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
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
}\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
visualTab.setBorder(new TitledBorder("Open new alignment"));\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.setMargin(new Insets(4, 2, 2, 0));\r
- fullID.setText("Full Sequence ID");\r
- fullScreen.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\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(new java.awt.Font("Verdana", Font.PLAIN, 11));\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(new java.awt.Font("Verdana", Font.PLAIN, 11));\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(new java.awt.Font("Verdana", Font.PLAIN, 11));\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_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
- colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- colour.setBounds(new Rectangle(148, 171, 154, 21));\r
- colourLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\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(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ fontLabel.setFont(verdana11);\r
fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
fontLabel.setText("Font ");\r
- fontSizeCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- fontSizeCB.setBounds(new Rectangle(317, 111, 49, 21));\r
- fontStyleCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- fontStyleCB.setBounds(new Rectangle(365, 111, 70, 21));\r
- fontNameCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- fontNameCB.setBounds(new Rectangle(148, 111, 169, 21));\r
- gapSymbolCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- gapSymbolCB.setBounds(new Rectangle(148, 141, 67, 21));\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(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(148, 232, 302, 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
- sortby.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- sortby.setBounds(new Rectangle(148, 200, 302, 21));\r
- sortLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\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, 138, 242));\r
+ jPanel2.setBounds(new Rectangle(7, 17, 158, 245));\r
jPanel2.setLayout(gridLayout2);\r
- gridLayout2.setRows(8);\r
- jPanel3.setBounds(new Rectangle(147, 46, 274, 26));\r
+ gridLayout2.setRows(9);\r
+ jPanel3.setBounds(new Rectangle(167, 41, 274, 26));\r
exportTab.setLayout(null);\r
- epsLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ epsLabel.setFont(verdana11);\r
epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
epsLabel.setText("EPS Rendering Style");\r
- epsLabel.setBounds(new Rectangle(3, 47, 134, 21));\r
- epsRendering.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- epsRendering.setBounds(new Rectangle(145, 47, 286, 21));\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(fullID);\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(jPanel3);\r
- jPanel3.add(conservation);\r
- jPanel3.add(quality);\r
- jPanel3.add(identity);\r
- visualTab.add(sortby);\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(gapSymbolCB);\r
+ visualTab.add(jPanel3);\r
+ jPanel3.add(conservation);\r
+ jPanel3.add(identity);\r
+ jPanel3.add(quality);\r
visualTab.add(jPanel2);\r
-\r
linkPanel.add(editLinkButtons, BorderLayout.EAST);\r
editLinkButtons.add(newLink, null);\r
editLinkButtons.add(editLink, null);\r
, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,\r
new Insets(15, 0, 0, 15), 307, 1));\r
\r
- exportTab.add(epsLabel);\r
- exportTab.add(epsRendering);\r
\r
jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0\r
, GridBagConstraints.WEST,\r
gapSymbolCB.setRenderer(dlcr);\r
\r
tabbedPane.add(visualTab, "Visual");\r
- tabbedPane.add(connectTab, "Connections");\r
- tabbedPane.add(exportTab, "Export");\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
git://source.jalview.org / jalview.git / blobdiff