxyPortHttpsTB, c);
+
+ gbc.gridy++;
+ proxyPanel.add(hpPanel, 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()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ saveProxySettings();
+ applyProxyButton.setEnabled(false);
+ }
+ });
+ gbc.gridy++;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.LINE_END;
+ proxyPanel.add(applyProxyButton, gbc);
+
+ return proxyPanel;
+ }
+
+ 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)
+ {
+ if (grabFocus)
+ proxyAuthPasswordPB.grabFocus();
+ proxyAuthPasswordPB.setBackground(Color.PINK);
+ }
+ else
+ {
+ proxyAuthPasswordPB.setBackground(Color.WHITE);
+ }
+ }
+
+ public void applyProxyButtonEnabled(boolean enabled)
+ {
+ applyProxyButton.setEnabled(enabled);
+ }
+
+ public void saveProxySettings()
+ {
+ // overridden in Preferences
+ }
+
+ private String displayUserHostPort(String user, String host, String port)
+ {
+ boolean hostBlank = (host == null || host.isEmpty());
+ boolean portBlank = (port == null || port.isEmpty());
+ if (hostBlank && portBlank)
+ {
+ return MessageManager.getString("label.none");
+ }
+
+ StringBuilder sb = new StringBuilder();
+ if (user != null)
+ {
+ sb.append(user.isEmpty() || user.indexOf(" ") > -1 ? '"' + user + '"'
+ : user);
+ sb.append("@");
+ }
+ sb.append(hostBlank ? "" : host);
+ if (!portBlank)
+ {
+ sb.append(":");
+ sb.append(port);
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Initialises the checkboxes in the Connections tab
+ */
+ private void initConnTabCheckboxes()
+ {
+ // Usage stats checkbox label
+ usagestats.setText(
+ MessageManager.getString("label.send_usage_statistics"));
+ usagestats.setFont(LABEL_FONT);
+ usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
+ usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
+
+ // Questionnaire checkbox label
+ questionnaire.setText(
+ MessageManager.getString("label.check_for_questionnaires"));
+ questionnaire.setFont(LABEL_FONT);
+ questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
+ questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
+
+ // Check for latest version checkbox label
+ versioncheck.setText(
+ MessageManager.getString("label.check_for_latest_version"));
+ versioncheck.setFont(LABEL_FONT);
+ versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
+ versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
+ }
+
+ /**
+ * Initialises the parent panel which contains the tabbed sections.
+ *
+ * @return
+ */
+ private JPanel initOkCancelPanel()
+ {
+ JButton ok = new JButton();
+ ok.setText(MessageManager.getString("action.ok"));
+ ok.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed(e);
+ }
+ });
+ JButton cancel = new JButton();
+ cancel.setText(MessageManager.getString("action.cancel"));
+ cancel.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ cancel_actionPerformed(e);
+ }
+ });
+ JPanel okCancelPanel = new JPanel();
+ okCancelPanel.add(ok);
+ okCancelPanel.add(cancel);
+ return okCancelPanel;
+ }
+
+ /**
+ * Initialises the Colours tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initColoursTab()
+ {
+ JPanel coloursTab = new JPanel();
+ coloursTab.setBorder(new TitledBorder(
+ MessageManager.getString("action.open_new_alignment")));
+ coloursTab.setLayout(new FlowLayout());
+ JLabel mincolourLabel = new JLabel();
+ mincolourLabel.setFont(LABEL_FONT);
mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- mincolourLabel.setText("Minimum Colour");
- minColour.setFont(verdana11);
+ mincolourLabel.setText(MessageManager.getString("label.min_colour"));
+ minColour.setFont(LABEL_FONT);
minColour.setBorder(BorderFactory.createEtchedBorder());
minColour.setPreferredSize(new Dimension(40, 20));
minColour.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
- minColour_actionPerformed();
+ minColour_actionPerformed(minColour);
}
});
- maxcolourLabel.setFont(verdana11);
+ JLabel maxcolourLabel = new JLabel();
+ maxcolourLabel.setFont(LABEL_FONT);
maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- maxcolourLabel.setText("Maximum Colour ");
- maxColour.setFont(verdana11);
+ maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
+ maxColour.setFont(LABEL_FONT);
maxColour.setBorder(BorderFactory.createEtchedBorder());
maxColour.setPreferredSize(new Dimension(40, 20));
maxColour.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
- maxColour_actionPerformed();
+ maxColour_actionPerformed(maxColour);
}
});
-
- startupCheckbox.setText("Open file");
- startupCheckbox.setFont(verdana11);
- startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
- startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
- startupCheckbox.setSelected(true);
- startupFileTextfield.setFont(verdana11);
- startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
- startupFileTextfield.addMouseListener(new MouseAdapter()
+
+ protColour.setFont(LABEL_FONT);
+ protColour.setBounds(new Rectangle(172, 225, 155, 21));
+ JLabel protColourLabel = new JLabel();
+ protColourLabel.setFont(LABEL_FONT);
+ protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ protColourLabel.setText(
+ MessageManager.getString("label.prot_alignment_colour") + " ");
+ JvSwingUtils.addtoLayout(coloursTab,
+ MessageManager
+ .getString("label.default_colour_scheme_for_alignment"),
+ protColourLabel, protColour);
+
+ nucColour.setFont(LABEL_FONT);
+ nucColour.setBounds(new Rectangle(172, 240, 155, 21));
+ JLabel nucColourLabel = new JLabel();
+ nucColourLabel.setFont(LABEL_FONT);
+ nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ nucColourLabel.setText(
+ MessageManager.getString("label.nuc_alignment_colour") + " ");
+ JvSwingUtils.addtoLayout(coloursTab,
+ MessageManager
+ .getString("label.default_colour_scheme_for_alignment"),
+ nucColourLabel, nucColour);
+
+ JPanel annotationShding = new JPanel();
+ annotationShding.setBorder(new TitledBorder(
+ MessageManager.getString("label.annotation_shading_default")));
+ annotationShding.setLayout(new GridLayout(1, 2));
+ JvSwingUtils.addtoLayout(annotationShding,
+ MessageManager.getString(
+ "label.default_minimum_colour_annotation_shading"),
+ mincolourLabel, minColour);
+ JvSwingUtils.addtoLayout(annotationShding,
+ MessageManager.getString(
+ "label.default_maximum_colour_annotation_shading"),
+ maxcolourLabel, maxColour);
+ coloursTab.add(annotationShding); // , FlowLayout.LEFT);
+ return coloursTab;
+ }
+
+ /**
+ * Initialises the Overview tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initOverviewTab()
+ {
+ JPanel overviewPanel = new JPanel();
+ overviewPanel.setBorder(new TitledBorder(
+ MessageManager.getString("label.overview_settings")));
+
+ gapColour.setFont(LABEL_FONT);
+ // fixing the border colours stops apparent colour bleed from the panel
+ gapColour.setBorder(
+ BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
+ gapColour.setPreferredSize(new Dimension(40, 20));
+ gapColour.addMouseListener(new MouseAdapter()
{
- public void mouseClicked(MouseEvent e)
+ @Override
+ public void mousePressed(MouseEvent e)
{
- if (e.getClickCount() > 1)
- {
- startupFileTextfield_mouseClicked();
- }
+ gapColour_actionPerformed(gapColour);
}
});
- connectTab.setLayout(gridBagLayout3);
- serverLabel.setText("Address");
- serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- serverLabel.setFont(verdana11);
- proxyServerTB.setFont(verdana11);
- proxyPortTB.setFont(verdana11);
- portLabel.setFont(verdana11);
- portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- portLabel.setText("Port");
- browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
- browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
- browserLabel.setText("Default Browser (Unix)");
- defaultBrowser.setFont(verdana11);
- defaultBrowser.setText("");
- usagestats.setText("Send usage statistics");
- usagestats.setFont(verdana11);
- usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
- usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
- questionnaire.setText("Check for questionnaires");
- questionnaire.setFont(verdana11);
- questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
- questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
- versioncheck.setText("Check for latest version");
- versioncheck.setFont(verdana11);
- versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
- versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
- newLink.setText("New");
- newLink.addActionListener(new java.awt.event.ActionListener()
+ hiddenColour.setFont(LABEL_FONT);
+ // fixing the border colours stops apparent colour bleed from the panel
+ hiddenColour.setBorder(
+ BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
+ hiddenColour.setPreferredSize(new Dimension(40, 20));
+ hiddenColour.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ hiddenColour_actionPerformed(hiddenColour);
+ }
+ });
+
+ useLegacyGap = new JCheckBox(
+ MessageManager.getString("label.ov_legacy_gap"));
+ useLegacyGap.setFont(LABEL_FONT);
+ useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
+ useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
+ gapLabel = new JLabel(MessageManager.getString("label.gap_colour"));
+ gapLabel.setFont(LABEL_FONT);
+ gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ gapLabel.setVerticalTextPosition(SwingConstants.TOP);
+ showHiddenAtStart = new JCheckBox(
+ MessageManager.getString("label.ov_show_hide_default"));
+ showHiddenAtStart.setFont(LABEL_FONT);
+ showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
+ showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
+ JLabel hiddenLabel = new JLabel(
+ MessageManager.getString("label.hidden_colour"));
+ hiddenLabel.setFont(LABEL_FONT);
+ hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
+
+ useLegacyGap.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- newLink_actionPerformed(e);
+ useLegacyGaps_actionPerformed(e);
}
});
- editLink.setText("Edit");
- editLink.addActionListener(new java.awt.event.ActionListener()
+
+ overviewPanel.setLayout(new GridBagLayout());
+ GridBagConstraints c1 = new GridBagConstraints();
+
+ c1.fill = GridBagConstraints.HORIZONTAL;
+ c1.gridx = 0;
+ c1.gridy = 0;
+ c1.weightx = 1;
+ c1.ipady = 20;
+ c1.anchor = GridBagConstraints.FIRST_LINE_START;
+ overviewPanel.add(useLegacyGap, c1);
+
+ GridBagConstraints c2 = new GridBagConstraints();
+ c2.fill = GridBagConstraints.HORIZONTAL;
+ c2.gridx = 1;
+ c2.gridy = 0;
+ c2.insets = new Insets(0, 15, 0, 10);
+ overviewPanel.add(gapLabel, c2);
+
+ GridBagConstraints c3 = new GridBagConstraints();
+ c3.fill = GridBagConstraints.HORIZONTAL;
+ c3.gridx = 2;
+ c3.gridy = 0;
+ c3.insets = new Insets(0, 0, 0, 15);
+ overviewPanel.add(gapColour, c3);
+
+ GridBagConstraints c4 = new GridBagConstraints();
+ c4.fill = GridBagConstraints.HORIZONTAL;
+ c4.gridx = 0;
+ c4.gridy = 1;
+ c4.weightx = 1;
+ overviewPanel.add(showHiddenAtStart, c4);
+
+ GridBagConstraints c5 = new GridBagConstraints();
+ c5.fill = GridBagConstraints.HORIZONTAL;
+ c5.gridx = 1;
+ c5.gridy = 1;
+ c5.insets = new Insets(0, 15, 0, 10);
+ overviewPanel.add(hiddenLabel, c5);
+
+ GridBagConstraints c6 = new GridBagConstraints();
+ c6.fill = GridBagConstraints.HORIZONTAL;
+ c6.gridx = 2;
+ c6.gridy = 1;
+ c6.insets = new Insets(0, 0, 0, 15);
+ overviewPanel.add(hiddenColour, c6);
+
+ JButton resetButton = new JButton(
+ MessageManager.getString("label.reset_to_defaults"));
+
+ resetButton.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ resetOvDefaults_actionPerformed(e);
+ }
+ });
+
+ GridBagConstraints c7 = new GridBagConstraints();
+ c7.fill = GridBagConstraints.NONE;
+ c7.gridx = 0;
+ c7.gridy = 2;
+ c7.insets = new Insets(10, 0, 0, 0);
+ c7.anchor = GridBagConstraints.WEST;
+ overviewPanel.add(resetButton, c7);
+
+ // Add padding so the panel doesn't look ridiculous
+ JPanel spacePanel = new JPanel();
+ overviewPanel.add(spacePanel,
+ new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
+ GridBagConstraints.WEST, GridBagConstraints.BOTH,
+ new Insets(0, 0, 0, 5), 0, 0));
+
+ return overviewPanel;
+ }
+
+ /**
+ * Initialises the Structure tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initStructureTab()
+ {
+ structureTab = new JPanel();
+
+ structureTab.setBorder(new TitledBorder(
+ MessageManager.getString("label.structure_options")));
+ structureTab.setLayout(null);
+ final int width = 420;
+ final int height = 22;
+ final int lineSpacing = 25;
+ int ypos = 15;
+
+ structFromPdb.setFont(LABEL_FONT);
+ structFromPdb
+ .setText(MessageManager.getString("label.struct_from_pdb"));
+ structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
+ structFromPdb.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ boolean selected = structFromPdb.isSelected();
+ // enable other options only when the first is checked
+ addSecondaryStructure.setEnabled(selected);
+ addTempFactor.setEnabled(selected);
+ }
+ });
+ structureTab.add(structFromPdb);
+
+ // indent checkboxes that are conditional on the first one
+ ypos += lineSpacing;
+ addSecondaryStructure.setFont(LABEL_FONT);
+ addSecondaryStructure
+ .setText(MessageManager.getString("label.autoadd_secstr"));
+ addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
+ structureTab.add(addSecondaryStructure);
+
+ ypos += lineSpacing;
+ addTempFactor.setFont(LABEL_FONT);
+ addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
+ addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
+ structureTab.add(addTempFactor);
+
+ ypos += lineSpacing;
+ JLabel viewerLabel = new JLabel();
+ viewerLabel.setFont(LABEL_FONT);
+ viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
+ viewerLabel.setBounds(new Rectangle(10, ypos, 220, height));
+ structureTab.add(viewerLabel);
+
+ /*
+ * add all external viewers as options here - check
+ * when selected whether the program is installed
+ */
+ structViewer.setFont(LABEL_FONT);
+ structViewer.setBounds(new Rectangle(190, ypos, 120, height));
+ structViewer.addItem(ViewerType.JMOL.name());
+ structViewer.addItem(ViewerType.CHIMERA.name());
+ structViewer.addItem(ViewerType.CHIMERAX.name());
+ structViewer.addItem(ViewerType.PYMOL.name());
+ structViewer.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ structureViewer_actionPerformed(
+ (String) structViewer.getSelectedItem());
+ }
+ });
+ structureTab.add(structViewer);
+
+ ypos += lineSpacing;
+ structureViewerPathLabel = new JLabel();
+ 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.setEnabled(false);
+ structureTab.add(structureViewerPathLabel);
+
+ structureViewerPath.setFont(LABEL_FONT);
+ structureViewerPath.setText("");
+ structureViewerPath.setEnabled(false);
+ final String tooltip = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.viewer_path_tip"));
+ structureViewerPath.setToolTipText(tooltip);
+ structureViewerPath.setBounds(new Rectangle(190, ypos, 290, height));
+ structureViewerPath.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (structureViewerPath.isEnabled() && e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser();
+ if (chosen != null)
+ {
+ structureViewerPath.setText(chosen);
+ }
+ }
+ }
+ });
+ structureTab.add(structureViewerPath);
+
+ ypos += lineSpacing;
+ nwMapping.setFont(LABEL_FONT);
+ nwMapping.setText(MessageManager.getString("label.nw_mapping"));
+ siftsMapping.setFont(LABEL_FONT);
+ siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
+ mappingMethod.add(nwMapping);
+ mappingMethod.add(siftsMapping);
+ JPanel mappingPanel = new JPanel();
+ mappingPanel.setFont(LABEL_FONT);
+ TitledBorder mmTitledBorder = new TitledBorder(
+ MessageManager.getString("label.mapping_method"));
+ mmTitledBorder.setTitleFont(LABEL_FONT);
+ mappingPanel.setBorder(mmTitledBorder);
+ mappingPanel.setBounds(new Rectangle(10, ypos, 472, 45));
+ // GridLayout mappingLayout = new GridLayout();
+ mappingPanel.setLayout(new GridLayout());
+ mappingPanel.add(nwMapping);
+ mappingPanel.add(siftsMapping);
+ structureTab.add(mappingPanel);
+
+ ypos += lineSpacing;
+ ypos += lineSpacing;
+ FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
+ PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
+ docFieldPref.setBounds(new Rectangle(10, ypos, 470, 120));
+ structureTab.add(docFieldPref);
+
+ /*
+ * hide Chimera options in JalviewJS
+ */
+ if (Platform.isJS())
+ {
+ structureViewerPathLabel.setVisible(false);
+ structureViewerPath.setVisible(false);
+ viewerLabel.setVisible(false);
+ structViewer.setVisible(false);
+ }
+
+ return structureTab;
+ }
+
+ /**
+ * Action on choosing a structure viewer from combobox options.
+ *
+ * @param selectedItem
+ */
+ protected void structureViewer_actionPerformed(String selectedItem)
+ {
+ }
+
+ /**
+ * Show a dialog for the user to choose a file. Returns the chosen path, or
+ * null on Cancel.
+ *
+ * @return
+ */
+ protected String openFileChooser()
+ {
+ 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"));
+ chooser.setToolTipText(MessageManager.getString("action.open"));
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JFileChooser.APPROVE_OPTION)
+ {
+ choice = chooser.getSelectedFile().getPath();
+ }
+ return choice;
+ }
+
+ /**
+ * Validate the structure tab preferences; if invalid, set focus on this tab.
