-/*\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
- /**\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(172, 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(172, 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(170, 236, 271, 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, 246));\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.LEADING);\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
- 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(startupFileTextfield);\r
- visualTab.add(sortby);\r
- visualTab.add(colour);\r
- visualTab.add(gapSymbolCB);\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, "visualTab");\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
-\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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.jbgui;
+
+import jalview.gui.JvSwingUtils;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import java.awt.Rectangle;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @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();
+ JPanel visual2Tab = new JPanel();
+
+ protected JCheckBox fullScreen = new JCheckBox();
+
+ protected JCheckBox conservation = new JCheckBox();
+
+ protected JCheckBox identity = new JCheckBox();
+
+ protected JCheckBox annotations = new JCheckBox();
+
+ protected JPanel minColour = new JPanel();
+ JLabel mincolourLabel = new JLabel();
+
+ protected JPanel maxColour = new JPanel();
+ JLabel maxcolourLabel = new JLabel();
+
+ JLabel gapLabel = new JLabel();
+
+ protected JComboBox colour = new JComboBox();
+
+ JLabel colourLabel = new JLabel();
+
+ JLabel fontLabel = new JLabel();
+
+ protected JComboBox fontSizeCB = new JComboBox();
+
+ protected JComboBox fontStyleCB = new JComboBox();
+
+ protected JComboBox fontNameCB = new JComboBox();
+
+ protected JComboBox gapSymbolCB = new JComboBox();
+
+ 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();
+
+ JButton editLink = new JButton();
+
+ JButton deleteLink = new JButton();
+
+ JScrollPane linkScrollPane = new JScrollPane();
+
+ JPanel linkPanel = new JPanel();
+
+ BorderLayout borderLayout2 = new BorderLayout();
+
+ JPanel editLinkButtons = new JPanel();
+
+ GridLayout gridLayout1 = new GridLayout();
+
+ protected JList linkNameList = new JList();
+
+ JPanel linkPanel2 = new JPanel();
+
+ BorderLayout borderLayout3 = new BorderLayout();
+
+ protected JCheckBox useProxy = new JCheckBox();
+
+ JPanel jPanel1 = new JPanel();
+
+ TitledBorder titledBorder1 = new TitledBorder("Proxy Server");
+
+ TitledBorder titledBorder2 = new TitledBorder("File Output");
+
+ GridBagLayout gridBagLayout2 = new GridBagLayout();
+
+ GridBagLayout gridBagLayout1 = new GridBagLayout();
+
+ GridBagLayout gridBagLayout3 = new GridBagLayout();
+
+ protected JComboBox sortby = new JComboBox();
+
+ JLabel sortLabel = new JLabel();
+
+ JPanel jPanel2 = new JPanel();
+ JPanel visual2panel = new JPanel();
+
+ GridLayout gridLayout2 = new GridLayout();
+
+ GridLayout gridLayout4 = new GridLayout();
+
+ JPanel annsettingsPanel = new JPanel();
+
+ JPanel autoAnnotSettings1 = new JPanel();
+
+ JPanel autoAnnotSettings2 = new JPanel();
+
+ JPanel autoAnnotSettings3 = new JPanel();
+
+ JPanel exportTab = new JPanel();
+
+ JLabel epsLabel = new JLabel();
+
+ protected JComboBox epsRendering = new JComboBox();
+
+ JLabel jLabel1 = new JLabel();
+
+ 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();
+
+ 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();
+
+ JPanel calcTab = new JPanel();
+
+ 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 followHighlight = new JCheckBox();
+
+ protected JCheckBox sortByTree= new JCheckBox();
+
+ /**
+ * Creates a new GPreferences object.
+ */
+ public GPreferences()
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception
+ * DOCUMENT ME!
+ */
+ private void jbInit() throws Exception
+ {
+ this.setLayout(borderLayout1);
+ ok.setText("OK");
+ ok.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed(e);
+ }
+ });
+ cancel.setText("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("Quality");
+ visualTab.setBorder(new TitledBorder("Open new alignment"));
+ visualTab.setLayout(null);
+ visual2Tab.setBorder(new TitledBorder("Open new alignment"));
+ visual2Tab.setLayout(new FlowLayout());
+ fullScreen.setFont(verdana11);
+ fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
+ fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
+ fullScreen.setText("Maximise Window");
+ conservation.setEnabled(false);
+ conservation.setFont(verdana11);
+ conservation.setHorizontalAlignment(SwingConstants.RIGHT);
+ conservation.setHorizontalTextPosition(SwingConstants.LEFT);
+ conservation.setSelected(true);
+ conservation.setText("Conservation");
+ identity.setEnabled(false);
+ identity.setFont(verdana11);
+ identity.setHorizontalAlignment(SwingConstants.RIGHT);
+ identity.setHorizontalTextPosition(SwingConstants.LEFT);
+ identity.setSelected(true);
+ identity.setText("Consensus");
+ showGroupbits.setFont(verdana11);
+ showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
+ showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
+ showGroupbits.setText("Show group:");
+ showConsensbits.setFont(verdana11);
+ showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensbits.setText("Consensus:");
+ showConsensHistogram.setEnabled(false);
+ showConsensHistogram.setFont(verdana11);
+ showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensHistogram.setSelected(true);
+ showConsensHistogram.setText("Histogram");
+ showConsensLogo.setEnabled(false);
+ showConsensLogo.setFont(verdana11);
+ showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
+ showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
+ showConsensLogo.setSelected(true);
+ showConsensLogo.setText("Logo");
+ showGroupConsensus.setEnabled(false);
+ showGroupConsensus.setFont(verdana11);
+ showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
+ showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
+ showGroupConsensus.setSelected(true);
+ showGroupConsensus.setText("Consensus");
+ showGroupConservation.setEnabled(false);
+ showGroupConservation.setFont(verdana11);
+ showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
+ showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
+ showGroupConservation.setSelected(true);
+ showGroupConservation.setText("Conservation");
+ showNpTooltip.setEnabled(true);
+ showNpTooltip.setFont(verdana11);
+ showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
+ showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
+ showNpTooltip.setSelected(true);
+ showNpTooltip.setText("Non-positional Features");
+ showDbRefTooltip.setEnabled(true);
+ showDbRefTooltip.setFont(verdana11);
+ showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
+ showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
+ showDbRefTooltip.setSelected(true);
+ showDbRefTooltip.setText("Database References");
+ annotations.setFont(verdana11);
+ annotations.setHorizontalAlignment(SwingConstants.RIGHT);
+ annotations.setHorizontalTextPosition(SwingConstants.LEADING);
+ annotations.setSelected(true);
+ annotations.setText("Show Annotations");
+ annotations.setBounds(new Rectangle(169, 12, 200, 23));
+ annotations.addActionListener(new ActionListener()
+ {
+ 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(verdana11);
+ showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
+ showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
+ showUnconserved.setSelected(true);
+ showUnconserved.setText("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("Share selection across views");
+ followHighlight.setFont(verdana11);
+ followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
+ followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
+ // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
+ followHighlight.setSelected(true);
+ followHighlight.setText("Scroll to highlighted regions");
+
+ gapLabel.setFont(verdana11);
+ gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ gapLabel.setText("Gap Symbol ");
+ colour.setFont(verdana11);
+ colour.setBounds(new Rectangle(172, 225, 155, 21));
+ colourLabel.setFont(verdana11);
+ colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ colourLabel.setText("Alignment Colour ");
+ fontLabel.setFont(verdana11);
+ fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ fontLabel.setText("Font ");
+ fontSizeCB.setFont(verdana11);
+ fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
+ fontStyleCB.setFont(verdana11);
+ fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
+ fontNameCB.setFont(verdana11);
+ fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
+ gapSymbolCB.setFont(verdana11);
+ gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
+ mincolourLabel.setFont(verdana11);
+ mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ mincolourLabel.setText("Minimum 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("Maximum 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();
+ }
+ });
+
+ startupCheckbox.setText("Open file");
+ startupCheckbox.setFont(verdana11);
+ startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
+ startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
+ startupCheckbox.setSelected(true);
+ startupFileTextfield.setFont(verdana11);
+ startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
+ startupFileTextfield.addMouseListener(new MouseAdapter()
+ {
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() > 1)
+ {
+ startupFileTextfield_mouseClicked();
+ }
+ }
+ });
+
+ connectTab.setLayout(gridBagLayout3);
+ serverLabel.setText("Address");
+ serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ serverLabel.setFont(verdana11);
+ proxyServerTB.setFont(verdana11);
+ proxyPortTB.setFont(verdana11);
+ portLabel.setFont(verdana11);
+ portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ portLabel.setText("Port");
+ browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
+ browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
+ browserLabel.setText("Default Browser (Unix)");
+ defaultBrowser.setFont(verdana11);
+ defaultBrowser.setText("");
+ usagestats.setText("Send usage statistics");
+ usagestats.setFont(verdana11);
+ usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
+ usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
+ questionnaire.setText("Check for questionnaires");
+ questionnaire.setFont(verdana11);
+ questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
+ questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
+ versioncheck.setText("Check for latest version");
+ versioncheck.setFont(verdana11);
+ versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
+ versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
+ newLink.setText("New");
+ newLink.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ newLink_actionPerformed(e);
+ }
+ });
+ editLink.setText("Edit");
+ editLink.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ editLink_actionPerformed(e);
+ }
+ });
+ deleteLink.setText("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);
+ }
+ });
+
+ linkScrollPane.setBorder(null);
+ linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
+ linkPanel.setLayout(borderLayout2);
+ editLinkButtons.setLayout(gridLayout1);
+ gridLayout1.setRows(3);
+ linkNameList.setFont(verdana11);
+ linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ linkPanel2.setLayout(borderLayout3);
+ linkURLList.setFont(verdana11);
+ linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+
+ defaultBrowser.addMouseListener(new MouseAdapter()
+ {
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() > 1)
+ {
+ defaultBrowser_mouseClicked(e);
+ }
+ }
+ });
+ useProxy.setFont(verdana11);
+ useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
+ useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
+ useProxy.setText("Use a proxy server");
+ useProxy.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ useProxy_actionPerformed();
+ }
+ });
+ jPanel1.setBorder(titledBorder1);
+ jPanel1.setLayout(gridBagLayout1);
+ sortby.setFont(verdana11);
+ sortby.setBounds(new Rectangle(172, 249, 155, 21));
+ sortLabel.setFont(verdana11);
+ sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ sortLabel.setText("Sort by ");
+ jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
+ jPanel2.setLayout(gridLayout2);
+ gridLayout2.setRows(12);
+ exportTab.setLayout(null);
+ epsLabel.setFont(verdana11);
+ epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ epsLabel.setText("EPS Rendering Style");
+ epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
+ epsRendering.setFont(verdana11);
+ epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
+ jLabel1.setFont(verdana11);
+ jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
+ jLabel1.setText("Append /start-end (/15-380)");
+ jLabel1.setFont(verdana11);
+ fastajv.setFont(verdana11);
+ fastajv.setHorizontalAlignment(SwingConstants.LEFT);
+ clustaljv.setText("Clustal ");
+ blcjv.setText("BLC ");
+ fastajv.setText("Fasta ");
+ msfjv.setText("MSF ");
+ pfamjv.setText("PFAM ");
+ pileupjv.setText("Pileup ");
+ msfjv.setFont(verdana11);
+ msfjv.setHorizontalAlignment(SwingConstants.LEFT);
+ pirjv.setText("PIR ");
+ jPanel11.setFont(verdana11);
+ jPanel11.setBorder(titledBorder2);
+ jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
+ jPanel11.setLayout(gridLayout3);
+ blcjv.setFont(verdana11);
+ blcjv.setHorizontalAlignment(SwingConstants.LEFT);
+ clustaljv.setFont(verdana11);
+ clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
+ pfamjv.setFont(verdana11);
+ pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
+ pileupjv.setFont(verdana11);
+ pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
+ pirjv.setFont(verdana11);
+ pirjv.setHorizontalAlignment(SwingConstants.LEFT);
+ seqLimit.setFont(verdana11);
+ seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
+ seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
+ seqLimit.setText("Full Sequence Id");
+ gridLayout3.setRows(8);
+ smoothFont.setFont(verdana11);
+ smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
+ smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
+ smoothFont.setText("Smooth Font");
+ calcTab.setLayout(null);
+ autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
+ autoCalculateConsCheck.setText("AutoCalculate Consensus");
+ autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
+ padGaps.setFont(JvSwingUtils.getLabelFont());
+ padGaps.setText("Pad Gaps When Editing");
+ padGaps.setBounds(new Rectangle(22, 94, 168, 23));
+ sortByTree.setFont(JvSwingUtils.getLabelFont());
+ sortByTree.setText("Sort With New Tree");
+ sortByTree.setToolTipText("When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.");
+ sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
+ modellerOutput.setFont(JvSwingUtils.getLabelFont());
+ modellerOutput.setText("Use Modeller Output");
+ modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+ dasPanel.setLayout(borderLayout4);
+ wsPanel.setLayout(borderLayout5);
+ wrap.setFont(JvSwingUtils.getLabelFont());
+ wrap.setHorizontalAlignment(SwingConstants.TRAILING);
+ wrap.setHorizontalTextPosition(SwingConstants.LEADING);
+ wrap.setText("Wrap Alignment");
+ rightAlign.setFont(JvSwingUtils.getLabelFont());
+ rightAlign.setForeground(Color.black);
+ rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
+ rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
+ rightAlign.setText("Right Align Ids");
+ idItalics.setFont(JvSwingUtils.getLabelFont());
+ idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
+ idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
+ idItalics.setText("Sequence Name Italics");
+ openoverv.setFont(JvSwingUtils.getLabelFont());
+ openoverv.setActionCommand("Open Overview");
+ openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
+ openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
+ openoverv.setText("Open Overview");
+ jPanel2.add(fullScreen);
+ jPanel2.add(openoverv);
+ jPanel2.add(seqLimit);
+ jPanel2.add(rightAlign);
+ jPanel2.add(fontLabel);
+ jPanel2.add(showUnconserved);
+ jPanel2.add(idItalics);
+ jPanel2.add(smoothFont);
+ jPanel2.add(gapLabel);
+ jPanel2.add(wrap);
+ jPanel2.add(sortLabel);
+ jPanel2.add(startupCheckbox);
+ visualTab.add(annotations);
+ visualTab.add(startupFileTextfield);
+ visualTab.add(sortby);
+ visualTab.add(gapSymbolCB);
+ visualTab.add(fontNameCB);
+ visualTab.add(fontSizeCB);
+ visualTab.add(fontStyleCB);
+ annsettingsPanel.setBounds(new Rectangle(173, 34, 300, 61));
+ annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
+ annsettingsPanel.add(autoAnnotSettings1);
+ annsettingsPanel.add(autoAnnotSettings2);
+ annsettingsPanel.add(autoAnnotSettings3);
+ autoAnnotSettings1.setLayout(new GridLayout(3, 1, 0, 0));
+ autoAnnotSettings2.setLayout(new GridLayout(3, 1, 0, 0));
+ autoAnnotSettings3.setLayout(new GridLayout(3, 1, 0, 0));
+ visualTab.add(annsettingsPanel);
+ Border jb = new EmptyBorder(1, 1, 4, 5);
+ quality.setBorder(jb);
+ conservation.setBorder(jb);
+ identity.setBorder(jb);
+ showConsensbits.setBorder(jb);
+ showGroupbits.setBorder(jb);
+ showGroupConsensus.setBorder(jb);
+ showGroupConservation.setBorder(jb);
+ showConsensHistogram.setBorder(jb);
+ showConsensLogo.setBorder(jb);
+
+ 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("Sequence ID Tooltip"));
+ tooltipSettings.setBounds(173, 130, 200, 62);
+ tooltipSettings.setLayout(new GridLayout(2, 1));
+ tooltipSettings.add(showDbRefTooltip);
+ tooltipSettings.add(showNpTooltip);
+ visualTab.add(tooltipSettings);
+ visualTab.add(jPanel2);
+ JvSwingUtils.addtoLayout(visual2Tab, "Default Colourscheme for alignment", colourLabel, colour);
+ JPanel annotationShding=new JPanel();
+ annotationShding.setBorder(new TitledBorder("Annotation Shading Default"));
+ annotationShding.setLayout(new GridLayout(1,2));
+ JvSwingUtils.addtoLayout(annotationShding, "Default Minimum Colour for annotation shading", mincolourLabel,minColour);
+ JvSwingUtils.addtoLayout(annotationShding,"Default Maximum Colour for annotation shading", maxcolourLabel, maxColour);
+ visual2Tab.add(annotationShding); // , FlowLayout.LEFT);
+
+// visual2panel.add(minColour);
+// visual2panel.add(maxColour);
+// visual2Tab.add(visual2panel);
+
+ linkPanel.add(editLinkButtons, BorderLayout.EAST);
+ editLinkButtons.add(newLink, null);
+ editLinkButtons.add(editLink, null);
+ editLinkButtons.add(deleteLink, null);
+ linkPanel.add(linkScrollPane, BorderLayout.CENTER);
+ linkScrollPane.getViewport().add(linkPanel2, null);
+ linkPanel2.add(linkURLList, BorderLayout.CENTER);
+ linkPanel2.add(linkNameList, BorderLayout.WEST);
+ okCancelPanel.add(ok);
+ okCancelPanel.add(cancel);
+ this.add(tabbedPane, java.awt.BorderLayout.CENTER);
+
+ this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
+ jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
+ 2, 4, 0), 5, 0));
+ jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
+ 0, 4, 0), 11, 6));
+ connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0,
+ GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
+ 16, 0, 0, 12), 359, -17));
+ connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0,
+ GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
+ 21, 0, 35, 12), 4, 6));
+ connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
+ new Insets(16, 0, 0, 0), 5, 1));
+ jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 4, 2), 54, 1));
+ jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 4, 0), 263, 1));
+ connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(15, 0, 0, 15), 307, 1));
+ connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 4, 2), 70, 1));
+ connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 4, 2), 70, 1));
+ connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0,
+ 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 4, 2), 70, 1));
+
+ jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
+ 2, 5, 185), 2, -4));
+ DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
+ dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
+ gapSymbolCB.setRenderer(dlcr);
+
+ tabbedPane.add(visualTab, "Visual");
+ tabbedPane.add(visual2Tab,"Colours");
+ tabbedPane.add(connectTab, "Connections");
+ tabbedPane.add(exportTab, "Output");
+ jPanel11.add(jLabel1);
+ jPanel11.add(blcjv);
+ jPanel11.add(clustaljv);
+ jPanel11.add(fastajv);
+ jPanel11.add(msfjv);
+ jPanel11.add(pfamjv);
+ jPanel11.add(pileupjv);
+ jPanel11.add(pirjv);
+ exportTab.add(modellerOutput);
+ tabbedPane.add(calcTab, "Editing");
+ calcTab.add(autoCalculateConsCheck);
+ calcTab.add(padGaps);
+ calcTab.add(sortByTree);
+
+ tabbedPane.add(dasPanel, "DAS Settings");
+ tabbedPane.add(wsPanel, "Web Services");
+
+ exportTab.add(epsLabel);
+ exportTab.add(epsRendering);
+ exportTab.add(jPanel11);
+ }
+
+ protected void maxColour_actionPerformed()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void minColour_actionPerformed()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ 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());
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff