2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.jbappletgui;
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22 import java.awt.event.*;
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25 public class GAlignFrame extends Frame {
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26 protected MenuBar alignFrameMenuBar = new MenuBar();
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27 protected Menu fileMenu = new Menu();
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28 protected MenuItem closeMenuItem = new MenuItem();
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29 protected Menu editMenu = new Menu();
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30 protected Menu viewMenu = new Menu();
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31 protected Menu colourMenu = new Menu();
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32 protected Menu calculateMenu = new Menu();
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33 protected MenuItem selectAllSequenceMenuItem = new MenuItem();
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34 protected MenuItem deselectAllSequenceMenuItem = new MenuItem();
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35 protected MenuItem invertSequenceMenuItem = new MenuItem();
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36 protected MenuItem remove2LeftMenuItem = new MenuItem();
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37 protected MenuItem remove2RightMenuItem = new MenuItem();
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38 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
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39 protected MenuItem removeAllGapsMenuItem = new MenuItem();
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40 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
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41 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
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42 protected MenuItem sortPairwiseMenuItem = new MenuItem();
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43 protected MenuItem sortIDMenuItem = new MenuItem();
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44 protected MenuItem sortGroupMenuItem = new MenuItem();
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45 protected MenuItem removeRedundancyMenuItem = new MenuItem();
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46 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
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47 protected MenuItem PCAMenuItem = new MenuItem();
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48 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
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49 protected MenuItem neighbourTreeMenuItem = new MenuItem();
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50 BorderLayout borderLayout1 = new BorderLayout();
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51 public Label statusBar = new Label();
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52 protected Menu outputTextboxMenu = new Menu();
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53 protected MenuItem clustalColour = new MenuItem();
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54 protected MenuItem zappoColour = new MenuItem();
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55 protected MenuItem taylorColour = new MenuItem();
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56 protected MenuItem hydrophobicityColour = new MenuItem();
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57 protected MenuItem helixColour = new MenuItem();
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58 protected MenuItem strandColour = new MenuItem();
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59 protected MenuItem turnColour = new MenuItem();
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60 protected MenuItem buriedColour = new MenuItem();
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61 protected MenuItem userDefinedColour = new MenuItem();
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62 protected MenuItem PIDColour = new MenuItem();
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63 protected MenuItem BLOSUM62Colour = new MenuItem();
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64 MenuItem njTreeBlosumMenuItem = new MenuItem();
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65 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
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66 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
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67 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
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68 MenuItem overviewMenuItem = new MenuItem();
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69 protected MenuItem undoMenuItem = new MenuItem();
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70 protected MenuItem redoMenuItem = new MenuItem();
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71 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
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72 MenuItem noColourmenuItem = new MenuItem();
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73 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
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74 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
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75 MenuItem findMenuItem = new MenuItem();
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76 Menu searchMenu = new Menu();
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77 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
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78 protected MenuItem nucleotideColour = new MenuItem();
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79 MenuItem deleteGroups = new MenuItem();
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80 MenuItem delete = new MenuItem();
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81 MenuItem copy = new MenuItem();
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82 MenuItem cut = new MenuItem();
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83 Menu Menu1 = new Menu();
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84 MenuItem pasteNew = new MenuItem();
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85 MenuItem pasteThis = new MenuItem();
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86 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
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87 protected MenuItem font = new MenuItem();
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88 protected CheckboxMenuItem fullSeqId = new CheckboxMenuItem();
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89 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
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90 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
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91 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
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92 MenuItem modifyPID = new MenuItem();
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93 MenuItem modifyConservation = new MenuItem();
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94 protected Menu sortByTreeMenu = new Menu();
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95 Menu sort = new Menu();