+ *
+ * @param e
+ */
+ protected boolean validateStructure(FocusEvent e)
+ {
+ if (!validateStructure())
+ {
+ e.getComponent().requestFocusInWindow();
+ return false;
+ }
+ return true;
+ }
+
+ protected boolean validateStructure()
+ {
+ return false;
+ }
+
+ /**
+ * Initialises the Visual tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initVisualTab()
+ {
+ JPanel visualTab = new JPanel();
+ visualTab.setBorder(new TitledBorder(
+ MessageManager.getString("action.open_new_alignment")));
+ visualTab.setLayout(null);
+ fullScreen.setFont(LABEL_FONT);
+ fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
+ fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
+ fullScreen.setText(MessageManager.getString("label.maximize_window"));
+ quality.setEnabled(false);
+ quality.setFont(LABEL_FONT);
+ quality.setHorizontalAlignment(SwingConstants.RIGHT);
+ quality.setHorizontalTextPosition(SwingConstants.LEFT);
+ quality.setSelected(true);
+ quality.setText(MessageManager.getString("label.quality"));
+ conservation.setEnabled(false);
+ conservation.setFont(LABEL_FONT);
+ conservation.setHorizontalAlignment(SwingConstants.RIGHT);
+ conservation.setHorizontalTextPosition(SwingConstants.LEFT);
+ conservation.setSelected(true);
+ conservation.setText(MessageManager.getString("label.conservation"));
+ identity.setEnabled(false);
+ identity.setFont(LABEL_FONT);
+ identity.setHorizontalAlignment(SwingConstants.RIGHT);
+ identity.setHorizontalTextPosition(SwingConstants.LEFT);
+ identity.setSelected(true);
+ identity.setText(MessageManager.getString("label.consensus"));
+ showOccupancy.setFont(LABEL_FONT);
+ showOccupancy.setEnabled(false);
+ showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
+ showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
+ showOccupancy.setSelected(true);
+ showOccupancy.setText(MessageManager.getString("label.occupancy"));
+
+ JLabel showGroupbits = new JLabel();
+ showGroupbits.setFont(LABEL_FONT);
+ showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
+ showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
+ showGroupbits
+ .setText(MessageManager.getString("action.show_group") + ":");
+ JLabel showConsensbits = new JLabel();
+ showConsensbits.setFont(LABEL_FONT);
+ showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensbits
+ .setText(MessageManager.getString("label.consensus") + ":");
+ showConsensHistogram.setEnabled(false);
+ showConsensHistogram.setFont(LABEL_FONT);
+ showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensHistogram.setSelected(true);
+ showConsensHistogram
+ .setText(MessageManager.getString("label.histogram"));
+ showConsensLogo.setEnabled(false);
+ showConsensLogo.setFont(LABEL_FONT);
+ showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensLogo.setSelected(true);
+ showConsensLogo.setText(MessageManager.getString("label.logo"));
+ showGroupConsensus.setEnabled(false);
+ showGroupConsensus.setFont(LABEL_FONT);
+ showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
+ showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
+ showGroupConsensus.setSelected(true);
+ showGroupConsensus.setText(MessageManager.getString("label.consensus"));
+ showGroupConservation.setEnabled(false);
+ showGroupConservation.setFont(LABEL_FONT);
+ showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
+ showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
+ showGroupConservation.setSelected(true);
+ showGroupConservation
+ .setText(MessageManager.getString("label.conservation"));
+ showNpTooltip.setEnabled(true);
+ showNpTooltip.setFont(LABEL_FONT);
+ showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
+ showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
+ showNpTooltip.setSelected(true);
+ showNpTooltip.setText(
+ MessageManager.getString("label.non_positional_features"));
+ showDbRefTooltip.setEnabled(true);
+ showDbRefTooltip.setFont(LABEL_FONT);
+ showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
+ showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
+ showDbRefTooltip.setSelected(true);
+ showDbRefTooltip
+ .setText(MessageManager.getString("label.database_references"));
+ annotations.setFont(LABEL_FONT);
+ annotations.setHorizontalAlignment(SwingConstants.RIGHT);
+ annotations.setHorizontalTextPosition(SwingConstants.LEFT);
+ annotations.setSelected(true);
+ annotations.setText(MessageManager.getString("label.show_annotations"));
+ // annotations.setBounds(new Rectangle(169, 12, 200, 23));
+ annotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ identity.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ showGroupConsensus.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ showUnconserved.setFont(LABEL_FONT);
+ showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
+ showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
+ showUnconserved.setSelected(true);
+ showUnconserved
+ .setText(MessageManager.getString("action.show_unconserved"));
+ showUnconserved.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showunconserved_actionPerformed(e);
+ }
+ });
+
+ // TODO these are not yet added to / action from Preferences
+ // JCheckBox shareSelections = new JCheckBox();
+ // shareSelections.setFont(verdana11);
+ // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
+ // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
+ // shareSelections.setSelected(true);
+ // shareSelections.setText(MessageManager
+ // .getString("label.share_selection_across_views"));
+ // JCheckBox followHighlight = new JCheckBox();
+ // followHighlight.setFont(verdana11);
+ // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
+ // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
+ // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
+ // followHighlight.setSelected(true);
+ // followHighlight.setText(MessageManager
+ // .getString("label.scroll_highlighted_regions"));
+
+ seqLimit.setFont(LABEL_FONT);
+ seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
+ seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
+ seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
+ smoothFont.setFont(LABEL_FONT);
+ smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
+ smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
+ smoothFont.setText(MessageManager.getString("label.smooth_font"));
+ scaleProteinToCdna.setFont(LABEL_FONT);
+ scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
+ scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
+ scaleProteinToCdna.setText(
+ MessageManager.getString("label.scale_protein_to_cdna"));
+ scaleProteinToCdna.setToolTipText(
+ MessageManager.getString("label.scale_protein_to_cdna_tip"));
+ JLabel gapLabel = new JLabel();
+ gapLabel.setFont(LABEL_FONT);
+ gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
+ JLabel fontLabel = new JLabel();
+ fontLabel.setFont(LABEL_FONT);
+ fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ fontLabel.setText(MessageManager.getString("label.font"));
+ fontSizeCB.setFont(LABEL_FONT);
+ fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
+ fontStyleCB.setFont(LABEL_FONT);
+ fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
+ fontNameCB.setFont(LABEL_FONT);
+ fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
+ gapSymbolCB.setFont(LABEL_FONT);
+ gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
+ DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
+ dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
+ gapSymbolCB.setRenderer(dlcr);
+
+ startupCheckbox.setText(MessageManager.getString("action.open_file"));
+ startupCheckbox.setFont(LABEL_FONT);
+ startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
+ startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
+ startupCheckbox.setSelected(true);
+ startupFileTextfield.setFont(LABEL_FONT);
+ startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
+ final String tooltip = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.double_click_to_browse"));
+ startupFileTextfield.setToolTipText(tooltip);
+ startupFileTextfield.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() > 1)
+ {
+ startupFileTextfield_mouseClicked();
+ }
+ }
+ });
+
+ sortby.setFont(LABEL_FONT);
+ sortby.setBounds(new Rectangle(172, 260, 155, 21));
+ JLabel sortLabel = new JLabel();
+ sortLabel.setFont(LABEL_FONT);
+ sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ sortLabel.setText(MessageManager.getString("label.sort_by"));
+ sortAnnBy.setFont(LABEL_FONT);
+ sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
+ JLabel sortAnnLabel = new JLabel();
+ sortAnnLabel.setFont(LABEL_FONT);
+ sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
