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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20 package jalview.appletgui;
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23 import java.awt.event.*;
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24 import java.util.Vector;
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26 import jalview.analysis.*;
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27 import jalview.datamodel.*;
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28 import jalview.schemes.*;
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30 public class APopupMenu
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31 extends java.awt.PopupMenu implements ActionListener, ItemListener
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33 Menu groupMenu = new Menu();
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34 protected MenuItem clustalColour = new MenuItem();
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35 protected MenuItem zappoColour = new MenuItem();
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36 protected MenuItem taylorColour = new MenuItem();
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37 protected MenuItem hydrophobicityColour = new MenuItem();
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38 protected MenuItem helixColour = new MenuItem();
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39 protected MenuItem strandColour = new MenuItem();
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40 protected MenuItem turnColour = new MenuItem();
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41 protected MenuItem buriedColour = new MenuItem();
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42 protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
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43 protected MenuItem userDefinedColour = new MenuItem();
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44 protected MenuItem PIDColour = new MenuItem();
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45 protected MenuItem BLOSUM62Colour = new MenuItem();
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46 MenuItem noColourmenuItem = new MenuItem();
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47 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
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49 final AlignmentPanel ap;
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50 MenuItem unGroupMenuItem = new MenuItem();
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51 MenuItem nucleotideMenuItem = new MenuItem();
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52 Menu colourMenu = new Menu();
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53 CheckboxMenuItem showBoxes = new CheckboxMenuItem();
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54 CheckboxMenuItem showText = new CheckboxMenuItem();
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55 CheckboxMenuItem showColourText = new CheckboxMenuItem();
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56 Menu editMenu = new Menu("Edit");
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57 MenuItem copy = new MenuItem("Copy (Jalview Only)");
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58 MenuItem cut = new MenuItem("Cut (Jalview Only)");
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59 MenuItem toUpper = new MenuItem("To Upper Case");
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60 MenuItem toLower = new MenuItem("To Lower Case");
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61 MenuItem toggleCase = new MenuItem("Toggle Case");
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63 public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
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65 ///////////////////////////////////////////////////////////
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66 // If this is activated from the sequence panel, the user may want to
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67 // edit or annotate a particular residue. Therefore display the residue menu
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69 // If from the IDPanel, we must display the sequence menu
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70 //////////////////////////////////////////////////////////
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80 e.printStackTrace();
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83 SequenceGroup sg = ap.av.getSelectionGroup();
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85 if (sg != null && sg.getSize()>0)
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87 showText.setState(sg.getDisplayText());
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88 showColourText.setState(sg.getColourText());
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89 showBoxes.setState(sg.getDisplayBoxes());
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90 if (!ap.av.alignment.getGroups().contains(sg))
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92 groupMenu.remove(unGroupMenuItem);
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104 Menu linkMenu = new Menu("Link");
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107 for(int i=0; i<links.size(); i++)
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109 link = links.elementAt(i).toString();
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110 final String target = link.substring(0, link.indexOf("|"));
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111 item = new MenuItem(target);
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115 if (link.indexOf("$SEQUENCE_ID$") > -1)
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117 String id = seq.getName();
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118 if (id.indexOf("|") > -1)
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119 id = id.substring(id.lastIndexOf("|") + 1);
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121 url = link.substring(link.indexOf("|") + 1,
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122 link.indexOf("$SEQUENCE_ID$"))
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124 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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127 url = link.substring(link.lastIndexOf("|")+1);
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129 item.addActionListener(new java.awt.event.ActionListener()
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131 public void actionPerformed(ActionEvent e)
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133 ap.alignFrame.showURL(url, target);
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136 linkMenu.add(item);
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142 item = new MenuItem("Show PDB Structure");
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143 item.addActionListener(new java.awt.event.ActionListener()
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145 public void actionPerformed(ActionEvent e)
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156 public void itemStateChanged(ItemEvent evt)
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158 if(evt.getSource()==abovePIDColour)
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159 abovePIDColour_itemStateChanged();
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160 else if(evt.getSource()==showColourText)
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161 showColourText_itemStateChanged();
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162 else if(evt.getSource()==showText)
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163 showText_itemStateChanged();
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164 else if(evt.getSource()==showBoxes)
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165 showBoxes_itemStateChanged() ;
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168 public void actionPerformed(ActionEvent evt)
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170 Object source = evt.getSource();
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171 if(source==clustalColour)
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172 clustalColour_actionPerformed();
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173 else if(source==zappoColour)
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174 zappoColour_actionPerformed();
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175 else if(source==taylorColour)
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176 taylorColour_actionPerformed();
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177 else if(source==hydrophobicityColour)
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178 hydrophobicityColour_actionPerformed();
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179 else if(source==helixColour)
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180 helixColour_actionPerformed();
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181 else if(source==strandColour)
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182 strandColour_actionPerformed();
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183 else if(source==clustalColour)
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184 turnColour_actionPerformed();
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185 else if(source==buriedColour)
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186 buriedColour_actionPerformed();
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187 else if(source==nucleotideMenuItem)
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188 nucleotideMenuItem_actionPerformed();
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190 else if(source==userDefinedColour)
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191 userDefinedColour_actionPerformed();
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192 else if(source==PIDColour)
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193 PIDColour_actionPerformed();
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194 else if(source==BLOSUM62Colour)
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195 BLOSUM62Colour_actionPerformed();
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196 else if(source==noColourmenuItem)
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197 noColourmenuItem_actionPerformed();
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198 else if(source==conservationMenuItem)
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199 conservationMenuItem_itemStateChanged();
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200 else if(source==unGroupMenuItem)
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201 unGroupMenuItem_actionPerformed();
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203 else if(source==copy)
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204 ap.alignFrame.copy_actionPerformed();
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205 else if(source==cut)
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206 ap.alignFrame.cut_actionPerformed();
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207 else if(source==toUpper || source==toLower || source==toggleCase)
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209 SequenceGroup sg = ap.av.getSelectionGroup();
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212 for (int g = 0; g < sg.getSize(); g++)
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214 if (source == toggleCase)
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215 sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
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217 sg.getSequenceAt(g).changeCase(source == toUpper, sg.getStartRes(),
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218 sg.getEndRes() + 1);
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220 ap.seqPanel.seqCanvas.repaint();
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226 void addPDB(Sequence seq)
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228 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
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229 cap.setText("Paste your PDB file here.");
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230 cap.setPDBImport(seq);
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231 Frame frame = new Frame();
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233 jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
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236 private void jbInit()
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239 groupMenu.setLabel("Group");
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240 groupMenu.setLabel("Define");
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242 unGroupMenuItem.setLabel("Remove Group");
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243 unGroupMenuItem.addActionListener(this);
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245 nucleotideMenuItem.setLabel("Nucleotide");
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246 nucleotideMenuItem.addActionListener(this);
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247 conservationMenuItem.addItemListener(this);
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248 abovePIDColour.addItemListener(this);
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249 colourMenu.setLabel("Group Colour");
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250 showBoxes.setLabel("Boxes");
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251 showBoxes.setState(true);
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252 showBoxes.addItemListener(this);
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254 showText.setLabel("Text");
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255 showText.addItemListener(this);
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256 showColourText.setLabel("Colour Text");
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257 showColourText.addItemListener(this);
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260 groupMenu.add(unGroupMenuItem);
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261 groupMenu.add(colourMenu);
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262 groupMenu.addSeparator();
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263 groupMenu.add(showBoxes);
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264 groupMenu.add(showText);
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265 groupMenu.add(showColourText);
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266 colourMenu.add(noColourmenuItem);
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267 colourMenu.add(clustalColour);
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268 colourMenu.add(BLOSUM62Colour);
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269 colourMenu.add(PIDColour);
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270 colourMenu.add(zappoColour);
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271 colourMenu.add(taylorColour);
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272 colourMenu.add(hydrophobicityColour);
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273 colourMenu.add(helixColour);
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274 colourMenu.add(strandColour);
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275 colourMenu.add(turnColour);
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276 colourMenu.add(buriedColour);
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277 colourMenu.add(nucleotideMenuItem);
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278 colourMenu.add(userDefinedColour);
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279 colourMenu.addSeparator();
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280 colourMenu.add(abovePIDColour);
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281 colourMenu.add(conservationMenuItem);
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283 noColourmenuItem.setLabel("None");
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284 noColourmenuItem.addActionListener(this);
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286 clustalColour.setLabel("Clustalx colours");
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287 clustalColour.addActionListener(this);
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288 zappoColour.setLabel("Zappo");
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289 zappoColour.addActionListener(this);
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290 taylorColour.setLabel("Taylor");
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291 taylorColour.addActionListener(this);
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292 hydrophobicityColour.setLabel("Hydrophobicity");
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293 hydrophobicityColour.addActionListener(this);
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294 helixColour.setLabel("Helix propensity");
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295 helixColour.addActionListener(this);
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296 strandColour.setLabel("Strand propensity");
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297 strandColour.addActionListener(this);
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298 turnColour.setLabel("Turn propensity");
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299 turnColour.addActionListener(this);
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300 buriedColour.setLabel("Buried Index");
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301 buriedColour.addActionListener(this);
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302 abovePIDColour.setLabel("Above % Identity");
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304 userDefinedColour.setLabel("User Defined");
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305 userDefinedColour.addActionListener(this);
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306 PIDColour.setLabel("Percentage Identity");
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307 PIDColour.addActionListener(this);
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308 BLOSUM62Colour.setLabel("BLOSUM62");
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309 BLOSUM62Colour.addActionListener(this);
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310 conservationMenuItem.setLabel("Conservation");
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313 editMenu.add(copy);
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314 copy.addActionListener(this);
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316 cut.addActionListener(this);
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317 editMenu.add(toUpper);
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318 toUpper.addActionListener(this);
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319 editMenu.add(toLower);
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320 toLower.addActionListener(this);
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321 editMenu.add(toggleCase);
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322 toggleCase.addActionListener(this);
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328 ap.seqPanel.seqCanvas.repaint();
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329 if(ap.overviewPanel!=null)
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330 ap.overviewPanel.updateOverviewImage();
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333 protected void clustalColour_actionPerformed()
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335 SequenceGroup sg = getGroup();
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336 sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
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340 protected void zappoColour_actionPerformed()
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342 getGroup().cs = new ZappoColourScheme();
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346 protected void taylorColour_actionPerformed()
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348 getGroup().cs = new TaylorColourScheme();
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352 protected void hydrophobicityColour_actionPerformed()
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354 getGroup().cs = new HydrophobicColourScheme();
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358 protected void helixColour_actionPerformed()
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360 getGroup().cs = new HelixColourScheme();
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364 protected void strandColour_actionPerformed()
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366 getGroup().cs = new StrandColourScheme();
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370 protected void turnColour_actionPerformed()
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372 getGroup().cs = new TurnColourScheme();
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376 protected void buriedColour_actionPerformed()
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378 getGroup().cs = new BuriedColourScheme();
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382 public void nucleotideMenuItem_actionPerformed()
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384 getGroup().cs = new NucleotideColourScheme();
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388 protected void abovePIDColour_itemStateChanged()
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390 SequenceGroup sg = getGroup();
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394 if (abovePIDColour.getState())
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396 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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397 ap.av.alignment.getWidth()));
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398 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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399 getGroup().getName());
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401 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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403 SliderPanel.showPIDSlider();
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406 else // remove PIDColouring
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408 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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415 protected void userDefinedColour_actionPerformed()
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417 new UserDefinedColours(ap, getGroup());
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420 protected void PIDColour_actionPerformed()
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422 SequenceGroup sg = getGroup();
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423 sg.cs = new PIDColourScheme();
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424 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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425 ap.av.alignment.getWidth()));
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429 protected void BLOSUM62Colour_actionPerformed()
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431 SequenceGroup sg = getGroup();
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433 sg.cs = new Blosum62ColourScheme();
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435 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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436 ap.av.alignment.getWidth()));
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441 protected void noColourmenuItem_actionPerformed()
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443 getGroup().cs = null;
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447 protected void conservationMenuItem_itemStateChanged()
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449 SequenceGroup sg = getGroup();
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453 if (conservationMenuItem.getState())
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456 Conservation c = new Conservation("Group",
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457 ResidueProperties.propHash, 3,
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459 ap.av.alignment.getWidth());
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462 c.verdict(false, ap.av.ConsPercGaps);
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464 sg.cs.setConservation(c);
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466 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
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467 SliderPanel.showConservationSlider();
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469 else // remove ConservationColouring
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471 sg.cs.setConservation(null);
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478 SequenceGroup getGroup()
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480 SequenceGroup sg = ap.av.getSelectionGroup();
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482 // this method won't add a new group if it already exists
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484 ap.av.alignment.addGroup(sg);
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489 void unGroupMenuItem_actionPerformed()
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491 SequenceGroup sg = ap.av.getSelectionGroup();
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492 ap.av.alignment.deleteGroup(sg);
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493 ap.av.setSelectionGroup(null);
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497 public void showColourText_itemStateChanged()
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499 getGroup().setColourText(showColourText.getState());
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503 public void showText_itemStateChanged()
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505 getGroup().setDisplayText(showText.getState());
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509 public void showBoxes_itemStateChanged()
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511 getGroup().setDisplayBoxes(showBoxes.getState());
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