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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22 import jalview.schemes.*;
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23 import jalview.datamodel.*;
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24 import jalview.analysis.*;
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25 import jalview.io.*;
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27 import java.awt.event.*;
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29 import java.io.InputStreamReader;
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30 import java.io.BufferedReader;
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31 import java.net.URL;
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34 public class AlignFrame extends Frame
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36 final AlignmentPanel alignPanel;
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37 public final AlignViewport viewport;
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38 int NEW_WINDOW_WIDTH = 700;
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39 int NEW_WINDOW_HEIGHT = 500;
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40 jalview.bin.JalviewLite applet;
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43 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title)
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47 }catch(Exception ex)
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49 ex.printStackTrace();
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51 this.applet = applet;
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52 viewport = new AlignViewport(al, applet);
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53 alignPanel = new AlignmentPanel(this, viewport);
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55 alignPanel.validate();
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59 String treeFile = applet.getParameter("treeFile");
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60 if (treeFile != null)
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64 jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
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65 getCodeBase() + treeFile, "URL");
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68 if (fin.getTree() != null)
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70 TreePanel tp = null;
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71 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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72 fin, "FromFile", applet.getCodeBase() + treeFile);
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73 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
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74 addTreeMenuItem(tp, treeFile);
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77 catch (Exception ex)
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79 ex.printStackTrace();
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83 String param = applet.getParameter("sortBy");
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86 if (param.equalsIgnoreCase("Id"))
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87 sortIDMenuItem_actionPerformed(null);
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88 else if (param.equalsIgnoreCase("Pairwise Identity"))
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89 sortPairwiseMenuItem_actionPerformed(null);
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92 param = applet.getParameter("wrap");
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95 if (param.equalsIgnoreCase("true"))
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97 wrapMenuItem.setState(true);
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98 wrapMenuItem_actionPerformed(null);
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104 param = applet.getParameter("windowWidth");
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107 int width = Integer.parseInt(param);
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108 NEW_WINDOW_WIDTH = width;
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110 param = applet.getParameter("windowHeight");
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113 int height = Integer.parseInt(param);
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114 NEW_WINDOW_HEIGHT = height;
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117 catch (Exception ex)
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122 this.addWindowListener(new WindowAdapter()
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124 public void windowClosing(WindowEvent e)
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126 closeMenuItem_actionPerformed(null);
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130 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
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132 public void propertyChange(java.beans.PropertyChangeEvent evt)
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134 if (evt.getPropertyName().equals("alignment"))
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136 alignmentChanged();
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141 jalview.bin.JalviewLite.addFrame(this, title,
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143 NEW_WINDOW_HEIGHT);
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152 * @param String DOCUMENT ME!
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155 public void parseFeaturesFile(String file)
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159 URL url = new URL(file);
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161 BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
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162 SequenceI seq = null;
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163 String line, type, desc, token;
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165 int index, start, end;
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166 StringTokenizer st;
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167 SequenceFeature sf;
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168 FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
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170 while ( (line = in.readLine()) != null)
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173 st = new StringTokenizer(line, "\t");
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174 if (st.countTokens() == 2)
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176 type = st.nextToken();
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177 UserColourScheme ucs = new UserColourScheme(st.nextToken());
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178 fr.setColour(type, ucs.findColour("A"));
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182 while (st.hasMoreElements())
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184 desc = st.nextToken();
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185 token = st.nextToken();
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186 if (!token.equals("ID_NOT_SPECIFIED"))
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188 index = viewport.alignment.findIndex(viewport.alignment.findName(
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194 index = Integer.parseInt(st.nextToken());
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197 start = Integer.parseInt(st.nextToken());
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198 end = Integer.parseInt(st.nextToken());
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200 seq = viewport.alignment.getSequenceAt(index);
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201 start = seq.findIndex(start) - 1;
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202 end = seq.findIndex(end) - 1;
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204 type = st.nextToken();
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206 if(fr.getColour(type)==null)
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208 // Probably the old style groups file
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209 UserColourScheme ucs = new UserColourScheme(type);
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210 fr.setColour(type, ucs.findColour("A"));
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213 sf = new SequenceFeature(type, desc, "", start, end);
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215 seq.addSequenceFeature(sf);
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219 viewport.showSequenceFeatures = true;
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220 ((Alignment)viewport.alignment).featuresAdded = true;
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222 alignPanel.repaint();
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225 catch (Exception ex)
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227 System.out.println("Error parsing groups file: " + ex);
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232 public void inputText_actionPerformed(ActionEvent e)
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234 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);
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235 Frame frame = new Frame();
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237 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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240 protected void outputText_actionPerformed(ActionEvent e)
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242 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);
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243 Frame frame = new Frame();
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245 jalview.bin.JalviewLite.addFrame(frame,
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246 "Alignment output - " + e.getActionCommand(),
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248 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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249 viewport.getAlignment().getSequences(),
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250 viewport.showJVSuffix));
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253 public void closeMenuItem_actionPerformed(ActionEvent e)
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255 PaintRefresher.components.remove(viewport.alignment);
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256 if(PaintRefresher.components.size()==0 && applet==null)
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260 Stack historyList = new Stack();
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261 Stack redoList = new Stack();
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263 void updateEditMenuBar()
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265 if (historyList.size() > 0)
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267 undoMenuItem.setEnabled(true);
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268 HistoryItem hi = (HistoryItem) historyList.peek();
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269 undoMenuItem.setLabel("Undo " + hi.getDescription());
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273 undoMenuItem.setEnabled(false);
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274 undoMenuItem.setLabel("Undo");
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277 if (redoList.size() > 0)
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279 redoMenuItem.setEnabled(true);
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280 HistoryItem hi = (HistoryItem) redoList.peek();
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281 redoMenuItem.setLabel("Redo " + hi.getDescription());
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285 redoMenuItem.setEnabled(false);
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286 redoMenuItem.setLabel("Redo");
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290 public void addHistoryItem(HistoryItem hi)
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292 historyList.push(hi);
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293 updateEditMenuBar();
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296 protected void undoMenuItem_actionPerformed(ActionEvent e)
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298 HistoryItem hi = (HistoryItem) historyList.pop();
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299 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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300 HistoryItem.HIDE));
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301 restoreHistoryItem(hi);
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302 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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305 protected void redoMenuItem_actionPerformed(ActionEvent e)
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307 HistoryItem hi = (HistoryItem) redoList.pop();
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308 restoreHistoryItem(hi);
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309 updateEditMenuBar();
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310 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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313 // used by undo and redo
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314 void restoreHistoryItem(HistoryItem hi)
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316 if (hi.getType() == HistoryItem.SORT)
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318 for (int i = 0; i < hi.getSequences().size(); i++)
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320 viewport.alignment.getSequences().setElementAt(hi.getSequences().
