/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
package jalview.jbgui;
import jalview.gui.JvSwingUtils;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource;
import jalview.util.MessageManager;
-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.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.BorderFactory;
+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.JList;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTabbedPane;
+import javax.swing.JTextField;
+import javax.swing.ListSelectionModel;
+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.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
/**
- * DOCUMENT ME!
+ * Base class for the Preferences panel.
*
* @author $author$
* @version $Revision$
*/
public class GPreferences extends JPanel
{
- JTabbedPane tabbedPane = new JTabbedPane();
-
- JButton ok = new JButton();
-
- JButton cancel = new JButton();
-
- JPanel okCancelPanel = new JPanel();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- protected JCheckBox quality = new JCheckBox();
-
- JPanel visualTab = new JPanel();
+ private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
- JPanel visual2Tab = new JPanel();
+ private static final Font LABEL_FONT_ITALIC = JvSwingUtils.getLabelFont(
+ false, true);
+ /*
+ * Visual tab components
+ */
protected JCheckBox fullScreen = new JCheckBox();
- protected JCheckBox conservation = new JCheckBox();
+ protected JCheckBox openoverv = new JCheckBox();
- protected JCheckBox identity = new JCheckBox();
+ protected JCheckBox seqLimit = new JCheckBox();
- protected JCheckBox annotations = new JCheckBox();
+ protected JCheckBox rightAlign = new JCheckBox();
- protected JPanel minColour = new JPanel();
+ protected JComboBox<String> fontSizeCB = new JComboBox<String>();
- JLabel mincolourLabel = new JLabel();
+ protected JComboBox<String> fontStyleCB = new JComboBox<String>();
- protected JPanel maxColour = new JPanel();
+ protected JComboBox<String> fontNameCB = new JComboBox<String>();
- JLabel maxcolourLabel = new JLabel();
+ protected JCheckBox showUnconserved = new JCheckBox();
- JLabel gapLabel = new JLabel();
+ protected JCheckBox idItalics = new JCheckBox();
- protected JComboBox colour = new JComboBox();
+ protected JCheckBox smoothFont = new JCheckBox();
- JLabel colourLabel = new JLabel();
+ protected JCheckBox scaleProteinToCdna = new JCheckBox();
- JLabel fontLabel = new JLabel();
+ protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
- protected JComboBox fontSizeCB = new JComboBox();
+ protected JCheckBox wrap = new JCheckBox();
- protected JComboBox fontStyleCB = new JComboBox();
+ protected JComboBox<String> sortby = new JComboBox<String>();
- protected JComboBox fontNameCB = new JComboBox();
+ protected JComboBox<String> sortAnnBy = new JComboBox<String>();
- protected JComboBox gapSymbolCB = new JComboBox();
+ protected JComboBox<String> sortAutocalc = new JComboBox<String>();
protected JCheckBox startupCheckbox = new JCheckBox();
protected JTextField startupFileTextfield = new JTextField();
- JPanel connectTab = new JPanel();
-
- JLabel serverLabel = new JLabel();
-
- protected JList linkURLList = new JList();
-
- protected JTextField proxyServerTB = new JTextField();
-
- protected JTextField proxyPortTB = new JTextField();
-
- JLabel portLabel = new JLabel();
-
- JLabel browserLabel = new JLabel();
-
- protected JTextField defaultBrowser = new JTextField();
-
- JButton newLink = new JButton();
+ // below are in the 'second column'
+ protected JCheckBox annotations = new JCheckBox();
- JButton editLink = new JButton();
+ protected JCheckBox quality = new JCheckBox();
- JButton deleteLink = new JButton();
+ protected JCheckBox conservation = new JCheckBox();
- JScrollPane linkScrollPane = new JScrollPane();
+ protected JCheckBox identity = new JCheckBox();
- JPanel linkPanel = new JPanel();
+ protected JCheckBox showGroupConsensus = new JCheckBox();
- BorderLayout borderLayout2 = new BorderLayout();
+ protected JCheckBox showGroupConservation = new JCheckBox();
- JPanel editLinkButtons = new JPanel();
+ protected JCheckBox showConsensHistogram = new JCheckBox();
- GridLayout gridLayout1 = new GridLayout();
+ protected JCheckBox showConsensLogo = new JCheckBox();
- protected JList linkNameList = new JList();
+ protected JCheckBox showDbRefTooltip = new JCheckBox();
- JPanel linkPanel2 = new JPanel();
+ protected JCheckBox showNpTooltip = new JCheckBox();
- BorderLayout borderLayout3 = new BorderLayout();
+ /*
+ * Structure tab and components
+ */
+ protected JPanel structureTab;
- protected JCheckBox useProxy = new JCheckBox();
