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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85 showText.setState(sg.getDisplayText());
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86 showColourText.setState(sg.getColourText());
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87 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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95 if (seq != null && links!=null)
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97 Menu linkMenu = new Menu("Link");
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100 for(int i=0; i<links.size(); i++)
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102 link = links.elementAt(i).toString();
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103 final String target = link.substring(0, link.indexOf("|"));
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104 item = new MenuItem(target);
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105 String id = seq.getName();
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106 if(id.indexOf("|")>-1)
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107 id = id.substring(id.lastIndexOf("|")+1);
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109 final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
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111 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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113 item.addActionListener(new java.awt.event.ActionListener()
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115 public void actionPerformed(ActionEvent e)
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117 ap.alignFrame.showURL(url, target);
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120 linkMenu.add(item);
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124 item = new MenuItem("Show PDB Structure");
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125 item.addActionListener(new java.awt.event.ActionListener()
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127 public void actionPerformed(ActionEvent e)
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139 public void itemStateChanged(ItemEvent evt)
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141 if(evt.getSource()==abovePIDColour)
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142 abovePIDColour_itemStateChanged();
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143 else if(evt.getSource()==showColourText)
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144 showColourText_itemStateChanged();
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145 else if(evt.getSource()==showText)
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146 showText_itemStateChanged();
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147 else if(evt.getSource()==showBoxes)
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148 showBoxes_itemStateChanged() ;
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151 public void actionPerformed(ActionEvent evt)
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153 Object source = evt.getSource();
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154 if(source==clustalColour)
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155 clustalColour_actionPerformed();
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156 else if(source==zappoColour)
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157 zappoColour_actionPerformed();
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158 else if(source==taylorColour)
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159 taylorColour_actionPerformed();
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160 else if(source==hydrophobicityColour)
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161 hydrophobicityColour_actionPerformed();
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162 else if(source==helixColour)
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163 helixColour_actionPerformed();
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164 else if(source==strandColour)
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165 strandColour_actionPerformed();
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166 else if(source==clustalColour)
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167 turnColour_actionPerformed();
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168 else if(source==buriedColour)
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169 buriedColour_actionPerformed();
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170 else if(source==nucleotideMenuItem)
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171 nucleotideMenuItem_actionPerformed();
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173 else if(source==userDefinedColour)
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174 userDefinedColour_actionPerformed();
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175 else if(source==PIDColour)
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176 PIDColour_actionPerformed();
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177 else if(source==BLOSUM62Colour)
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178 BLOSUM62Colour_actionPerformed();
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179 else if(source==noColourmenuItem)
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180 noColourmenuItem_actionPerformed();
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181 else if(source==conservationMenuItem)
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182 conservationMenuItem_itemStateChanged();
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183 else if(source==unGroupMenuItem)
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184 unGroupMenuItem_actionPerformed();
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186 else if(source==copy)
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187 ap.alignFrame.copy_actionPerformed();
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188 else if(source==cut)
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189 ap.alignFrame.cut_actionPerformed();
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190 else if(source==toUpper)
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192 SequenceGroup sg = ap.av.getSelectionGroup();
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195 for (int g = 0; g < sg.getSize(); g++)
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197 sg.getSequenceAt(g).changeCase(true, sg.getStartRes(),
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198 sg.getEndRes() + 1);
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200 ap.seqPanel.seqCanvas.repaint();
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203 else if(source==toLower)
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205 SequenceGroup sg = ap.av.getSelectionGroup();
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208 for (int g = 0; g < sg.getSize(); g++)
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210 sg.getSequenceAt(g).changeCase(false, sg.getStartRes(),
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211 sg.getEndRes() + 1);
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213 ap.seqPanel.seqCanvas.repaint();
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219 void addPDB(Sequence seq)
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221 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
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222 cap.setText("Paste your PDB file here.");
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223 cap.setPDBImport(seq);
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224 Frame frame = new Frame();
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226 jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
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229 private void jbInit()
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232 groupMenu.setLabel("Group");
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233 groupMenu.setLabel("Define");
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235 unGroupMenuItem.setLabel("Remove Group");
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236 unGroupMenuItem.addActionListener(this);
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238 nucleotideMenuItem.setLabel("Nucleotide");
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239 nucleotideMenuItem.addActionListener(this);
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240 conservationMenuItem.addItemListener(this);
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241 abovePIDColour.addItemListener(this);
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242 colourMenu.setLabel("Group Colour");
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243 showBoxes.setLabel("Boxes");
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244 showBoxes.setState(true);
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245 showBoxes.addItemListener(this);
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247 showText.setLabel("Text");
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248 showText.addItemListener(this);
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249 showColourText.setLabel("Colour Text");
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250 showColourText.addItemListener(this);
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253 groupMenu.add(unGroupMenuItem);
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254 groupMenu.add(colourMenu);
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255 groupMenu.addSeparator();
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256 groupMenu.add(showBoxes);
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257 groupMenu.add(showText);
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258 groupMenu.add(showColourText);
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259 colourMenu.add(noColourmenuItem);
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260 colourMenu.add(clustalColour);
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261 colourMenu.add(BLOSUM62Colour);
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262 colourMenu.add(PIDColour);
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263 colourMenu.add(zappoColour);
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264 colourMenu.add(taylorColour);
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265 colourMenu.add(hydrophobicityColour);
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266 colourMenu.add(helixColour);
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267 colourMenu.add(strandColour);
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268 colourMenu.add(turnColour);
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269 colourMenu.add(buriedColour);
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270 colourMenu.add(nucleotideMenuItem);
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271 colourMenu.add(userDefinedColour);
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272 colourMenu.addSeparator();
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273 colourMenu.add(abovePIDColour);
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274 colourMenu.add(conservationMenuItem);
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276 noColourmenuItem.setLabel("None");
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277 noColourmenuItem.addActionListener(this);
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279 clustalColour.setLabel("Clustalx colours");
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280 clustalColour.addActionListener(this);
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281 zappoColour.setLabel("Zappo");
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282 zappoColour.addActionListener(this);
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283 taylorColour.setLabel("Taylor");
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284 taylorColour.addActionListener(this);
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285 hydrophobicityColour.setLabel("Hydrophobicity");
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286 hydrophobicityColour.addActionListener(this);
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287 helixColour.setLabel("Helix propensity");
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288 helixColour.addActionListener(this);
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289 strandColour.setLabel("Strand propensity");
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290 strandColour.addActionListener(this);
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291 turnColour.setLabel("Turn propensity");
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292 turnColour.addActionListener(this);
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293 buriedColour.setLabel("Buried Index");
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294 buriedColour.addActionListener(this);
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295 abovePIDColour.setLabel("Above % Identity");
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297 userDefinedColour.setLabel("User Defined");
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298 userDefinedColour.addActionListener(this);
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299 PIDColour.setLabel("Percentage Identity");
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300 PIDColour.addActionListener(this);
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301 BLOSUM62Colour.setLabel("BLOSUM62");
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302 BLOSUM62Colour.addActionListener(this);
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303 conservationMenuItem.setLabel("Conservation");
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306 editMenu.add(copy);
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307 copy.addActionListener(this);
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309 cut.addActionListener(this);
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310 editMenu.add(toUpper);
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311 toUpper.addActionListener(this);
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312 editMenu.add(toLower);
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313 toLower.addActionListener(this);
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319 ap.seqPanel.seqCanvas.repaint();
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320 if(ap.overviewPanel!=null)
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321 ap.overviewPanel.updateOverviewImage();
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324 protected void clustalColour_actionPerformed()
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326 SequenceGroup sg = getGroup();
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327 sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
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331 protected void zappoColour_actionPerformed()
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333 getGroup().cs = new ZappoColourScheme();
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337 protected void taylorColour_actionPerformed()
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339 getGroup().cs = new TaylorColourScheme();
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343 protected void hydrophobicityColour_actionPerformed()
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345 getGroup().cs = new HydrophobicColourScheme();
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349 protected void helixColour_actionPerformed()
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351 getGroup().cs = new HelixColourScheme();
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355 protected void strandColour_actionPerformed()
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357 getGroup().cs = new StrandColourScheme();
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361 protected void turnColour_actionPerformed()
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363 getGroup().cs = new TurnColourScheme();
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367 protected void buriedColour_actionPerformed()
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369 getGroup().cs = new BuriedColourScheme();
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373 public void nucleotideMenuItem_actionPerformed()
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375 getGroup().cs = new NucleotideColourScheme();
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379 protected void abovePIDColour_itemStateChanged()
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381 SequenceGroup sg = getGroup();
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385 if (abovePIDColour.getState())
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387 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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388 ap.av.alignment.getWidth()));
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389 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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390 getGroup().getName());
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392 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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394 SliderPanel.showPIDSlider();
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397 else // remove PIDColouring
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399 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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406 protected void userDefinedColour_actionPerformed()
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408 new UserDefinedColours(ap, getGroup());
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411 protected void PIDColour_actionPerformed()
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413 SequenceGroup sg = getGroup();
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414 sg.cs = new PIDColourScheme();
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415 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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416 ap.av.alignment.getWidth()));
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420 protected void BLOSUM62Colour_actionPerformed()
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422 SequenceGroup sg = getGroup();
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424 sg.cs = new Blosum62ColourScheme();
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426 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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427 ap.av.alignment.getWidth()));
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432 protected void noColourmenuItem_actionPerformed()
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434 getGroup().cs = null;
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438 protected void conservationMenuItem_itemStateChanged()
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440 SequenceGroup sg = getGroup();
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444 if (conservationMenuItem.getState())
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447 Conservation c = new Conservation("Group",
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448 ResidueProperties.propHash, 3,
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450 ap.av.alignment.getWidth());
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453 c.verdict(false, ap.av.ConsPercGaps);
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455 sg.cs.setConservation(c);
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457 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
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458 SliderPanel.showConservationSlider();
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460 else // remove ConservationColouring
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462 sg.cs.setConservation(null);
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469 SequenceGroup getGroup()
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471 SequenceGroup sg = ap.av.getSelectionGroup();
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473 // this method won't add a new group if it already exists
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475 ap.av.alignment.addGroup(sg);
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480 void unGroupMenuItem_actionPerformed()
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482 SequenceGroup sg = ap.av.getSelectionGroup();
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483 ap.av.alignment.deleteGroup(sg);
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484 ap.av.setSelectionGroup(null);
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488 public void showColourText_itemStateChanged()
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490 getGroup().setColourText(showColourText.getState());
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494 public void showText_itemStateChanged()
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496 getGroup().setDisplayText(showText.getState());
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500 public void showBoxes_itemStateChanged()
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502 getGroup().setDisplayBoxes(showBoxes.getState());
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