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326 for (int i = 0; i < hi.getSequences().size(); i++)
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328 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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329 if (restore.getLength() == 0)
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331 // log.System.out.println(hi.getHidden().elementAt(i));
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332 restore.setSequence(hi.getHidden().elementAt(i).toString());
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333 viewport.alignment.getSequences().insertElementAt(
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335 hi.getAlignIndex(i));
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339 restore.setSequence(hi.getHidden().elementAt(i).toString());
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342 if (hi.getType() == HistoryItem.PASTE)
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344 for (int i = viewport.alignment.getHeight() - 1;
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345 i > hi.getSequences().size() - 1; i--)
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347 viewport.alignment.deleteSequence(i);
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352 updateEditMenuBar();
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354 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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357 public void moveSelectedSequences(boolean up)
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359 SequenceGroup sg = viewport.getSelectionGroup();
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367 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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369 SequenceI seq = viewport.alignment.getSequenceAt(i);
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370 if (!sg.sequences.contains(seq))
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375 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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376 if (sg.sequences.contains(temp))
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381 viewport.alignment.getSequences().setElementAt(temp, i);
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382 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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387 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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389 SequenceI seq = viewport.alignment.getSequenceAt(i);
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390 if (!sg.sequences.contains(seq))
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395 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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396 if (sg.sequences.contains(temp))
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401 viewport.alignment.getSequences().setElementAt(temp, i);
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402 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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406 alignPanel.repaint();
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409 StringBuffer copiedSequences;
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410 protected void copy_actionPerformed(ActionEvent e)
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412 if (viewport.getSelectionGroup() == null)
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417 SequenceGroup sg = viewport.getSelectionGroup();
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418 copiedSequences = new StringBuffer();
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419 Hashtable orderedSeqs = new Hashtable();
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420 for (int i = 0; i < sg.getSize(); i++)
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422 SequenceI seq = sg.getSequenceAt(i);
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423 int index = viewport.alignment.findIndex(seq);
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424 orderedSeqs.put(index + "", seq);
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427 int index = 0, startRes, endRes;
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430 for (int i = 0; i < sg.getSize(); i++)
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432 SequenceI seq = null;
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434 while (seq == null)
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436 if (orderedSeqs.containsKey(index + ""))
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438 seq = (SequenceI) orderedSeqs.get(index + "");
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450 //Returns residue following index if gap
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451 startRes = seq.findPosition(sg.getStartRes());
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454 //Need to find the residue preceeding index if gap
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457 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
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459 ch = seq.getCharAt(j);
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460 if (!jalview.util.Comparison.isGap( (ch)))
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468 endRes += seq.getStart() -1;
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471 copiedSequences.append(seq.getName() + "\t" +
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474 seq.getSequence(sg.getStartRes(),
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475 sg.getEndRes() + 1) + "\n");
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480 protected void pasteNew_actionPerformed(ActionEvent e)
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485 protected void pasteThis_actionPerformed(ActionEvent e)
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487 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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488 HistoryItem.PASTE));
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492 void paste(boolean newAlignment)
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496 if (copiedSequences == null)
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501 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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502 Vector seqs = new Vector();
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503 while (st.hasMoreElements())
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505 String name = st.nextToken();
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506 int start = Integer.parseInt(st.nextToken());
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507 int end = Integer.parseInt(st.nextToken());
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508 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
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512 viewport.alignment.addSequence(sequence);
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516 seqs.addElement(sequence);
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522 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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523 for (int i = 0; i < seqs.size(); i++)
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525 newSeqs[i] = (SequenceI) seqs.elementAt(i);
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528 String newtitle = new String("Copied sequences");
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529 if (getTitle().startsWith("Copied sequences"))
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531 newtitle = getTitle();
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535 newtitle = newtitle.concat("- from " + getTitle());
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537 AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);
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539 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
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540 NEW_WINDOW_HEIGHT);
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544 viewport.setEndSeq(viewport.alignment.getHeight());
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545 viewport.alignment.getWidth();
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546 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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550 catch (Exception ex)
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551 {} // could be anything being pasted in here
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555 protected void cut_actionPerformed(ActionEvent e)
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557 copy_actionPerformed(null);
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558 delete_actionPerformed(null);
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561 protected void delete_actionPerformed(ActionEvent e)
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563 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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564 HistoryItem.HIDE));
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565 if (viewport.getSelectionGroup() == null)
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571 SequenceGroup sg = viewport.getSelectionGroup();
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572 boolean allSequences = false;
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573 if(sg.sequences.size()==viewport.alignment.getHeight())
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574 allSequences = true;
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576 for (int i = 0; i < sg.sequences.size(); i++)
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578 SequenceI seq = sg.getSequenceAt(i);
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579 int index = viewport.getAlignment().findIndex(seq);
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580 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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582 // If the cut affects all sequences, remove highlighted columns
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585 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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586 sg.getEndRes() + 1);
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590 if (seq.getSequence().length() < 1)
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592 viewport.getAlignment().deleteSequence(seq);
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596 viewport.getAlignment().getSequences().setElementAt(seq, index);
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600 viewport.setSelectionGroup(null);
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601 viewport.alignment.deleteGroup(sg);
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602 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
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603 if (viewport.getAlignment().getHeight() < 1)
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607 this.setVisible(false);
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609 catch (Exception ex)
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612 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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616 protected void deleteGroups_actionPerformed(ActionEvent e)
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618 viewport.alignment.deleteAllGroups();