+ sortAutocalc.setFont(LABEL_FONT);
+ sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
+
+ JPanel annsettingsPanel = new JPanel();
+ annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
+ annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
+ annsettingsPanel.setBorder(new EtchedBorder());
+ visualTab.add(annsettingsPanel);
+ Border jb = new EmptyBorder(1, 1, 4, 5);
+ annotations.setBorder(jb);
+ showOccupancy.setBorder(jb);
+ quality.setBorder(jb);
+ conservation.setBorder(jb);
+ identity.setBorder(jb);
+ showConsensbits.setBorder(jb);
+ showGroupbits.setBorder(jb);
+ showGroupConsensus.setBorder(jb);
+ showGroupConservation.setBorder(jb);
+ showConsensHistogram.setBorder(jb);
+ showConsensLogo.setBorder(jb);
+
+ JPanel autoAnnotSettings = new JPanel();
+ annsettingsPanel.add(autoAnnotSettings);
+ autoAnnotSettings.setLayout(new GridLayout(0, 2));
+ autoAnnotSettings.add(annotations);
+ autoAnnotSettings.add(quality);
+ // second row of autoannotation box
+ autoAnnotSettings = new JPanel();
+ annsettingsPanel.add(autoAnnotSettings);
+
+ autoAnnotSettings.setLayout(new GridLayout(0, 3));
+ autoAnnotSettings.add(conservation);
+ autoAnnotSettings.add(identity);
+ autoAnnotSettings.add(showOccupancy);
+ autoAnnotSettings.add(showGroupbits);
+ autoAnnotSettings.add(showGroupConservation);
+ autoAnnotSettings.add(showGroupConsensus);
+ autoAnnotSettings.add(showConsensbits);
+ autoAnnotSettings.add(showConsensHistogram);
+ autoAnnotSettings.add(showConsensLogo);
+
+ JPanel tooltipSettings = new JPanel();
+ tooltipSettings.setBorder(new TitledBorder(
+ MessageManager.getString("label.sequence_id_tooltip")));
+ tooltipSettings.setBounds(173, 140, 220, 62);
+ tooltipSettings.setLayout(new GridLayout(2, 1));
+ tooltipSettings.add(showDbRefTooltip);
+ tooltipSettings.add(showNpTooltip);
+ visualTab.add(tooltipSettings);
+
+ wrap.setFont(LABEL_FONT);
+ wrap.setHorizontalAlignment(SwingConstants.TRAILING);
+ wrap.setHorizontalTextPosition(SwingConstants.LEADING);
+ wrap.setText(MessageManager.getString("label.wrap_alignment"));
+ rightAlign.setFont(LABEL_FONT);
+ rightAlign.setForeground(Color.black);
+ rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
+ rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
+ rightAlign.setText(MessageManager.getString("label.right_align_ids"));
+ idItalics.setFont(LABEL_FONT_ITALIC);
+ idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
+ idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
+ idItalics.setText(
+ MessageManager.getString("label.sequence_name_italics"));
+ openoverv.setFont(LABEL_FONT);
+ openoverv.setActionCommand(
+ MessageManager.getString("label.open_overview"));
+ openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
+ openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
+ openoverv.setText(MessageManager.getString("label.open_overview"));
+ JPanel jPanel2 = new JPanel();
+ jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
+ jPanel2.setLayout(new GridLayout(14, 1));
+ jPanel2.add(fullScreen);
+ jPanel2.add(openoverv);
+ jPanel2.add(seqLimit);
+ jPanel2.add(rightAlign);
+ jPanel2.add(fontLabel);
+ jPanel2.add(showUnconserved);
+ jPanel2.add(idItalics);
+ jPanel2.add(smoothFont);
+ jPanel2.add(scaleProteinToCdna);
+ jPanel2.add(gapLabel);
+ jPanel2.add(wrap);
+ jPanel2.add(sortLabel);
+ jPanel2.add(sortAnnLabel);
+ jPanel2.add(startupCheckbox);
+ visualTab.add(jPanel2);
+ visualTab.add(startupFileTextfield);
+ visualTab.add(sortby);
+ visualTab.add(sortAnnBy);
+ visualTab.add(sortAutocalc);
+ visualTab.add(gapSymbolCB);
+ visualTab.add(fontNameCB);
+ visualTab.add(fontSizeCB);
+ visualTab.add(fontStyleCB);
+
+ if (Platform.isJS())
+ {
+ startupCheckbox.setVisible(false);
+ startupFileTextfield.setVisible(false);
+ }
+
+ return visualTab;
+ }
+
+ /**
+ * Load the saved Backups options EXCEPT "Enabled" and "Scheme"
+ */
+
+ protected void loadLastSavedBackupsOptions()
+ {
+ BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
+ .getSavedBackupEntry();
+ enableBackupFiles.setSelected(
+ Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
+
+ BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
+ .createBackupFilesPresetEntry(Cache
+ .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null));
+ if (backupfilesCustomEntry == null)
+ {
+ backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT);
+ }
+ BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
+ BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM,
+ backupfilesCustomEntry);
+
+ setComboIntStringKey(backupfilesPresetsCombo,
+ Cache.getDefault(BackupFiles.NS + "_PRESET",
+ BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT));
+
+ backupsSetOptions(savedPreset);
+
+ backupsOptionsSetEnabled();
+ 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
+ .getSavedBackupEntry();
+ boolean savedSuffixReverse = bfpe.reverse;
+ int savedSuffixDigits = bfpe.digits;
+ String savedSuffixTemplate = bfpe.suffix;
+
+ boolean nowSuffixReverse = suffixReverse.isSelected();
+ int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3);
+ String nowSuffixTemplate = suffixTemplate.getText();
+ return nowSuffixReverse != savedSuffixReverse
+ && nowSuffixDigits == savedSuffixDigits
+ && nowSuffixTemplate != null
+ && 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.
+ *
+ * @return
+ */
+ private JPanel initBackupsTab()
+ {
+ JPanel backupsTab = new JPanel();
+ backupsTab.setBorder(new TitledBorder(
+ MessageManager.getString("label.backup_files")));
+ backupsTab.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;
+
+ initBackupsTabPresetsPanel();
+ initBackupsTabSuffixPanel();
+ initBackupsTabKeepFilesPanel();
+ initBackupsTabFilenameExamplesPanel();
+
+ enableBackupFiles.setFont(LABEL_FONT_BOLD);
+ enableBackupFiles
+ .setText(MessageManager.getString("label.enable_backupfiles"));
+ enableBackupFiles.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // enable other options only when the first is checked
+ backupsOptionsSetEnabled();
+ }
+ });
+
+ // enable checkbox 1 col
+ gbc.gridwidth = 1;
+ gbc.gridheight = 1;
+ gbc.gridx = 0;
+ gbc.gridy = 0; // row 0
+ backupsTab.add(enableBackupFiles, gbc);
+
+ // summary of scheme box (over two rows)
+ gbc.gridx = 1;
+ gbc.weightx = 0.0;
+ gbc.gridheight = 2;
+ gbc.anchor = GridBagConstraints.FIRST_LINE_END;
+ gbc.fill = GridBagConstraints.BOTH;
+ backupsTab.add(exampleFilesPanel, gbc);
+ gbc.gridheight = 1;
+ gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+ gbc.fill = GridBagConstraints.NONE;
+
+ // fill empty space on right
+ gbc.gridx++;
+ gbc.weightx = 1.0;
+ backupsTab.add(new JPanel(), gbc);
+
+ // schemes box
+ gbc.weightx = 0.0;
+ gbc.gridx = 0;
+ gbc.gridy++; // row 1
+ backupsTab.add(presetsPanel, gbc);
+
+ // now using whole row
+ gbc.gridwidth = 2;
+ gbc.gridheight = 1;
+ // keep files box
+ gbc.gridx = 0;
+ gbc.gridy++; // row 2
+ backupsTab.add(keepfilesPanel, gbc);
+
+ // filename strategy box
+ gbc.gridy++; // row 3
+ backupsTab.add(suffixPanel, gbc);
+
+ // fill empty space
+ gbc.gridy++; // row 4
+ gbc.weighty = 1.0;
+ backupsTab.add(new JPanel(), gbc);
+
+ backupsOptionsSetEnabled();
+ return backupsTab;
+ }
+
+ private JPanel initBackupsTabPresetsPanel()
+ {
+
+ String title = MessageManager.getString("label.schemes");
+
+ presetsPanel.setLayout(new GridBagLayout());
+
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.weightx = 0.0;
+ gbc.weighty = 0.0;
+ gbc.anchor = GridBagConstraints.BASELINE_LEADING;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.gridwidth = 1;
+ gbc.gridheight = 1;
+
+ // "Scheme: "
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+
+ presetsComboLabel = new JLabel(title + ":");
+ presetsPanel.add(presetsComboLabel, gbc);
+
+ List<Object> entries = Arrays.asList(
+ (Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
+ List<String> tooltips = Arrays.asList(
+ BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
+ backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
+ tooltips);
+ /*
+ for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++)
+ {
+ backupfilesPresetsCombo
+ .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]);
+ }
+ */
+
+ backupfilesPresetsCombo.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ int key = getComboIntStringKey(backupfilesPresetsCombo);
+ if (!customiseCheckbox.isSelected())
+ {
+ backupfilesPresetsComboLastSelected = key;
+ }
+ if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
+ {
+ if (customiseCheckbox.isSelected())
+ {
+ // got here by clicking on customiseCheckbox so don't change the
+ // values
+ backupfilesCustomOptionsSetEnabled();
+ }
+ else
+ {