+ protected JCheckBox structFromPdb = new JCheckBox();
- JPanel jPanel1 = new JPanel();
+ protected JCheckBox useRnaView = new JCheckBox();
- TitledBorder titledBorder1 = new TitledBorder(MessageManager.getString("label.proxy_server"));
+ protected JCheckBox addSecondaryStructure = new JCheckBox();
- TitledBorder titledBorder2 = new TitledBorder(MessageManager.getString("label.file_output"));
+ protected JCheckBox addTempFactor = new JCheckBox();
- GridBagLayout gridBagLayout2 = new GridBagLayout();
+ protected JComboBox<String> structViewer = new JComboBox<String>();
- GridBagLayout gridBagLayout1 = new GridBagLayout();
+ protected JTextField chimeraPath = new JTextField();
- GridBagLayout gridBagLayout3 = new GridBagLayout();
+ /*
+ * Colours tab components
+ */
+ protected JPanel minColour = new JPanel();
- protected JComboBox sortby = new JComboBox();
+ protected JPanel maxColour = new JPanel();
- JLabel sortLabel = new JLabel();
+ protected JComboBox<String> protColour = new JComboBox<String>();
- JPanel jPanel2 = new JPanel();
+ protected JComboBox<String> nucColour = new JComboBox<String>();
- JPanel visual2panel = new JPanel();
+ /*
+ * Connections tab components
+ */
+ protected JList linkURLList = new JList();
- GridLayout gridLayout2 = new GridLayout();
+ protected JTextField proxyServerTB = new JTextField();
- GridLayout gridLayout4 = new GridLayout();
+ protected JTextField proxyPortTB = new JTextField();
- JPanel annsettingsPanel = new JPanel();
+ protected JTextField defaultBrowser = new JTextField();
- JPanel autoAnnotSettings1 = new JPanel();
+ protected JList linkNameList = new JList();
- JPanel autoAnnotSettings2 = new JPanel();
+ protected JCheckBox useProxy = new JCheckBox();
- JPanel autoAnnotSettings3 = new JPanel();
+ protected JCheckBox usagestats = new JCheckBox();
- JPanel exportTab = new JPanel();
+ protected JCheckBox questionnaire = new JCheckBox();
- JLabel epsLabel = new JLabel();
+ protected JCheckBox versioncheck = new JCheckBox();
- protected JComboBox epsRendering = new JComboBox();
+ /*
+ * Output tab components
+ */
+ protected JComboBox<String> epsRendering = new JComboBox<String>();
protected JLabel userIdWidthlabel = new JLabel();
protected JTextField userIdWidth = new JTextField();
- JLabel jLabel1 = new JLabel();
-
protected JCheckBox blcjv = new JCheckBox();
protected JCheckBox pileupjv = new JCheckBox();
protected JCheckBox pfamjv = new JCheckBox();
- FlowLayout flowLayout1 = new FlowLayout();
-
protected JCheckBox pirjv = new JCheckBox();
- JPanel jPanel11 = new JPanel();
-
- Font verdana11 = JvSwingUtils.getLabelFont();
-
- protected JCheckBox seqLimit = new JCheckBox();
-
- GridLayout gridLayout3 = new GridLayout();
-
- protected JCheckBox smoothFont = new JCheckBox();
+ protected JCheckBox modellerOutput = new JCheckBox();
- JPanel calcTab = new JPanel();
+ protected JCheckBox embbedBioJSON = new JCheckBox();
+ /*
+ * Editing tab components
+ */
protected JCheckBox autoCalculateConsCheck = new JCheckBox();
protected JCheckBox padGaps = new JCheckBox();
- protected JCheckBox modellerOutput = new JCheckBox();
-
- protected JPanel dasPanel = new JPanel();
-
- BorderLayout borderLayout4 = new BorderLayout();
-
- protected JPanel wsPanel = new JPanel();
-
- BorderLayout borderLayout5 = new BorderLayout();
-
- protected JCheckBox wrap = new JCheckBox();
-
- protected JCheckBox rightAlign = new JCheckBox();
-
- protected JCheckBox showUnconserved = new JCheckBox();
-
- protected JCheckBox showDbRefTooltip = new JCheckBox();
-
- protected JCheckBox showNpTooltip = new JCheckBox();
-
- protected JCheckBox idItalics = new JCheckBox();
-
- protected JCheckBox openoverv = new JCheckBox();
-
- protected JCheckBox usagestats = new JCheckBox();
-
- protected JCheckBox questionnaire = new JCheckBox();
-
- protected JCheckBox versioncheck = new JCheckBox();
-
- protected JLabel showGroupbits = new JLabel();
-
- protected JLabel showConsensbits = new JLabel();
-
- protected JCheckBox showConsensLogo = new JCheckBox();
-
- protected JCheckBox showConsensHistogram = new JCheckBox();
-
- protected JCheckBox showGroupConsensus = new JCheckBox();
-
- protected JCheckBox showGroupConservation = new JCheckBox();
-
- protected JCheckBox shareSelections = new JCheckBox();
+ protected JCheckBox sortByTree = new JCheckBox();
- protected JCheckBox followHighlight = new JCheckBox();
+ /*
+ * DAS Settings tab
+ */
+ protected JPanel dasTab = new JPanel();
- protected JCheckBox sortByTree = new JCheckBox();
+ /*
+ * Web Services tab
+ */
+ protected JPanel wsTab = new JPanel();
/**
* 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(MessageManager.getString("action.ok"));
- ok.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- ok_actionPerformed(e);
- }
- });
- cancel.setText(MessageManager.getString("action.cancel"));
- cancel.addActionListener(new ActionListener()
- {
- 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(MessageManager.getString("label.quality"));
- visualTab.setBorder(new TitledBorder(MessageManager.getString("action.open_new_aligmnent")));
- visualTab.setLayout(null);
- visual2Tab.setBorder(new TitledBorder(MessageManager.getString("action.open_new_aligmnent")));
- visual2Tab.setLayout(new FlowLayout());
- fullScreen.setFont(verdana11);
- fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
- fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
- fullScreen.setText(MessageManager.getString("label.maximize_window"));
- conservation.setEnabled(false);
- conservation.setFont(verdana11);
- conservation.setHorizontalAlignment(SwingConstants.RIGHT);
- conservation.setHorizontalTextPosition(SwingConstants.LEFT);
- conservation.setSelected(true);
- conservation.setText(MessageManager.getString("label.conservation"));
- identity.setEnabled(false);
- identity.setFont(verdana11);
- identity.setHorizontalAlignment(SwingConstants.RIGHT);
- identity.setHorizontalTextPosition(SwingConstants.LEFT);
- identity.setSelected(true);
- identity.setText(MessageManager.getString("label.consensus"));
- showGroupbits.setFont(verdana11);
- showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
- showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupbits.setText(MessageManager.getString("action.show_group") + ":");
- showConsensbits.setFont(verdana11);
- showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
- showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showConsensbits.setText(MessageManager.getString("label.consensus") + ":");
- showConsensHistogram.setEnabled(false);
- showConsensHistogram.setFont(verdana11);
- showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
- showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
- showConsensHistogram.setSelected(true);
- showConsensHistogram.setText(MessageManager.getString("label.histogram"));
- showConsensLogo.setEnabled(false);
- showConsensLogo.setFont(verdana11);
- showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
- showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
- showConsensLogo.setSelected(true);
- showConsensLogo.setText(MessageManager.getString("label.logo"));
- showGroupConsensus.setEnabled(false);
- showGroupConsensus.setFont(verdana11);
- showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
- showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupConsensus.setSelected(true);
- showGroupConsensus.setText(MessageManager.getString("label.consensus"));
- showGroupConservation.setEnabled(false);
- showGroupConservation.setFont(verdana11);
- showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
- showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupConservation.setSelected(true);
- showGroupConservation.setText(MessageManager.getString("label.conservation"));
- showNpTooltip.setEnabled(true);
- showNpTooltip.setFont(verdana11);
- showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
- showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
- showNpTooltip.setSelected(true);
- showNpTooltip.setText(MessageManager.getString("label.non_positional_features"));
- showDbRefTooltip.setEnabled(true);
- showDbRefTooltip.setFont(verdana11);
- showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
- showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
- showDbRefTooltip.setSelected(true);
- showDbRefTooltip.setText(MessageManager.getString("label.database_references"));
- annotations.setFont(verdana11);
- annotations.setHorizontalAlignment(SwingConstants.RIGHT);
- annotations.setHorizontalTextPosition(SwingConstants.LEADING);
- annotations.setSelected(true);
- annotations.setText(MessageManager.getString("label.show_annotations"));
- annotations.setBounds(new Rectangle(169, 12, 200, 23));
- annotations.addActionListener(new ActionListener()
+ final JTabbedPane tabbedPane = new JTabbedPane();
+ this.setLayout(new BorderLayout());
+ 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(initStructureTab(),
+ MessageManager.getString("label.structure"));
+
+ tabbedPane.add(initConnectionsTab(),
+ MessageManager.getString("label.connections"));
+
+ tabbedPane.add(initOutputTab(),
+ MessageManager.getString("label.output"));
+
+ tabbedPane.add(initEditingTab(),
+ MessageManager.getString("label.editing"));
+
+ /*
+ * See DasSourceBrowser for the real work of configuring this tab.