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96 Menu calculate = new Menu();
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97 MenuItem inputText = new MenuItem();
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98 Menu helpMenu = new Menu();
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99 MenuItem documentation = new MenuItem();
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100 MenuItem about = new MenuItem();
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102 public GAlignFrame() {
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105 setMenuBar(alignFrameMenuBar);
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109 // dynamically fill save as menu with available formats
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110 for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {
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111 item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(
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113 item.addActionListener(new java.awt.event.ActionListener() {
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114 public void actionPerformed(ActionEvent e) {
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115 saveAs_actionPerformed(e);
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119 item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(
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121 item.addActionListener(new java.awt.event.ActionListener() {
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122 public void actionPerformed(ActionEvent e) {
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123 outputText_actionPerformed(e);
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127 outputTextboxMenu.add(item);
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129 } catch (Exception e) {
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130 e.printStackTrace();
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134 private void jbInit() throws Exception {
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135 fileMenu.setLabel("File");
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136 closeMenuItem.setLabel("Close");
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137 closeMenuItem.addActionListener(new java.awt.event.ActionListener() {
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138 public void actionPerformed(ActionEvent e) {
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139 closeMenuItem_actionPerformed(e);
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142 editMenu.setLabel("Edit");
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143 viewMenu.setLabel("View");
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144 colourMenu.setLabel("Colour");
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145 calculateMenu.setLabel("Calculate");
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146 selectAllSequenceMenuItem.setLabel("Select all");
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147 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
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148 public void actionPerformed(ActionEvent e) {
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149 selectAllSequenceMenuItem_actionPerformed(e);
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152 deselectAllSequenceMenuItem.setLabel("Deselect All");
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153 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
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154 public void actionPerformed(ActionEvent e) {
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155 deselectAllSequenceMenuItem_actionPerformed(e);
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158 invertSequenceMenuItem.setLabel("Invert Selection");
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159 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
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160 public void actionPerformed(ActionEvent e) {
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161 invertSequenceMenuItem_actionPerformed(e);
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164 remove2LeftMenuItem.setLabel("Remove Left");
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165 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {
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166 public void actionPerformed(ActionEvent e) {
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167 remove2LeftMenuItem_actionPerformed(e);
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170 remove2RightMenuItem.setLabel("Remove Right");
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171 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {
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172 public void actionPerformed(ActionEvent e) {
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173 remove2RightMenuItem_actionPerformed(e);
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176 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
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177 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {
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178 public void actionPerformed(ActionEvent e) {
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179 removeGappedColumnMenuItem_actionPerformed(e);
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182 removeAllGapsMenuItem.setLabel("Remove All Gaps");
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183 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {
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184 public void actionPerformed(ActionEvent e) {
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185 removeAllGapsMenuItem_actionPerformed(e);
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188 viewBoxesMenuItem.setLabel("Boxes");
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189 viewBoxesMenuItem.setState(true);
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190 viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() {
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191 public void itemStateChanged(ItemEvent e) {
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192 viewBoxesMenuItem_actionPerformed(null);
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195 viewTextMenuItem.setLabel("Text");
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196 viewTextMenuItem.setState(true);
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197 viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() {
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198 public void itemStateChanged(ItemEvent e) {
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199 viewTextMenuItem_actionPerformed(null);
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202 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
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203 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {
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204 public void actionPerformed(ActionEvent e) {
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205 sortPairwiseMenuItem_actionPerformed(e);
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208 sortIDMenuItem.setLabel("by ID");
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209 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {
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210 public void actionPerformed(ActionEvent e) {
