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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62 public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
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64 ///////////////////////////////////////////////////////////
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65 // If this is activated from the sequence panel, the user may want to
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66 // edit or annotate a particular residue. Therefore display the residue menu
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68 // If from the IDPanel, we must display the sequence menu
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69 //////////////////////////////////////////////////////////
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79 e.printStackTrace();
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82 SequenceGroup sg = ap.av.getSelectionGroup();
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84 if (sg != null && sg.getSize()>0)
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86 showText.setState(sg.getDisplayText());
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87 showColourText.setState(sg.getColourText());
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88 showBoxes.setState(sg.getDisplayBoxes());
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95 if (!ap.av.alignment.getGroups().contains(sg))
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97 groupMenu.remove(unGroupMenuItem);
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100 if (seq != null && links!=null)
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102 Menu linkMenu = new Menu("Link");
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105 for(int i=0; i<links.size(); i++)
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107 link = links.elementAt(i).toString();
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108 final String target = link.substring(0, link.indexOf("|"));
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109 item = new MenuItem(target);
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110 String id = seq.getName();
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111 if(id.indexOf("|")>-1)
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112 id = id.substring(id.lastIndexOf("|")+1);
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114 final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
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116 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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118 item.addActionListener(new java.awt.event.ActionListener()
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120 public void actionPerformed(ActionEvent e)
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122 ap.alignFrame.showURL(url, target);
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125 linkMenu.add(item);
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129 item = new MenuItem("Show PDB Structure");
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130 item.addActionListener(new java.awt.event.ActionListener()
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132 public void actionPerformed(ActionEvent e)
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144 public void itemStateChanged(ItemEvent evt)
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146 if(evt.getSource()==abovePIDColour)
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147 abovePIDColour_itemStateChanged();
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148 else if(evt.getSource()==showColourText)
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149 showColourText_itemStateChanged();
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150 else if(evt.getSource()==showText)
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151 showText_itemStateChanged();
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152 else if(evt.getSource()==showBoxes)
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153 showBoxes_itemStateChanged() ;
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156 public void actionPerformed(ActionEvent evt)
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158 Object source = evt.getSource();
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159 if(source==clustalColour)
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160 clustalColour_actionPerformed();
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161 else if(source==zappoColour)
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162 zappoColour_actionPerformed();
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163 else if(source==taylorColour)
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164 taylorColour_actionPerformed();
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165 else if(source==hydrophobicityColour)
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166 hydrophobicityColour_actionPerformed();
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167 else if(source==helixColour)
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168 helixColour_actionPerformed();
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169 else if(source==strandColour)
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170 strandColour_actionPerformed();
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171 else if(source==clustalColour)
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172 turnColour_actionPerformed();
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173 else if(source==buriedColour)
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174 buriedColour_actionPerformed();
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175 else if(source==nucleotideMenuItem)
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176 nucleotideMenuItem_actionPerformed();
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178 else if(source==userDefinedColour)
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179 userDefinedColour_actionPerformed();
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180 else if(source==PIDColour)
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181 PIDColour_actionPerformed();
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182 else if(source==BLOSUM62Colour)
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183 BLOSUM62Colour_actionPerformed();
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184 else if(source==noColourmenuItem)
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185 noColourmenuItem_actionPerformed();
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186 else if(source==conservationMenuItem)
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187 conservationMenuItem_itemStateChanged();
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188 else if(source==unGroupMenuItem)
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189 unGroupMenuItem_actionPerformed();
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191 else if(source==copy)
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192 ap.alignFrame.copy_actionPerformed();
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193 else if(source==cut)
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194 ap.alignFrame.cut_actionPerformed();
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195 else if(source==toUpper)
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197 SequenceGroup sg = ap.av.getSelectionGroup();
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200 for (int g = 0; g < sg.getSize(); g++)
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202 sg.getSequenceAt(g).changeCase(true, sg.getStartRes(),
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203 sg.getEndRes() + 1);
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205 ap.seqPanel.seqCanvas.repaint();
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208 else if(source==toLower)
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210 SequenceGroup sg = ap.av.getSelectionGroup();
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213 for (int g = 0; g < sg.getSize(); g++)
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215 sg.getSequenceAt(g).changeCase(false, sg.getStartRes(),
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216 sg.getEndRes() + 1);
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218 ap.seqPanel.seqCanvas.repaint();
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224 void addPDB(Sequence seq)
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226 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
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227 cap.setText("Paste your PDB file here.");
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228 cap.setPDBImport(seq);
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229 Frame frame = new Frame();
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231 jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
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234 private void jbInit()
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237 groupMenu.setLabel("Group");
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238 groupMenu.setLabel("Define");
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240 unGroupMenuItem.setLabel("Remove Group");
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241 unGroupMenuItem.addActionListener(this);
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243 nucleotideMenuItem.setLabel("Nucleotide");
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244 nucleotideMenuItem.addActionListener(this);
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245 conservationMenuItem.addItemListener(this);
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246 abovePIDColour.addItemListener(this);
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247 colourMenu.setLabel("Group Colour");
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248 showBoxes.setLabel("Boxes");
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249 showBoxes.setState(true);
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250 showBoxes.addItemListener(this);
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252 showText.setLabel("Text");
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253 showText.addItemListener(this);
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254 showColourText.setLabel("Colour Text");
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255 showColourText.addItemListener(this);
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258 groupMenu.add(unGroupMenuItem);
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259 groupMenu.add(colourMenu);
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260 groupMenu.addSeparator();
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261 groupMenu.add(showBoxes);
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262 groupMenu.add(showText);
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263 groupMenu.add(showColourText);
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264 colourMenu.add(noColourmenuItem);
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265 colourMenu.add(clustalColour);
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266 colourMenu.add(BLOSUM62Colour);
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267 colourMenu.add(PIDColour);
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268 colourMenu.add(zappoColour);
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269 colourMenu.add(taylorColour);
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270 colourMenu.add(hydrophobicityColour);
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271 colourMenu.add(helixColour);
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272 colourMenu.add(strandColour);
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273 colourMenu.add(turnColour);
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274 colourMenu.add(buriedColour);
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275 colourMenu.add(nucleotideMenuItem);
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276 colourMenu.add(userDefinedColour);
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277 colourMenu.addSeparator();
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278 colourMenu.add(abovePIDColour);
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279 colourMenu.add(conservationMenuItem);
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281 noColourmenuItem.setLabel("None");
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282 noColourmenuItem.addActionListener(this);
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284 clustalColour.setLabel("Clustalx colours");
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285 clustalColour.addActionListener(this);
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286 zappoColour.setLabel("Zappo");
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287 zappoColour.addActionListener(this);
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288 taylorColour.setLabel("Taylor");
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289 taylorColour.addActionListener(this);
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290 hydrophobicityColour.setLabel("Hydrophobicity");
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291 hydrophobicityColour.addActionListener(this);
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292 helixColour.setLabel("Helix propensity");
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293 helixColour.addActionListener(this);
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294 strandColour.setLabel("Strand propensity");
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295 strandColour.addActionListener(this);
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296 turnColour.setLabel("Turn propensity");
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297 turnColour.addActionListener(this);
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298 buriedColour.setLabel("Buried Index");
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299 buriedColour.addActionListener(this);
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300 abovePIDColour.setLabel("Above % Identity");
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302 userDefinedColour.setLabel("User Defined");
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303 userDefinedColour.addActionListener(this);
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304 PIDColour.setLabel("Percentage Identity");
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305 PIDColour.addActionListener(this);
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306 BLOSUM62Colour.setLabel("BLOSUM62");
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307 BLOSUM62Colour.addActionListener(this);
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308 conservationMenuItem.setLabel("Conservation");
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311 editMenu.add(copy);
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312 copy.addActionListener(this);
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314 cut.addActionListener(this);
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315 editMenu.add(toUpper);
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316 toUpper.addActionListener(this);
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317 editMenu.add(toLower);
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318 toLower.addActionListener(this);
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324 ap.seqPanel.seqCanvas.repaint();
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325 if(ap.overviewPanel!=null)
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326 ap.overviewPanel.updateOverviewImage();
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329 protected void clustalColour_actionPerformed()
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331 SequenceGroup sg = getGroup();
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332 sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
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336 protected void zappoColour_actionPerformed()
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338 getGroup().cs = new ZappoColourScheme();
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342 protected void taylorColour_actionPerformed()
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344 getGroup().cs = new TaylorColourScheme();
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348 protected void hydrophobicityColour_actionPerformed()
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350 getGroup().cs = new HydrophobicColourScheme();
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354 protected void helixColour_actionPerformed()
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356 getGroup().cs = new HelixColourScheme();
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360 protected void strandColour_actionPerformed()
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362 getGroup().cs = new StrandColourScheme();
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366 protected void turnColour_actionPerformed()
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368 getGroup().cs = new TurnColourScheme();
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372 protected void buriedColour_actionPerformed()
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374 getGroup().cs = new BuriedColourScheme();
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378 public void nucleotideMenuItem_actionPerformed()
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380 getGroup().cs = new NucleotideColourScheme();
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384 protected void abovePIDColour_itemStateChanged()
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386 SequenceGroup sg = getGroup();
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390 if (abovePIDColour.getState())
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392 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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393 ap.av.alignment.getWidth()));
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394 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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395 getGroup().getName());
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397 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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399 SliderPanel.showPIDSlider();
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402 else // remove PIDColouring
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404 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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411 protected void userDefinedColour_actionPerformed()
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413 new UserDefinedColours(ap, getGroup());
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416 protected void PIDColour_actionPerformed()
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418 SequenceGroup sg = getGroup();
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419 sg.cs = new PIDColourScheme();
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420 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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421 ap.av.alignment.getWidth()));
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425 protected void BLOSUM62Colour_actionPerformed()
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427 SequenceGroup sg = getGroup();
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429 sg.cs = new Blosum62ColourScheme();
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431 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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432 ap.av.alignment.getWidth()));
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437 protected void noColourmenuItem_actionPerformed()
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439 getGroup().cs = null;
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443 protected void conservationMenuItem_itemStateChanged()
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445 SequenceGroup sg = getGroup();
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449 if (conservationMenuItem.getState())
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452 Conservation c = new Conservation("Group",
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453 ResidueProperties.propHash, 3,
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455 ap.av.alignment.getWidth());
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458 c.verdict(false, ap.av.ConsPercGaps);
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460 sg.cs.setConservation(c);
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462 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
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463 SliderPanel.showConservationSlider();
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465 else // remove ConservationColouring
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467 sg.cs.setConservation(null);
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474 SequenceGroup getGroup()
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476 SequenceGroup sg = ap.av.getSelectionGroup();
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478 // this method won't add a new group if it already exists
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480 ap.av.alignment.addGroup(sg);
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485 void unGroupMenuItem_actionPerformed()
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487 SequenceGroup sg = ap.av.getSelectionGroup();
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488 ap.av.alignment.deleteGroup(sg);
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489 ap.av.setSelectionGroup(null);
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493 public void showColourText_itemStateChanged()
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495 getGroup().setColourText(showColourText.getState());
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499 public void showText_itemStateChanged()
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501 getGroup().setDisplayText(showText.getState());
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505 public void showBoxes_itemStateChanged()
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507 getGroup().setDisplayBoxes(showBoxes.getState());
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