+ */
+ dasTab.setLayout(new BorderLayout());
+ tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
+
+ /*
+ * See WsPreferences for the real work of configuring this tab.
+ */
+ wsTab.setLayout(new BorderLayout());
+ tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
+
+ /*
+ * Handler to validate a tab before leaving it - currently only for
+ * Structure.
+ */
+ 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();
}
+
});
- identity.addActionListener(new ActionListener()
+ }
+
+ /**
+ * 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 tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initOutputTab()
+ {
+ JPanel outputTab = new JPanel();
+ outputTab.setLayout(null);
+ JLabel epsLabel = new JLabel();
+ epsLabel.setFont(LABEL_FONT);
+ epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
+ epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
+ epsRendering.setFont(LABEL_FONT);
+ epsRendering.setBounds(new Rectangle(154, 34, 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, 72, 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, 96, 188, 23));
+ autoIdWidth.addActionListener(new ActionListener()
{
+
+ @Override
public void actionPerformed(ActionEvent e)
{
- annotations_actionPerformed(e);
+ autoIdWidth_actionPerformed();
}
});
- showGroupConsensus.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, 120, 168, 23));
+ userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
+ userIdWidth.setText("");
+ userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
+ userIdWidth.addActionListener(new ActionListener()
{
+
+ @Override
public void actionPerformed(ActionEvent e)
{
- annotations_actionPerformed(e);
- }
- });
- showUnconserved.setFont(verdana11);
- showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
- showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
- showUnconserved.setSelected(true);
- showUnconserved.setText(MessageManager.getString("action.show_unconserved"));
- showUnconserved.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- showunconserved_actionPerformed(e);
- }
- });
- // / TODO: fit these in to preferences panel!!!!!
- shareSelections.setFont(verdana11);
- shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
- shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
- shareSelections.setSelected(true);
- shareSelections.setText(MessageManager.getString("label.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(MessageManager.getString("label.scroll_highlighted_regions"));
-
- gapLabel.setFont(verdana11);
- gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
- colour.setFont(verdana11);
- colour.setBounds(new Rectangle(172, 225, 155, 21));
- colourLabel.setFont(verdana11);
- colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- colourLabel.setText(MessageManager.getString("label.alignment_colour") + " ");
- fontLabel.setFont(verdana11);
- fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- fontLabel.setText(MessageManager.getString("label.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);
- mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- mincolourLabel.setText(MessageManager.getString("label.min_colour"));
- minColour.setFont(verdana11);
- minColour.setBorder(BorderFactory.createEtchedBorder());
- minColour.setPreferredSize(new Dimension(40, 20));
- minColour.addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent e)
- {
- minColour_actionPerformed();
- }
- });
- maxcolourLabel.setFont(verdana11);
- maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
- maxColour.setFont(verdana11);
- maxColour.setBorder(BorderFactory.createEtchedBorder());
- maxColour.setPreferredSize(new Dimension(40, 20));
- maxColour.addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent e)
- {
- maxColour_actionPerformed();
+ userIdWidth_actionPerformed();
}
});
+ modellerOutput.setFont(LABEL_FONT);
+ modellerOutput.setText(MessageManager
+ .getString("label.use_modeller_output"));
+ modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+ embbedBioJSON.setFont(LABEL_FONT);
+ embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
+ embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
- startupCheckbox.setText(MessageManager.getString("action.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()
- {
- public void mouseClicked(MouseEvent e)
- {
- if (e.getClickCount() > 1)
- {
- startupFileTextfield_mouseClicked();
- }
- }
- });
+ 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);
+ outputTab.add(embbedBioJSON);
+ outputTab.add(epsLabel);