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619 viewport.setSelectionGroup(null);
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621 alignPanel.repaint();
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624 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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626 SequenceGroup sg = new SequenceGroup();
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627 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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629 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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631 sg.setEndRes(viewport.alignment.getWidth()-1);
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632 viewport.setSelectionGroup(sg);
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633 alignPanel.repaint();
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634 PaintRefresher.Refresh(null, viewport.alignment);
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637 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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639 viewport.setSelectionGroup(null);
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640 viewport.getColumnSelection().clear();
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641 viewport.setSelectionGroup(null);
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642 alignPanel.repaint();
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643 PaintRefresher.Refresh(null, viewport.alignment);
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646 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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648 SequenceGroup sg = viewport.getSelectionGroup();
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649 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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651 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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654 PaintRefresher.Refresh(null, viewport.alignment);
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657 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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659 ColumnSelection colSel = viewport.getColumnSelection();
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660 if (colSel.size() > 0)
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662 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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663 HistoryItem.HIDE));
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664 int min = colSel.getMin();
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665 viewport.getAlignment().trimLeft(min);
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666 colSel.compensateForEdit(0, min);
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668 if (viewport.getSelectionGroup() != null)
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670 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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673 Vector groups = viewport.alignment.getGroups();
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674 for (int i = 0; i < groups.size(); i++)
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676 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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677 if (!sg.adjustForRemoveLeft(min))
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679 viewport.alignment.deleteGroup(sg);
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682 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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686 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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688 ColumnSelection colSel = viewport.getColumnSelection();
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689 if (colSel.size() > 0)
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691 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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692 HistoryItem.HIDE));
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693 int max = colSel.getMax();
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694 viewport.getAlignment().trimRight(max);
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695 if (viewport.getSelectionGroup() != null)
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697 viewport.getSelectionGroup().adjustForRemoveRight(max);
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700 Vector groups = viewport.alignment.getGroups();
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701 for (int i = 0; i < groups.size(); i++)
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703 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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704 if (!sg.adjustForRemoveRight(max))
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706 viewport.alignment.deleteGroup(sg);
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709 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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714 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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716 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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717 viewport.alignment,
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718 HistoryItem.HIDE));
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720 //This is to maintain viewport position on first residue
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721 //of first sequence
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722 SequenceI seq = viewport.alignment.getSequenceAt(0);
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723 int startRes = seq.findPosition(viewport.startRes);
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725 viewport.getAlignment().removeGaps();
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727 viewport.setStartRes(seq.findIndex(startRes)-1);
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729 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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732 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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734 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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735 HistoryItem.HIDE));
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737 //This is to maintain viewport position on first residue
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738 //of first sequence
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739 SequenceI seq = viewport.alignment.getSequenceAt(0);
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740 int startRes = seq.findPosition(viewport.startRes);
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747 int start=0, end = viewport.alignment.getWidth();
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749 if (viewport.getSelectionGroup() != null
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750 && viewport.getSelectionGroup().sequences != null
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751 && viewport.getSelectionGroup().sequences.size()>0)
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753 seqs = viewport.getSelectionGroup().sequences;
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754 start = viewport.getSelectionGroup().getStartRes();
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755 end = viewport.getSelectionGroup().getEndRes()+1;
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758 seqs = viewport.alignment.getSequences();
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760 for (int i = 0; i < seqs.size(); i++)
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762 current = (SequenceI) seqs.elementAt(i);
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763 jSize = current.getLength();
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765 // Removing a range is much quicker than removing gaps
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766 // one by one for long sequences
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768 int rangeStart=-1, rangeEnd=-1;
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772 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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789 current.deleteChars(rangeStart, rangeEnd);
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790 j-=rangeEnd-rangeStart;
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791 jSize-=rangeEnd-rangeStart;
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799 while (j < end && j < jSize);
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802 current.deleteChars(rangeStart, rangeEnd);
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805 viewport.setStartRes(seq.findIndex(startRes)-1);
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806 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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809 public void alignmentChanged()
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811 viewport.updateConsensus();
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812 viewport.updateConservation ();
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813 resetAllColourSchemes();
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814 if(alignPanel.overviewPanel!=null)
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815 alignPanel.overviewPanel.updateOverviewImage();
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816 alignPanel.repaint();
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819 void resetAllColourSchemes()
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821 ColourSchemeI cs = viewport.globalColourScheme;
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824 if (cs instanceof ClustalxColourScheme)
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826 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
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827 resetClustalX(viewport.alignment.getSequences(),
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828 viewport.alignment.getWidth());
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831 cs.setConsensus(viewport.vconsensus);
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832 if (cs.conservationApplied())
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834 Alignment al = (Alignment) viewport.alignment;
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835 Conservation c = new Conservation("All",
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836 ResidueProperties.propHash, 3,
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837 al.getSequences(), 0,
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838 al.getWidth() - 1);
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840 c.verdict(false, viewport.ConsPercGaps);
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842 cs.setConservation(c);
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846 int s, sSize = viewport.alignment.getGroups().size();
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847 for(s=0; s<sSize; s++)
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849 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
