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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148 public AlignViewport getAlignViewport()
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153 public SeqCanvas getSeqcanvas()
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155 return alignPanel.seqPanel.seqCanvas;
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162 * @param String DOCUMENT ME!
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165 public void parseFeaturesFile(String file)
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169 URL url = new URL(file);
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171 BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
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172 SequenceI seq = null;
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173 String line, type, desc, token;
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175 int index, start, end;
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176 StringTokenizer st;
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177 SequenceFeature sf;
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178 FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
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180 while ( (line = in.readLine()) != null)
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183 st = new StringTokenizer(line, "\t");
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184 if (st.countTokens() == 2)
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186 type = st.nextToken();
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187 UserColourScheme ucs = new UserColourScheme(st.nextToken());
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188 fr.setColour(type, ucs.findColour("A"));
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192 while (st.hasMoreElements())
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194 desc = st.nextToken();
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195 token = st.nextToken();
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196 if (!token.equals("ID_NOT_SPECIFIED"))
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198 index = viewport.alignment.findIndex(viewport.alignment.findName(
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204 index = Integer.parseInt(st.nextToken());
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207 start = Integer.parseInt(st.nextToken());
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208 end = Integer.parseInt(st.nextToken());
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210 seq = viewport.alignment.getSequenceAt(index);
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211 start = seq.findIndex(start) - 1;
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212 end = seq.findIndex(end) - 1;
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214 type = st.nextToken();
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216 if(fr.getColour(type)==null)
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218 // Probably the old style groups file
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219 UserColourScheme ucs = new UserColourScheme(type);
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220 fr.setColour(type, ucs.findColour("A"));
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223 sf = new SequenceFeature(type, desc, "", start, end);
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225 seq.addSequenceFeature(sf);
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229 viewport.showSequenceFeatures = true;
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231 alignPanel.repaint();
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234 catch (Exception ex)
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236 System.out.println("Error parsing groups file: " + ex);
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241 public void inputText_actionPerformed(ActionEvent e)
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243 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);
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244 Frame frame = new Frame();
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246 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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249 protected void outputText_actionPerformed(ActionEvent e)
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251 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);
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252 Frame frame = new Frame();
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254 jalview.bin.JalviewLite.addFrame(frame,
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255 "Alignment output - " + e.getActionCommand(),
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257 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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258 viewport.getAlignment().getSequences(),
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259 viewport.showJVSuffix));
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262 public void closeMenuItem_actionPerformed(ActionEvent e)
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264 PaintRefresher.components.remove(viewport.alignment);
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265 if(PaintRefresher.components.size()==0 && applet==null)
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269 Stack historyList = new Stack();
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270 Stack redoList = new Stack();
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272 void updateEditMenuBar()
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274 if (historyList.size() > 0)
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276 undoMenuItem.setEnabled(true);
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277 HistoryItem hi = (HistoryItem) historyList.peek();
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278 undoMenuItem.setLabel("Undo " + hi.getDescription());
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282 undoMenuItem.setEnabled(false);
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283 undoMenuItem.setLabel("Undo");
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286 if (redoList.size() > 0)
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288 redoMenuItem.setEnabled(true);
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289 HistoryItem hi = (HistoryItem) redoList.peek();
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290 redoMenuItem.setLabel("Redo " + hi.getDescription());
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294 redoMenuItem.setEnabled(false);
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295 redoMenuItem.setLabel("Redo");
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299 public void addHistoryItem(HistoryItem hi)
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301 historyList.push(hi);
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302 updateEditMenuBar();
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305 protected void undoMenuItem_actionPerformed(ActionEvent e)
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307 HistoryItem hi = (HistoryItem) historyList.pop();
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308 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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309 HistoryItem.HIDE));
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310 restoreHistoryItem(hi);
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311 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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314 protected void redoMenuItem_actionPerformed(ActionEvent e)
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316 HistoryItem hi = (HistoryItem) redoList.pop();
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317 restoreHistoryItem(hi);
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318 updateEditMenuBar();
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319 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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322 // used by undo and redo
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323 void restoreHistoryItem(HistoryItem hi)
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325 if (hi.getType() == HistoryItem.SORT)
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327 for (int i = 0; i < hi.getSequences().size(); i++)
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329 viewport.alignment.getSequences().setElementAt(hi.getSequences().
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335 for (int i = 0; i < hi.getSequences().size(); i++)
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337 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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338 if (restore.getLength() == 0)
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340 // log.System.out.println(hi.getHidden().elementAt(i));
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341 restore.setSequence(hi.getHidden().elementAt(i).toString());
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342 viewport.alignment.getSequences().insertElementAt(
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344 hi.getAlignIndex(i));
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348 restore.setSequence(hi.getHidden().elementAt(i).toString());
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351 if (hi.getType() == HistoryItem.PASTE)
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353 for (int i = viewport.alignment.getHeight() - 1;
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354 i > hi.getSequences().size() - 1; i--)
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356 viewport.alignment.deleteSequence(i);
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361 updateEditMenuBar();
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363 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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366 public void moveSelectedSequences(boolean up)
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368 SequenceGroup sg = viewport.getSelectionGroup();
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376 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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378 SequenceI seq = viewport.alignment.getSequenceAt(i);
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379 if (!sg.sequences.contains(seq))
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384 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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385 if (sg.sequences.contains(temp))
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390 viewport.alignment.getSequences().setElementAt(temp, i);
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391 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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396 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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398 SequenceI seq = viewport.alignment.getSequenceAt(i);
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399 if (!sg.sequences.contains(seq))
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404 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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405 if (sg.sequences.contains(temp))
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410 viewport.alignment.getSequences().setElementAt(temp, i);
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411 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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415 alignPanel.repaint();
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418 StringBuffer copiedSequences;
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419 protected void copy_actionPerformed(ActionEvent e)
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421 if (viewport.getSelectionGroup() == null)
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426 SequenceGroup sg = viewport.getSelectionGroup();
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427 copiedSequences = new StringBuffer();
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428 Hashtable orderedSeqs = new Hashtable();
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429 for (int i = 0; i < sg.getSize(); i++)
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431 SequenceI seq = sg.getSequenceAt(i);
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432 int index = viewport.alignment.findIndex(seq);
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433 orderedSeqs.put(index + "", seq);
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436 int index = 0, startRes, endRes;
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439 for (int i = 0; i < sg.getSize(); i++)
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441 SequenceI seq = null;
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443 while (seq == null)
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445 if (orderedSeqs.containsKey(index + ""))
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447 seq = (SequenceI) orderedSeqs.get(index + "");
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459 //Returns residue following index if gap
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460 startRes = seq.findPosition(sg.getStartRes());
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463 //Need to find the residue preceeding index if gap
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466 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
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468 ch = seq.getCharAt(j);
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469 if (!jalview.util.Comparison.isGap( (ch)))
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477 endRes += seq.getStart() -1;
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480 copiedSequences.append(seq.getName() + "\t" +
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483 seq.getSequence(sg.getStartRes(),
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484 sg.getEndRes() + 1) + "\n");
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489 protected void pasteNew_actionPerformed(ActionEvent e)
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494 protected void pasteThis_actionPerformed(ActionEvent e)
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496 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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497 HistoryItem.PASTE));
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501 void paste(boolean newAlignment)
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505 if (copiedSequences == null)
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510 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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511 Vector seqs = new Vector();
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512 while (st.hasMoreElements())
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514 String name = st.nextToken();
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515 int start = Integer.parseInt(st.nextToken());
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516 int end = Integer.parseInt(st.nextToken());
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517 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
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521 viewport.alignment.addSequence(sequence);
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525 seqs.addElement(sequence);
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531 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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532 for (int i = 0; i < seqs.size(); i++)
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534 newSeqs[i] = (SequenceI) seqs.elementAt(i);
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537 String newtitle = new String("Copied sequences");
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538 if (getTitle().startsWith("Copied sequences"))
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540 newtitle = getTitle();
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544 newtitle = newtitle.concat("- from " + getTitle());
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546 AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);
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548 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
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549 NEW_WINDOW_HEIGHT);
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553 viewport.setEndSeq(viewport.alignment.getHeight());
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554 viewport.alignment.getWidth();
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555 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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559 catch (Exception ex)
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560 {} // could be anything being pasted in here
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564 protected void cut_actionPerformed(ActionEvent e)
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566 copy_actionPerformed(null);
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567 delete_actionPerformed(null);
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570 protected void delete_actionPerformed(ActionEvent e)
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572 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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573 HistoryItem.HIDE));
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574 if (viewport.getSelectionGroup() == null)
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580 SequenceGroup sg = viewport.getSelectionGroup();
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581 boolean allSequences = false;
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582 if(sg.sequences.size()==viewport.alignment.getHeight())
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583 allSequences = true;
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585 for (int i = 0; i < sg.sequences.size(); i++)
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587 SequenceI seq = sg.getSequenceAt(i);
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588 int index = viewport.getAlignment().findIndex(seq);
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589 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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591 // If the cut affects all sequences, remove highlighted columns
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594 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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595 sg.getEndRes() + 1);
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599 if (seq.getSequence().length() < 1)
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601 viewport.getAlignment().deleteSequence(seq);
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605 viewport.getAlignment().getSequences().setElementAt(seq, index);
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609 viewport.setSelectionGroup(null);
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610 viewport.alignment.deleteGroup(sg);
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611 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
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612 if (viewport.getAlignment().getHeight() < 1)
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616 this.setVisible(false);
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618 catch (Exception ex)
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621 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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625 protected void deleteGroups_actionPerformed(ActionEvent e)
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627 viewport.alignment.deleteAllGroups();
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628 viewport.setSelectionGroup(null);
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630 alignPanel.repaint();
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633 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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635 SequenceGroup sg = new SequenceGroup();
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636 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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638 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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640 sg.setEndRes(viewport.alignment.getWidth()-1);
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641 viewport.setSelectionGroup(sg);
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642 alignPanel.repaint();
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643 PaintRefresher.Refresh(null, viewport.alignment);
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646 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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648 viewport.setSelectionGroup(null);
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649 viewport.getColumnSelection().clear();
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650 viewport.setSelectionGroup(null);
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651 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
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652 alignPanel.repaint();
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653 PaintRefresher.Refresh(null, viewport.alignment);
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656 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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658 SequenceGroup sg = viewport.getSelectionGroup();
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659 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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661 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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664 PaintRefresher.Refresh(null, viewport.alignment);
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667 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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669 ColumnSelection colSel = viewport.getColumnSelection();
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670 if (colSel.size() > 0)
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672 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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673 HistoryItem.HIDE));
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674 int min = colSel.getMin();
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675 viewport.getAlignment().trimLeft(min);
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676 colSel.compensateForEdit(0, min);
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678 if (viewport.getSelectionGroup() != null)
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680 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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683 Vector groups = viewport.alignment.getGroups();
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684 for (int i = 0; i < groups.size(); i++)
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686 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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687 if (!sg.adjustForRemoveLeft(min))
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689 viewport.alignment.deleteGroup(sg);
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692 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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696 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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698 ColumnSelection colSel = viewport.getColumnSelection();
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699 if (colSel.size() > 0)
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701 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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702 HistoryItem.HIDE));
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703 int max = colSel.getMax();
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704 viewport.getAlignment().trimRight(max);
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705 if (viewport.getSelectionGroup() != null)
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707 viewport.getSelectionGroup().adjustForRemoveRight(max);
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710 Vector groups = viewport.alignment.getGroups();
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711 for (int i = 0; i < groups.size(); i++)
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713 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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714 if (!sg.adjustForRemoveRight(max))
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716 viewport.alignment.deleteGroup(sg);
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719 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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724 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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726 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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727 viewport.alignment,
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728 HistoryItem.HIDE));
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730 //This is to maintain viewport position on first residue
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731 //of first sequence
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732 SequenceI seq = viewport.alignment.getSequenceAt(0);
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733 int startRes = seq.findPosition(viewport.startRes);
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735 viewport.getAlignment().removeGaps();
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737 viewport.setStartRes(seq.findIndex(startRes)-1);
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739 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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742 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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744 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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745 HistoryItem.HIDE));
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747 //This is to maintain viewport position on first residue
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748 //of first sequence
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749 SequenceI seq = viewport.alignment.getSequenceAt(0);
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750 int startRes = seq.findPosition(viewport.startRes);
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757 int start=0, end = viewport.alignment.getWidth();
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759 if (viewport.getSelectionGroup() != null
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760 && viewport.getSelectionGroup().sequences != null
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761 && viewport.getSelectionGroup().sequences.size()>0)
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763 seqs = viewport.getSelectionGroup().sequences;
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764 start = viewport.getSelectionGroup().getStartRes();
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765 end = viewport.getSelectionGroup().getEndRes()+1;
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768 seqs = viewport.alignment.getSequences();
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770 for (int i = 0; i < seqs.size(); i++)
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772 current = (SequenceI) seqs.elementAt(i);
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773 jSize = current.getLength();
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775 // Removing a range is much quicker than removing gaps
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776 // one by one for long sequences
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778 int rangeStart=-1, rangeEnd=-1;
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782 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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799 current.deleteChars(rangeStart, rangeEnd);
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800 j-=rangeEnd-rangeStart;
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801 jSize-=rangeEnd-rangeStart;
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809 while (j < end && j < jSize);
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812 current.deleteChars(rangeStart, rangeEnd);
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815 viewport.setStartRes(seq.findIndex(startRes)-1);
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816 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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819 public void alignmentChanged()
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821 viewport.updateConsensus();
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822 viewport.updateConservation ();
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823 resetAllColourSchemes();
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824 if(alignPanel.overviewPanel!=null)
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825 alignPanel.overviewPanel.updateOverviewImage();
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826 alignPanel.repaint();
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829 void resetAllColourSchemes()
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831 ColourSchemeI cs = viewport.globalColourScheme;