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211 sortIDMenuItem_actionPerformed(e);
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214 sortGroupMenuItem.setLabel("by Group");
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215 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {
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216 public void actionPerformed(ActionEvent e) {
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217 sortGroupMenuItem_actionPerformed(e);
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220 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
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221 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {
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222 public void actionPerformed(ActionEvent e) {
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223 removeRedundancyMenuItem_actionPerformed(e);
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226 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
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227 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {
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228 public void actionPerformed(ActionEvent e) {
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229 pairwiseAlignmentMenuItem_actionPerformed(e);
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232 PCAMenuItem.setLabel("Principal Component Analysis");
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233 PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {
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234 public void actionPerformed(ActionEvent e) {
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235 PCAMenuItem_actionPerformed(e);
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238 averageDistanceTreeMenuItem.setLabel(
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239 "Average Distance Using % Identity");
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240 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
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241 public void actionPerformed(ActionEvent e) {
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242 averageDistanceTreeMenuItem_actionPerformed(e);
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245 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
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246 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
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247 public void actionPerformed(ActionEvent e) {
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248 neighbourTreeMenuItem_actionPerformed(e);
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251 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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252 statusBar.setBackground(Color.white);
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253 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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254 statusBar.setText("Status bar");
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255 outputTextboxMenu.setLabel("Output to Textbox");
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256 clustalColour.setLabel("Clustalx");
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258 clustalColour.addActionListener(new java.awt.event.ActionListener() {
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259 public void actionPerformed(ActionEvent e) {
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260 clustalColour_actionPerformed(e);
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263 zappoColour.setLabel("Zappo");
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264 zappoColour.addActionListener(new java.awt.event.ActionListener() {
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265 public void actionPerformed(ActionEvent e) {
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266 zappoColour_actionPerformed(e);
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269 taylorColour.setLabel("Taylor");
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270 taylorColour.addActionListener(new java.awt.event.ActionListener() {
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271 public void actionPerformed(ActionEvent e) {
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272 taylorColour_actionPerformed(e);
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275 hydrophobicityColour.setLabel("Hydrophobicity");
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276 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {
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277 public void actionPerformed(ActionEvent e) {
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278 hydrophobicityColour_actionPerformed(e);
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281 helixColour.setLabel("Helix Propensity");
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282 helixColour.addActionListener(new java.awt.event.ActionListener() {
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283 public void actionPerformed(ActionEvent e) {
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284 helixColour_actionPerformed(e);
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287 strandColour.setLabel("Strand Propensity");
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288 strandColour.addActionListener(new java.awt.event.ActionListener() {
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289 public void actionPerformed(ActionEvent e) {
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290 strandColour_actionPerformed(e);
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293 turnColour.setLabel("Turn Propensity");
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294 turnColour.addActionListener(new java.awt.event.ActionListener() {
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295 public void actionPerformed(ActionEvent e) {
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296 turnColour_actionPerformed(e);
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299 buriedColour.setLabel("Buried Index");
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300 buriedColour.addActionListener(new java.awt.event.ActionListener() {
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301 public void actionPerformed(ActionEvent e) {
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302 buriedColour_actionPerformed(e);
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305 userDefinedColour.setLabel("User Defined...");
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306 userDefinedColour.addActionListener(new java.awt.event.ActionListener() {
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307 public void actionPerformed(ActionEvent e) {
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308 userDefinedColour_actionPerformed(e);
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311 PIDColour.setLabel("Percentage Identity");
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312 PIDColour.addActionListener(new java.awt.event.ActionListener() {
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313 public void actionPerformed(ActionEvent e) {
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314 PIDColour_actionPerformed(e);
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317 BLOSUM62Colour.setLabel("BLOSUM62 Score");
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318 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {
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319 public void actionPerformed(ActionEvent e) {
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320 BLOSUM62Colour_actionPerformed(e);
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323 avDistanceTreeBlosumMenuItem.setLabel(
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324 "Average Distance Using BLOSUM62");
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325 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {
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326 public void actionPerformed(ActionEvent e) {
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327 avTreeBlosumMenuItem_actionPerformed(e);
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330 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
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331 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {
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332 public void actionPerformed(ActionEvent e) {
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333 njTreeBlosumMenuItem_actionPerformed(e);
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336 annotationPanelMenuItem.setActionCommand("");
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337 annotationPanelMenuItem.setState(true);
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338 annotationPanelMenuItem.setLabel("Show Annotations");
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339 annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() {
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340 public void itemStateChanged(ItemEvent e) {
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341 annotationPanelMenuItem_actionPerformed(null);
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344 colourTextMenuItem.setLabel("Colour Text");
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345 colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() {
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346 public void itemStateChanged(ItemEvent e) {
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347 colourTextMenuItem_actionPerformed(null);
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350 overviewMenuItem.setLabel("Overview Window");
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351 overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {
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352 public void actionPerformed(ActionEvent e) {
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353 overviewMenuItem_actionPerformed(e);
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356 undoMenuItem.setEnabled(false);
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357 undoMenuItem.setLabel("Undo");
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358 undoMenuItem.addActionListener(new java.awt.event.ActionListener() {
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359 public void actionPerformed(ActionEvent e) {
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360 undoMenuItem_actionPerformed(e);
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363 redoMenuItem.setEnabled(false);
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364 redoMenuItem.setLabel("Redo");
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365 redoMenuItem.addActionListener(new java.awt.event.ActionListener() {
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366 public void actionPerformed(ActionEvent e) {
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367 redoMenuItem_actionPerformed(e);
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370 conservationMenuItem.setLabel("by Conservation");
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371 conservationMenuItem.addItemListener(new java.awt.event.ItemListener() {
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372 public void itemStateChanged(ItemEvent e) {
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373 conservationMenuItem_actionPerformed(null);
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376 noColourmenuItem.setLabel("None");
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377 noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {
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378 public void actionPerformed(ActionEvent e) {
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379 noColourmenuItem_actionPerformed(e);
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382 wrapMenuItem.setLabel("Wrap");
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383 wrapMenuItem.addItemListener(new java.awt.event.ItemListener() {
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384 public void itemStateChanged(ItemEvent e) {
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385 wrapMenuItem_actionPerformed(null);
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388 renderGapsMenuItem.setLabel("Show Gaps");
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389 renderGapsMenuItem.setState(true);
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390 renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() {
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391 public void itemStateChanged(ItemEvent e) {
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392 renderGapsMenuItem_actionPerformed(null);
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395 findMenuItem.setLabel("Find...");
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396 findMenuItem.addActionListener(new java.awt.event.ActionListener() {
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397 public void actionPerformed(ActionEvent e) {
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398 findMenuItem_actionPerformed(e);
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401 searchMenu.setLabel("Search");
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403 abovePIDThreshold.setLabel("Above Identity Threshold");
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404 abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() {
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405 public void itemStateChanged(ItemEvent e) {
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406 abovePIDThreshold_actionPerformed(null);
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409 nucleotideColour.setLabel("Nucleotide");
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410 nucleotideColour.addActionListener(new java.awt.event.ActionListener() {
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411 public void actionPerformed(ActionEvent e) {
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412 nucleotideColour_actionPerformed(e);
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415 deleteGroups.setLabel("Undefine Groups");
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416 deleteGroups.addActionListener(new java.awt.event.ActionListener() {
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417 public void actionPerformed(ActionEvent e) {
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418 deleteGroups_actionPerformed(e);
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421 copy.setLabel("Copy");
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422 copy.addActionListener(new java.awt.event.ActionListener() {
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423 public void actionPerformed(ActionEvent e) {
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424 copy_actionPerformed(e);
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427 cut.setLabel("Cut");
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428 cut.addActionListener(new java.awt.event.ActionListener() {
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429 public void actionPerformed(ActionEvent e) {
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430 cut_actionPerformed(e);
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433 delete.setLabel("Delete");
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434 delete.addActionListener(new java.awt.event.ActionListener() {
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435 public void actionPerformed(ActionEvent e) {
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436 delete_actionPerformed(e);
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439 Menu1.setLabel("Paste");
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440 pasteNew.setLabel("To New Alignment");
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441 pasteNew.addActionListener(new java.awt.event.ActionListener() {
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442 public void actionPerformed(ActionEvent e) {
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443 pasteNew_actionPerformed(e);
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446 pasteThis.setLabel("Add To This Alignment");
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447 pasteThis.addActionListener(new java.awt.event.ActionListener() {
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448 public void actionPerformed(ActionEvent e) {
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449 pasteThis_actionPerformed(e);
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452 applyToAllGroups.setLabel("Apply Colour To All Groups");
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453 applyToAllGroups.setState(true);
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454 applyToAllGroups.addItemListener(new java.awt.event.ItemListener() {
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455 public void itemStateChanged(ItemEvent e) {
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456 applyToAllGroups_actionPerformed(null);
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459 font.setLabel("Font...");
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460 font.addActionListener(new java.awt.event.ActionListener() {
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461 public void actionPerformed(ActionEvent e) {
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462 font_actionPerformed(e);
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465 fullSeqId.setLabel("Show Full Sequence ID");
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466 fullSeqId.setState(true);
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467 fullSeqId.addItemListener(new java.awt.event.ItemListener() {
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468 public void itemStateChanged(ItemEvent e) {
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469 fullSeqId_actionPerformed(null);
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472 scaleAbove.setLabel("Scale Above");
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473 scaleAbove.setState(true);
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474 scaleAbove.addItemListener(new java.awt.event.ItemListener() {
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475 public void itemStateChanged(ItemEvent e) {
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476 scaleAbove_actionPerformed(null);
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479 scaleLeft.setEnabled(false);
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480 scaleLeft.setState(true);
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481 scaleLeft.setLabel("Scale Left");
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482 scaleLeft.addItemListener(new java.awt.event.ItemListener() {
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483 public void itemStateChanged(ItemEvent e) {
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484 scaleLeft_actionPerformed(null);
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487 scaleRight.setEnabled(false);
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488 scaleRight.setState(true);
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489 scaleRight.setLabel("Scale Right");
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490 scaleRight.addItemListener(new java.awt.event.ItemListener() {
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491 public void itemStateChanged(ItemEvent e) {
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492 scaleRight_actionPerformed(null);
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495 modifyPID.setLabel("Modify Identity Threshold...");
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496 modifyPID.addActionListener(new java.awt.event.ActionListener() {
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497 public void actionPerformed(ActionEvent e) {
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498 modifyPID_actionPerformed(e);
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501 modifyConservation.setLabel("Modify Conservation Threshold...");
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502 modifyConservation.addActionListener(new java.awt.event.ActionListener() {
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503 public void actionPerformed(ActionEvent e) {
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504 modifyConservation_actionPerformed(e);
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507 sortByTreeMenu.setLabel("By Tree Order");
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508 sort.setLabel("Sort");
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509 calculate.setLabel("Calculate Tree");
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510 inputText.setLabel("Input from textbox");
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511 inputText.addActionListener(new java.awt.event.ActionListener() {
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512 public void actionPerformed(ActionEvent e) {
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513 inputText_actionPerformed(e);
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517 helpMenu.setLabel("Help");
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518 documentation.setLabel("Documentation");
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519 documentation.addActionListener(new java.awt.event.ActionListener() {
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520 public void actionPerformed(ActionEvent e) {
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521 documentation_actionPerformed(e);
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525 about.setLabel("About...");
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526 about.addActionListener(new java.awt.event.ActionListener() {
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527 public void actionPerformed(ActionEvent e) {
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528 about_actionPerformed(e);
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532 alignFrameMenuBar.add(fileMenu);
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533 alignFrameMenuBar.add(editMenu);
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534 alignFrameMenuBar.add(searchMenu);
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535 alignFrameMenuBar.add(viewMenu);
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536 alignFrameMenuBar.add(colourMenu);
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537 alignFrameMenuBar.add(calculateMenu);
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538 alignFrameMenuBar.add(helpMenu);
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539 fileMenu.add(inputText);
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540 fileMenu.add(outputTextboxMenu);
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541 fileMenu.addSeparator();
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542 fileMenu.add(closeMenuItem);
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543 editMenu.add(undoMenuItem);
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544 editMenu.add(redoMenuItem);
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546 editMenu.add(copy);
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547 editMenu.add(Menu1);
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548 editMenu.add(delete);
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549 editMenu.addSeparator();
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550 editMenu.add(selectAllSequenceMenuItem);
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551 editMenu.add(deselectAllSequenceMenuItem);
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552 editMenu.add(invertSequenceMenuItem);
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553 editMenu.add(deleteGroups);
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554 editMenu.addSeparator();
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555 editMenu.add(remove2LeftMenuItem);
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556 editMenu.add(remove2RightMenuItem);
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557 editMenu.add(removeGappedColumnMenuItem);
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558 editMenu.add(removeAllGapsMenuItem);
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559 editMenu.add(removeRedundancyMenuItem);
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560 searchMenu.add(findMenuItem);
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561 viewMenu.add(font);
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562 viewMenu.addSeparator();
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563 viewMenu.add(wrapMenuItem);
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564 viewMenu.add(scaleAbove);
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565 viewMenu.add(scaleLeft);
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566 viewMenu.add(scaleRight);
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567 viewMenu.addSeparator();
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568 viewMenu.add(fullSeqId);
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569 viewMenu.add(viewBoxesMenuItem);
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570 viewMenu.add(viewTextMenuItem);
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571 viewMenu.add(colourTextMenuItem);
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572 viewMenu.add(renderGapsMenuItem);
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573 viewMenu.add(annotationPanelMenuItem);
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574 viewMenu.addSeparator();
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575 viewMenu.add(overviewMenuItem);
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576 colourMenu.add(applyToAllGroups);
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577 colourMenu.addSeparator();
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578 colourMenu.add(noColourmenuItem);
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579 colourMenu.add(clustalColour);
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580 colourMenu.add(BLOSUM62Colour);
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581 colourMenu.add(PIDColour);
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582 colourMenu.add(zappoColour);
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583 colourMenu.add(taylorColour);
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584 colourMenu.add(hydrophobicityColour);
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585 colourMenu.add(helixColour);
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586 colourMenu.add(strandColour);
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587 colourMenu.add(turnColour);
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588 colourMenu.add(buriedColour);
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589 colourMenu.add(nucleotideColour);
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590 colourMenu.add(userDefinedColour);
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591 colourMenu.addSeparator();
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592 colourMenu.add(conservationMenuItem);
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593 colourMenu.add(modifyConservation);
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594 colourMenu.add(abovePIDThreshold);
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595 colourMenu.add(modifyPID);
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596 calculateMenu.add(sort);
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597 calculateMenu.add(calculate);
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598 calculateMenu.addSeparator();
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599 calculateMenu.add(pairwiseAlignmentMenuItem);
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600 calculateMenu.add(PCAMenuItem);
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601 this.add(statusBar, BorderLayout.SOUTH);
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602 Menu1.add(pasteNew);
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603 Menu1.add(pasteThis);
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604 sort.add(sortIDMenuItem);
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605 sort.add(sortByTreeMenu);
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606 sort.add(sortGroupMenuItem);
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607 sort.add(sortPairwiseMenuItem);
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608 calculate.add(averageDistanceTreeMenuItem);
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609 calculate.add(neighbourTreeMenuItem);
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610 calculate.add(avDistanceTreeBlosumMenuItem);
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611 calculate.add(njTreeBlosumMenuItem);
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612 helpMenu.add(documentation);
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613 helpMenu.add(about);
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616 protected void saveAs_actionPerformed(ActionEvent e) {
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619 protected void outputText_actionPerformed(ActionEvent e) {
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622 protected void htmlMenuItem_actionPerformed(ActionEvent e) {
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625 protected void closeMenuItem_actionPerformed(ActionEvent e) {
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628 protected void redoMenuItem_actionPerformed(ActionEvent e) {
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631 protected void undoMenuItem_actionPerformed(ActionEvent e) {
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634 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) {
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637 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) {
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640 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) {
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643 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) {
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646 protected void remove2RightMenuItem_actionPerformed(ActionEvent e) {
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649 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) {
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652 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) {
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655 protected void wrapMenuItem_actionPerformed(ActionEvent e) {
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658 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) {
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661 protected void viewTextMenuItem_actionPerformed(ActionEvent e) {
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664 protected void colourTextMenuItem_actionPerformed(ActionEvent e) {
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667 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) {
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670 protected void overviewMenuItem_actionPerformed(ActionEvent e) {
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673 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) {
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676 protected void sortIDMenuItem_actionPerformed(ActionEvent e) {
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679 protected void sortGroupMenuItem_actionPerformed(ActionEvent e) {
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682 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) {
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685 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) {
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688 protected void PCAMenuItem_actionPerformed(ActionEvent e) {
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691 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) {
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694 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) {
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697 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) {
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700 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) {
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703 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) {
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706 protected void clustalColour_actionPerformed(ActionEvent e) {
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709 protected void zappoColour_actionPerformed(ActionEvent e) {
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712 protected void taylorColour_actionPerformed(ActionEvent e) {
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715 protected void hydrophobicityColour_actionPerformed(ActionEvent e) {
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718 protected void helixColour_actionPerformed(ActionEvent e) {
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721 protected void strandColour_actionPerformed(ActionEvent e) {
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724 protected void turnColour_actionPerformed(ActionEvent e) {
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727 protected void buriedColour_actionPerformed(ActionEvent e) {
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730 protected void userDefinedColour_actionPerformed(ActionEvent e) {
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733 protected void PIDColour_actionPerformed(ActionEvent e) {
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736 protected void BLOSUM62Colour_actionPerformed(ActionEvent e) {
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739 protected void noColourmenuItem_actionPerformed(ActionEvent e) {
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742 protected void conservationMenuItem_actionPerformed(ActionEvent e) {
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745 protected void printMenuItem_actionPerformed(ActionEvent e) {
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748 protected void renderGapsMenuItem_actionPerformed(ActionEvent e) {
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751 protected void findMenuItem_actionPerformed(ActionEvent e) {
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754 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
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757 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) {
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760 protected void nucleotideColour_actionPerformed(ActionEvent e) {
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763 protected void deleteGroups_actionPerformed(ActionEvent e) {
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766 protected void copy_actionPerformed(ActionEvent e) {
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769 protected void cut_actionPerformed(ActionEvent e) {
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772 protected void delete_actionPerformed(ActionEvent e) {
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775 protected void pasteNew_actionPerformed(ActionEvent e) {
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778 protected void pasteThis_actionPerformed(ActionEvent e) {
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781 protected void applyToAllGroups_actionPerformed(ActionEvent e) {
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784 protected void createPNG_actionPerformed(ActionEvent e) {
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787 protected void font_actionPerformed(ActionEvent e) {
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790 protected void fullSeqId_actionPerformed(ActionEvent e) {
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793 protected void epsFile_actionPerformed(ActionEvent e) {
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796 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
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799 protected void jpred_actionPerformed(ActionEvent e) {
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802 protected void scaleAbove_actionPerformed(ActionEvent e) {
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805 protected void scaleLeft_actionPerformed(ActionEvent e) {
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808 protected void scaleRight_actionPerformed(ActionEvent e) {
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811 protected void modifyPID_actionPerformed(ActionEvent e) {
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814 protected void modifyConservation_actionPerformed(ActionEvent e) {
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817 protected void preferences_actionPerformed(ActionEvent e) {
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820 protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
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823 protected void inputText_actionPerformed(ActionEvent e) {
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826 protected void documentation_actionPerformed(ActionEvent e) {
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829 protected void about_actionPerformed(ActionEvent e) {
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