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850 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
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852 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
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854 sg.recalcConservation();
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860 public void findMenuItem_actionPerformed(ActionEvent e)
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862 new Finder(alignPanel);
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865 public void font_actionPerformed(ActionEvent e)
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867 new FontChooser(alignPanel);
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871 public void seqLimits_itemStateChanged(ItemEvent e)
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873 viewport.setShowJVSuffix(seqLimits.getState());
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874 alignPanel.fontChanged();
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875 alignPanel.repaint();
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879 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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881 viewport.setColourText(colourTextMenuItem.getState());
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882 alignPanel.repaint();
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885 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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887 viewport.setWrapAlignment(wrapMenuItem.getState());
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888 alignPanel.setWrapAlignment(wrapMenuItem.getState());
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889 scaleAbove.setEnabled(wrapMenuItem.getState());
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890 scaleLeft.setEnabled(wrapMenuItem.getState());
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891 scaleRight.setEnabled(wrapMenuItem.getState());
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892 alignPanel.repaint();
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895 protected void scaleAbove_actionPerformed(ActionEvent e)
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897 viewport.setScaleAboveWrapped(scaleAbove.getState());
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898 alignPanel.repaint();
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901 protected void scaleLeft_actionPerformed(ActionEvent e)
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903 viewport.setScaleLeftWrapped(scaleLeft.getState());
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904 alignPanel.repaint();
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907 protected void scaleRight_actionPerformed(ActionEvent e)
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909 viewport.setScaleRightWrapped(scaleRight.getState());
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910 alignPanel.repaint();
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913 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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915 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
916 alignPanel.repaint();
\r
919 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
921 viewport.setShowText(viewTextMenuItem.getState());
\r
922 alignPanel.repaint();
\r
925 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
927 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
928 alignPanel.repaint();
\r
931 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
933 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
934 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
937 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
939 if (alignPanel.overviewPanel != null)
\r
944 Frame frame = new Frame();
\r
945 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
946 frame.add(overview);
\r
947 // +50 must allow for applet frame window
\r
948 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
949 overview.preferredSize().width,
\r
950 overview.preferredSize().height + 50);
\r
953 frame.addWindowListener(new WindowAdapter()
\r
955 public void windowClosing(WindowEvent e)
\r
957 alignPanel.setOverviewPanel(null);
\r
961 alignPanel.setOverviewPanel(overview);
\r
965 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
967 changeColour(null);
\r
970 public void clustalColour_actionPerformed(ActionEvent e)
\r
972 abovePIDThreshold.setState(false);
\r
973 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
974 viewport.alignment.getWidth()));
\r
977 public void zappoColour_actionPerformed(ActionEvent e)
\r
979 changeColour(new ZappoColourScheme());
\r
982 public void taylorColour_actionPerformed(ActionEvent e)
\r
984 changeColour(new TaylorColourScheme());
\r
987 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
989 changeColour(new HydrophobicColourScheme());
\r
992 public void helixColour_actionPerformed(ActionEvent e)
\r
994 changeColour(new HelixColourScheme());
\r
997 public void strandColour_actionPerformed(ActionEvent e)
\r
999 changeColour(new StrandColourScheme());
\r
1002 public void turnColour_actionPerformed(ActionEvent e)
\r
1004 changeColour(new TurnColourScheme());
\r
1007 public void buriedColour_actionPerformed(ActionEvent e)
\r
1009 changeColour(new BuriedColourScheme());
\r
1012 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1014 changeColour(new NucleotideColourScheme());
\r
1017 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1019 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1022 void changeColour(ColourSchemeI cs)
\r
1024 int threshold = 0;
\r
1028 if (viewport.getAbovePIDThreshold())
\r
1030 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1032 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1034 viewport.setGlobalColourScheme(cs);
\r
1038 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1041 if (viewport.getConservationSelected())
\r
1044 Alignment al = (Alignment) viewport.alignment;
\r
1045 Conservation c = new Conservation("All",
\r
1046 ResidueProperties.propHash, 3,
\r
1047 al.getSequences(), 0,
\r
1048 al.getWidth() - 1);
\r
1051 c.verdict(false, viewport.ConsPercGaps);
\r
1053 cs.setConservation(c);
\r
1055 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1061 cs.setConservation(null);
\r
1064 cs.setConsensus(viewport.vconsensus);
\r
1067 viewport.setGlobalColourScheme(cs);
\r
1069 if (viewport.getColourAppliesToAllGroups())
\r
1071 Vector groups = viewport.alignment.getGroups();
\r
1072 for (int i = 0; i < groups.size(); i++)
\r
1074 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1081 if (cs instanceof ClustalxColourScheme)
\r
1083 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1089 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1091 catch (Exception ex)
\r
1093 ex.printStackTrace();
\r
1098 if (viewport.getAbovePIDThreshold()
\r
1099 || cs instanceof PIDColourScheme
\r
1100 || cs instanceof Blosum62ColourScheme)
\r
1102 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1103 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
1106 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1108 if (viewport.getConservationSelected())
\r
1110 Conservation c = new Conservation("Group",
\r
1111 ResidueProperties.propHash, 3,
\r
1113 viewport.alignment.getWidth() - 1);
\r
1115 c.verdict(false, viewport.ConsPercGaps);
\r
1116 sg.cs.setConservation(c);
\r
1120 sg.cs.setConservation(null);
\r
1121 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1128 if (alignPanel.getOverviewPanel() != null)
\r
1130 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1133 alignPanel.repaint();
\r
1138 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1140 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1142 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1144 SliderPanel.showPIDSlider();
\r
1148 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1150 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1152 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1154 SliderPanel.showConservationSlider();
\r
1158 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1160 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1162 viewport.setAbovePIDThreshold(false);
\r
1163 abovePIDThreshold.setState(false);
\r
1165 changeColour(viewport.getGlobalColourScheme());
\r
1167 modifyConservation_actionPerformed(null);
\r
1170 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1172 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1174 conservationMenuItem.setState(false);
\r
1175 viewport.setConservationSelected(false);
\r
1177 changeColour(viewport.getGlobalColourScheme());
\r
1179 modifyPID_actionPerformed(null);
\r
1182 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1184 new UserDefinedColours(alignPanel, null);
\r
1187 public void PIDColour_actionPerformed(ActionEvent e)
\r
1189 changeColour(new PIDColourScheme());
\r
1192 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1194 changeColour(new Blosum62ColourScheme());
\r
1197 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1199 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1200 HistoryItem.SORT));
\r
1201 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1202 viewport.getAlignment().getSequenceAt(0));
\r
1203 alignPanel.repaint();
\r
1206 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1208 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1209 HistoryItem.SORT));
\r
1210 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1211 alignPanel.repaint();
\r
1214 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1216 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1217 HistoryItem.SORT));
\r
1218 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1219 alignPanel.repaint();
\r
1223 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1225 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
1226 Frame frame = new Frame();
\r
1228 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
1233 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1235 if (viewport.getSelectionGroup().getSize() > 1)
\r
1237 Frame frame = new Frame();
\r
1238 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1239 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1243 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1245 //are the sequences aligned?
\r
1246 if (!viewport.alignment.isAligned())
\r
1248 SequenceI current;
\r
1249 int Width = viewport.getAlignment().getWidth();
\r
1251 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1254 current = viewport.getAlignment().getSequenceAt(i);
\r
1256 if (current.getLength() < Width)
\r
1258 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1261 alignPanel.repaint();
\r
1264 if ( (viewport.getSelectionGroup() != null &&
\r
1265 viewport.getSelectionGroup().getSize() < 4 &&
\r
1266 viewport.getSelectionGroup().getSize() > 0)
\r
1267 || viewport.getAlignment().getHeight() < 4)
\r
1274 new PCAPanel(viewport);
\r
1276 catch (java.lang.OutOfMemoryError ex)
\r
1282 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1284 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1287 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1289 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1292 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1294 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1297 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1299 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1302 void NewTreePanel(String type, String pwType, String title)
\r
1304 //are the sequences aligned?
\r
1305 if (!viewport.alignment.isAligned())
\r
1307 SequenceI current;
\r
1308 int Width = viewport.getAlignment().getWidth();
\r
1310 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1313 current = viewport.getAlignment().getSequenceAt(i);
\r
1315 if (current.getLength() < Width)
\r
1317 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1320 alignPanel.repaint();
\r
1324 final TreePanel tp;
\r
1325 if (viewport.getSelectionGroup() != null &&
\r
1326 viewport.getSelectionGroup().getSize() > 3)
\r
1328 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1330 0, viewport.alignment.getWidth());
\r
1334 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1335 type, pwType, 0, viewport.alignment.getWidth());
\r
1338 addTreeMenuItem(tp, title);
\r
1340 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1343 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1345 final MenuItem item = new MenuItem(title);
\r
1346 sortByTreeMenu.add(item);
\r
1347 item.addActionListener(new java.awt.event.ActionListener()
\r
1349 public void actionPerformed(ActionEvent e)
\r
1351 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1352 HistoryItem.SORT));
\r
1353 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1354 alignPanel.repaint();
\r
1358 treePanel.addWindowListener(new WindowAdapter()
\r
1360 public void windowClosing(WindowEvent e)
\r
1362 sortByTreeMenu.remove(item);
\r
1367 protected void documentation_actionPerformed(ActionEvent e)
\r
1369 showURL("http://www.jalview.org/help.html");
\r
1372 protected void about_actionPerformed(ActionEvent e)
\r
1375 class AboutPanel extends Canvas
\r
1378 public AboutPanel(String version)
\r
1379 { this.version = version; }
\r
1381 public void paint(Graphics g)
\r
1383 g.setColor(Color.white);
\r
1384 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1385 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1386 FontMetrics fm = g.getFontMetrics();
\r
1387 int fh = fm.getHeight();
\r
1389 g.setColor(Color.black);
\r
1390 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1391 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1392 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1393 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1395 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1398 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1400 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1401 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1403 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1407 String version = "test";
\r
1408 java.net.URL url = getClass().getResource("/.build_properties");
\r
1413 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1414 url.openStream()));
\r
1416 while ( (line = reader.readLine()) != null)
\r
1418 if (line.indexOf("VERSION") > -1)
\r
1420 version = line.substring(line.indexOf("=") + 1);
\r
1424 catch (Exception ex)
\r
1426 ex.printStackTrace();
\r
1431 Frame frame = new Frame();
\r
1432 frame.add(new AboutPanel(version));
\r
1433 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1438 * Displays the given URL in a new browser window
\r
1440 * @param url URL to display in browser window.
\r
1441 * <br>New window will be named "HELP_WINDOW"
\r
1443 public void showURL(String url)
\r
1445 showURL(url, "HELP");
\r
1448 public void showURL(String url, String target)
\r
1450 if (applet == null)
\r
1452 System.out.println("Not running as applet - no browser available.");
\r
1458 applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1461 catch (Exception ex)
\r
1463 ex.printStackTrace();
\r
1469 //////////////////////////////////////////////////////////////////////////////////
\r
1470 //JBuilder Graphics here
\r
1472 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1473 protected Menu fileMenu = new Menu();
\r
1474 protected MenuItem closeMenuItem = new MenuItem();
\r
1475 protected Menu editMenu = new Menu();
\r
1476 protected Menu viewMenu = new Menu();
\r
1477 protected Menu colourMenu = new Menu();
\r
1478 protected Menu calculateMenu = new Menu();
\r
1479 protected MenuItem selectAllSequenceMenuItem = new MenuItem();
\r
1480 protected MenuItem deselectAllSequenceMenuItem = new MenuItem();
\r
1481 protected MenuItem invertSequenceMenuItem = new MenuItem();
\r
1482 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1483 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1484 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1485 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1486 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1487 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1488 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1489 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1490 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1491 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1492 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1493 protected MenuItem PCAMenuItem = new MenuItem();
\r
1494 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1495 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1496 BorderLayout borderLayout1 = new BorderLayout();
\r
1497 public Label statusBar = new Label();
\r
1498 protected Menu outputTextboxMenu = new Menu();
\r
1499 protected MenuItem clustalColour = new MenuItem();
\r
1500 protected MenuItem zappoColour = new MenuItem();
\r
1501 protected MenuItem taylorColour = new MenuItem();
\r
1502 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1503 protected MenuItem helixColour = new MenuItem();
\r
1504 protected MenuItem strandColour = new MenuItem();
\r
1505 protected MenuItem turnColour = new MenuItem();
\r
1506 protected MenuItem buriedColour = new MenuItem();
\r
1507 protected MenuItem userDefinedColour = new MenuItem();
\r
1508 protected MenuItem PIDColour = new MenuItem();
\r
1509 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1510 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1511 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1512 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1513 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1514 MenuItem overviewMenuItem = new MenuItem();
\r
1515 protected MenuItem undoMenuItem = new MenuItem();
\r
1516 protected MenuItem redoMenuItem = new MenuItem();
\r
1517 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1518 MenuItem noColourmenuItem = new MenuItem();
\r
1519 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1520 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1521 MenuItem findMenuItem = new MenuItem();
\r
1522 Menu searchMenu = new Menu();
\r
1523 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1524 protected MenuItem nucleotideColour = new MenuItem();
\r
1525 MenuItem deleteGroups = new MenuItem();
\r
1526 MenuItem delete = new MenuItem();
\r
1527 MenuItem copy = new MenuItem();
\r
1528 MenuItem cut = new MenuItem();
\r
1529 Menu Menu1 = new Menu();
\r
1530 MenuItem pasteNew = new MenuItem();
\r
1531 MenuItem pasteThis = new MenuItem();
\r
1532 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
1533 protected MenuItem font = new MenuItem();
\r
1534 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
1535 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
1536 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
1537 MenuItem modifyPID = new MenuItem();
\r
1538 MenuItem modifyConservation = new MenuItem();
\r
1539 protected Menu sortByTreeMenu = new Menu();
\r
1540 Menu sort = new Menu();
\r
1541 Menu calculate = new Menu();
\r
1542 MenuItem inputText = new MenuItem();
\r
1543 Menu helpMenu = new Menu();
\r
1544 MenuItem documentation = new MenuItem();
\r
1545 MenuItem about = new MenuItem();
\r
1546 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
1548 private void jbInit() throws Exception {
\r
1550 setMenuBar(alignFrameMenuBar);
\r
1554 // dynamically fill save as menu with available formats
\r
1555 for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)
\r
1558 item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
\r
1561 item.addActionListener(new java.awt.event.ActionListener()
\r
1563 public void actionPerformed(ActionEvent e)
\r
1565 outputText_actionPerformed(e);
\r
1569 outputTextboxMenu.add(item);
\r
1573 fileMenu.setLabel("File");
\r
1574 closeMenuItem.setLabel("Close");
\r
1575 closeMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1576 public void actionPerformed(ActionEvent e) {
\r
1577 closeMenuItem_actionPerformed(e);
\r
1580 editMenu.setLabel("Edit");
\r
1581 viewMenu.setLabel("View");
\r
1582 colourMenu.setLabel("Colour");
\r
1583 calculateMenu.setLabel("Calculate");
\r
1584 selectAllSequenceMenuItem.setLabel("Select all");
\r
1585 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1586 public void actionPerformed(ActionEvent e) {
\r
1587 selectAllSequenceMenuItem_actionPerformed(e);
\r
1590 deselectAllSequenceMenuItem.setLabel("Deselect All");
\r
1591 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1592 public void actionPerformed(ActionEvent e) {
\r
1593 deselectAllSequenceMenuItem_actionPerformed(e);
\r
1596 invertSequenceMenuItem.setLabel("Invert Selection");
\r
1597 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1598 public void actionPerformed(ActionEvent e) {
\r
1599 invertSequenceMenuItem_actionPerformed(e);
\r
1602 remove2LeftMenuItem.setLabel("Remove Left");
\r
1603 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1604 public void actionPerformed(ActionEvent e) {
\r
1605 remove2LeftMenuItem_actionPerformed(e);
\r
1608 remove2RightMenuItem.setLabel("Remove Right");
\r
1609 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1610 public void actionPerformed(ActionEvent e) {
\r
1611 remove2RightMenuItem_actionPerformed(e);
\r
1614 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
1615 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1616 public void actionPerformed(ActionEvent e) {
\r
1617 removeGappedColumnMenuItem_actionPerformed(e);
\r
1620 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
1621 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1622 public void actionPerformed(ActionEvent e) {
\r
1623 removeAllGapsMenuItem_actionPerformed(e);
\r
1626 viewBoxesMenuItem.setLabel("Boxes");
\r
1627 viewBoxesMenuItem.setState(true);
\r
1628 viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1629 public void itemStateChanged(ItemEvent e) {
\r
1630 viewBoxesMenuItem_actionPerformed(null);
\r
1633 viewTextMenuItem.setLabel("Text");
\r
1634 viewTextMenuItem.setState(true);
\r
1635 viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1636 public void itemStateChanged(ItemEvent e) {
\r
1637 viewTextMenuItem_actionPerformed(null);
\r
1640 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
1641 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1642 public void actionPerformed(ActionEvent e) {
\r
1643 sortPairwiseMenuItem_actionPerformed(e);
\r
1646 sortIDMenuItem.setLabel("by ID");
\r
1647 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1648 public void actionPerformed(ActionEvent e) {
\r
1649 sortIDMenuItem_actionPerformed(e);
\r
1652 sortGroupMenuItem.setLabel("by Group");
\r
1653 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1654 public void actionPerformed(ActionEvent e) {
\r
1655 sortGroupMenuItem_actionPerformed(e);
\r
1658 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
1659 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1660 public void actionPerformed(ActionEvent e) {
\r
1661 removeRedundancyMenuItem_actionPerformed(e);
\r
1664 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
1665 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1666 public void actionPerformed(ActionEvent e) {
\r
1667 pairwiseAlignmentMenuItem_actionPerformed(e);
\r
1670 PCAMenuItem.setLabel("Principal Component Analysis");
\r
1671 PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1672 public void actionPerformed(ActionEvent e) {
\r
1673 PCAMenuItem_actionPerformed(e);
\r
1676 averageDistanceTreeMenuItem.setLabel(
\r
1677 "Average Distance Using % Identity");
\r
1678 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1679 public void actionPerformed(ActionEvent e) {
\r
1680 averageDistanceTreeMenuItem_actionPerformed(e);
\r
1683 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
1684 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1685 public void actionPerformed(ActionEvent e) {
\r
1686 neighbourTreeMenuItem_actionPerformed(e);
\r
1689 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1690 statusBar.setBackground(Color.white);
\r
1691 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1692 statusBar.setText("Status bar");
\r
1693 outputTextboxMenu.setLabel("Output to Textbox");
\r
1694 clustalColour.setLabel("Clustalx");
\r
1696 clustalColour.addActionListener(new java.awt.event.ActionListener() {
\r
1697 public void actionPerformed(ActionEvent e) {
\r
1698 clustalColour_actionPerformed(e);
\r
1701 zappoColour.setLabel("Zappo");
\r
1702 zappoColour.addActionListener(new java.awt.event.ActionListener() {
\r
1703 public void actionPerformed(ActionEvent e) {
\r
1704 zappoColour_actionPerformed(e);
\r
1707 taylorColour.setLabel("Taylor");
\r
1708 taylorColour.addActionListener(new java.awt.event.ActionListener() {
\r
1709 public void actionPerformed(ActionEvent e) {
\r
1710 taylorColour_actionPerformed(e);
\r
1713 hydrophobicityColour.setLabel("Hydrophobicity");
\r
1714 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {
\r
1715 public void actionPerformed(ActionEvent e) {
\r
1716 hydrophobicityColour_actionPerformed(e);
\r
1719 helixColour.setLabel("Helix Propensity");
\r
1720 helixColour.addActionListener(new java.awt.event.ActionListener() {
\r
1721 public void actionPerformed(ActionEvent e) {
\r
1722 helixColour_actionPerformed(e);
\r
1725 strandColour.setLabel("Strand Propensity");
\r
1726 strandColour.addActionListener(new java.awt.event.ActionListener() {
\r
1727 public void actionPerformed(ActionEvent e) {
\r
1728 strandColour_actionPerformed(e);
\r
1731 turnColour.setLabel("Turn Propensity");
\r
1732 turnColour.addActionListener(new java.awt.event.ActionListener() {
\r
1733 public void actionPerformed(ActionEvent e) {
\r
1734 turnColour_actionPerformed(e);
\r
1737 buriedColour.setLabel("Buried Index");
\r
1738 buriedColour.addActionListener(new java.awt.event.ActionListener() {
\r
1739 public void actionPerformed(ActionEvent e) {
\r
1740 buriedColour_actionPerformed(e);
\r
1743 userDefinedColour.setLabel("User Defined...");
\r
1744 userDefinedColour.addActionListener(new java.awt.event.ActionListener() {
\r
1745 public void actionPerformed(ActionEvent e) {
\r
1746 userDefinedColour_actionPerformed(e);
\r
1749 PIDColour.setLabel("Percentage Identity");
\r
1750 PIDColour.addActionListener(new java.awt.event.ActionListener() {
\r
1751 public void actionPerformed(ActionEvent e) {
\r
1752 PIDColour_actionPerformed(e);
\r
1755 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
1756 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {
\r
1757 public void actionPerformed(ActionEvent e) {
\r
1758 BLOSUM62Colour_actionPerformed(e);
\r
1761 avDistanceTreeBlosumMenuItem.setLabel(
\r
1762 "Average Distance Using BLOSUM62");
\r
1763 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1764 public void actionPerformed(ActionEvent e) {
\r
1765 avTreeBlosumMenuItem_actionPerformed(e);
\r
1768 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
1769 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1770 public void actionPerformed(ActionEvent e) {
\r
1771 njTreeBlosumMenuItem_actionPerformed(e);
\r
1774 annotationPanelMenuItem.setActionCommand("");
\r
1775 annotationPanelMenuItem.setState(true);
\r
1776 annotationPanelMenuItem.setLabel("Show Annotations");
\r
1777 annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1778 public void itemStateChanged(ItemEvent e) {
\r
1779 annotationPanelMenuItem_actionPerformed(null);
\r
1782 colourTextMenuItem.setLabel("Colour Text");
\r
1783 colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1784 public void itemStateChanged(ItemEvent e) {
\r
1785 colourTextMenuItem_actionPerformed(null);
\r
1788 overviewMenuItem.setLabel("Overview Window");
\r
1789 overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1790 public void actionPerformed(ActionEvent e) {
\r
1791 overviewMenuItem_actionPerformed(e);
\r
1794 undoMenuItem.setEnabled(false);
\r
1795 undoMenuItem.setLabel("Undo");
\r
1796 undoMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1797 public void actionPerformed(ActionEvent e) {
\r
1798 undoMenuItem_actionPerformed(e);
\r
1801 redoMenuItem.setEnabled(false);
\r
1802 redoMenuItem.setLabel("Redo");
\r
1803 redoMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1804 public void actionPerformed(ActionEvent e) {
\r
1805 redoMenuItem_actionPerformed(e);
\r
1808 conservationMenuItem.setLabel("by Conservation");
\r
1809 conservationMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1810 public void itemStateChanged(ItemEvent e) {
\r
1811 conservationMenuItem_actionPerformed(null);
\r
1814 noColourmenuItem.setLabel("None");
\r
1815 noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1816 public void actionPerformed(ActionEvent e) {
\r
1817 noColourmenuItem_actionPerformed(e);
\r
1820 wrapMenuItem.setLabel("Wrap");
\r
1821 wrapMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1822 public void itemStateChanged(ItemEvent e) {
\r
1823 wrapMenuItem_actionPerformed(null);
\r
1826 renderGapsMenuItem.setLabel("Show Gaps");
\r
1827 renderGapsMenuItem.setState(true);
\r
1828 renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1829 public void itemStateChanged(ItemEvent e) {
\r
1830 renderGapsMenuItem_actionPerformed(null);
\r
1833 findMenuItem.setLabel("Find...");
\r
1834 findMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1835 public void actionPerformed(ActionEvent e) {
\r
1836 findMenuItem_actionPerformed(e);
\r
1839 searchMenu.setLabel("Search");
\r
1841 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
1842 abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() {
\r
1843 public void itemStateChanged(ItemEvent e) {
\r
1844 abovePIDThreshold_actionPerformed(null);
\r
1847 nucleotideColour.setLabel("Nucleotide");
\r
1848 nucleotideColour.addActionListener(new java.awt.event.ActionListener() {
\r
1849 public void actionPerformed(ActionEvent e) {
\r
1850 nucleotideColour_actionPerformed(e);
\r
1853 deleteGroups.setLabel("Undefine Groups");
\r
1854 deleteGroups.addActionListener(new java.awt.event.ActionListener() {
\r
1855 public void actionPerformed(ActionEvent e) {
\r
1856 deleteGroups_actionPerformed(e);
\r
1859 copy.setLabel("Copy");
\r
1860 copy.addActionListener(new java.awt.event.ActionListener() {
\r
1861 public void actionPerformed(ActionEvent e) {
\r
1862 copy_actionPerformed(e);
\r
1865 cut.setLabel("Cut");
\r
1866 cut.addActionListener(new java.awt.event.ActionListener() {
\r
1867 public void actionPerformed(ActionEvent e) {
\r
1868 cut_actionPerformed(e);
\r
1871 delete.setLabel("Delete");
\r
1872 delete.addActionListener(new java.awt.event.ActionListener() {
\r
1873 public void actionPerformed(ActionEvent e) {
\r
1874 delete_actionPerformed(e);
\r
1877 Menu1.setLabel("Paste");
\r
1878 pasteNew.setLabel("To New Alignment");
\r
1879 pasteNew.addActionListener(new java.awt.event.ActionListener() {
\r
1880 public void actionPerformed(ActionEvent e) {
\r
1881 pasteNew_actionPerformed(e);
\r
1884 pasteThis.setLabel("Add To This Alignment");
\r
1885 pasteThis.addActionListener(new java.awt.event.ActionListener() {
\r
1886 public void actionPerformed(ActionEvent e) {
\r
1887 pasteThis_actionPerformed(e);
\r
1890 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
1891 applyToAllGroups.setState(true);
\r
1892 applyToAllGroups.addItemListener(new java.awt.event.ItemListener() {
\r
1893 public void itemStateChanged(ItemEvent e) {
\r
1894 applyToAllGroups_actionPerformed(null);
\r
1897 font.setLabel("Font...");
\r
1898 font.addActionListener(new java.awt.event.ActionListener() {
\r
1899 public void actionPerformed(ActionEvent e) {
\r
1900 font_actionPerformed(e);
\r
1903 scaleAbove.setLabel("Scale Above");
\r
1904 scaleAbove.setState(true);
\r
1905 scaleAbove.addItemListener(new java.awt.event.ItemListener() {
\r
1906 public void itemStateChanged(ItemEvent e) {
\r
1907 scaleAbove_actionPerformed(null);
\r
1910 scaleLeft.setEnabled(false);
\r
1911 scaleLeft.setState(true);
\r
1912 scaleLeft.setLabel("Scale Left");
\r
1913 scaleLeft.addItemListener(new java.awt.event.ItemListener() {
\r
1914 public void itemStateChanged(ItemEvent e) {
\r
1915 scaleLeft_actionPerformed(null);
\r
1918 scaleRight.setEnabled(false);
\r
1919 scaleRight.setState(true);
\r
1920 scaleRight.setLabel("Scale Right");
\r
1921 scaleRight.addItemListener(new java.awt.event.ItemListener() {
\r
1922 public void itemStateChanged(ItemEvent e) {
\r
1923 scaleRight_actionPerformed(null);
\r
1926 modifyPID.setLabel("Modify Identity Threshold...");
\r
1927 modifyPID.addActionListener(new java.awt.event.ActionListener() {
\r
1928 public void actionPerformed(ActionEvent e) {
\r
1929 modifyPID_actionPerformed(e);
\r
1932 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
1933 modifyConservation.addActionListener(new java.awt.event.ActionListener() {
\r
1934 public void actionPerformed(ActionEvent e) {
\r
1935 modifyConservation_actionPerformed(e);
\r
1938 sortByTreeMenu.setLabel("By Tree Order");
\r
1939 sort.setLabel("Sort");
\r
1940 calculate.setLabel("Calculate Tree");
\r
1941 inputText.setLabel("Input from textbox");
\r
1942 inputText.addActionListener(new java.awt.event.ActionListener() {
\r
1943 public void actionPerformed(ActionEvent e) {
\r
1944 inputText_actionPerformed(e);
\r
1948 helpMenu.setLabel("Help");
\r
1949 documentation.setLabel("Documentation");
\r
1950 documentation.addActionListener(new java.awt.event.ActionListener() {
\r
1951 public void actionPerformed(ActionEvent e) {
\r
1952 documentation_actionPerformed(e);
\r
1956 about.setLabel("About...");
\r
1957 about.addActionListener(new java.awt.event.ActionListener() {
\r
1958 public void actionPerformed(ActionEvent e) {
\r
1959 about_actionPerformed(e);
\r
1962 seqLimits.setState(true);
\r
1963 seqLimits.setLabel("Show Sequence Limits");
\r
1964 seqLimits.addItemListener(new ItemListener()
\r
1966 public void itemStateChanged(ItemEvent e)
\r
1968 seqLimits_itemStateChanged(e);
\r
1972 alignFrameMenuBar.add(fileMenu);
\r
1973 alignFrameMenuBar.add(editMenu);
\r
1974 alignFrameMenuBar.add(searchMenu);
\r
1975 alignFrameMenuBar.add(viewMenu);
\r
1976 alignFrameMenuBar.add(colourMenu);
\r
1977 alignFrameMenuBar.add(calculateMenu);
\r
1978 alignFrameMenuBar.add(helpMenu);
\r
1979 fileMenu.add(inputText);
\r
1980 fileMenu.add(outputTextboxMenu);
\r
1981 fileMenu.addSeparator();
\r
1982 fileMenu.add(closeMenuItem);
\r
1983 editMenu.add(undoMenuItem);
\r
1984 editMenu.add(redoMenuItem);
\r
1985 editMenu.add(cut);
\r
1986 editMenu.add(copy);
\r
1987 editMenu.add(Menu1);
\r
1988 editMenu.add(delete);
\r
1989 editMenu.addSeparator();
\r
1990 editMenu.add(selectAllSequenceMenuItem);
\r
1991 editMenu.add(deselectAllSequenceMenuItem);
\r
1992 editMenu.add(invertSequenceMenuItem);
\r
1993 editMenu.add(deleteGroups);
\r
1994 editMenu.addSeparator();
\r
1995 editMenu.add(remove2LeftMenuItem);
\r
1996 editMenu.add(remove2RightMenuItem);
\r
1997 editMenu.add(removeGappedColumnMenuItem);
\r
1998 editMenu.add(removeAllGapsMenuItem);
\r
1999 editMenu.add(removeRedundancyMenuItem);
\r
2000 searchMenu.add(findMenuItem);
\r
2001 viewMenu.add(font);
\r
2002 viewMenu.addSeparator();
\r
2003 viewMenu.add(seqLimits);
\r
2004 viewMenu.addSeparator();
\r
2005 viewMenu.add(wrapMenuItem);
\r
2006 viewMenu.add(scaleAbove);
\r
2007 viewMenu.add(scaleLeft);
\r
2008 viewMenu.add(scaleRight);
\r
2009 viewMenu.addSeparator();
\r
2010 viewMenu.add(viewBoxesMenuItem);
\r
2011 viewMenu.add(viewTextMenuItem);
\r
2012 viewMenu.add(colourTextMenuItem);
\r
2013 viewMenu.add(renderGapsMenuItem);
\r
2014 viewMenu.add(annotationPanelMenuItem);
\r
2015 viewMenu.addSeparator();
\r
2016 viewMenu.add(overviewMenuItem);
\r
2017 colourMenu.add(applyToAllGroups);
\r
2018 colourMenu.addSeparator();
\r
2019 colourMenu.add(noColourmenuItem);
\r
2020 colourMenu.add(clustalColour);
\r
2021 colourMenu.add(BLOSUM62Colour);
\r
2022 colourMenu.add(PIDColour);
\r
2023 colourMenu.add(zappoColour);
\r
2024 colourMenu.add(taylorColour);
\r
2025 colourMenu.add(hydrophobicityColour);
\r
2026 colourMenu.add(helixColour);
\r
2027 colourMenu.add(strandColour);
\r
2028 colourMenu.add(turnColour);
\r
2029 colourMenu.add(buriedColour);
\r
2030 colourMenu.add(nucleotideColour);
\r
2031 colourMenu.add(userDefinedColour);
\r
2032 colourMenu.addSeparator();
\r
2033 colourMenu.add(conservationMenuItem);
\r
2034 colourMenu.add(modifyConservation);
\r
2035 colourMenu.add(abovePIDThreshold);
\r
2036 colourMenu.add(modifyPID);
\r
2037 calculateMenu.add(sort);
\r
2038 calculateMenu.add(calculate);
\r
2039 calculateMenu.addSeparator();
\r
2040 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2041 calculateMenu.add(PCAMenuItem);
\r
2042 this.add(statusBar, BorderLayout.SOUTH);
\r
2043 Menu1.add(pasteNew);
\r
2044 Menu1.add(pasteThis);
\r
2045 sort.add(sortIDMenuItem);
\r
2046 sort.add(sortByTreeMenu);
\r
2047 sort.add(sortGroupMenuItem);
\r
2048 sort.add(sortPairwiseMenuItem);
\r
2049 calculate.add(averageDistanceTreeMenuItem);
\r
2050 calculate.add(neighbourTreeMenuItem);
\r
2051 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2052 calculate.add(njTreeBlosumMenuItem);
\r
2053 helpMenu.add(documentation);
\r
2054 helpMenu.add(about);
\r