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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25 import jalview.analysis.*;
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26 import jalview.datamodel.*;
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27 import jalview.schemes.*;
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29 public class APopupMenu
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30 extends java.awt.PopupMenu
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32 Menu groupMenu = new Menu();
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33 protected MenuItem clustalColour = new MenuItem();
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34 protected MenuItem zappoColour = new MenuItem();
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35 protected MenuItem taylorColour = new MenuItem();
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36 protected MenuItem hydrophobicityColour = new MenuItem();
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37 protected MenuItem helixColour = new MenuItem();
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38 protected MenuItem strandColour = new MenuItem();
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39 protected MenuItem turnColour = new MenuItem();
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40 protected MenuItem buriedColour = new MenuItem();
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41 protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
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42 protected MenuItem userDefinedColour = new MenuItem();
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43 protected MenuItem PIDColour = new MenuItem();
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44 protected MenuItem BLOSUM62Colour = new MenuItem();
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45 MenuItem noColourmenuItem = new MenuItem();
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46 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
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49 Menu sequenceMenu = new Menu();
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50 MenuItem sequenceName = new MenuItem();
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52 MenuItem unGroupMenuItem = new MenuItem();
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53 MenuItem nucleotideMenuItem = new MenuItem();
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54 Menu colourMenu = new Menu();
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55 CheckboxMenuItem showBoxes = new CheckboxMenuItem();
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56 CheckboxMenuItem showText = new CheckboxMenuItem();
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57 CheckboxMenuItem showColourText = new CheckboxMenuItem();
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59 public APopupMenu(AlignmentPanel ap, Sequence seq)
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61 ///////////////////////////////////////////////////////////
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62 // If this is activated from the sequence panel, the user may want to
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63 // edit or annotate a particular residue. Therefore display the residue menu
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65 // If from the IDPanel, we must display the sequence menu
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66 //////////////////////////////////////////////////////////
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77 e.printStackTrace();
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80 SequenceGroup sg = ap.av.getSelectionGroup();
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83 showText.setState(sg.getDisplayText());
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84 showColourText.setState(sg.getColourText());
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85 showBoxes.setState(sg.getDisplayBoxes());
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88 if (!ap.av.alignment.getGroups().contains(sg))
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90 groupMenu.remove(unGroupMenuItem);
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95 remove(sequenceMenu);
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100 private void jbInit()
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103 groupMenu.setLabel("Group");
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104 groupMenu.setLabel("Define");
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106 sequenceMenu.setLabel("Sequence");
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107 sequenceName.setLabel("Edit name");
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108 unGroupMenuItem.setLabel("Remove Group");
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109 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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111 public void actionPerformed(ActionEvent e)
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113 unGroupMenuItem_actionPerformed(e);
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117 nucleotideMenuItem.setLabel("Nucleotide");
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118 nucleotideMenuItem.addActionListener(new ActionListener()
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120 public void actionPerformed(ActionEvent e)
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122 nucleotideMenuItem_actionPerformed(e);
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125 conservationMenuItem.addItemListener(new ItemListener()
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127 public void itemStateChanged(ItemEvent itemEvent)
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129 conservationMenuItem_itemStateChanged(itemEvent);
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132 abovePIDColour.addItemListener(new ItemListener()
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134 public void itemStateChanged(ItemEvent itemEvent)
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136 abovePIDColour_itemStateChanged(itemEvent);
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139 colourMenu.setLabel("Group Colour");
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140 showBoxes.setLabel("Boxes");
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141 showBoxes.setState(true);
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142 showBoxes.addItemListener(new ItemListener()
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144 public void itemStateChanged(ItemEvent itemEvent)
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146 showBoxes_itemStateChanged(itemEvent);
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150 showText.setLabel("Text");
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151 showText.addItemListener(new ItemListener()
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153 public void itemStateChanged(ItemEvent itemEvent)
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155 showText_itemStateChanged(itemEvent);
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158 showColourText.setLabel("Colour Text");
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159 showColourText.addItemListener(new ItemListener()
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161 public void itemStateChanged(ItemEvent itemEvent)
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163 showColourText_itemStateChanged(itemEvent);
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168 this.add(sequenceMenu);
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169 groupMenu.add(unGroupMenuItem);
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170 groupMenu.add(colourMenu);
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171 groupMenu.addSeparator();
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172 groupMenu.add(showBoxes);
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173 groupMenu.add(showText);
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174 groupMenu.add(showColourText);
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175 sequenceMenu.add(sequenceName);
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176 colourMenu.add(noColourmenuItem);
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177 colourMenu.add(clustalColour);
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178 colourMenu.add(BLOSUM62Colour);
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179 colourMenu.add(PIDColour);
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180 colourMenu.add(zappoColour);
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181 colourMenu.add(taylorColour);
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182 colourMenu.add(hydrophobicityColour);
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183 colourMenu.add(helixColour);
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184 colourMenu.add(strandColour);
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185 colourMenu.add(turnColour);
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186 colourMenu.add(buriedColour);
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187 colourMenu.add(nucleotideMenuItem);
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188 colourMenu.add(userDefinedColour);
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189 colourMenu.addSeparator();
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190 colourMenu.add(abovePIDColour);
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191 colourMenu.add(conservationMenuItem);
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193 noColourmenuItem.setLabel("None");
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194 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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196 public void actionPerformed(ActionEvent e)
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198 noColourmenuItem_actionPerformed(e);
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202 clustalColour.setLabel("Clustalx colours");
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203 clustalColour.addActionListener(new java.awt.event.ActionListener()
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205 public void actionPerformed(ActionEvent e)
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207 clustalColour_actionPerformed(e);
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210 zappoColour.setLabel("Zappo");
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211 zappoColour.addActionListener(new java.awt.event.ActionListener()
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213 public void actionPerformed(ActionEvent e)
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215 zappoColour_actionPerformed(e);
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218 taylorColour.setLabel("Taylor");
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219 taylorColour.addActionListener(new java.awt.event.ActionListener()
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221 public void actionPerformed(ActionEvent e)
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223 taylorColour_actionPerformed(e);
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226 hydrophobicityColour.setLabel("Hydrophobicity");
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227 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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229 public void actionPerformed(ActionEvent e)
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231 hydrophobicityColour_actionPerformed(e);
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234 helixColour.setLabel("Helix propensity");
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235 helixColour.addActionListener(new java.awt.event.ActionListener()
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237 public void actionPerformed(ActionEvent e)
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239 helixColour_actionPerformed(e);
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242 strandColour.setLabel("Strand propensity");
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243 strandColour.addActionListener(new java.awt.event.ActionListener()
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245 public void actionPerformed(ActionEvent e)
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247 strandColour_actionPerformed(e);
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250 turnColour.setLabel("Turn propensity");
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251 turnColour.addActionListener(new java.awt.event.ActionListener()
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253 public void actionPerformed(ActionEvent e)
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255 turnColour_actionPerformed(e);
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258 buriedColour.setLabel("Buried Index");
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259 buriedColour.addActionListener(new java.awt.event.ActionListener()
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261 public void actionPerformed(ActionEvent e)
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263 buriedColour_actionPerformed(e);
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266 abovePIDColour.setLabel("Above % Identity");
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268 userDefinedColour.setLabel("User Defined");
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269 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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271 public void actionPerformed(ActionEvent e)
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273 userDefinedColour_actionPerformed(e);
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276 PIDColour.setLabel("Percentage Identity");
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277 PIDColour.addActionListener(new java.awt.event.ActionListener()
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279 public void actionPerformed(ActionEvent e)
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281 PIDColour_actionPerformed(e);
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284 BLOSUM62Colour.setLabel("BLOSUM62");
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285 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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287 public void actionPerformed(ActionEvent e)
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289 BLOSUM62Colour_actionPerformed(e);
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292 conservationMenuItem.setLabel("Conservation");
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298 SequenceGroup sg = getGroup();
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299 SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
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300 if (superG != null)
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302 superG.setSuperGroupProperties(sg);
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305 ap.seqPanel.seqCanvas.repaint();
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308 protected void clustalColour_actionPerformed(ActionEvent e)
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310 SequenceGroup sg = getGroup();
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311 sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
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315 protected void zappoColour_actionPerformed(ActionEvent e)
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317 getGroup().cs = new ZappoColourScheme();
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321 protected void taylorColour_actionPerformed(ActionEvent e)
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323 getGroup().cs = new TaylorColourScheme();
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327 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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329 getGroup().cs = new HydrophobicColourScheme();
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333 protected void helixColour_actionPerformed(ActionEvent e)
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335 getGroup().cs = new HelixColourScheme();
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339 protected void strandColour_actionPerformed(ActionEvent e)
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341 getGroup().cs = new StrandColourScheme();
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345 protected void turnColour_actionPerformed(ActionEvent e)
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347 getGroup().cs = new TurnColourScheme();
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351 protected void buriedColour_actionPerformed(ActionEvent e)
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353 getGroup().cs = new BuriedColourScheme();
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357 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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359 getGroup().cs = new NucleotideColourScheme();
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363 protected void abovePIDColour_itemStateChanged(ItemEvent ie)
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365 SequenceGroup sg = getGroup();
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366 if (abovePIDColour.getState())
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368 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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369 ap.av.alignment.getWidth()));
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370 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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371 getGroup().getName());
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372 if (sg.cs instanceof ResidueColourScheme)
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374 ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
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376 else if (sg.cs instanceof ScoreColourScheme)
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378 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
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381 SliderPanel.showPIDSlider();
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384 else // remove PIDColouring
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386 ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
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387 rcs.setThreshold(0);
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395 protected void userDefinedColour_actionPerformed(ActionEvent e)
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397 new UserDefinedColours(ap, getGroup());
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400 protected void PIDColour_actionPerformed(ActionEvent e)
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402 SequenceGroup sg = getGroup();
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403 sg.cs = new PIDColourScheme();
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404 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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405 ap.av.alignment.getWidth()));
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409 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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411 SequenceGroup sg = getGroup();
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413 sg.cs = new Blosum62ColourScheme();
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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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421 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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423 getGroup().cs = null;
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427 protected void conservationMenuItem_itemStateChanged(ItemEvent ie)
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429 SequenceGroup sg = getGroup();
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431 if (conservationMenuItem.getState())
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434 Conservation c = new Conservation("Group",
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435 ResidueProperties.propHash, 3,
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437 ap.av.alignment.getWidth());
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440 c.verdict(false, ap.av.ConsPercGaps);
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441 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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445 SliderPanel.setConservationSlider(ap, ccs, sg.getName());
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446 SliderPanel.showConservationSlider();
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448 else // remove ConservationColouring
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450 ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;
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457 protected void analyze_actionPerformed(ActionEvent e)
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459 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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460 Frame frame = new Frame();
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462 jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);
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463 SequenceGroup sg = getGroup();
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464 StringBuffer sb = new StringBuffer();
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466 for (int i = 0; i < sg.sequences.size(); i++)
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468 Sequence tmp = (Sequence) sg.sequences.elementAt(i);
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469 sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
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473 sb.append("Something amazing will happen soon");
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474 cap.setText(sb.toString());
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478 SequenceGroup getGroup()
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480 SequenceGroup sg = ap.av.getSelectionGroup();
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482 // this method won't add a new group if it already exists
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483 ap.av.alignment.addGroup(sg);
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488 void unGroupMenuItem_actionPerformed(ActionEvent e)
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490 SequenceGroup sg = ap.av.getSelectionGroup();
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491 ap.av.alignment.deleteGroup(sg);
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492 ap.av.setSelectionGroup(null);
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496 public void showColourText_itemStateChanged(ItemEvent itemEvent)
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498 getGroup().setColourText(showColourText.getState());
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502 public void showText_itemStateChanged(ItemEvent itemEvent)
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504 getGroup().setDisplayText(showText.getState());
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508 public void showBoxes_itemStateChanged(ItemEvent itemEvent)
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510 getGroup().setDisplayBoxes(showBoxes.getState());
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