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 dbref = 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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101 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
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103 public GAlignFrame() {
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106 setMenuBar(alignFrameMenuBar);
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110 // dynamically fill save as menu with available formats
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111 for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++) {
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112 item = new MenuItem((String) jalview.io.AppletFormatAdapter.formats.elementAt(
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114 item.addActionListener(new java.awt.event.ActionListener() {
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115 public void actionPerformed(ActionEvent e) {
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116 saveAs_actionPerformed(e);
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120 item = new MenuItem((String) jalview.io.AppletFormatAdapter.formats.elementAt(
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122 item.addActionListener(new java.awt.event.ActionListener() {
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123 public void actionPerformed(ActionEvent e) {
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124 outputText_actionPerformed(e);
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128 outputTextboxMenu.add(item);
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130 } catch (Exception e) {
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131 e.printStackTrace();
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135 private void jbInit() throws Exception {
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136 fileMenu.setLabel("File");
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137 closeMenuItem.setLabel("Close");
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138 closeMenuItem.addActionListener(new java.awt.event.ActionListener() {
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139 public void actionPerformed(ActionEvent e) {
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140 closeMenuItem_actionPerformed(e);
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143 editMenu.setLabel("Edit");
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144 viewMenu.setLabel("View");
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145 colourMenu.setLabel("Colour");
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146 calculateMenu.setLabel("Calculate");
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147 selectAllSequenceMenuItem.setLabel("Select all");
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148 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
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149 public void actionPerformed(ActionEvent e) {
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150 selectAllSequenceMenuItem_actionPerformed(e);
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153 deselectAllSequenceMenuItem.setLabel("Deselect All");
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154 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
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155 public void actionPerformed(ActionEvent e) {
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156 deselectAllSequenceMenuItem_actionPerformed(e);
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159 invertSequenceMenuItem.setLabel("Invert Selection");
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160 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
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161 public void actionPerformed(ActionEvent e) {
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162 invertSequenceMenuItem_actionPerformed(e);
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165 remove2LeftMenuItem.setLabel("Remove Left");
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166 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {
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167 public void actionPerformed(ActionEvent e) {
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168 remove2LeftMenuItem_actionPerformed(e);
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171 remove2RightMenuItem.setLabel("Remove Right");
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172 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {
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173 public void actionPerformed(ActionEvent e) {
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174 remove2RightMenuItem_actionPerformed(e);
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177 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
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178 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {
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179 public void actionPerformed(ActionEvent e) {
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180 removeGappedColumnMenuItem_actionPerformed(e);
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183 removeAllGapsMenuItem.setLabel("Remove All Gaps");
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184 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {
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185 public void actionPerformed(ActionEvent e) {
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186 removeAllGapsMenuItem_actionPerformed(e);
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189 viewBoxesMenuItem.setLabel("Boxes");
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190 viewBoxesMenuItem.setState(true);
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191 viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() {
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192 public void itemStateChanged(ItemEvent e) {
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193 viewBoxesMenuItem_actionPerformed(null);
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196 viewTextMenuItem.setLabel("Text");
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197 viewTextMenuItem.setState(true);
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198 viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() {
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199 public void itemStateChanged(ItemEvent e) {
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200 viewTextMenuItem_actionPerformed(null);
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203 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
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204 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {
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205 public void actionPerformed(ActionEvent e) {
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206 sortPairwiseMenuItem_actionPerformed(e);
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209 sortIDMenuItem.setLabel("by ID");
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210 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {
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211 public void actionPerformed(ActionEvent e) {
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212 sortIDMenuItem_actionPerformed(e);
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215 sortGroupMenuItem.setLabel("by Group");
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216 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {
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217 public void actionPerformed(ActionEvent e) {
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218 sortGroupMenuItem_actionPerformed(e);
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221 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
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222 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {
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223 public void actionPerformed(ActionEvent e) {
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224 removeRedundancyMenuItem_actionPerformed(e);
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227 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
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228 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {
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229 public void actionPerformed(ActionEvent e) {
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230 pairwiseAlignmentMenuItem_actionPerformed(e);
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233 PCAMenuItem.setLabel("Principal Component Analysis");
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234 PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {
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235 public void actionPerformed(ActionEvent e) {
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236 PCAMenuItem_actionPerformed(e);
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239 averageDistanceTreeMenuItem.setLabel(
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240 "Average Distance Using % Identity");
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241 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
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242 public void actionPerformed(ActionEvent e) {
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243 averageDistanceTreeMenuItem_actionPerformed(e);
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246 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
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247 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
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248 public void actionPerformed(ActionEvent e) {
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249 neighbourTreeMenuItem_actionPerformed(e);
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252 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
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253 statusBar.setBackground(Color.white);
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254 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
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255 statusBar.setText("Status bar");
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256 outputTextboxMenu.setLabel("Output to Textbox");
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257 clustalColour.setLabel("Clustalx");
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259 clustalColour.addActionListener(new java.awt.event.ActionListener() {
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260 public void actionPerformed(ActionEvent e) {
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261 clustalColour_actionPerformed(e);
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264 zappoColour.setLabel("Zappo");
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265 zappoColour.addActionListener(new java.awt.event.ActionListener() {
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266 public void actionPerformed(ActionEvent e) {
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267 zappoColour_actionPerformed(e);
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270 taylorColour.setLabel("Taylor");
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271 taylorColour.addActionListener(new java.awt.event.ActionListener() {
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272 public void actionPerformed(ActionEvent e) {
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273 taylorColour_actionPerformed(e);
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276 hydrophobicityColour.setLabel("Hydrophobicity");
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277 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {
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278 public void actionPerformed(ActionEvent e) {
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279 hydrophobicityColour_actionPerformed(e);
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282 helixColour.setLabel("Helix Propensity");
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283 helixColour.addActionListener(new java.awt.event.ActionListener() {
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284 public void actionPerformed(ActionEvent e) {
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285 helixColour_actionPerformed(e);
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288 strandColour.setLabel("Strand Propensity");
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289 strandColour.addActionListener(new java.awt.event.ActionListener() {
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290 public void actionPerformed(ActionEvent e) {
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291 strandColour_actionPerformed(e);
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294 turnColour.setLabel("Turn Propensity");
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295 turnColour.addActionListener(new java.awt.event.ActionListener() {
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296 public void actionPerformed(ActionEvent e) {
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297 turnColour_actionPerformed(e);
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300 buriedColour.setLabel("Buried Index");
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301 buriedColour.addActionListener(new java.awt.event.ActionListener() {
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302 public void actionPerformed(ActionEvent e) {
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303 buriedColour_actionPerformed(e);
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306 userDefinedColour.setLabel("User Defined...");
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307 userDefinedColour.addActionListener(new java.awt.event.ActionListener() {
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308 public void actionPerformed(ActionEvent e) {
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309 userDefinedColour_actionPerformed(e);
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312 PIDColour.setLabel("Percentage Identity");
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313 PIDColour.addActionListener(new java.awt.event.ActionListener() {
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314 public void actionPerformed(ActionEvent e) {
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315 PIDColour_actionPerformed(e);
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318 BLOSUM62Colour.setLabel("BLOSUM62 Score");
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319 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {
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320 public void actionPerformed(ActionEvent e) {
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321 BLOSUM62Colour_actionPerformed(e);
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324 avDistanceTreeBlosumMenuItem.setLabel(
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325 "Average Distance Using BLOSUM62");
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326 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {
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327 public void actionPerformed(ActionEvent e) {
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328 avTreeBlosumMenuItem_actionPerformed(e);
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331 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
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332 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {
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333 public void actionPerformed(ActionEvent e) {
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334 njTreeBlosumMenuItem_actionPerformed(e);
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337 annotationPanelMenuItem.setActionCommand("");
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338 annotationPanelMenuItem.setState(true);
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339 annotationPanelMenuItem.setLabel("Show Annotations");
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340 annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() {
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341 public void itemStateChanged(ItemEvent e) {
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342 annotationPanelMenuItem_actionPerformed(null);
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345 colourTextMenuItem.setLabel("Colour Text");
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346 colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() {
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347 public void itemStateChanged(ItemEvent e) {
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348 colourTextMenuItem_actionPerformed(null);
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351 overviewMenuItem.setLabel("Overview Window");
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352 overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {
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353 public void actionPerformed(ActionEvent e) {
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354 overviewMenuItem_actionPerformed(e);
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357 undoMenuItem.setEnabled(false);
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358 undoMenuItem.setLabel("Undo");
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359 undoMenuItem.addActionListener(new java.awt.event.ActionListener() {
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360 public void actionPerformed(ActionEvent e) {
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361 undoMenuItem_actionPerformed(e);
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364 redoMenuItem.setEnabled(false);
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365 redoMenuItem.setLabel("Redo");
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366 redoMenuItem.addActionListener(new java.awt.event.ActionListener() {
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367 public void actionPerformed(ActionEvent e) {
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368 redoMenuItem_actionPerformed(e);
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371 conservationMenuItem.setLabel("by Conservation");
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372 conservationMenuItem.addItemListener(new java.awt.event.ItemListener() {
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373 public void itemStateChanged(ItemEvent e) {
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374 conservationMenuItem_actionPerformed(null);
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377 noColourmenuItem.setLabel("None");
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378 noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {
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379 public void actionPerformed(ActionEvent e) {
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380 noColourmenuItem_actionPerformed(e);
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383 wrapMenuItem.setLabel("Wrap");
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384 wrapMenuItem.addItemListener(new java.awt.event.ItemListener() {
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385 public void itemStateChanged(ItemEvent e) {
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386 wrapMenuItem_actionPerformed(null);
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389 renderGapsMenuItem.setLabel("Show Gaps");
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390 renderGapsMenuItem.setState(true);
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391 renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() {
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392 public void itemStateChanged(ItemEvent e) {
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393 renderGapsMenuItem_actionPerformed(null);
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396 findMenuItem.setLabel("Find...");
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397 findMenuItem.addActionListener(new java.awt.event.ActionListener() {
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398 public void actionPerformed(ActionEvent e) {
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399 findMenuItem_actionPerformed(e);
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402 searchMenu.setLabel("Search");
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404 abovePIDThreshold.setLabel("Above Identity Threshold");
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405 abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() {
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406 public void itemStateChanged(ItemEvent e) {
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407 abovePIDThreshold_actionPerformed(null);
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410 nucleotideColour.setLabel("Nucleotide");
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411 nucleotideColour.addActionListener(new java.awt.event.ActionListener() {
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412 public void actionPerformed(ActionEvent e) {
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413 nucleotideColour_actionPerformed(e);
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416 deleteGroups.setLabel("Undefine Groups");
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417 deleteGroups.addActionListener(new java.awt.event.ActionListener() {
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418 public void actionPerformed(ActionEvent e) {
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419 deleteGroups_actionPerformed(e);
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422 copy.setLabel("Copy");
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423 copy.addActionListener(new java.awt.event.ActionListener() {
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424 public void actionPerformed(ActionEvent e) {
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425 copy_actionPerformed(e);
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428 cut.setLabel("Cut");
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429 cut.addActionListener(new java.awt.event.ActionListener() {
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430 public void actionPerformed(ActionEvent e) {
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431 cut_actionPerformed(e);
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434 delete.setLabel("Delete");
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435 delete.addActionListener(new java.awt.event.ActionListener() {
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436 public void actionPerformed(ActionEvent e) {
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437 delete_actionPerformed(e);
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440 Menu1.setLabel("Paste");
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441 pasteNew.setLabel("To New Alignment");
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442 pasteNew.addActionListener(new java.awt.event.ActionListener() {
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443 public void actionPerformed(ActionEvent e) {
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444 pasteNew_actionPerformed(e);
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447 pasteThis.setLabel("Add To This Alignment");
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448 pasteThis.addActionListener(new java.awt.event.ActionListener() {
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449 public void actionPerformed(ActionEvent e) {
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450 pasteThis_actionPerformed(e);
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453 applyToAllGroups.setLabel("Apply Colour To All Groups");
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454 applyToAllGroups.setState(true);
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455 applyToAllGroups.addItemListener(new java.awt.event.ItemListener() {
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456 public void itemStateChanged(ItemEvent e) {
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457 applyToAllGroups_actionPerformed(null);
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460 font.setLabel("Font...");
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461 font.addActionListener(new java.awt.event.ActionListener() {
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462 public void actionPerformed(ActionEvent e) {
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463 font_actionPerformed(e);
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466 dbref.setLabel("ShowSequence DB Refs");
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467 dbref.setActionCommand("");
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468 dbref.setState(true);
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469 dbref.addItemListener(new java.awt.event.ItemListener() {
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470 public void itemStateChanged(ItemEvent e) {
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471 dbref_actionPerformed(e);
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474 scaleAbove.setLabel("Scale Above");
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475 scaleAbove.setState(true);
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476 scaleAbove.addItemListener(new java.awt.event.ItemListener() {
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477 public void itemStateChanged(ItemEvent e) {
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478 scaleAbove_actionPerformed(null);
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481 scaleLeft.setEnabled(false);
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482 scaleLeft.setState(true);
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483 scaleLeft.setLabel("Scale Left");
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484 scaleLeft.addItemListener(new java.awt.event.ItemListener() {
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485 public void itemStateChanged(ItemEvent e) {
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486 scaleLeft_actionPerformed(null);
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489 scaleRight.setEnabled(false);
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490 scaleRight.setState(true);
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491 scaleRight.setLabel("Scale Right");
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492 scaleRight.addItemListener(new java.awt.event.ItemListener() {
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493 public void itemStateChanged(ItemEvent e) {
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494 scaleRight_actionPerformed(null);
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497 modifyPID.setLabel("Modify Identity Threshold...");
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498 modifyPID.addActionListener(new java.awt.event.ActionListener() {
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499 public void actionPerformed(ActionEvent e) {
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500 modifyPID_actionPerformed(e);
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503 modifyConservation.setLabel("Modify Conservation Threshold...");
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504 modifyConservation.addActionListener(new java.awt.event.ActionListener() {
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505 public void actionPerformed(ActionEvent e) {
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506 modifyConservation_actionPerformed(e);
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509 sortByTreeMenu.setLabel("By Tree Order");
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510 sort.setLabel("Sort");
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511 calculate.setLabel("Calculate Tree");
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512 inputText.setLabel("Input from textbox");
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513 inputText.addActionListener(new java.awt.event.ActionListener() {
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514 public void actionPerformed(ActionEvent e) {
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515 inputText_actionPerformed(e);
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519 helpMenu.setLabel("Help");
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520 documentation.setLabel("Documentation");
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521 documentation.addActionListener(new java.awt.event.ActionListener() {
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522 public void actionPerformed(ActionEvent e) {
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523 documentation_actionPerformed(e);
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527 about.setLabel("About...");
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528 about.addActionListener(new java.awt.event.ActionListener() {
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529 public void actionPerformed(ActionEvent e) {
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530 about_actionPerformed(e);
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533 seqLimits.setState(true);
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534 seqLimits.setLabel("Show Sequence Limits");
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535 seqLimits.addItemListener(new ItemListener()
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537 public void itemStateChanged(ItemEvent e)
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539 seqLimits_itemStateChanged(e);
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543 alignFrameMenuBar.add(fileMenu);
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544 alignFrameMenuBar.add(editMenu);
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545 alignFrameMenuBar.add(searchMenu);
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546 alignFrameMenuBar.add(viewMenu);
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547 alignFrameMenuBar.add(colourMenu);
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548 alignFrameMenuBar.add(calculateMenu);
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549 alignFrameMenuBar.add(helpMenu);
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550 fileMenu.add(inputText);
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551 fileMenu.add(outputTextboxMenu);
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552 fileMenu.addSeparator();
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553 fileMenu.add(closeMenuItem);
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554 editMenu.add(undoMenuItem);
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555 editMenu.add(redoMenuItem);
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557 editMenu.add(copy);
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558 editMenu.add(Menu1);
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559 editMenu.add(delete);
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560 editMenu.addSeparator();
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561 editMenu.add(selectAllSequenceMenuItem);
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562 editMenu.add(deselectAllSequenceMenuItem);
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563 editMenu.add(invertSequenceMenuItem);
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564 editMenu.add(deleteGroups);
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565 editMenu.addSeparator();
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566 editMenu.add(remove2LeftMenuItem);
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567 editMenu.add(remove2RightMenuItem);
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568 editMenu.add(removeGappedColumnMenuItem);
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569 editMenu.add(removeAllGapsMenuItem);
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570 editMenu.add(removeRedundancyMenuItem);
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571 searchMenu.add(findMenuItem);
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572 viewMenu.add(font);
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573 viewMenu.addSeparator();
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574 viewMenu.add(dbref);
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575 viewMenu.add(seqLimits);
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576 viewMenu.addSeparator();
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577 viewMenu.add(wrapMenuItem);
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578 viewMenu.add(scaleAbove);
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579 viewMenu.add(scaleLeft);
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580 viewMenu.add(scaleRight);
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581 viewMenu.addSeparator();
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582 viewMenu.add(viewBoxesMenuItem);
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583 viewMenu.add(viewTextMenuItem);
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584 viewMenu.add(colourTextMenuItem);
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585 viewMenu.add(renderGapsMenuItem);
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586 viewMenu.add(annotationPanelMenuItem);
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587 viewMenu.addSeparator();
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588 viewMenu.add(overviewMenuItem);
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589 colourMenu.add(applyToAllGroups);
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590 colourMenu.addSeparator();
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591 colourMenu.add(noColourmenuItem);
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592 colourMenu.add(clustalColour);
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593 colourMenu.add(BLOSUM62Colour);
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594 colourMenu.add(PIDColour);
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595 colourMenu.add(zappoColour);
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596 colourMenu.add(taylorColour);
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597 colourMenu.add(hydrophobicityColour);
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598 colourMenu.add(helixColour);
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599 colourMenu.add(strandColour);
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600 colourMenu.add(turnColour);
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601 colourMenu.add(buriedColour);
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602 colourMenu.add(nucleotideColour);
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603 colourMenu.add(userDefinedColour);
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604 colourMenu.addSeparator();
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605 colourMenu.add(conservationMenuItem);
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606 colourMenu.add(modifyConservation);
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607 colourMenu.add(abovePIDThreshold);
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608 colourMenu.add(modifyPID);
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609 calculateMenu.add(sort);
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610 calculateMenu.add(calculate);
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611 calculateMenu.addSeparator();
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612 calculateMenu.add(pairwiseAlignmentMenuItem);
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613 calculateMenu.add(PCAMenuItem);
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614 this.add(statusBar, BorderLayout.SOUTH);
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615 Menu1.add(pasteNew);
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616 Menu1.add(pasteThis);
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617 sort.add(sortIDMenuItem);
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618 sort.add(sortByTreeMenu);
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619 sort.add(sortGroupMenuItem);
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620 sort.add(sortPairwiseMenuItem);
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621 calculate.add(averageDistanceTreeMenuItem);
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622 calculate.add(neighbourTreeMenuItem);
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623 calculate.add(avDistanceTreeBlosumMenuItem);
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624 calculate.add(njTreeBlosumMenuItem);
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625 helpMenu.add(documentation);
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626 helpMenu.add(about);
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629 protected void saveAs_actionPerformed(ActionEvent e) {
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632 protected void outputText_actionPerformed(ActionEvent e) {
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635 protected void htmlMenuItem_actionPerformed(ActionEvent e) {
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638 protected void closeMenuItem_actionPerformed(ActionEvent e) {
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641 protected void redoMenuItem_actionPerformed(ActionEvent e) {
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644 protected void undoMenuItem_actionPerformed(ActionEvent e) {
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647 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) {
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650 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) {
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653 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) {
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656 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) {
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659 protected void remove2RightMenuItem_actionPerformed(ActionEvent e) {
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662 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) {
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665 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) {
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668 protected void wrapMenuItem_actionPerformed(ActionEvent e) {
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671 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) {
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674 protected void viewTextMenuItem_actionPerformed(ActionEvent e) {
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677 protected void colourTextMenuItem_actionPerformed(ActionEvent e) {
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680 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) {
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683 protected void overviewMenuItem_actionPerformed(ActionEvent e) {
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686 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) {
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689 protected void sortIDMenuItem_actionPerformed(ActionEvent e) {
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692 protected void sortGroupMenuItem_actionPerformed(ActionEvent e) {
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695 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) {
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698 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) {
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701 protected void PCAMenuItem_actionPerformed(ActionEvent e) {
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704 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) {
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707 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) {
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710 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) {
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713 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) {
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716 protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) {
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719 protected void clustalColour_actionPerformed(ActionEvent e) {
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722 protected void zappoColour_actionPerformed(ActionEvent e) {
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725 protected void taylorColour_actionPerformed(ActionEvent e) {
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728 protected void hydrophobicityColour_actionPerformed(ActionEvent e) {
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731 protected void helixColour_actionPerformed(ActionEvent e) {
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734 protected void strandColour_actionPerformed(ActionEvent e) {
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737 protected void turnColour_actionPerformed(ActionEvent e) {
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740 protected void buriedColour_actionPerformed(ActionEvent e) {
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743 protected void userDefinedColour_actionPerformed(ActionEvent e) {
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746 protected void PIDColour_actionPerformed(ActionEvent e) {
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749 protected void BLOSUM62Colour_actionPerformed(ActionEvent e) {
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752 protected void noColourmenuItem_actionPerformed(ActionEvent e) {
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755 protected void conservationMenuItem_actionPerformed(ActionEvent e) {
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758 protected void printMenuItem_actionPerformed(ActionEvent e) {
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761 protected void renderGapsMenuItem_actionPerformed(ActionEvent e) {
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764 protected void findMenuItem_actionPerformed(ActionEvent e) {
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767 protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
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770 public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) {
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773 protected void nucleotideColour_actionPerformed(ActionEvent e) {
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776 protected void deleteGroups_actionPerformed(ActionEvent e) {
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779 protected void copy_actionPerformed(ActionEvent e) {
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782 protected void cut_actionPerformed(ActionEvent e) {
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785 protected void delete_actionPerformed(ActionEvent e) {
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788 protected void pasteNew_actionPerformed(ActionEvent e) {
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791 protected void pasteThis_actionPerformed(ActionEvent e) {
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794 protected void applyToAllGroups_actionPerformed(ActionEvent e) {
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797 protected void createPNG_actionPerformed(ActionEvent e) {
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800 protected void font_actionPerformed(ActionEvent e) {
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803 protected void epsFile_actionPerformed(ActionEvent e) {
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806 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
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809 protected void jpred_actionPerformed(ActionEvent e) {
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812 protected void scaleAbove_actionPerformed(ActionEvent e) {
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815 protected void scaleLeft_actionPerformed(ActionEvent e) {
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818 protected void scaleRight_actionPerformed(ActionEvent e) {
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821 protected void modifyPID_actionPerformed(ActionEvent e) {
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824 protected void modifyConservation_actionPerformed(ActionEvent e) {
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827 protected void preferences_actionPerformed(ActionEvent e) {
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830 protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
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833 protected void inputText_actionPerformed(ActionEvent e) {
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836 protected void documentation_actionPerformed(ActionEvent e) {
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839 protected void about_actionPerformed(ActionEvent e) {
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842 public void dbref_actionPerformed(ItemEvent e)
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847 public void seqLimits_itemStateChanged(ItemEvent e)
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