+ 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, 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
+ 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