+ backupsTabUpdatePresets();
+ backupfilesCustomOptionsSetEnabled();
+ }
+ }
+ else
+ {
+ customiseCheckbox.setSelected(false);
+ backupsTabUpdatePresets();
+ backupfilesCustomOptionsSetEnabled();
+ }
+ }
+ });
+
+ // dropdown list of preset schemes
+ gbc.gridx = 1;
+ presetsPanel.add(backupfilesPresetsCombo, gbc);
+
+ revertButton.setText(MessageManager.getString("label.cancel_changes"));
+ revertButton.setToolTipText(
+ MessageManager.getString("label.cancel_changes_description"));
+ revertButton.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ backupsSetOptions(
+ BackupFilesPresetEntry.backupfilesPresetEntriesValues.get(
+ BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM));
+ backupfilesCustomOptionsSetEnabled();
+ }
+
+ });
+ revertButton.setFont(LABEL_FONT);
+
+ customiseCheckbox.setFont(LABEL_FONT);
+ customiseCheckbox.setText(MessageManager.getString("label.customise"));
+ customiseCheckbox.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ int currently = getComboIntStringKey(backupfilesPresetsCombo);
+ if (customiseCheckbox.isSelected())
+ {
+ backupfilesPresetsComboLastSelected = currently;
+ setComboIntStringKey(backupfilesPresetsCombo,
+ BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
+ }
+ else
+ {
+ setComboIntStringKey(backupfilesPresetsCombo,
+ backupfilesPresetsComboLastSelected);
+
+ }
+ backupfilesCustomOptionsSetEnabled();
+ }
+ });
+ customiseCheckbox.setToolTipText(
+ MessageManager.getString("label.customise_description"));
+
+ // customise checkbox
+ gbc.gridx = 0;
+ gbc.gridy++;
+ presetsPanel.add(customiseCheckbox, gbc);
+
+ // "Cancel changes" button (aligned with combo box above)
+ gbc.gridx = 1;
+ presetsPanel.add(revertButton, gbc);
+
+ return presetsPanel;
+ }
+
+ private JPanel initBackupsTabFilenameExamplesPanel()
+ {
+ String title = MessageManager.getString("label.scheme_examples");
+ TitledBorder tb = new TitledBorder(title);
+ exampleFilesPanel.setBorder(tb);
+ exampleFilesPanel.setLayout(new GridBagLayout());
+
+ backupfilesExampleLabel.setEditable(false);
+ backupfilesExampleLabel
+ .setBackground(exampleFilesPanel.getBackground());
+
+ updateBackupFilesExampleLabel();
+
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.weightx = 1.0;
+ gbc.weighty = 1.0;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+
+ exampleFilesPanel.add(backupfilesExampleLabel, gbc);
+ return exampleFilesPanel;
+ }
+
+ private void backupsTabUpdatePresets()
+ {
+ IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
+ .getSelectedItem();
+ int key = entry.k;
+ String value = entry.v;
+
+ if (BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .containsKey(key))
+ {
+ backupsSetOptions(
+ BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .get(key));
+ }
+ else
+ {
+ Console.error(
+ "Preset '" + value + "' [key:" + key + "] not implemented");
+ }
+
+ // Custom options will now be enabled when the customiseCheckbox is checked
+ // (performed above)
+ // backupfilesCustomOptionsSetEnabled();
+ updateBackupFilesExampleLabel();
+ }
+
+ protected int getComboIntStringKey(
+ JComboBox<Object> backupfilesPresetsCombo2)
+ {
+ IntKeyStringValueEntry e;
+ try
+ {
+ e = (IntKeyStringValueEntry) backupfilesPresetsCombo2
+ .getSelectedItem();
+ } catch (Exception ex)
+ {
+ Console.error(
+ "Problem casting Combo entry to IntKeyStringValueEntry.");
+ e = null;
+ }
+ return e != null ? e.k : 0;
+ }
+
+ protected void setComboIntStringKey(
+ JComboBox<Object> backupfilesPresetsCombo2, int key)
+ {
+ for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
+ {
+ IntKeyStringValueEntry e;
+ try
+ {
+ e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
+ } catch (Exception ex)
+ {
+ Console.error(
+ "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
+ continue;
+ }
+ if (e.k == key)
+ {
+ backupfilesPresetsCombo2.setSelectedIndex(i);
+ break;
+ }
+ }
+ // backupsTabUpdatePresets();
+ }
+
+ private JPanel initBackupsTabSuffixPanel()
+ {
+ suffixPanel.setBorder(new TitledBorder(
+ MessageManager.getString("label.backup_filename_strategy")));
+ suffixPanel.setLayout(new GridBagLayout());
+
+ suffixTemplateLabel
+ .setText(MessageManager.getString("label.append_to_filename"));
+ suffixTemplateLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ suffixTemplateLabel.setFont(LABEL_FONT);
+
+ final String tooltip = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.append_to_filename_tooltip"));
+ suffixTemplate.setToolTipText(tooltip);
+ suffixTemplate.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ updateBackupFilesExampleLabel();
+ backupfilesCustomOptionsSetEnabled();
+ backupfilesRevertButtonSetEnabled(true);
+ }
+
+ });
+ suffixTemplate.addKeyListener(new KeyListener()
+ {
+ @Override
+ public void keyReleased(KeyEvent e)
+ {
+ updateBackupFilesExampleLabel();
+ backupfilesCustomOptionsSetEnabled();
+ backupfilesRevertButtonSetEnabled(true);
+ }
+
+ @Override
+ public void keyPressed(KeyEvent e)
+ {
+ }
+
+ // disable use of ':' or '/' or '\'
+ @Override
+ public void keyTyped(KeyEvent e)
+ {
+ char c = e.getKeyChar();
+ if (c == ':' || c == '/' || c == '\\')
+ {
+ // don't process ':' or '/' or '\'
+ e.consume();
+ }
+ }
+
+ });
+
+ // digits spinner
+ suffixDigitsLabel
+ .setText(MessageManager.getString("label.index_digits"));
+ suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ suffixDigitsLabel.setFont(LABEL_FONT);
+ ChangeListener c = new ChangeListener()
+ {
+ @Override
+ public void stateChanged(ChangeEvent e)
+ {
+ backupfilesRevertButtonSetEnabled(true);
+ updateBackupFilesExampleLabel();
+ }
+
+ };
+ setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN,
+ BackupFilesPresetEntry.DIGITSMAX, 3, c);
+
+ suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"),
+ MessageManager.getString("label.increment_index"));
+ suffixReverse.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ boolean okay = true;
+ if (warnAboutSuffixReverseChange())
+ {
+ // Warning popup
+ okay = confirmSuffixReverseChange();
+ }
+ if (okay)
+ {
+ backupfilesRevertButtonSetEnabled(true);
+ updateBackupFilesExampleLabel();
+ }
+ else
+ {
+ boolean savedSuffixReverse = BackupFilesPresetEntry
+ .getSavedBackupEntry().reverse;
+ suffixReverse.setSelected(savedSuffixReverse);
+ }
+ }
+ });
+
+ GridBagConstraints sgbc = new GridBagConstraints();
+
+ // first row (template text box)
+ sgbc.anchor = GridBagConstraints.WEST;
+ sgbc.gridx = 0;
+ sgbc.gridy = 0;
+ sgbc.gridwidth = 1;
+ sgbc.gridheight = 1;
+ sgbc.weightx = 1.0;
+ sgbc.weighty = 0.0;
+ sgbc.fill = GridBagConstraints.NONE;
+ suffixPanel.add(suffixTemplateLabel, sgbc);
+
+ sgbc.gridx = 1;
+ sgbc.fill = GridBagConstraints.HORIZONTAL;
+ suffixPanel.add(suffixTemplate, sgbc);
+
+ // second row (number of digits spinner)
+ sgbc.gridy = 1;
+
+ sgbc.gridx = 0;
+ sgbc.fill = GridBagConstraints.NONE;
+ suffixPanel.add(suffixDigitsLabel, sgbc);
+
+ sgbc.gridx = 1;
+ sgbc.fill = GridBagConstraints.HORIZONTAL;
+ suffixPanel.add(suffixDigitsSpinner, sgbc);
+
+ // third row (forward order radio selection)
+ sgbc.gridx = 0;
+ sgbc.gridy = 2;
+ sgbc.gridwidth = GridBagConstraints.REMAINDER;
+ sgbc.fill = GridBagConstraints.HORIZONTAL;
+ suffixPanel.add(suffixReverse.getFalseButton(), sgbc);
+
+ // fourth row (reverse order radio selection)
+ sgbc.gridy = 3;
+ suffixPanel.add(suffixReverse.getTrueButton(), sgbc);
+ return suffixPanel;
+ }
+
+ private boolean confirmSuffixReverseChange()
+ {
+ boolean ret = false;
+ String warningMessage = MessageManager
+ .getString("label.warning_confirm_change_reverse");
+ int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
+ warningMessage,
+ MessageManager.getString("label.change_increment_decrement"),
+ JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
+
+ ret = (confirm == JvOptionPane.YES_OPTION);
+ return ret;
+ }
+
+ private JPanel initBackupsTabKeepFilesPanel()
+ {
+ keepfilesPanel.setBorder(
+ new TitledBorder(MessageManager.getString("label.keep_files")));
+ keepfilesPanel.setLayout(new GridBagLayout());
+
+ backupfilesKeepAll.setLabels(
+ MessageManager.getString("label.keep_all_backup_files"),
+ MessageManager.getString(
+ "label.keep_only_this_number_of_backup_files"));
+ backupfilesKeepAll.addTrueActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- editLink_actionPerformed(e);
+ backupfilesRevertButtonSetEnabled(true);
+ updateBackupFilesExampleLabel();
}
});
- deleteLink.setText("Delete");
- deleteLink.addActionListener(new java.awt.event.ActionListener()
+ backupfilesKeepAll.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- deleteLink_actionPerformed(e);
+ backupfilesRevertButtonSetEnabled(true);
+ keepRollMaxOptionsEnabled();
