/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 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
import javax.swing.border.TitledBorder;\r
import java.awt.event.*;\r
import javax.swing.event.*;\r
-\r
+import java.awt.Font;\r
+import java.awt.Rectangle;\r
+import java.awt.Insets;\r
\r
/**\r
* DOCUMENT ME!\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 fullScreen = new JCheckBox();\r
protected JCheckBox conservation = new JCheckBox();\r
protected JCheckBox identity = new JCheckBox();\r
protected JCheckBox annotations = new JCheckBox();\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
/**\r
* Creates a new GPreferences object.\r
*/\r
}\r
});\r
quality.setEnabled(false);\r
- quality.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ quality.setFont(verdana11);\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
+ 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
- fullScreen.setBounds(new Rectangle(5, 29, 132, 23));\r
- conservation.setEnabled(false);\r
- conservation.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\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
- 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.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
- identity.setBounds(new Rectangle(326, 53, 99, 23));\r
- annotations.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ annotations.setFont(verdana11);\r
annotations.setHorizontalAlignment(SwingConstants.RIGHT);\r
annotations.setHorizontalTextPosition(SwingConstants.LEFT);\r
- annotations.setSelected(true);\r
+ annotations.setMargin(new Insets(2, 2, 2, 0));\r
+ annotations.setSelected(true);\r
annotations.setText("Show Annotations");\r
- annotations.setBounds(new Rectangle(10, 53, 128, 23));\r
- annotations.addActionListener(new ActionListener()\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.setFont(verdana11);\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
+ gapLabel.setText("Gap Symbol ");\r
+ colour.setFont(verdana11);\r
+ colour.setBounds(new Rectangle(172, 188, 155, 21));\r
+ colourLabel.setFont(verdana11);\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
+ colourLabel.setText("Colour ");\r
+ fontLabel.setFont(verdana11);\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
+ fontLabel.setText("Font ");\r
+ fontSizeCB.setFont(verdana11);\r
+ fontSizeCB.setBounds(new Rectangle(317, 92, 49, 21));\r
+ fontStyleCB.setFont(verdana11);\r
+ fontStyleCB.setBounds(new Rectangle(364, 92, 70, 21));\r
+ fontNameCB.setFont(verdana11);\r
+ fontNameCB.setBounds(new Rectangle(171, 92, 147, 21));\r
+ gapSymbolCB.setFont(verdana11);\r
+ gapSymbolCB.setBounds(new Rectangle(172, 163, 69, 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.setFont(verdana11);\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(122, 202, 309, 20));\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
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
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
}\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
- 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
- visualTab.add(startupFileTextfield);\r
-\r
- tabbedPane.add(visualTab, "Visual");\r
- tabbedPane.add(connectTab, "Connections");\r
+ sortby.setFont(verdana11);\r
+ sortby.setBounds(new Rectangle(171, 213, 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(10);\r
+ jPanel3.setBounds(new Rectangle(169, 39, 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.setMargin(new Insets(2, 2, 2, 0));\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
+ jPanel2.add(fullScreen);\r
\r
+ jPanel2.add(annotations);\r
+ jPanel2.add(seqLimit);\r
+ jPanel2.add(fontLabel);\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(sortby);\r
+ visualTab.add(gapSymbolCB);\r
+ visualTab.add(colour);\r
+ visualTab.add(fontNameCB);\r
+ visualTab.add(fontSizeCB);\r
+ visualTab.add(fontStyleCB);\r
+ visualTab.add(jPanel3);\r
+ visualTab.add(startupFileTextfield);\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
linkPanel2.add(linkNameList, BorderLayout.WEST);\r
okCancelPanel.add(ok);\r
okCancelPanel.add(cancel);\r
- this.add(tabbedPane, java.awt.BorderLayout.CENTER);\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
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
DefaultListCellRenderer dlcr = new DefaultListCellRenderer();\r
dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);\r
gapSymbolCB.setRenderer(dlcr);\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
+ exportTab.add(epsLabel);\r
+ exportTab.add(epsRendering);\r
+ exportTab.add(jPanel11);\r
+ }\r
\r
/**\r
* DOCUMENT ME!\r