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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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 ap, 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 final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
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102 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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104 item.addActionListener(new java.awt.event.ActionListener()
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106 public void actionPerformed(ActionEvent e)
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108 jalview.bin.JalviewLite.showURL(url, target);
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111 linkMenu.add(item);
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117 private void jbInit()
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120 groupMenu.setLabel("Group");
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121 groupMenu.setLabel("Define");
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123 unGroupMenuItem.setLabel("Remove Group");
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124 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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126 public void actionPerformed(ActionEvent e)
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128 unGroupMenuItem_actionPerformed(e);
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132 nucleotideMenuItem.setLabel("Nucleotide");
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133 nucleotideMenuItem.addActionListener(new ActionListener()
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135 public void actionPerformed(ActionEvent e)
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137 nucleotideMenuItem_actionPerformed(e);
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140 conservationMenuItem.addItemListener(new ItemListener()
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142 public void itemStateChanged(ItemEvent itemEvent)
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144 conservationMenuItem_itemStateChanged(itemEvent);
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147 abovePIDColour.addItemListener(new ItemListener()
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149 public void itemStateChanged(ItemEvent itemEvent)
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151 abovePIDColour_itemStateChanged(itemEvent);
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154 colourMenu.setLabel("Group Colour");
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155 showBoxes.setLabel("Boxes");
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156 showBoxes.setState(true);
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157 showBoxes.addItemListener(new ItemListener()
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159 public void itemStateChanged(ItemEvent itemEvent)
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161 showBoxes_itemStateChanged(itemEvent);
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165 showText.setLabel("Text");
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166 showText.addItemListener(new ItemListener()
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168 public void itemStateChanged(ItemEvent itemEvent)
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170 showText_itemStateChanged(itemEvent);
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173 showColourText.setLabel("Colour Text");
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174 showColourText.addItemListener(new ItemListener()
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176 public void itemStateChanged(ItemEvent itemEvent)
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178 showColourText_itemStateChanged(itemEvent);
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183 groupMenu.add(unGroupMenuItem);
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184 groupMenu.add(colourMenu);
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185 groupMenu.addSeparator();
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186 groupMenu.add(showBoxes);
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187 groupMenu.add(showText);
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188 groupMenu.add(showColourText);
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189 colourMenu.add(noColourmenuItem);
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190 colourMenu.add(clustalColour);
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191 colourMenu.add(BLOSUM62Colour);
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192 colourMenu.add(PIDColour);
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193 colourMenu.add(zappoColour);
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194 colourMenu.add(taylorColour);
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195 colourMenu.add(hydrophobicityColour);
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196 colourMenu.add(helixColour);
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197 colourMenu.add(strandColour);
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198 colourMenu.add(turnColour);
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199 colourMenu.add(buriedColour);
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200 colourMenu.add(nucleotideMenuItem);
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201 colourMenu.add(userDefinedColour);
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202 colourMenu.addSeparator();
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203 colourMenu.add(abovePIDColour);
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204 colourMenu.add(conservationMenuItem);
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206 noColourmenuItem.setLabel("None");
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207 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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209 public void actionPerformed(ActionEvent e)
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211 noColourmenuItem_actionPerformed(e);
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215 clustalColour.setLabel("Clustalx colours");
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216 clustalColour.addActionListener(new java.awt.event.ActionListener()
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218 public void actionPerformed(ActionEvent e)
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220 clustalColour_actionPerformed(e);
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223 zappoColour.setLabel("Zappo");
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224 zappoColour.addActionListener(new java.awt.event.ActionListener()
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226 public void actionPerformed(ActionEvent e)
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228 zappoColour_actionPerformed(e);
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231 taylorColour.setLabel("Taylor");
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232 taylorColour.addActionListener(new java.awt.event.ActionListener()
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234 public void actionPerformed(ActionEvent e)
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236 taylorColour_actionPerformed(e);
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239 hydrophobicityColour.setLabel("Hydrophobicity");
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240 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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242 public void actionPerformed(ActionEvent e)
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244 hydrophobicityColour_actionPerformed(e);
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247 helixColour.setLabel("Helix propensity");
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248 helixColour.addActionListener(new java.awt.event.ActionListener()
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250 public void actionPerformed(ActionEvent e)
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252 helixColour_actionPerformed(e);
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255 strandColour.setLabel("Strand propensity");
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256 strandColour.addActionListener(new java.awt.event.ActionListener()
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258 public void actionPerformed(ActionEvent e)
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260 strandColour_actionPerformed(e);
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263 turnColour.setLabel("Turn propensity");
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264 turnColour.addActionListener(new java.awt.event.ActionListener()
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266 public void actionPerformed(ActionEvent e)
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268 turnColour_actionPerformed(e);
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271 buriedColour.setLabel("Buried Index");
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272 buriedColour.addActionListener(new java.awt.event.ActionListener()
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274 public void actionPerformed(ActionEvent e)
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276 buriedColour_actionPerformed(e);
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279 abovePIDColour.setLabel("Above % Identity");
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281 userDefinedColour.setLabel("User Defined");
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282 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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284 public void actionPerformed(ActionEvent e)
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286 userDefinedColour_actionPerformed(e);
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289 PIDColour.setLabel("Percentage Identity");
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290 PIDColour.addActionListener(new java.awt.event.ActionListener()
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292 public void actionPerformed(ActionEvent e)
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294 PIDColour_actionPerformed(e);
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297 BLOSUM62Colour.setLabel("BLOSUM62");
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298 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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300 public void actionPerformed(ActionEvent e)
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302 BLOSUM62Colour_actionPerformed(e);
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305 conservationMenuItem.setLabel("Conservation");
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311 SequenceGroup sg = getGroup();
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314 SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
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316 if (superG != null)
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318 superG.setSuperGroupProperties(sg);
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321 ap.seqPanel.seqCanvas.repaint();
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324 protected void clustalColour_actionPerformed(ActionEvent e)
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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(ActionEvent e)
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333 getGroup().cs = new ZappoColourScheme();
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337 protected void taylorColour_actionPerformed(ActionEvent e)
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339 getGroup().cs = new TaylorColourScheme();
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343 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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345 getGroup().cs = new HydrophobicColourScheme();
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349 protected void helixColour_actionPerformed(ActionEvent e)
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351 getGroup().cs = new HelixColourScheme();
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355 protected void strandColour_actionPerformed(ActionEvent e)
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357 getGroup().cs = new StrandColourScheme();
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361 protected void turnColour_actionPerformed(ActionEvent e)
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363 getGroup().cs = new TurnColourScheme();
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367 protected void buriedColour_actionPerformed(ActionEvent e)
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369 getGroup().cs = new BuriedColourScheme();
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373 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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375 getGroup().cs = new NucleotideColourScheme();
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379 protected void abovePIDColour_itemStateChanged(ItemEvent ie)
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381 SequenceGroup sg = getGroup();
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382 if (abovePIDColour.getState())
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384 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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385 ap.av.alignment.getWidth()));
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386 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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387 getGroup().getName());
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388 if (sg.cs instanceof ResidueColourScheme)
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390 ( (ResidueColourScheme) sg.cs).setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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392 else if (sg.cs instanceof ScoreColourScheme)
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394 ( (ScoreColourScheme) sg.cs).setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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397 SliderPanel.showPIDSlider();
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400 else // remove PIDColouring
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402 ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
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403 rcs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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411 protected void userDefinedColour_actionPerformed(ActionEvent e)
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413 new UserDefinedColours(ap, getGroup());
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416 protected void PIDColour_actionPerformed(ActionEvent e)
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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(ActionEvent e)
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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(ActionEvent e)
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439 getGroup().cs = null;
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443 protected void conservationMenuItem_itemStateChanged(ItemEvent ie)
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445 SequenceGroup sg = getGroup();
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447 if (conservationMenuItem.getState())
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450 Conservation c = new Conservation("Group",
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451 ResidueProperties.propHash, 3,
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453 ap.av.alignment.getWidth());
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456 c.verdict(false, ap.av.ConsPercGaps);
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457 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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461 SliderPanel.setConservationSlider(ap, ccs, sg.getName());
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462 SliderPanel.showConservationSlider();
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464 else // remove ConservationColouring
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466 ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;
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473 protected void analyze_actionPerformed(ActionEvent e)
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475 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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476 Frame frame = new Frame();
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478 jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);
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479 SequenceGroup sg = getGroup();
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480 StringBuffer sb = new StringBuffer();
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482 for (int i = 0; i < sg.sequences.size(); i++)
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484 Sequence tmp = (Sequence) sg.sequences.elementAt(i);
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485 sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
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489 sb.append("Something amazing will happen soon");
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490 cap.setText(sb.toString());
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494 SequenceGroup getGroup()
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496 SequenceGroup sg = ap.av.getSelectionGroup();
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498 // this method won't add a new group if it already exists
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500 ap.av.alignment.addGroup(sg);
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505 void unGroupMenuItem_actionPerformed(ActionEvent e)
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507 SequenceGroup sg = ap.av.getSelectionGroup();
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508 ap.av.alignment.deleteGroup(sg);
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509 ap.av.setSelectionGroup(null);
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513 public void showColourText_itemStateChanged(ItemEvent itemEvent)
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515 getGroup().setColourText(showColourText.getState());
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519 public void showText_itemStateChanged(ItemEvent itemEvent)
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521 getGroup().setDisplayText(showText.getState());
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525 public void showBoxes_itemStateChanged(ItemEvent itemEvent)
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527 getGroup().setDisplayBoxes(showBoxes.getState());
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