+ outputTab.add(epsRendering);
+ outputTab.add(jPanel11);
+ return outputTab;
+ }
- connectTab.setLayout(gridBagLayout3);
+ /**
+ * Initialises the Connections tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initConnectionsTab()
+ {
+ JPanel connectTab = new JPanel();
+ connectTab.setLayout(new GridBagLayout());
+ JLabel serverLabel = new JLabel();
serverLabel.setText(MessageManager.getString("label.address"));
serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- serverLabel.setFont(verdana11);
- proxyServerTB.setFont(verdana11);
- proxyPortTB.setFont(verdana11);
- portLabel.setFont(verdana11);
+ serverLabel.setFont(LABEL_FONT);
+ proxyServerTB.setFont(LABEL_FONT);
+ proxyPortTB.setFont(LABEL_FONT);
+ JLabel portLabel = new JLabel();
+ portLabel.setFont(LABEL_FONT);
portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
portLabel.setText(MessageManager.getString("label.port"));
+ JLabel browserLabel = new JLabel();
browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
- browserLabel.setText(MessageManager.getString("label.default_browser_unix"));
- defaultBrowser.setFont(verdana11);
+ browserLabel.setText(MessageManager
+ .getString("label.default_browser_unix"));
+ defaultBrowser.setFont(LABEL_FONT);
defaultBrowser.setText("");
- usagestats.setText(MessageManager.getString("label.send_usage_statistics"));
- usagestats.setFont(verdana11);
+ usagestats.setText(MessageManager
+ .getString("label.send_usage_statistics"));
+ usagestats.setFont(LABEL_FONT);
usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
- questionnaire.setText(MessageManager.getString("label.check_for_questionnaires"));
- questionnaire.setFont(verdana11);
+ questionnaire.setText(MessageManager
+ .getString("label.check_for_questionnaires"));
+ questionnaire.setFont(LABEL_FONT);
questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
- versioncheck.setText(MessageManager.getString("label.check_for_latest_version"));
- versioncheck.setFont(verdana11);
+ versioncheck.setText(MessageManager
+ .getString("label.check_for_latest_version"));
+ versioncheck.setFont(LABEL_FONT);
versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
+ JButton newLink = new JButton();
newLink.setText(MessageManager.getString("action.new"));
newLink.addActionListener(new java.awt.event.ActionListener()
{
newLink_actionPerformed(e);
}
});
+ JButton editLink = new JButton();
editLink.setText(MessageManager.getString("action.edit"));
editLink.addActionListener(new java.awt.event.ActionListener()
{
editLink_actionPerformed(e);
}
});
+ JButton deleteLink = new JButton();
deleteLink.setText(MessageManager.getString("action.delete"));
deleteLink.addActionListener(new java.awt.event.ActionListener()
{
}
});
+ JScrollPane linkScrollPane = new JScrollPane();
linkScrollPane.setBorder(null);
- linkPanel.setBorder(new TitledBorder(MessageManager.getString("label.url_linkfrom_sequence_id")));
- linkPanel.setLayout(borderLayout2);
+ JPanel linkPanel = new JPanel();
+ linkPanel.setBorder(new TitledBorder(MessageManager
+ .getString("label.url_linkfrom_sequence_id")));
+ linkPanel.setLayout(new BorderLayout());
+ GridLayout gridLayout1 = new GridLayout();
+ JPanel editLinkButtons = new JPanel();
editLinkButtons.setLayout(gridLayout1);
gridLayout1.setRows(3);
- linkNameList.setFont(verdana11);
+ linkNameList.setFont(LABEL_FONT);
linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ BorderLayout borderLayout3 = new BorderLayout();
+ JPanel linkPanel2 = new JPanel();
linkPanel2.setLayout(borderLayout3);
- linkURLList.setFont(verdana11);
+ linkURLList.setFont(LABEL_FONT);
linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
defaultBrowser.addMouseListener(new MouseAdapter()
}
}
});
- useProxy.setFont(verdana11);
+ useProxy.setFont(LABEL_FONT);
useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
useProxy.setText(MessageManager.getString("label.use_proxy_server"));
useProxy_actionPerformed();
}
});
+ 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);
+ JPanel jPanel1 = new JPanel();
+ TitledBorder titledBorder1 = new TitledBorder(
+ MessageManager.getString("label.proxy_server"));
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(MessageManager.getString("label.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(MessageManager.getString("label.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(MessageManager.getString("label.append_start_end"));
- jLabel1.setFont(verdana11);
- fastajv.setFont(verdana11);
- 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(verdana11);