+ updateBackupFilesExampleLabel();
}
});
- linkURLList.addListSelectionListener(new ListSelectionListener()
+ ChangeListener c = new ChangeListener()
{
- public void valueChanged(ListSelectionEvent e)
+ @Override
+ public void stateChanged(ChangeEvent e)
{
- int index = linkURLList.getSelectedIndex();
- linkNameList.setSelectedIndex(index);
+ backupfilesRevertButtonSetEnabled(true);
+ updateBackupFilesExampleLabel();
}
- });
- linkNameList.addListSelectionListener(new ListSelectionListener()
+ };
+ setIntegerSpinner(backupfilesRollMaxSpinner,
+ BackupFilesPresetEntry.ROLLMAXMIN,
+ BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c);
+
+ backupfilesConfirmDelete.setLabels(
+ MessageManager.getString("label.always_ask"),
+ MessageManager.getString("label.auto_delete"));
+ backupfilesConfirmDelete.addActionListener(new ActionListener()
{
- public void valueChanged(ListSelectionEvent e)
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- int index = linkNameList.getSelectedIndex();
- linkURLList.setSelectedIndex(index);
+ backupfilesRevertButtonSetEnabled(true);
}
});
+ // update the enabled section
+ keepRollMaxOptionsEnabled();
+
+ GridBagConstraints kgbc = new GridBagConstraints();
+
+ // first row (template text box)
+ kgbc.anchor = GridBagConstraints.WEST;
+ kgbc.gridx = 0;
+ kgbc.gridy = 0;
+ kgbc.gridwidth = GridBagConstraints.REMAINDER;
+ kgbc.gridheight = 1;
+ kgbc.weightx = 1.0;
+ kgbc.weighty = 0.0;
+ kgbc.fill = GridBagConstraints.HORIZONTAL;
+ keepfilesPanel.add(backupfilesKeepAll.getTrueButton(), kgbc);
+
+ // second row
+ kgbc.gridy = 1;
+
+ kgbc.gridx = 0;
+ kgbc.gridwidth = GridBagConstraints.RELATIVE;
+ keepfilesPanel.add(backupfilesKeepAll.getFalseButton(), kgbc);
+
+ kgbc.gridx = 1;
+ kgbc.gridwidth = GridBagConstraints.REMAINDER;
+ keepfilesPanel.add(backupfilesRollMaxSpinner, kgbc);
+
+ // third row (indented)
+ kgbc.gridy = 2;
+ kgbc.insets = new Insets(0, 20, 0, 0);
+
+ kgbc.gridx = 0;
+ kgbc.gridwidth = GridBagConstraints.REMAINDER;
+ kgbc.fill = GridBagConstraints.HORIZONTAL;
+ kgbc.weightx = 1.0;
+
+ JPanel jp = new JPanel();
+ jp.setLayout(new FlowLayout());
+ oldBackupFilesLabel.setText(
+ MessageManager.getString("label.autodelete_old_backup_files"));
+ oldBackupFilesLabel.setFont(LABEL_FONT);
+ oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ jp.add(oldBackupFilesLabel);
+ jp.add(backupfilesConfirmDelete.getTrueButton());
+ jp.add(backupfilesConfirmDelete.getFalseButton());
+ keepfilesPanel.add(jp, kgbc);
+
+ return keepfilesPanel;
+ }
- linkScrollPane.setBorder(null);
- linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
- linkPanel.setLayout(borderLayout2);
- editLinkButtons.setLayout(gridLayout1);
- gridLayout1.setRows(3);
- linkNameList.setFont(verdana11);
- linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
- linkPanel2.setLayout(borderLayout3);
- linkURLList.setFont(verdana11);
- linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-
- defaultBrowser.addMouseListener(new MouseAdapter()
+ protected void updateBackupFilesExampleLabel()
+ {
+ int exampleindex = 12;
+ String base = MessageManager.getString("label.filename") + ".fa";
+ if (base == null || base.length() == 0)
{
- public void mouseClicked(MouseEvent e)
+ base = "file_name.fa";
+ }
+
+ boolean reverse = suffixReverse.isSelected();
+ boolean keepAll = backupfilesKeepAll.isSelected();
+ int rollMax = 4;
+ String suffix = suffixTemplate.getText();
+ int digits = 3;
+
+ backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC);
+ if (suffix == null || suffix.length() == 0)
+ {
+ backupfilesExampleLabel
+ .setText(MessageManager.getString("label.no_backup_files"));
+ backupfilesExampleLabel.setFont(LABEL_FONT_BOLD);
+ return;
+ }
+
+ rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 4);
+ rollMax = rollMax < 1 ? 1 : rollMax;
+
+ if (suffix.indexOf(BackupFiles.NUM_PLACEHOLDER) == -1)
+ {
+ rollMax = 1;
+ }
+
+ digits = getSpinnerInt(suffixDigitsSpinner, 3);
+ digits = digits < 1 ? 1 : digits;
+
+ int lowersurround = 2;
+ int uppersurround = 0;
+ StringBuilder exampleSB = new StringBuilder();
+ boolean firstLine = true;
+ int lineNumber = 0;
+ if (reverse)
+ {
+
+ int min = 1;
+ int max = keepAll ? exampleindex : rollMax;
+ for (int index = min; index <= max; index++)
{
- if (e.getClickCount() > 1)
+ if (index == min + lowersurround && index < max - uppersurround - 1)
+ {
+ exampleSB.append("\n...");
+ lineNumber++;
+ }
+ else if (index > min + lowersurround && index < max - uppersurround)
+ {
+ // nothing
+ }
+ else
{
- defaultBrowser_mouseClicked(e);
+ if (firstLine)
+ {
+ firstLine = false;
+ }
+ else
+ {
+ exampleSB.append("\n");
+ lineNumber++;
+ }
+ exampleSB.append(BackupFilenameParts.getBackupFilename(index,
+ base, suffix, digits));
+ if (min == max)
+ {
+ // no extra text needed
+ }
+ else if (index == min)
+ {
+ String newest = MessageManager.getString("label.braced_newest");
+ if (newest != null && newest.length() > 0)
+ {
+ exampleSB.append(" " + newest);
+ }
+ }
+ else if (index == max)
+ {
+ String oldest = MessageManager.getString("label.braced_oldest");
+ if (oldest != null && oldest.length() > 0)
+ {
+ exampleSB.append(" " + oldest);
+ }
+ }
}
}
- });
- useProxy.setFont(verdana11);
- useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
- useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
- useProxy.setText("Use a proxy server");
- useProxy.addActionListener(new ActionListener()
+ }
+ else
{
- public void actionPerformed(ActionEvent e)
+
+ int min = (keepAll || exampleindex - rollMax < 0) ? 1
+ : exampleindex - rollMax + 1;
+ int max = exampleindex;
+
+ for (int index = min; index <= max; index++)
{
- useProxy_actionPerformed();
+
+ if (index == min + lowersurround && index < max - uppersurround - 1)
+ {
+ exampleSB.append("\n...");
+ lineNumber++;
+ }
+ else if (index > min + lowersurround && index < max - uppersurround)
+ {
+ // nothing
+ }
+ else
+ {
+ if (firstLine)
+ {
+ firstLine = false;
+ }
+ else
+ {
+ exampleSB.append("\n");
+ lineNumber++;
+ }
+ exampleSB.append(BackupFilenameParts.getBackupFilename(index,
+ base, suffix, digits));
+ if (min == max)
+ {
+ // no extra text needed
+ }
+ else if (index == min)
+ {
+ String oldest = MessageManager.getString("label.braced_oldest");
+ if (oldest != null && oldest.length() > 0)
+ {
+ exampleSB.append(" " + oldest);
+ }
+ }
+ else if (index == max)
+ {
+ String newest = MessageManager.getString("label.braced_newest");
+ if (newest != null && newest.length() > 0)
+ {
+ exampleSB.append(" " + newest);
+ }
+ }
+ }
}
- });
- jPanel1.setBorder(titledBorder1);
- jPanel1.setLayout(gridBagLayout1);
- sortby.setFont(verdana11);
- sortby.setBounds(new Rectangle(172, 249, 155, 21));
- sortLabel.setFont(verdana11);
- sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- sortLabel.setText("Sort by ");
- jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
- jPanel2.setLayout(gridLayout2);
- gridLayout2.setRows(12);
- exportTab.setLayout(null);
- epsLabel.setFont(verdana11);
- epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- epsLabel.setText("EPS Rendering Style");
- epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
- epsRendering.setFont(verdana11);
- epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
- jLabel1.setFont(verdana11);
- jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
- jLabel1.setText("Append /start-end (/15-380)");
- jLabel1.setFont(verdana11);
- fastajv.setFont(verdana11);
- fastajv.setHorizontalAlignment(SwingConstants.LEFT);
- clustaljv.setText("Clustal ");
- blcjv.setText("BLC ");
- fastajv.setText("Fasta ");
- msfjv.setText("MSF ");
- pfamjv.setText("PFAM ");
- pileupjv.setText("Pileup ");
- msfjv.setFont(verdana11);
- msfjv.setHorizontalAlignment(SwingConstants.LEFT);
- pirjv.setText("PIR ");
- jPanel11.setFont(verdana11);
- jPanel11.setBorder(titledBorder2);
- jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
- jPanel11.setLayout(gridLayout3);
- blcjv.setFont(verdana11);
- blcjv.setHorizontalAlignment(SwingConstants.LEFT);
- clustaljv.setFont(verdana11);
- clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
- pfamjv.setFont(verdana11);
- pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
- pileupjv.setFont(verdana11);
- pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
- pirjv.setFont(verdana11);
- pirjv.setHorizontalAlignment(SwingConstants.LEFT);
- seqLimit.setFont(verdana11);
- seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
- seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
- seqLimit.setText("Full Sequence Id");
- gridLayout3.setRows(8);
- smoothFont.setFont(verdana11);
- smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
- smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
- smoothFont.setText("Smooth Font");
- calcTab.setLayout(null);
- autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
- autoCalculateConsCheck.setText("AutoCalculate Consensus");
- autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
- padGaps.setFont(JvSwingUtils.getLabelFont());
- padGaps.setText("Pad Gaps When Editing");
- padGaps.setBounds(new Rectangle(22, 94, 168, 23));
- sortByTree.setFont(JvSwingUtils.getLabelFont());
- sortByTree.setText("Sort With New Tree");
- sortByTree.setToolTipText("When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.");
- sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
-
- autoIdWidth.setFont(JvSwingUtils.getLabelFont());
- autoIdWidth.setText("Automatically set ID width");
- autoIdWidth.setToolTipText("<html>"+JvSwingUtils.wrapTooltip("Adjusts the width of the generated EPS or PNG file to ensure even the longest sequence ID or annotation label is displayed")+"</html>");
- autoIdWidth.setBounds(new Rectangle(228, 96,188,23));
- autoIdWidth.addActionListener(new ActionListener()
+
+ }
+
+ // add some extra empty lines to pad out the example files box. ugh, please
+ // tell
+ // me how to do this better
+ int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
+ if (remainingLines > 0)
{
-
- @Override
- public void actionPerformed(ActionEvent e)
+ for (int i = 0; i < remainingLines; i++)
{
- autoIdWidth_actionPerformed();
+ exampleSB.append("\n ");
+ lineNumber++;
}
- });
- userIdWidthlabel.setFont(JvSwingUtils.getLabelFont());
- userIdWidthlabel.setText("Figure ID column width");
- userIdWidth
- .setToolTipText("<html>"+JvSwingUtils
- .wrapTooltip("Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set")+"</html>");
- userIdWidthlabel
- .setToolTipText("<html>"+JvSwingUtils
- .wrapTooltip("Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set")+"</html>");
- userIdWidthlabel.setBounds(new Rectangle(236, 120,168,23));
- userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
- userIdWidth.setText("");
- userIdWidth.setBounds(new Rectangle(232,144,84,23));
- userIdWidth.addActionListener(new ActionListener()
+ }
+
+ backupfilesExampleLabel.setText(exampleSB.toString());
+ }
+
+ protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
+ boolean useExistingVal, ChangeListener c)
+ {
+ int i = def;
+ if (useExistingVal)
{
-
- @Override
- public void actionPerformed(ActionEvent e)
+ try
{
- userIdWidth_actionPerformed();
+ i = ((Integer) s.getValue()).intValue();
+ } catch (Exception e)
+ {
+ Console.error(
+ "Exception casting the initial value of s.getValue()");
}
- });
- modellerOutput.setFont(JvSwingUtils.getLabelFont());
- modellerOutput.setText("Use Modeller Output");
- modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+ }
- dasPanel.setLayout(borderLayout4);
- wsPanel.setLayout(borderLayout5);
- wrap.setFont(JvSwingUtils.getLabelFont());
- wrap.setHorizontalAlignment(SwingConstants.TRAILING);
- wrap.setHorizontalTextPosition(SwingConstants.LEADING);
- wrap.setText("Wrap Alignment");
- rightAlign.setFont(JvSwingUtils.getLabelFont());
- rightAlign.setForeground(Color.black);
- rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
- rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
- rightAlign.setText("Right Align Ids");
- idItalics.setFont(JvSwingUtils.getLabelFont());
- idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
- idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
- idItalics.setText("Sequence Name Italics");
- openoverv.setFont(JvSwingUtils.getLabelFont());
- openoverv.setActionCommand("Open Overview");
- openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
- openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
- openoverv.setText("Open Overview");
- jPanel2.add(fullScreen);
- jPanel2.add(openoverv);
- jPanel2.add(seqLimit);
- jPanel2.add(rightAlign);
- jPanel2.add(fontLabel);
- jPanel2.add(showUnconserved);
- jPanel2.add(idItalics);
- jPanel2.add(smoothFont);
- jPanel2.add(gapLabel);
- jPanel2.add(wrap);
- jPanel2.add(sortLabel);
- jPanel2.add(startupCheckbox);
- visualTab.add(annotations);
- visualTab.add(startupFileTextfield);
- visualTab.add(sortby);
- visualTab.add(gapSymbolCB);
- visualTab.add(fontNameCB);
- visualTab.add(fontSizeCB);
- visualTab.add(fontStyleCB);
- annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
- annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
- annsettingsPanel.add(autoAnnotSettings1);
- annsettingsPanel.add(autoAnnotSettings2);
- annsettingsPanel.add(autoAnnotSettings3);
- autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
- autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
- autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
- visualTab.add(annsettingsPanel);
- Border jb = new EmptyBorder(1, 1, 4, 5);
- quality.setBorder(jb);
- conservation.setBorder(jb);
- identity.setBorder(jb);
- showConsensbits.setBorder(jb);
- showGroupbits.setBorder(jb);
- showGroupConsensus.setBorder(jb);
- showGroupConservation.setBorder(jb);
- showConsensHistogram.setBorder(jb);
- showConsensLogo.setBorder(jb);
+ setIntegerSpinner(s, min, max, i, c);
+ }
- autoAnnotSettings2.add(conservation);
- autoAnnotSettings1.add(quality);
- autoAnnotSettings3.add(identity);
- autoAnnotSettings1.add(showGroupbits);
- autoAnnotSettings3.add(showGroupConsensus);
- autoAnnotSettings2.add(showGroupConservation);
- autoAnnotSettings1.add(showConsensbits);
- autoAnnotSettings2.add(showConsensHistogram);
- autoAnnotSettings3.add(showConsensLogo);
+ protected void setIntegerSpinner(JSpinner s, int min, int max, int def,
+ ChangeListener c)
+ {
+ // integer spinner for number of digits
+ if (def > max)
+ {
+ max = def;
+ }
+ if (def < min)
+ {
+ def = min;
+ }
+ SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
+ s.setModel(sModel);
- JPanel tooltipSettings = new JPanel();
- tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
- tooltipSettings.setBounds(173, 130, 200, 62);
- tooltipSettings.setLayout(new GridLayout(2, 1));
- tooltipSettings.add(showDbRefTooltip);
- tooltipSettings.add(showNpTooltip);
- visualTab.add(tooltipSettings);
- visualTab.add(jPanel2);
- JvSwingUtils.addtoLayout(visual2Tab, "Default Colourscheme for alignment", colourLabel, colour);
- JPanel annotationShding=new JPanel();
- annotationShding.setBorder(new TitledBorder("Annotation Shading Default"));
- annotationShding.setLayout(new GridLayout(1,2));
- JvSwingUtils.addtoLayout(annotationShding, "Default Minimum Colour for annotation shading", mincolourLabel,minColour);
- JvSwingUtils.addtoLayout(annotationShding,"Default Maximum Colour for annotation shading", maxcolourLabel, maxColour);
- visual2Tab.add(annotationShding); // , FlowLayout.LEFT);
-
-// visual2panel.add(minColour);
-// visual2panel.add(maxColour);
-// visual2Tab.add(visual2panel);
-
- linkPanel.add(editLinkButtons, BorderLayout.EAST);
- editLinkButtons.add(newLink, null);
- editLinkButtons.add(editLink, null);
- editLinkButtons.add(deleteLink, null);
- linkPanel.add(linkScrollPane, BorderLayout.CENTER);
- linkScrollPane.getViewport().add(linkPanel2, null);
- linkPanel2.add(linkURLList, BorderLayout.CENTER);
- linkPanel2.add(linkNameList, BorderLayout.WEST);
- okCancelPanel.add(ok);
- okCancelPanel.add(cancel);
- this.add(tabbedPane, java.awt.BorderLayout.CENTER);
-
- this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
- jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 2, 4, 0), 5, 0));
- jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 0, 4, 0), 11, 6));
- connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
- 16, 0, 0, 12), 359, -17));
- connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
- 21, 0, 35, 12), 4, 6));
- connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
- new Insets(16, 0, 0, 0), 5, 1));
- jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 54, 1));
- jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 0), 263, 1));
- connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(15, 0, 0, 15), 307, 1));
- connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 70, 1));
- connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 70, 1));
- connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 4, 2), 70, 1));
-
- jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 2, 5, 185), 2, -4));
- DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
- dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
- gapSymbolCB.setRenderer(dlcr);
+ s.addChangeListener(c);
- tabbedPane.add(visualTab, "Visual");
- tabbedPane.add(visual2Tab,"Colours");
