/*\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
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 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.*;\r
+import javax.swing.border.*;\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
+public class GPreferences\r
+ extends JPanel\r
{\r
- JTabbedPane tabbedPane = new JTabbedPane();\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 fullID = new JCheckBox();\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
+ 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 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
+ protected JPanel dasPanel = new JPanel();\r
+ BorderLayout borderLayout4 = new BorderLayout();\r
+ protected JCheckBox wrap = new JCheckBox();\r
+ protected JCheckBox rightAlign = new JCheckBox();\r
+ protected JCheckBox idItalics = new JCheckBox();\r
/**\r
- * Creates a new GPreferences object.\r
- */\r
- public GPreferences()\r
+ * Creates a new GPreferences object.\r
+ */\r
+ public GPreferences()\r
+ {\r
+ try\r
{\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\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
+ * DOCUMENT ME!\r
+ *\r
+ * @throws Exception DOCUMENT ME!\r
+ */\r
+ private void jbInit()\r
+ 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.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.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, 225, 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(319, 111, 49, 21));\r
+ fontStyleCB.setFont(verdana11);\r
+ fontStyleCB.setBounds(new Rectangle(367, 111, 70, 21));\r
+ fontNameCB.setFont(verdana11);\r
+ fontNameCB.setBounds(new Rectangle(172, 111, 147, 21));\r
+ gapSymbolCB.setFont(verdana11);\r
+ gapSymbolCB.setBounds(new Rectangle(172, 204, 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(172, 273, 270, 20));\r
+ startupFileTextfield.addMouseListener(new MouseAdapter()\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(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- quality.setHorizontalAlignment(SwingConstants.RIGHT);\r
- quality.setHorizontalTextPosition(SwingConstants.LEFT);\r
- quality.setSelected(true);\r
- quality.setText("Quality");\r
- quality.setBounds(new Rectangle(248, 53, 81, 23));\r
- visualTab.setBorder(new TitledBorder("Open new alignment"));\r
- visualTab.setBounds(new Rectangle(9, 20, 442, 241));\r
- visualTab.setLayout(null);\r
- fullID.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- fullID.setHorizontalAlignment(SwingConstants.RIGHT);\r
- fullID.setHorizontalTextPosition(SwingConstants.LEFT);\r
- fullID.setText("Full Sequence ID");\r
- fullID.setBounds(new Rectangle(9, 78, 129, 23));\r
- fullScreen.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);\r
- fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);\r
- fullScreen.setText("Maximise Window");\r
- fullScreen.setBounds(new Rectangle(5, 29, 132, 23));\r
- conservation.setEnabled(false);\r
- conservation.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- conservation.setHorizontalAlignment(SwingConstants.RIGHT);\r
- conservation.setHorizontalTextPosition(SwingConstants.LEFT);\r
- conservation.setSelected(true);\r
- conservation.setText("Conservation");\r
- conservation.setBounds(new Rectangle(137, 53, 113, 23));\r
- identity.setEnabled(false);\r
- identity.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- identity.setHorizontalAlignment(SwingConstants.RIGHT);\r
- identity.setHorizontalTextPosition(SwingConstants.LEFT);\r
- identity.setSelected(true);\r
- identity.setText("Consensus");\r
- identity.setBounds(new Rectangle(326, 53, 99, 23));\r
- annotations.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- annotations.setHorizontalAlignment(SwingConstants.RIGHT);\r
- annotations.setHorizontalTextPosition(SwingConstants.LEFT);\r
- annotations.setSelected(true);\r
- annotations.setText("Show Annotations");\r
- annotations.setBounds(new Rectangle(10, 53, 128, 23));\r
- annotations.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- annotations_actionPerformed(e);\r
- }\r
- });\r
- gapLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
- gapLabel.setText("Gap Symbol");\r
- gapLabel.setBounds(new Rectangle(41, 142, 76, 15));\r
- colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- colour.setBounds(new Rectangle(121, 168, 154, 21));\r
- colourLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
- colourLabel.setText("Colour");\r
- colourLabel.setBounds(new Rectangle(60, 172, 58, 15));\r
- fontLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
- fontLabel.setText("Font");\r
- fontLabel.setBounds(new Rectangle(83, 114, 34, 15));\r
- fontSizeCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- fontSizeCB.setBounds(new Rectangle(304, 109, 49, 21));\r
- fontStyleCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- fontStyleCB.setBounds(new Rectangle(353, 109, 80, 21));\r
- fontNameCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- fontNameCB.setBounds(new Rectangle(121, 109, 183, 21));\r
- gapSymbolCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- gapSymbolCB.setBounds(new Rectangle(121, 140, 67, 21));\r
- startupCheckbox.setText("Open file");\r
- startupCheckbox.setBounds(new Rectangle(4, 200, 115, 23));\r
- startupCheckbox.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);\r
- startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);\r
- startupCheckbox.setSelected(true);\r
- startupFileTextfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- startupFileTextfield.setBounds(new Rectangle(121, 200, 309, 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
+ public void mouseClicked(MouseEvent e)\r
+ {\r
+ if (e.getClickCount() > 1)\r
+ {\r
+ startupFileTextfield_mouseClicked();\r
+ }\r
+ }\r
+ });\r
\r
- connectTab.setLayout(gridBagLayout3);\r
+ connectTab.setLayout(gridBagLayout3);\r
serverLabel.setText("Address");\r
serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
- serverLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- proxyServerTB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- proxyPortTB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- portLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\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(new java.awt.Font("Verdana", Font.PLAIN, 11));\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.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\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.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\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.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\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
+ 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
+ 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(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
+ linkNameList.setFont(verdana11);\r
linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
linkPanel2.setLayout(borderLayout3);\r
- linkURLList.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ linkURLList.setFont(verdana11);\r
linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
\r
defaultBrowser.addMouseListener(new MouseAdapter()\r
public void mouseClicked(MouseEvent e)\r
{\r
if (e.getClickCount() > 1)\r
- {\r
- defaultBrowser_mouseClicked(e);\r
- }\r
+ {\r
+ defaultBrowser_mouseClicked(e);\r
+ }\r
}\r
});\r
- useProxy.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ useProxy.setFont(verdana11);\r
useProxy.setHorizontalAlignment(SwingConstants.RIGHT);\r
useProxy.setHorizontalTextPosition(SwingConstants.LEADING);\r
useProxy.setText("Use a proxy server");\r
});\r
jPanel1.setBorder(titledBorder1);\r
jPanel1.setLayout(gridBagLayout1);\r
- sortby.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- sortby.setBounds(new Rectangle(122, 232, 308, 21));\r
- sortLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ sortby.setFont(verdana11);\r
+ sortby.setBounds(new Rectangle(172, 249, 155, 21));\r
+ sortLabel.setFont(verdana11);\r
sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
- sortLabel.setText("Sort by");\r
- sortLabel.setBounds(new Rectangle(53, 235, 64, 15));\r
- visualTab.add(annotations);\r
- visualTab.add(conservation);\r
- visualTab.add(quality);\r
- visualTab.add(fullID);\r
- visualTab.add(gapSymbolCB);\r
- visualTab.add(fontLabel);\r
- visualTab.add(fontNameCB);\r
- visualTab.add(colourLabel);\r
- visualTab.add(gapLabel);\r
- visualTab.add(colour);\r
- visualTab.add(fontSizeCB);\r
- visualTab.add(fontStyleCB);\r
- visualTab.add(identity);\r
- visualTab.add(fullScreen);\r
- visualTab.add(startupCheckbox);\r
+ sortLabel.setText("Sort by ");\r
+ jPanel2.setBounds(new Rectangle(7, 17, 158, 278));\r
+ jPanel2.setLayout(gridLayout2);\r
+ gridLayout2.setRows(12);\r
+ jPanel3.setBounds(new Rectangle(173, 35, 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
+ dasPanel.setLayout(borderLayout4);\r
+ wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ wrap.setHorizontalAlignment(SwingConstants.TRAILING);\r
+ wrap.setHorizontalTextPosition(SwingConstants.LEADING);\r
+ wrap.setText("Wrap Alignment");\r
+ rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ rightAlign.setForeground(Color.black);\r
+ rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);\r
+ rightAlign.setText("Right Align Ids");\r
+ idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ idItalics.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ idItalics.setHorizontalTextPosition(SwingConstants.LEADING);\r
+ idItalics.setText("Sequence Name Italics");\r
+ jPanel2.add(fullScreen);\r
+ jPanel2.add(annotations);\r
+ jPanel2.add(seqLimit);\r
+ jPanel2.add(rightAlign);\r
+ jPanel2.add(fontLabel);\r
+ jPanel2.add(idItalics);\r
+ jPanel2.add(smoothFont);\r
+ jPanel2.add(wrap);\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(sortLabel);\r
-\r
- tabbedPane.add(visualTab, "Visual");\r
- tabbedPane.add(connectTab, "Connections");\r
-\r
+ visualTab.add(colour);\r
+ visualTab.add(gapSymbolCB);\r
+ visualTab.add(jPanel3);\r
+ visualTab.add(fontNameCB);\r
+ visualTab.add(fontSizeCB);\r
+ visualTab.add(fontStyleCB);\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
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
+ 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
+ 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
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
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
+ dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);\r
+ gapSymbolCB.setRenderer(dlcr);\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void ok_actionPerformed(ActionEvent e)\r
- {\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
+ tabbedPane.add(dasPanel, "DAS Settings");\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void cancel_actionPerformed(ActionEvent e)\r
- {\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 annotations_actionPerformed(ActionEvent e)\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
- public void startupFileTextfield_mouseClicked()\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
+ * DOCUMENT ME!\r
+ */\r
+ public void startupFileTextfield_mouseClicked()\r
+ {\r
+ }\r
\r
- public void newLink_actionPerformed(ActionEvent e) {\r
+ public void newLink_actionPerformed(ActionEvent e)\r
+ {\r
\r
}\r
\r
- public void editLink_actionPerformed(ActionEvent e) {\r
+ public void editLink_actionPerformed(ActionEvent e)\r
+ {\r
\r
}\r
\r
- public void deleteLink_actionPerformed(ActionEvent e) {\r
+ public void deleteLink_actionPerformed(ActionEvent e)\r
+ {\r
\r
}\r
\r
\r
public void useProxy_actionPerformed()\r
{\r
- proxyServerTB.setEnabled(useProxy.isSelected());\r
- proxyPortTB.setEnabled(useProxy.isSelected());\r
+ proxyServerTB.setEnabled(useProxy.isSelected());\r
+ proxyPortTB.setEnabled(useProxy.isSelected());\r
}\r
+\r
}\r