- jLabel1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- jLabel1.setHorizontalAlignment(SwingConstants.RIGHT);\r
- jLabel1.setText("Gap Symbol");\r
- jLabel1.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
- jLabel2.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- jLabel2.setHorizontalAlignment(SwingConstants.RIGHT);\r
- jLabel2.setText("Colour");\r
- jLabel2.setBounds(new Rectangle(60, 172, 58, 15));\r
- jLabel3.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- jLabel3.setHorizontalAlignment(SwingConstants.RIGHT);\r
- jLabel3.setText("Font");\r
- jLabel3.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
- jPanel2.add(annotations);\r
- jPanel2.add(conservation);\r
- jPanel2.add(quality);\r
- jPanel2.add(fullID);\r
- jPanel2.add(gapSymbolCB);\r
- jPanel2.add(jLabel1);\r
- jPanel2.add(fontNameCB);\r
- jPanel2.add(jLabel2);\r
- jPanel2.add(jLabel3);\r
- jPanel2.add(colour);\r
- jPanel2.add(fontSizeCB);\r
- jPanel2.add(fontStyleCB);\r
- jPanel2.add(identity);\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
+ 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
+ {\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
+ {\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
+ {\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
+ 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(172, 249, 155, 21));\r
+ sortLabel.setFont(verdana11);\r
+ sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);\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
+ openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ openoverv.setActionCommand("Open Overview");\r
+ openoverv.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ openoverv.setHorizontalTextPosition(SwingConstants.LEADING);\r
+ openoverv.setText("Open Overview Window");\r
+ openoverv.setBounds(new Rectangle(169, 17, 200, 23));\r