- tabbedPane.add(connectTab, "Connections");
- tabbedPane.add(exportTab, "Output");
- jPanel11.add(jLabel1);
- jPanel11.add(blcjv);
- jPanel11.add(clustaljv);
- jPanel11.add(fastajv);
- jPanel11.add(msfjv);
- jPanel11.add(pfamjv);
- jPanel11.add(pileupjv);
- jPanel11.add(pirjv);
- exportTab.add(autoIdWidth);
- exportTab.add(userIdWidth);
- exportTab.add(userIdWidthlabel);
- exportTab.add(modellerOutput);
- tabbedPane.add(calcTab, "Editing");
- calcTab.add(autoCalculateConsCheck);
- calcTab.add(padGaps);
- calcTab.add(sortByTree);
-
- tabbedPane.add(dasPanel, "DAS Settings");
- tabbedPane.add(wsPanel, "Web Services");
-
- exportTab.add(epsLabel);
- exportTab.add(epsRendering);
- exportTab.add(jPanel11);
+ }
+
+ protected static int getSpinnerInt(JSpinner s, int def)
+ {
+ int i = def;
+ try
+ {
+ s.commitEdit();
+ i = (Integer) s.getValue();
+ } catch (Exception e)
+ {
+ Console.error("Failed casting (Integer) JSpinner s.getValue()");
+ }
+ return i;
+ }
+
+ private void keepRollMaxOptionsEnabled()
+ {
+ boolean enabled = backupfilesKeepAll.isEnabled()
+ && !backupfilesKeepAll.isSelected();
+ oldBackupFilesLabel.setEnabled(enabled);
+ backupfilesRollMaxSpinner.setEnabled(enabled);
+ backupfilesConfirmDelete.setEnabled(enabled);
+ }
+
+ private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
+ {
+ boolean enabled = tryEnabled && enableBackupFiles.isSelected()
+ && customiseCheckbox.isSelected() && suffixTemplate.getText()
+ .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
+ keepfilesPanel.setEnabled(enabled);
+ backupfilesKeepAll.setEnabled(enabled);
+ oldBackupFilesLabel.setEnabled(enabled);
+ keepRollMaxOptionsEnabled();
+ }
+
+ private void backupfilesSuffixTemplateDigitsSetEnabled()
+ {
+ boolean enabled = suffixTemplate.isEnabled() && suffixTemplate.getText()
+ .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
+ suffixDigitsLabel.setEnabled(enabled);
+ suffixDigitsSpinner.setEnabled(enabled);
+ suffixReverse.setEnabled(enabled);
+ }
+
+ private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled)
+ {
+ boolean enabled = tryEnabled && enableBackupFiles.isSelected()
+ && customiseCheckbox.isSelected();
+ suffixPanel.setEnabled(enabled);
+ suffixTemplateLabel.setEnabled(enabled);
+ suffixTemplate.setEnabled(enabled);
+ backupfilesSuffixTemplateDigitsSetEnabled();
+ }
+
+ private void backupfilesRevertButtonSetEnabled(boolean tryEnabled)
+ {
+ boolean enabled = tryEnabled && enableBackupFiles.isSelected()
+ && customiseCheckbox.isSelected() && backupfilesCustomChanged();
+ revertButton.setEnabled(enabled);
+ }
+
+ private boolean backupfilesCustomChanged()
+ {
+ BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
+ BackupFilesPresetEntry current = getBackupfilesCurrentEntry();
+ return !custom.equals(current);
+ }
+
+ protected BackupFilesPresetEntry getBackupfilesCurrentEntry()
+ {
+ String suffix = suffixTemplate.getText();
+ int digits = getSpinnerInt(suffixDigitsSpinner, 3);
+ boolean reverse = suffixReverse.isSelected();
+ boolean keepAll = backupfilesKeepAll.isSelected();
+ int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3);
+ boolean confirmDelete = backupfilesConfirmDelete.isSelected();
+
+ BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
+ reverse, keepAll, rollMax, confirmDelete);
+
+ return bfpe;
+ }
+
+ protected void backupfilesCustomOptionsSetEnabled()
+ {
+ boolean enabled = customiseCheckbox.isSelected();
+
+ backupfilesRevertButtonSetEnabled(enabled);
+ backupfilesSuffixTemplateSetEnabled(enabled);
+ backupfilesKeepAllSetEnabled(enabled);
+ }
+
+ private void backupfilesSummarySetEnabled()
+ {
+ boolean enabled = enableBackupFiles.isSelected();
+ backupfilesExampleLabel.setEnabled(enabled);
+ exampleFilesPanel.setEnabled(enabled);
+ }
+
+ private void backupfilesPresetsSetEnabled()
+ {
+ boolean enabled = enableBackupFiles.isSelected();
+ presetsPanel.setEnabled(enabled);
+ presetsComboLabel.setEnabled(enabled);
+ backupfilesPresetsCombo.setEnabled(enabled);
+ customiseCheckbox.setEnabled(enabled);
+ revertButton.setEnabled(enabled);
+ }
+
+ protected void backupsOptionsSetEnabled()
+ {
+ backupfilesPresetsSetEnabled();
+ backupfilesSummarySetEnabled();
+ backupfilesCustomOptionsSetEnabled();
+ }
+
+ protected void backupsSetOptions(String suffix, int digits,
+ boolean reverse, boolean keepAll, int rollMax,
+ boolean confirmDelete)
+ {
+ suffixTemplate.setText(suffix);
+ suffixDigitsSpinner.setValue(digits);
+ suffixReverse.setSelected(reverse);
+ backupfilesKeepAll.setSelected(keepAll);
+ backupfilesRollMaxSpinner.setValue(rollMax);
+ backupfilesConfirmDelete.setSelected(confirmDelete);
+ }
+
+ protected void backupsSetOptions(BackupFilesPresetEntry p)
+ {
+ backupsSetOptions(p.suffix, p.digits, p.reverse, p.keepAll, p.rollMax,
+ p.confirmDelete);
}
protected void autoIdWidth_actionPerformed()
{
// TODO Auto-generated method stub
-
+
}
protected void userIdWidth_actionPerformed()
{
// TODO Auto-generated method stub
-
+
}
- protected void maxColour_actionPerformed()
+ protected void maxColour_actionPerformed(JPanel panel)
{
- // TODO Auto-generated method stub
-
}
- protected void minColour_actionPerformed()
+ protected void minColour_actionPerformed(JPanel panel)
+ {
+ }
+
+ protected void gapColour_actionPerformed(JPanel panel)
+ {
+ }
+
+ protected void hiddenColour_actionPerformed(JPanel panel)
{
- // TODO Auto-generated method stub
-
}
protected void showunconserved_actionPerformed(ActionEvent e)
}
+ protected void useLegacyGaps_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void resetOvDefaults_actionPerformed(ActionEvent e)
+ {
+ }
+
/**
* DOCUMENT ME!
*
}
- public void defaultBrowser_mouseClicked(MouseEvent e)
+ public void linkURLList_keyTyped(KeyEvent e)
{
}
- public void linkURLList_keyTyped(KeyEvent e)
+ public void setProxyAuthEnabled()
+ {
+ boolean enabled = proxyAuth.isSelected() && proxyAuth.isEnabled();
+ proxyAuthUsernameLabel.setEnabled(enabled);
+ proxyAuthPasswordLabel.setEnabled(enabled);
+ passwordNotStoredLabel.setEnabled(enabled);
+ proxyAuthUsernameTB.setEnabled(enabled);
+ proxyAuthPasswordPB.setEnabled(enabled);
+ }
+
+ public void setCustomProxyEnabled()
+ {
+ boolean enabled = customProxy.isSelected();
+ portLabel.setEnabled(enabled);
+ serverLabel.setEnabled(enabled);
+ portLabel2.setEnabled(enabled);
+ serverLabel2.setEnabled(enabled);
+ httpLabel.setEnabled(enabled);
+ httpsLabel.setEnabled(enabled);
+ proxyServerHttpTB.setEnabled(enabled);
+ proxyPortHttpTB.setEnabled(enabled);
+ proxyServerHttpsTB.setEnabled(enabled);
+ proxyPortHttpsTB.setEnabled(enabled);
+ proxyAuth.setEnabled(enabled);
+ setProxyAuthEnabled();
+ }
+
+ public void proxyType_actionPerformed()
{
+ setCustomProxyEnabled();
+ proxyAuthPasswordCheckHighlight(true);
+ applyProxyButtonEnabled(true);
+ }
+ public void proxyAuth_actionPerformed()
+ {
+ setProxyAuthEnabled();
+ proxyAuthPasswordCheckHighlight(true);
+ applyProxyButtonEnabled(true);
}
- public void useProxy_actionPerformed()
+ /**
+ * Customer renderer for JTable: supports column of radio buttons
+ */
+ public class RadioButtonRenderer extends JRadioButton
+ implements TableCellRenderer
{
- proxyServerTB.setEnabled(useProxy.isSelected());
- proxyPortTB.setEnabled(useProxy.isSelected());
+ public RadioButtonRenderer()
+ {
+ setHorizontalAlignment(CENTER);
+ setToolTipText(MessageManager.getString("label.urltooltip"));
+ }
+
+ @Override
+ public Component getTableCellRendererComponent(JTable table,
+ Object value, boolean isSelected, boolean hasFocus, int row,
+ int column)
+ {
+ setSelected((boolean) value);
+
+ // set colours to match rest of table
+ if (isSelected)
+ {
+ setBackground(table.getSelectionBackground());
+ setForeground(table.getSelectionForeground());
+ }
+ else
+ {
+ setBackground(table.getBackground());
+ setForeground(table.getForeground());
+ }
+ return this;
+ }
}
+ /**
+ * Customer cell editor for JTable: supports column of radio buttons in
+ * conjunction with renderer
+ */
+ public class RadioButtonEditor extends AbstractCellEditor
+ implements TableCellEditor
+ {
+ private JRadioButton button = new JRadioButton();
+
+ public RadioButtonEditor()
+ {
+ button.setHorizontalAlignment(SwingConstants.CENTER);
+ this.button.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ fireEditingStopped();
+ }
+ });
+ }
+
+ @Override
+ public Component getTableCellEditorComponent(JTable table, Object value,
+ boolean isSelected, int row, int column)
+ {
+ button.setSelected((boolean) value);
+ return button;
+ }
+
+ @Override
+ public Object getCellEditorValue()
+ {
+ return button.isSelected();
+ }
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff