-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.jbgui;\r
-\r
-import java.awt.*;\r
-\r
-import javax.swing.*;\r
-import javax.swing.border.TitledBorder;\r
-import java.awt.event.*;\r
-import javax.swing.event.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class GPreferences extends JPanel\r
-{\r
- JTabbedPane tabbedPane = new JTabbedPane();\r
-\r
- JButton ok = new JButton();\r
- JButton cancel = new JButton();\r
- JPanel okCancelPanel = new JPanel();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- protected JCheckBox quality = new JCheckBox();\r
- JPanel visualTab = new JPanel();\r
- protected JCheckBox fullScreen = new JCheckBox();\r
- protected JCheckBox conservation = new JCheckBox();\r
- protected JCheckBox identity = new JCheckBox();\r
- protected JCheckBox annotations = new JCheckBox();\r
- JLabel gapLabel = new JLabel();\r
- protected JComboBox colour = new JComboBox();\r
- JLabel colourLabel = new JLabel();\r
- JLabel fontLabel = new JLabel();\r
- protected JComboBox fontSizeCB = new JComboBox();\r
- protected JComboBox fontStyleCB = new JComboBox();\r
- protected JComboBox fontNameCB = new JComboBox();\r
- protected JComboBox gapSymbolCB = new JComboBox();\r
- protected JCheckBox startupCheckbox = new JCheckBox();\r
- protected JTextField startupFileTextfield = new JTextField();\r
- JPanel connectTab = new JPanel();\r
- JLabel serverLabel = new JLabel();\r
- protected JList linkURLList = new JList();\r
- protected JTextField proxyServerTB = new JTextField();\r
- protected JTextField proxyPortTB = new JTextField();\r
- JLabel portLabel = new JLabel();\r
- JLabel browserLabel = new JLabel();\r
- protected JTextField defaultBrowser = new JTextField();\r
- JButton newLink = new JButton();\r
- JButton editLink = new JButton();\r
- JButton deleteLink = new JButton();\r
- JScrollPane linkScrollPane = new JScrollPane();\r
- JPanel linkPanel = new JPanel();\r
- BorderLayout borderLayout2 = new BorderLayout();\r
- JPanel editLinkButtons = new JPanel();\r
- GridLayout gridLayout1 = new GridLayout();\r
- protected JList linkNameList = new JList();\r
- JPanel linkPanel2 = new JPanel();\r
- BorderLayout borderLayout3 = new BorderLayout();\r
- protected JCheckBox useProxy = new JCheckBox();\r
- JPanel jPanel1 = new JPanel();\r
- TitledBorder titledBorder1 = new TitledBorder("Proxy Server");\r
- TitledBorder titledBorder2 = new TitledBorder("File Output");\r
- GridBagLayout gridBagLayout2 = new GridBagLayout();\r
- GridBagLayout gridBagLayout1 = new GridBagLayout();\r
- GridBagLayout gridBagLayout3 = new GridBagLayout();\r
- protected JComboBox sortby = new JComboBox();\r
- JLabel sortLabel = new JLabel();\r
- JPanel jPanel2 = new JPanel();\r
- GridLayout gridLayout2 = new GridLayout();\r
- JPanel jPanel3 = new JPanel();\r
- JPanel exportTab = new JPanel();\r
- JLabel epsLabel = new JLabel();\r
- protected JComboBox epsRendering = new JComboBox();\r
- JLabel jLabel1 = new JLabel();\r
- protected JCheckBox blcjv = new JCheckBox();\r
- protected JCheckBox pileupjv = new JCheckBox();\r
- protected JCheckBox clustaljv = new JCheckBox();\r
- protected JCheckBox msfjv = new JCheckBox();\r
- protected JCheckBox fastajv = new JCheckBox();\r
- protected JCheckBox pfamjv = new JCheckBox();\r
- FlowLayout flowLayout1 = new FlowLayout();\r
- protected JCheckBox pirjv = new JCheckBox();\r
- JPanel jPanel11 = new JPanel();\r
- Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);\r
- protected JCheckBox seqLimit = new JCheckBox();\r
- GridLayout gridLayout3 = new GridLayout();\r
- protected JCheckBox smoothFont = new JCheckBox();\r
- JPanel calcTab = new JPanel();\r
- protected JCheckBox autoCalculateConsCheck = new JCheckBox();\r
- protected JCheckBox padGaps = new JCheckBox();\r
- protected JCheckBox modellerOutput = new JCheckBox();\r
- /**\r
- * Creates a new GPreferences object.\r
- */\r
- public GPreferences()\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @throws Exception DOCUMENT ME!\r
- */\r
- private void jbInit() throws Exception\r
- {\r
- this.setLayout(borderLayout1);\r
- ok.setText("OK");\r
- ok.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ok_actionPerformed(e);\r
- }\r
- });\r
- cancel.setText("Cancel");\r
- cancel.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- cancel_actionPerformed(e);\r
- }\r
- });\r
- quality.setEnabled(false);\r
- quality.setFont(verdana11);\r
- quality.setHorizontalAlignment(SwingConstants.RIGHT);\r
- quality.setHorizontalTextPosition(SwingConstants.LEFT);\r
- quality.setSelected(true);\r
- quality.setText("Quality");\r
- visualTab.setBorder(new TitledBorder("Open new alignment"));\r
- visualTab.setLayout(null);\r
- fullScreen.setFont(verdana11);\r
- fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);\r
- fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);\r
- fullScreen.setMargin(new Insets(2, 2, 2, 0));\r
- fullScreen.setText("Maximise Window");\r
- conservation.setEnabled(false);\r
- conservation.setFont(verdana11);\r
- conservation.setHorizontalAlignment(SwingConstants.RIGHT);\r
- conservation.setHorizontalTextPosition(SwingConstants.LEFT);\r
- conservation.setSelected(true);\r
- conservation.setText("Conservation");\r
- identity.setEnabled(false);\r
- identity.setFont(verdana11);\r
- identity.setHorizontalAlignment(SwingConstants.RIGHT);\r
- identity.setHorizontalTextPosition(SwingConstants.LEFT);\r
- identity.setSelected(true);\r
- identity.setText("Consensus");\r
- annotations.setFont(verdana11);\r
- annotations.setHorizontalAlignment(SwingConstants.RIGHT);\r
- annotations.setHorizontalTextPosition(SwingConstants.LEFT);\r
- annotations.setMargin(new Insets(2, 4, 2, 0));\r
- annotations.setSelected(true);\r
- annotations.setText("Show Annotations");\r
- annotations.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- annotations_actionPerformed(e);\r
- }\r
- });\r
- gapLabel.setFont(verdana11);\r
- gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
- gapLabel.setText("Gap Symbol ");\r
- colour.setFont(verdana11);\r
- colour.setBounds(new Rectangle(171, 180, 155, 21));\r
- colourLabel.setFont(verdana11);\r
- colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
- colourLabel.setText("Colour ");\r
- fontLabel.setFont(verdana11);\r
- fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
- fontLabel.setText("Font ");\r
- fontSizeCB.setFont(verdana11);\r
- fontSizeCB.setBounds(new Rectangle(318, 100, 49, 21));\r
- fontStyleCB.setFont(verdana11);\r
- fontStyleCB.setBounds(new Rectangle(366, 100, 70, 21));\r
- fontNameCB.setFont(verdana11);\r
- fontNameCB.setBounds(new Rectangle(171, 100, 147, 21));\r
- gapSymbolCB.setFont(verdana11);\r
- gapSymbolCB.setBounds(new Rectangle(171, 153, 69, 21));\r
- startupCheckbox.setText("Open file");\r
- startupCheckbox.setFont(verdana11);\r
- startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);\r
- startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);\r