- msfjv.setHorizontalAlignment(SwingConstants.LEFT);
- pirjv.setText(MessageManager.getString("label.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(MessageManager.getString("label.full_sequence_id"));
- gridLayout3.setRows(8);
- smoothFont.setFont(verdana11);
- smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
- smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
- smoothFont.setText(MessageManager.getString("label.smooth_font"));
- calcTab.setLayout(null);
- autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
- autoCalculateConsCheck.setText(MessageManager.getString("label.autocalculate_consensus"));
- autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
- padGaps.setFont(JvSwingUtils.getLabelFont());
- padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
- padGaps.setBounds(new Rectangle(22, 94, 168, 23));
- sortByTree.setFont(JvSwingUtils.getLabelFont());
- 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));
+ jPanel1.setLayout(new GridBagLayout());
+ 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(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
+ 2, 5, 185), 2, -4));
+ 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));
+ return connectTab;
+ }
- autoIdWidth.setFont(JvSwingUtils.getLabelFont());
- autoIdWidth.setText(MessageManager.getString("label.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()
+ /**
+ * 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()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed(e);
+ }
+ });
+ JButton cancel = new JButton();
+ cancel.setText(MessageManager.getString("action.cancel"));
+ cancel.addActionListener(new ActionListener()
{
+ 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(MessageManager.getString("label.min_colour"));
+ minColour.setFont(LABEL_FONT);
+ minColour.setBorder(BorderFactory.createEtchedBorder());
+ minColour.setPreferredSize(new Dimension(40, 20));
+ minColour.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent e)
+ {
+ minColour_actionPerformed(minColour);
+ }
+ });
+ JLabel maxcolourLabel = new JLabel();
+ maxcolourLabel.setFont(LABEL_FONT);
+ maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ 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()
+ {
+ public void mousePressed(MouseEvent e)
+ {
+ maxColour_actionPerformed(maxColour);
+ }
+ });
+
+ 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 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 = 400;
+ final int height = 22;
+ final int lineSpacing = 25;
+ int ypos = 30;
+
+ 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)
{
- autoIdWidth_actionPerformed();
+ boolean selected = structFromPdb.isSelected();
+ // enable other options only when the first is checked
+ useRnaView.setEnabled(selected);
+ addSecondaryStructure.setEnabled(selected);
+ addTempFactor.setEnabled(selected);
}
});
- userIdWidthlabel.setFont(JvSwingUtils.getLabelFont());
- userIdWidthlabel.setText(MessageManager.getString("label.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()
+ structureTab.add(structFromPdb);
+
+ // indent checkboxes that are conditional on the first one
+ ypos += lineSpacing;
+ useRnaView.setFont(LABEL_FONT);
+ useRnaView.setText(MessageManager.getString("label.use_rnaview"));
+ useRnaView.setBounds(new Rectangle(25, ypos, width, height));
+ structureTab.add(useRnaView);
+
+ ypos += lineSpacing;
+ addSecondaryStructure.setFont(LABEL_FONT);
+ addSecondaryStructure.setText(MessageManager
+ .getString("label.autoadd_secstr"));
+ 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, 200, height));
+ structureTab.add(viewerLabel);
+
+ structViewer.setFont(LABEL_FONT);
+ structViewer.setBounds(new Rectangle(160, ypos, 120, height));
+ structViewer.addItem(ViewerType.JMOL.name());
+ structViewer.addItem(ViewerType.CHIMERA.name());
+ structViewer.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
- userIdWidth_actionPerformed();
+ structureViewer_actionPerformed((String) structViewer
+ .getSelectedItem());
}
});
- modellerOutput.setFont(JvSwingUtils.getLabelFont());
- modellerOutput.setText(MessageManager.getString("label.use_modeller_output"));
- modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+ structureTab.add(structViewer);
+
+ ypos += lineSpacing;
+ JLabel pathLabel = new JLabel();
+ pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
+ pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ pathLabel.setText(MessageManager.getString("label.chimera_path"));
+ final String tooltip = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.chimera_path_tip"));
+ pathLabel.setToolTipText(tooltip);
+ pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
+ structureTab.add(pathLabel);
+
+ chimeraPath.setFont(LABEL_FONT);
+ chimeraPath.setText("");
+ chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
+ chimeraPath.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser();
+ if (chosen != null)
+ {
+ chimeraPath.setText(chosen);
+ }
+ }
+ }
+ });
+ structureTab.add(chimeraPath);
+
+ ypos += lineSpacing;
+ // scrl_pdbDocFieldConfig.setPreferredSize(new Dimension(450, 100));
+ // scrl_pdbDocFieldConfig
+ // .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+ // scrl_pdbDocFieldConfig.setBounds();
+ PDBDocFieldPreferences docFieldPref = new PDBDocFieldPreferences(
+ PreferenceSource.PREFERENCES);
+ docFieldPref.setBounds(new Rectangle(10, ypos + 5, 450, 120));
+ structureTab.add(docFieldPref);
+
+ 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();
+
+ // 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"));
+ 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.LEADING);
+ annotations.setSelected(true);
+ annotations.setText(MessageManager.getString("label.show_annotations"));
+ annotations.setBounds(new Rectangle(169, 12, 200, 23));
+ annotations.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ identity.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ showGroupConsensus.addActionListener(new ActionListener()
+ {
+ 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()
+ {
+ 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);
- dasPanel.setLayout(borderLayout4);
- wsPanel.setLayout(borderLayout5);
- wrap.setFont(JvSwingUtils.getLabelFont());
+ 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));
+ startupFileTextfield.addMouseListener(new MouseAdapter()
+ {
+ 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, 34, 320, 75));
+ annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
+ annsettingsPanel.setBorder(new EtchedBorder());
+ 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);
+
+ JPanel autoAnnotSettings = new JPanel();
+ autoAnnotSettings.setLayout(new GridLayout(3, 3));
+ annsettingsPanel.add(autoAnnotSettings);
+ autoAnnotSettings.add(quality);
+ autoAnnotSettings.add(conservation);
+ autoAnnotSettings.add(identity);
+ 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(JvSwingUtils.getLabelFont());
+ 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(JvSwingUtils.getLabelFont());
+ idItalics.setFont(LABEL_FONT_ITALIC);
idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
- idItalics.setText(MessageManager.getString("label.sequence_name_italics"));
- openoverv.setFont(JvSwingUtils.getLabelFont());
- openoverv.setActionCommand(MessageManager.getString("label.open_overview"));
+ 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(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(annotations);
visualTab.add(startupFileTextfield);
visualTab.add(sortby);
+ visualTab.add(sortAnnBy);
+ visualTab.add(sortAutocalc);
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);
-
- 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);
-
- JPanel tooltipSettings = new JPanel();
- tooltipSettings.setBorder(new TitledBorder(MessageManager.getString("label.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,
- MessageManager.getString("label.default_colour_scheme_for_alignment"), colourLabel, colour);
- 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);
- 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);
-
- tabbedPane.add(visualTab, MessageManager.getString("label.visual"));
- tabbedPane.add(visual2Tab, MessageManager.getString("label.colours"));
- tabbedPane.add(connectTab, MessageManager.getString("label.connections"));
- tabbedPane.add(exportTab, MessageManager.getString("label.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, MessageManager.getString("label.editing"));
- calcTab.add(autoCalculateConsCheck);
- calcTab.add(padGaps);
- calcTab.add(sortByTree);
-
- tabbedPane.add(dasPanel, MessageManager.getString("label.das_settings"));
- tabbedPane.add(wsPanel, MessageManager.getString("label.web_services"));
-
- exportTab.add(epsLabel);
- exportTab.add(epsRendering);
- exportTab.add(jPanel11);
+ return visualTab;
}
protected void autoIdWidth_actionPerformed()
}
- 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)
{
- // TODO Auto-generated method stub
-
}
protected void showunconserved_actionPerformed(ActionEvent e)
git://source.jalview.org / jalview.git / blobdiff