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
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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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57 public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
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59 ///////////////////////////////////////////////////////////
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60 // If this is activated from the sequence panel, the user may want to
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61 // edit or annotate a particular residue. Therefore display the residue menu
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63 // If from the IDPanel, we must display the sequence menu
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64 //////////////////////////////////////////////////////////
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74 e.printStackTrace();
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77 SequenceGroup sg = ap.av.getSelectionGroup();
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80 showText.setState(sg.getDisplayText());
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81 showColourText.setState(sg.getColourText());
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82 showBoxes.setState(sg.getDisplayBoxes());
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85 if (!ap.av.alignment.getGroups().contains(sg))
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87 groupMenu.remove(unGroupMenuItem);
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90 if (seq != null && links!=null)
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92 Menu linkMenu = new Menu("Link");
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95 for(int i=0; i<links.size(); i++)
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97 link = links.elementAt(i).toString();
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98 final String target = link.substring(0, link.indexOf("|"));
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99 item = new MenuItem(target);
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100 String id = seq.getName();
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101 if(id.indexOf("|")>-1)
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102 id = id.substring(id.lastIndexOf("|")+1);
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104 final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
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106 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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108 item.addActionListener(new java.awt.event.ActionListener()
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110 public void actionPerformed(ActionEvent e)
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112 ap.alignFrame.showURL(url, target);
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115 linkMenu.add(item);
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119 item = new MenuItem("Show PDB Structure");
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120 item.addActionListener(new java.awt.event.ActionListener()
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122 public void actionPerformed(ActionEvent e)
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134 void addPDB(Sequence seq)
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136 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame.applet);
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137 cap.setText("Paste your PDB file here.");
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138 cap.setPDBImport(seq, ap.seqPanel.seqCanvas);
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139 Frame frame = new Frame();
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141 jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
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144 private void jbInit()
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147 groupMenu.setLabel("Group");
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148 groupMenu.setLabel("Define");
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150 unGroupMenuItem.setLabel("Remove Group");
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151 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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153 public void actionPerformed(ActionEvent e)
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155 unGroupMenuItem_actionPerformed(e);
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159 nucleotideMenuItem.setLabel("Nucleotide");
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160 nucleotideMenuItem.addActionListener(new ActionListener()
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162 public void actionPerformed(ActionEvent e)
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164 nucleotideMenuItem_actionPerformed(e);
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167 conservationMenuItem.addItemListener(new ItemListener()
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169 public void itemStateChanged(ItemEvent itemEvent)
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171 conservationMenuItem_itemStateChanged(itemEvent);
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174 abovePIDColour.addItemListener(new ItemListener()
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176 public void itemStateChanged(ItemEvent itemEvent)
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178 abovePIDColour_itemStateChanged(itemEvent);
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181 colourMenu.setLabel("Group Colour");
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182 showBoxes.setLabel("Boxes");
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183 showBoxes.setState(true);
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184 showBoxes.addItemListener(new ItemListener()
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186 public void itemStateChanged(ItemEvent itemEvent)
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188 showBoxes_itemStateChanged(itemEvent);
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192 showText.setLabel("Text");
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193 showText.addItemListener(new ItemListener()
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195 public void itemStateChanged(ItemEvent itemEvent)
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197 showText_itemStateChanged(itemEvent);
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200 showColourText.setLabel("Colour Text");
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201 showColourText.addItemListener(new ItemListener()
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203 public void itemStateChanged(ItemEvent itemEvent)
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205 showColourText_itemStateChanged(itemEvent);
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210 groupMenu.add(unGroupMenuItem);
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211 groupMenu.add(colourMenu);
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212 groupMenu.addSeparator();
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213 groupMenu.add(showBoxes);
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214 groupMenu.add(showText);
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215 groupMenu.add(showColourText);
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216 colourMenu.add(noColourmenuItem);
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217 colourMenu.add(clustalColour);
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218 colourMenu.add(BLOSUM62Colour);
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219 colourMenu.add(PIDColour);
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220 colourMenu.add(zappoColour);
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221 colourMenu.add(taylorColour);
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222 colourMenu.add(hydrophobicityColour);
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223 colourMenu.add(helixColour);
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224 colourMenu.add(strandColour);
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225 colourMenu.add(turnColour);
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226 colourMenu.add(buriedColour);
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227 colourMenu.add(nucleotideMenuItem);
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228 colourMenu.add(userDefinedColour);
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229 colourMenu.addSeparator();
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230 colourMenu.add(abovePIDColour);
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231 colourMenu.add(conservationMenuItem);
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233 noColourmenuItem.setLabel("None");
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234 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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236 public void actionPerformed(ActionEvent e)
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238 noColourmenuItem_actionPerformed(e);
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242 clustalColour.setLabel("Clustalx colours");
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243 clustalColour.addActionListener(new java.awt.event.ActionListener()
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245 public void actionPerformed(ActionEvent e)
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247 clustalColour_actionPerformed(e);
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250 zappoColour.setLabel("Zappo");
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251 zappoColour.addActionListener(new java.awt.event.ActionListener()
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253 public void actionPerformed(ActionEvent e)
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255 zappoColour_actionPerformed(e);
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258 taylorColour.setLabel("Taylor");
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259 taylorColour.addActionListener(new java.awt.event.ActionListener()
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261 public void actionPerformed(ActionEvent e)
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263 taylorColour_actionPerformed(e);
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266 hydrophobicityColour.setLabel("Hydrophobicity");
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267 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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269 public void actionPerformed(ActionEvent e)
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271 hydrophobicityColour_actionPerformed(e);
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274 helixColour.setLabel("Helix propensity");
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275 helixColour.addActionListener(new java.awt.event.ActionListener()
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277 public void actionPerformed(ActionEvent e)
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279 helixColour_actionPerformed(e);
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282 strandColour.setLabel("Strand propensity");
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283 strandColour.addActionListener(new java.awt.event.ActionListener()
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285 public void actionPerformed(ActionEvent e)
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287 strandColour_actionPerformed(e);
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290 turnColour.setLabel("Turn propensity");
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291 turnColour.addActionListener(new java.awt.event.ActionListener()
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293 public void actionPerformed(ActionEvent e)
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295 turnColour_actionPerformed(e);
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298 buriedColour.setLabel("Buried Index");
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299 buriedColour.addActionListener(new java.awt.event.ActionListener()
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301 public void actionPerformed(ActionEvent e)
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303 buriedColour_actionPerformed(e);
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306 abovePIDColour.setLabel("Above % Identity");
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308 userDefinedColour.setLabel("User Defined");
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309 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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311 public void actionPerformed(ActionEvent e)
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313 userDefinedColour_actionPerformed(e);
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316 PIDColour.setLabel("Percentage Identity");
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317 PIDColour.addActionListener(new java.awt.event.ActionListener()
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319 public void actionPerformed(ActionEvent e)
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321 PIDColour_actionPerformed(e);
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324 BLOSUM62Colour.setLabel("BLOSUM62");
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325 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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327 public void actionPerformed(ActionEvent e)
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329 BLOSUM62Colour_actionPerformed(e);
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332 conservationMenuItem.setLabel("Conservation");
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338 SequenceGroup sg = getGroup();
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341 SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
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343 if (superG != null)
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345 superG.setSuperGroupProperties(sg);
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348 ap.seqPanel.seqCanvas.repaint();
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349 if(ap.overviewPanel!=null)
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350 ap.overviewPanel.updateOverviewImage();
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353 protected void clustalColour_actionPerformed(ActionEvent e)
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355 SequenceGroup sg = getGroup();
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356 sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
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360 protected void zappoColour_actionPerformed(ActionEvent e)
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362 getGroup().cs = new ZappoColourScheme();
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366 protected void taylorColour_actionPerformed(ActionEvent e)
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368 getGroup().cs = new TaylorColourScheme();
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372 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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374 getGroup().cs = new HydrophobicColourScheme();
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378 protected void helixColour_actionPerformed(ActionEvent e)
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380 getGroup().cs = new HelixColourScheme();
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384 protected void strandColour_actionPerformed(ActionEvent e)
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386 getGroup().cs = new StrandColourScheme();
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390 protected void turnColour_actionPerformed(ActionEvent e)
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392 getGroup().cs = new TurnColourScheme();
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396 protected void buriedColour_actionPerformed(ActionEvent e)
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398 getGroup().cs = new BuriedColourScheme();
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402 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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404 getGroup().cs = new NucleotideColourScheme();
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408 protected void abovePIDColour_itemStateChanged(ItemEvent ie)
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410 SequenceGroup sg = getGroup();
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414 if (abovePIDColour.getState())
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416 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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417 ap.av.alignment.getWidth()));
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418 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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419 getGroup().getName());
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421 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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423 SliderPanel.showPIDSlider();
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426 else // remove PIDColouring
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428 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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435 protected void userDefinedColour_actionPerformed(ActionEvent e)
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437 new UserDefinedColours(ap, getGroup());
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440 protected void PIDColour_actionPerformed(ActionEvent e)
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442 SequenceGroup sg = getGroup();
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443 sg.cs = new PIDColourScheme();
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444 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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445 ap.av.alignment.getWidth()));
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449 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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451 SequenceGroup sg = getGroup();
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453 sg.cs = new Blosum62ColourScheme();
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455 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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456 ap.av.alignment.getWidth()));
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461 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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463 getGroup().cs = null;
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467 protected void conservationMenuItem_itemStateChanged(ItemEvent ie)
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469 SequenceGroup sg = getGroup();
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473 if (conservationMenuItem.getState())
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476 Conservation c = new Conservation("Group",
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477 ResidueProperties.propHash, 3,
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479 ap.av.alignment.getWidth());
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482 c.verdict(false, ap.av.ConsPercGaps);
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484 sg.cs.setConservation(c);
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486 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
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487 SliderPanel.showConservationSlider();
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489 else // remove ConservationColouring
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491 sg.cs.setConservation(null);
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498 SequenceGroup getGroup()
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500 SequenceGroup sg = ap.av.getSelectionGroup();
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502 // this method won't add a new group if it already exists
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504 ap.av.alignment.addGroup(sg);
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509 void unGroupMenuItem_actionPerformed(ActionEvent e)
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511 SequenceGroup sg = ap.av.getSelectionGroup();
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512 ap.av.alignment.deleteGroup(sg);
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513 ap.av.setSelectionGroup(null);
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517 public void showColourText_itemStateChanged(ItemEvent itemEvent)
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519 getGroup().setColourText(showColourText.getState());
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523 public void showText_itemStateChanged(ItemEvent itemEvent)
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525 getGroup().setDisplayText(showText.getState());
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529 public void showBoxes_itemStateChanged(ItemEvent itemEvent)
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531 getGroup().setDisplayBoxes(showBoxes.getState());
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