- startupCheckbox.setSelected(true);\r
- startupFileTextfield.setFont(verdana11);\r
- startupFileTextfield.setBounds(new Rectangle(171, 236, 270, 20));\r
- startupFileTextfield.addMouseListener(new MouseAdapter()\r
- {\r
- public void mouseClicked(MouseEvent e)\r
- {\r
- if (e.getClickCount() > 1)\r
- {\r
- startupFileTextfield_mouseClicked();\r
- }\r
- }\r
- });\r
-\r
- connectTab.setLayout(gridBagLayout3);\r
- serverLabel.setText("Address");\r
- serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
- serverLabel.setFont(verdana11);\r
- proxyServerTB.setFont(verdana11);\r
- proxyPortTB.setFont(verdana11);\r
- portLabel.setFont(verdana11);\r
- portLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
- portLabel.setText("Port");\r
- browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));\r
- browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);\r
- browserLabel.setText("Default Browser (Unix)");\r
- defaultBrowser.setFont(verdana11);\r
- defaultBrowser.setText("");\r
- newLink.setText("New");\r
- newLink.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- newLink_actionPerformed(e);\r
- }\r
- });\r
- editLink.setText("Edit");\r
- editLink.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- editLink_actionPerformed(e);\r
- }\r
- });\r
- deleteLink.setText("Delete");\r
- deleteLink.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- deleteLink_actionPerformed(e);\r
- }\r
- });\r
-\r
- linkURLList.addListSelectionListener(new ListSelectionListener()\r
- {\r
- public void valueChanged(ListSelectionEvent e)\r
- {\r
- int index = linkURLList.getSelectedIndex();\r
- linkNameList.setSelectedIndex(index);\r
- }\r
- });\r
-\r
- linkNameList.addListSelectionListener(new ListSelectionListener()\r
- {\r
- public void valueChanged(ListSelectionEvent e)\r
- {\r
- int index = linkNameList.getSelectedIndex();\r
- linkURLList.setSelectedIndex(index);\r
- }\r
- });\r
-\r
- linkScrollPane.setBorder(null);\r
- linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));\r
- linkPanel.setLayout(borderLayout2);\r
- editLinkButtons.setLayout(gridLayout1);\r
- gridLayout1.setRows(3);\r
- linkNameList.setFont(verdana11);\r
- linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
- linkPanel2.setLayout(borderLayout3);\r
- linkURLList.setFont(verdana11);\r
- linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
-\r
- defaultBrowser.addMouseListener(new MouseAdapter()\r
- {\r
- public void mouseClicked(MouseEvent e)\r
- {\r
- if (e.getClickCount() > 1)\r
- {\r
- defaultBrowser_mouseClicked(e);\r
- }\r
- }\r
- });\r
- useProxy.setFont(verdana11);\r
- useProxy.setHorizontalAlignment(SwingConstants.RIGHT);\r
- useProxy.setHorizontalTextPosition(SwingConstants.LEADING);\r
- useProxy.setText("Use a proxy server");\r
- useProxy.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- useProxy_actionPerformed();\r
- }\r
- });\r
- jPanel1.setBorder(titledBorder1);\r
- jPanel1.setLayout(gridBagLayout1);\r
- sortby.setFont(verdana11);\r
- sortby.setBounds(new Rectangle(171, 208, 155, 21));\r
- sortLabel.setFont(verdana11);\r
- sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
- sortLabel.setText("Sort by ");\r
- jPanel2.setBounds(new Rectangle(7, 17, 158, 245));\r
- jPanel2.setLayout(gridLayout2);\r
- gridLayout2.setRows(9);\r
- jPanel3.setBounds(new Rectangle(167, 41, 274, 26));\r
- exportTab.setLayout(null);\r
- epsLabel.setFont(verdana11);\r
- epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
- epsLabel.setText("EPS Rendering Style");\r
- epsLabel.setBounds(new Rectangle(9, 31, 140, 24));\r
- epsRendering.setFont(verdana11);\r
- epsRendering.setBounds(new Rectangle(154, 34, 187, 21));\r
- jLabel1.setFont(verdana11);\r
- jLabel1.setHorizontalAlignment(SwingConstants.CENTER);\r
- jLabel1.setText("Append /start-end (/15-380)");\r
- jLabel1.setFont(verdana11);\r
- fastajv.setFont(verdana11);\r
- fastajv.setHorizontalAlignment(SwingConstants.LEFT);\r
- clustaljv.setText("Clustal ");\r
- blcjv.setText("BLC ");\r
- fastajv.setText("Fasta ");\r
- msfjv.setText("MSF ");\r
- pfamjv.setText("PFAM ");\r
- pileupjv.setText("Pileup ");\r
- msfjv.setFont(verdana11);\r
- msfjv.setHorizontalAlignment(SwingConstants.LEFT);\r
- pirjv.setText("PIR ");\r
- jPanel11.setFont(verdana11);\r
- jPanel11.setBorder(titledBorder2);\r
- jPanel11.setBounds(new Rectangle(30, 72, 196, 182));\r
- jPanel11.setLayout(gridLayout3);\r
- blcjv.setFont(verdana11);\r
- blcjv.setHorizontalAlignment(SwingConstants.LEFT);\r
- clustaljv.setFont(verdana11);\r
- clustaljv.setHorizontalAlignment(SwingConstants.LEFT);\r
- pfamjv.setFont(verdana11);\r
- pfamjv.setHorizontalAlignment(SwingConstants.LEFT);\r
- pileupjv.setFont(verdana11);\r
- pileupjv.setHorizontalAlignment(SwingConstants.LEFT);\r
- pirjv.setFont(verdana11);\r
- pirjv.setHorizontalAlignment(SwingConstants.LEFT);\r
- seqLimit.setFont(verdana11);\r
- seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);\r
- seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);\r
- seqLimit.setText("Full Sequence Id");\r
- gridLayout3.setRows(8);\r
- smoothFont.setFont(verdana11);\r
- smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);\r
- smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);\r
- smoothFont.setText("Smooth Font");\r
- calcTab.setLayout(null);\r
- autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- autoCalculateConsCheck.setText("AutoCalculate Consensus");\r
- autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));\r
- padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- padGaps.setText("Pad gaps when editing");\r
- padGaps.setBounds(new Rectangle(22, 94, 168, 23));\r
- modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- modellerOutput.setText("Use Modeller Output");\r
- modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));\r
- jPanel2.add(fullScreen);\r
-\r
- jPanel2.add(annotations);\r
- jPanel2.add(seqLimit);\r
- jPanel2.add(fontLabel);\r
- jPanel2.add(smoothFont);\r
- jPanel2.add(gapLabel);\r
- jPanel2.add(colourLabel);\r
- jPanel2.add(sortLabel);\r
- jPanel2.add(startupCheckbox);\r
- visualTab.add(colour);\r
- visualTab.add(gapSymbolCB);\r
- visualTab.add(startupFileTextfield);\r
- visualTab.add(sortby);\r
- visualTab.add(fontNameCB);\r
- visualTab.add(fontSizeCB);\r
- visualTab.add(fontStyleCB);\r
- visualTab.add(jPanel3);\r
- jPanel3.add(conservation);\r
- jPanel3.add(identity);\r
- jPanel3.add(quality);\r
- visualTab.add(jPanel2);\r
- linkPanel.add(editLinkButtons, BorderLayout.EAST);\r
- editLinkButtons.add(newLink, null);\r
- editLinkButtons.add(editLink, null);\r
- editLinkButtons.add(deleteLink, null);\r
- linkPanel.add(linkScrollPane, BorderLayout.CENTER);\r
- linkScrollPane.getViewport().add(linkPanel2, null);\r
- linkPanel2.add(linkURLList, BorderLayout.CENTER);\r
- linkPanel2.add(linkNameList, BorderLayout.WEST);\r
- okCancelPanel.add(ok);\r
- okCancelPanel.add(cancel);\r
