+ 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
+ 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(openoverv);\r
+ visualTab.add(startupFileTextfield);\r
+ visualTab.add(sortby);\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