- this.add(tabbedPane, java.awt.BorderLayout.CENTER);\r
-\r
- this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);\r
- jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0\r
- , GridBagConstraints.WEST, GridBagConstraints.NONE,\r
- new Insets(0, 2, 4, 0), 5, 0));\r
- jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0\r
- , GridBagConstraints.WEST,\r
- GridBagConstraints.NONE,\r
- new Insets(0, 0, 4, 0), 11, 6));\r
- connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0\r
- , GridBagConstraints.CENTER, GridBagConstraints.BOTH,\r
- new Insets(16, 0, 0, 12), 359, -17));\r
- connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0\r
- , GridBagConstraints.CENTER, GridBagConstraints.BOTH,\r
- new Insets(21, 0, 35, 12), 4, 6));\r
- connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0\r
- , GridBagConstraints.WEST, GridBagConstraints.NONE,\r
- new Insets(16, 0, 0, 0), 5, 1));\r
- jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0\r
- , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,\r
- new Insets(0, 2, 4, 2), 54, 1));\r
- jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0\r
- , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,\r
- new Insets(0, 2, 4, 0), 263, 1));\r
- connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0\r
- , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,\r
- new Insets(15, 0, 0, 15), 307, 1));\r
-\r
-\r
- jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0\r
- , GridBagConstraints.WEST,\r
- GridBagConstraints.NONE,\r
- new Insets(0, 2, 5, 185), 2,\r
- -4));\r
- DefaultListCellRenderer dlcr = new DefaultListCellRenderer();\r
- dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);\r
- gapSymbolCB.setRenderer(dlcr);\r
-\r
- tabbedPane.add(visualTab, "Visual");\r
- tabbedPane.add(connectTab,"Connections");\r
- tabbedPane.add(exportTab, "Output");\r
- jPanel11.add(jLabel1);\r
- jPanel11.add(blcjv);\r
- jPanel11.add(clustaljv);\r
- jPanel11.add(fastajv);\r
- jPanel11.add(msfjv);\r
- jPanel11.add(pfamjv);\r
- jPanel11.add(pileupjv);\r
- jPanel11.add(pirjv);\r
- exportTab.add(modellerOutput);\r
- tabbedPane.add(calcTab, "Editing");\r
- calcTab.add(autoCalculateConsCheck);\r
- calcTab.add(padGaps);\r
-\r
- exportTab.add(epsLabel);\r
- exportTab.add(epsRendering);\r
- exportTab.add(jPanel11);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void ok_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void cancel_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void annotations_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void startupFileTextfield_mouseClicked()\r
- {\r
- }\r
-\r
-\r
- public void newLink_actionPerformed(ActionEvent e) {\r
-\r
- }\r
-\r
- public void editLink_actionPerformed(ActionEvent e) {\r
-\r
- }\r
-\r
- public void deleteLink_actionPerformed(ActionEvent e) {\r
-\r
- }\r
-\r
- public void defaultBrowser_mouseClicked(MouseEvent e)\r
- {\r
-\r
- }\r
-\r
- public void linkURLList_keyTyped(KeyEvent e)\r
- {\r
-\r
- }\r
-\r
- public void useProxy_actionPerformed()\r
- {\r
- proxyServerTB.setEnabled(useProxy.isSelected());\r
- proxyPortTB.setEnabled(useProxy.isSelected());\r
- }\r
-}\r
+/*
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.jbgui;
+
+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;
+
+import jalview.gui.JvSwingUtils;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource;
+import jalview.util.MessageManager;
+
+/**
+ * Base class for the Preferences panel.
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class GPreferences extends JPanel
+{
+ private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
+
+ private static final Font LABEL_FONT_ITALIC = JvSwingUtils
+ .getLabelFont(false, true);
+
+ /*
+ * Visual tab components
+ */
+ protected JCheckBox fullScreen = new JCheckBox();
+
+ protected JCheckBox openoverv = new JCheckBox();
+
+ protected JCheckBox seqLimit = new JCheckBox();
+
+ protected JCheckBox rightAlign = new JCheckBox();
+
+ protected JComboBox<String> fontSizeCB = new JComboBox<String>();
+
+ protected JComboBox<String> fontStyleCB = new JComboBox<String>();
+
+ protected JComboBox<String> fontNameCB = new JComboBox<String>();
+
+ 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<String>();
+
+ protected JCheckBox wrap = new JCheckBox();
+
+ protected JComboBox<String> sortby = new JComboBox<String>();
+
+ protected JComboBox<String> sortAnnBy = new JComboBox<String>();
+
+ protected JComboBox<String> sortAutocalc = new JComboBox<String>();
+
+ 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 showGroupConsensus = new JCheckBox();
+
+ protected JCheckBox showGroupConservation = new JCheckBox();
+
+ protected JCheckBox showConsensHistogram = new JCheckBox();
+
+ protected JCheckBox showConsensLogo = new JCheckBox();
+
+ protected JCheckBox showDbRefTooltip = new JCheckBox();
+
+ protected JCheckBox showNpTooltip = new JCheckBox();
+
+ /*
+ * Structure tab and components
+ */
+ protected JPanel structureTab;
+
+ protected JCheckBox structFromPdb = new JCheckBox();
+
+ protected JCheckBox useRnaView = new JCheckBox();
+
+ protected JCheckBox addSecondaryStructure = new JCheckBox();
+
+ protected JCheckBox addTempFactor = new JCheckBox();
+
+ protected JComboBox<String> structViewer = new JComboBox<String>();
+
+ protected JTextField chimeraPath = new JTextField();
+
+
+ /*
+ * Colours tab components
+ */
+ protected JPanel minColour = new JPanel();
+
+ protected JPanel maxColour = new JPanel();
+
+ protected JComboBox<String> protColour = new JComboBox<String>();
+
+ protected JComboBox<String> nucColour = new JComboBox<String>();
+
+ /*
+ * Connections tab components
+ */
+ protected JList linkURLList = new JList();
+
+ protected JTextField proxyServerTB = new JTextField();
+
+ protected JTextField proxyPortTB = new JTextField();
+
+ protected JTextField defaultBrowser = new JTextField();
+
+ protected JList linkNameList = new JList();
+
+ protected JCheckBox useProxy = new JCheckBox();
+
+ protected JCheckBox usagestats = new JCheckBox();
+
+ protected JCheckBox questionnaire = new JCheckBox();
+
+ protected JCheckBox versioncheck = new JCheckBox();
+
+ /*
+ * Output tab components
+ */
+ protected JComboBox<String> epsRendering = new JComboBox<String>();
+
+ protected JLabel userIdWidthlabel = new JLabel();
+
+ protected JCheckBox autoIdWidth = new JCheckBox();
+
+ protected JTextField userIdWidth = new JTextField();
+
+ protected JCheckBox blcjv = new JCheckBox();
+
+ protected JCheckBox pileupjv = new JCheckBox();
+
+ protected JCheckBox clustaljv = new JCheckBox();
+
+ protected JCheckBox msfjv = new JCheckBox();
+
+ protected JCheckBox fastajv = new JCheckBox();
+
+ protected JCheckBox pfamjv = new JCheckBox();
+
+ protected JCheckBox pirjv = new JCheckBox();
+
+ protected JCheckBox modellerOutput = new JCheckBox();
+
+ /*
+ * Editing tab components
+ */
+ protected JCheckBox autoCalculateConsCheck = new JCheckBox();
+
+ protected JCheckBox padGaps = new JCheckBox();
+
+ protected JCheckBox sortByTree = new JCheckBox();
+
+ /*
+ * DAS Settings tab
+ */
+ protected JPanel dasTab = new JPanel();
+
+ /*
+ * Web Services tab
+ */
+ protected JPanel wsTab = new JPanel();
+
+ /**
+ * Creates a new GPreferences object.
+ */
+ public GPreferences()
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * Construct the panel and its tabbed sub-panels.
+ *
+ * @throws Exception
+ */
+ private void jbInit() throws Exception
+ {
+ 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()
+ {
+ private Component lastTab;
+
+ @Override
+ public void stateChanged(ChangeEvent e)
+ {
+ if (lastTab == structureTab
+ && tabbedPane.getSelectedComponent() != structureTab)
+ {
+ if (!validateStructure())
+ {
+ tabbedPane.setSelectedComponent(structureTab);
+ return;
+ }
+ }
+ lastTab = tabbedPane.getSelectedComponent();
+ }
+
+ });
+ }
+
+ /**
+ * 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)
+ {
+ autoIdWidth_actionPerformed();
+ }
+ });
+ 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)
+ {
+ userIdWidth_actionPerformed();
+ }
+ });
+ 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(epsLabel);
+ outputTab.add(epsRendering);
+ outputTab.add(jPanel11);
+ modellerOutput.setFont(LABEL_FONT);
+ modellerOutput.setText(MessageManager
+ .getString("label.use_modeller_output"));
+ modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+ return outputTab;
+ }
+
+ /**
+ * 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(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(LABEL_FONT);
+ defaultBrowser.setText("");
+ 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(LABEL_FONT);
+ questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
+ questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
+ 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()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ newLink_actionPerformed(e);
+ }
+ });
+ JButton editLink = new JButton();
+ editLink.setText(MessageManager.getString("action.edit"));
+ editLink.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ editLink_actionPerformed(e);
+ }
+ });
+ JButton deleteLink = new JButton();
+ deleteLink.setText(MessageManager.getString("action.delete"));
+ deleteLink.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ deleteLink_actionPerformed(e);
+ }
+ });
+
+ linkURLList.addListSelectionListener(new ListSelectionListener()
+ {
+ public void valueChanged(ListSelectionEvent e)
+ {
+ int index = linkURLList.getSelectedIndex();
+ linkNameList.setSelectedIndex(index);
+ }
+ });
+
+ linkNameList.addListSelectionListener(new ListSelectionListener()
+ {
+ public void valueChanged(ListSelectionEvent e)
+ {
+ int index = linkNameList.getSelectedIndex();
+ linkURLList.setSelectedIndex(index);
+ }
+ });
+
+ JScrollPane linkScrollPane = new JScrollPane();
+ linkScrollPane.setBorder(null);
+ 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(LABEL_FONT);
+ linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ BorderLayout borderLayout3 = new BorderLayout();
+ JPanel linkPanel2 = new JPanel();
+ linkPanel2.setLayout(borderLayout3);
+ linkURLList.setFont(LABEL_FONT);
+ linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+
+ defaultBrowser.addMouseListener(new MouseAdapter()
+ {
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() > 1)
+ {
+ defaultBrowser_mouseClicked(e);
+ }
+ }
+ });
+ useProxy.setFont(LABEL_FONT);
+ useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
+ useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
+ useProxy.setText(MessageManager.getString("label.use_proxy_server"));
+ useProxy.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ 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(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;
+ }
+
+ /**
+ * 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)
+ {
+ boolean selected = structFromPdb.isSelected();
+ // enable other options only when the first is checked
+ useRnaView.setEnabled(selected);
+ addSecondaryStructure.setEnabled(selected);
+ addTempFactor.setEnabled(selected);
+ }
+ });
+ 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)
+ {
+ structureViewer_actionPerformed((String) structViewer
+ .getSelectedItem());
+ }
+ });
+ 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);
+
+ 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(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(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);
+ return visualTab;
+ }
+
+ protected void autoIdWidth_actionPerformed()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void userIdWidth_actionPerformed()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void maxColour_actionPerformed(JPanel panel)
+ {
+ }
+
+ protected void minColour_actionPerformed(JPanel panel)
+ {
+ }
+
+ protected void showunconserved_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void ok_actionPerformed(ActionEvent e)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void cancel_actionPerformed(ActionEvent e)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void annotations_actionPerformed(ActionEvent e)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void startupFileTextfield_mouseClicked()
+ {
+ }
+
+ public void newLink_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void editLink_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void deleteLink_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void defaultBrowser_mouseClicked(MouseEvent e)
+ {
+
+ }
+
+ public void linkURLList_keyTyped(KeyEvent e)
+ {
+
+ }
+
+ public void useProxy_actionPerformed()
+ {
+ proxyServerTB.setEnabled(useProxy.isSelected());
+ proxyPortTB.setEnabled(useProxy.isSelected());
+ }
+
+}