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834 if (cs instanceof ClustalxColourScheme)
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836 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
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837 resetClustalX(viewport.alignment.getSequences(),
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838 viewport.alignment.getWidth());
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841 cs.setConsensus(viewport.vconsensus);
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842 if (cs.conservationApplied())
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844 Alignment al = (Alignment) viewport.alignment;
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845 Conservation c = new Conservation("All",
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846 ResidueProperties.propHash, 3,
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847 al.getSequences(), 0,
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848 al.getWidth() - 1);
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850 c.verdict(false, viewport.ConsPercGaps);
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852 cs.setConservation(c);
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856 int s, sSize = viewport.alignment.getGroups().size();
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857 for(s=0; s<sSize; s++)
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859 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
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860 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
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862 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
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864 sg.recalcConservation();
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870 public void findMenuItem_actionPerformed(ActionEvent e)
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872 new Finder(alignPanel);
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875 public void font_actionPerformed(ActionEvent e)
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877 new FontChooser(alignPanel);
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881 public void seqLimits_itemStateChanged(ItemEvent e)
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883 viewport.setShowJVSuffix(seqLimits.getState());
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884 alignPanel.fontChanged();
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885 alignPanel.repaint();
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889 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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891 viewport.setColourText(colourTextMenuItem.getState());
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892 alignPanel.repaint();
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895 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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897 viewport.setWrapAlignment(wrapMenuItem.getState());
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898 alignPanel.setWrapAlignment(wrapMenuItem.getState());
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899 scaleAbove.setEnabled(wrapMenuItem.getState());
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900 scaleLeft.setEnabled(wrapMenuItem.getState());
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901 scaleRight.setEnabled(wrapMenuItem.getState());
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902 alignPanel.repaint();
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905 protected void scaleAbove_actionPerformed(ActionEvent e)
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907 viewport.setScaleAboveWrapped(scaleAbove.getState());
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908 alignPanel.repaint();
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911 protected void scaleLeft_actionPerformed(ActionEvent e)
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913 viewport.setScaleLeftWrapped(scaleLeft.getState());
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914 alignPanel.repaint();
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917 protected void scaleRight_actionPerformed(ActionEvent e)
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919 viewport.setScaleRightWrapped(scaleRight.getState());
\r
920 alignPanel.repaint();
\r
923 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
925 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
926 alignPanel.repaint();
\r
929 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
931 viewport.setShowText(viewTextMenuItem.getState());
\r
932 alignPanel.repaint();
\r
935 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
937 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
938 alignPanel.repaint();
\r
941 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
943 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
944 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
947 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
949 if (alignPanel.overviewPanel != null)
\r
954 Frame frame = new Frame();
\r
955 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
956 frame.add(overview);
\r
957 // +50 must allow for applet frame window
\r
958 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
959 overview.preferredSize().width,
\r
960 overview.preferredSize().height + 50);
\r
963 frame.addWindowListener(new WindowAdapter()
\r
965 public void windowClosing(WindowEvent e)
\r
967 alignPanel.setOverviewPanel(null);
\r
971 alignPanel.setOverviewPanel(overview);
\r
975 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
977 changeColour(null);
\r
980 public void clustalColour_actionPerformed(ActionEvent e)
\r
982 abovePIDThreshold.setState(false);
\r
983 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
984 viewport.alignment.getWidth()));
\r
987 public void zappoColour_actionPerformed(ActionEvent e)
\r
989 changeColour(new ZappoColourScheme());
\r
992 public void taylorColour_actionPerformed(ActionEvent e)
\r
994 changeColour(new TaylorColourScheme());
\r
997 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
999 changeColour(new HydrophobicColourScheme());
\r
1002 public void helixColour_actionPerformed(ActionEvent e)
\r
1004 changeColour(new HelixColourScheme());
\r
1007 public void strandColour_actionPerformed(ActionEvent e)
\r
1009 changeColour(new StrandColourScheme());
\r
1012 public void turnColour_actionPerformed(ActionEvent e)
\r
1014 changeColour(new TurnColourScheme());
\r
1017 public void buriedColour_actionPerformed(ActionEvent e)
\r
1019 changeColour(new BuriedColourScheme());
\r
1022 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1024 changeColour(new NucleotideColourScheme());
\r
1027 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1029 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1032 void changeColour(ColourSchemeI cs)
\r
1034 int threshold = 0;
\r
1038 if (viewport.getAbovePIDThreshold())
\r
1040 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1042 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1044 viewport.setGlobalColourScheme(cs);
\r
1048 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1051 if (viewport.getConservationSelected())
\r
1054 Alignment al = (Alignment) viewport.alignment;
\r
1055 Conservation c = new Conservation("All",
\r
1056 ResidueProperties.propHash, 3,
\r
1057 al.getSequences(), 0,
\r
1058 al.getWidth() - 1);
\r
1061 c.verdict(false, viewport.ConsPercGaps);
\r
1063 cs.setConservation(c);
\r
1065 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1071 cs.setConservation(null);
\r
1074 cs.setConsensus(viewport.vconsensus);
\r
1077 viewport.setGlobalColourScheme(cs);
\r
1079 if (viewport.getColourAppliesToAllGroups())
\r
1081 Vector groups = viewport.alignment.getGroups();
\r
1082 for (int i = 0; i < groups.size(); i++)
\r
1084 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1091 if (cs instanceof ClustalxColourScheme)
\r
1093 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1099 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1101 catch (Exception ex)
\r
1103 ex.printStackTrace();
\r
1108 if (viewport.getAbovePIDThreshold()
\r
1109 || cs instanceof PIDColourScheme
\r
1110 || cs instanceof Blosum62ColourScheme)
\r
1112 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1113 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
1116 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1118 if (viewport.getConservationSelected())
\r
1120 Conservation c = new Conservation("Group",
\r
1121 ResidueProperties.propHash, 3,
\r
1123 viewport.alignment.getWidth() - 1);
\r
1125 c.verdict(false, viewport.ConsPercGaps);
\r
1126 sg.cs.setConservation(c);
\r
1130 sg.cs.setConservation(null);
\r
1131 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1138 if (alignPanel.getOverviewPanel() != null)
\r
1140 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1143 alignPanel.repaint();
\r
1148 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1150 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1152 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1154 SliderPanel.showPIDSlider();
\r
1158 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1160 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1162 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1164 SliderPanel.showConservationSlider();
\r
1168 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1170 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1172 viewport.setAbovePIDThreshold(false);
\r
1173 abovePIDThreshold.setState(false);
\r
1175 changeColour(viewport.getGlobalColourScheme());
\r
1177 modifyConservation_actionPerformed(null);
\r
1180 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1182 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1184 conservationMenuItem.setState(false);
\r
1185 viewport.setConservationSelected(false);
\r
1187 changeColour(viewport.getGlobalColourScheme());
\r
1189 modifyPID_actionPerformed(null);
\r
1192 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1194 new UserDefinedColours(alignPanel, null);
\r
1197 public void PIDColour_actionPerformed(ActionEvent e)
\r
1199 changeColour(new PIDColourScheme());
\r
1202 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1204 changeColour(new Blosum62ColourScheme());
\r
1207 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1209 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1210 HistoryItem.SORT));
\r
1211 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1212 viewport.getAlignment().getSequenceAt(0));
\r
1213 alignPanel.repaint();
\r
1216 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1218 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1219 HistoryItem.SORT));
\r
1220 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1221 alignPanel.repaint();
\r
1224 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1226 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1227 HistoryItem.SORT));
\r
1228 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1229 alignPanel.repaint();
\r
1233 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1235 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
1236 Frame frame = new Frame();
\r
1238 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
1243 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1245 if (viewport.getSelectionGroup().getSize() > 1)
\r
1247 Frame frame = new Frame();
\r
1248 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1249 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1253 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1255 //are the sequences aligned?
\r
1256 if (!viewport.alignment.isAligned())
\r
1258 SequenceI current;
\r
1259 int Width = viewport.getAlignment().getWidth();
\r
1261 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1264 current = viewport.getAlignment().getSequenceAt(i);
\r
1266 if (current.getLength() < Width)
\r
1268 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1271 alignPanel.repaint();
\r
1274 if ( (viewport.getSelectionGroup() != null &&
\r
1275 viewport.getSelectionGroup().getSize() < 4 &&
\r
1276 viewport.getSelectionGroup().getSize() > 0)
\r
1277 || viewport.getAlignment().getHeight() < 4)
\r
1284 new PCAPanel(viewport);
\r
1286 catch (java.lang.OutOfMemoryError ex)
\r
1292 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1294 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1297 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1299 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1302 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1304 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1307 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1309 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1312 void NewTreePanel(String type, String pwType, String title)
\r
1314 //are the sequences aligned?
\r
1315 if (!viewport.alignment.isAligned())
\r
1317 SequenceI current;
\r
1318 int Width = viewport.getAlignment().getWidth();
\r
1320 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1323 current = viewport.getAlignment().getSequenceAt(i);
\r
1325 if (current.getLength() < Width)
\r
1327 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1330 alignPanel.repaint();
\r
1334 final TreePanel tp;
\r
1335 if (viewport.getSelectionGroup() != null &&
\r
1336 viewport.getSelectionGroup().getSize() > 3)
\r
1338 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1340 0, viewport.alignment.getWidth());
\r
1344 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1345 type, pwType, 0, viewport.alignment.getWidth());
\r
1348 addTreeMenuItem(tp, title);
\r
1350 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1353 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1355 final MenuItem item = new MenuItem(title);
\r
1356 sortByTreeMenu.add(item);
\r
1357 item.addActionListener(new java.awt.event.ActionListener()
\r
1359 public void actionPerformed(ActionEvent e)
\r
1361 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1362 HistoryItem.SORT));
\r
1363 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1364 alignPanel.repaint();
\r
1368 treePanel.addWindowListener(new WindowAdapter()
\r
1370 public void windowClosing(WindowEvent e)
\r
1372 sortByTreeMenu.remove(item);
\r
1377 protected void documentation_actionPerformed(ActionEvent e)
\r
1379 showURL("http://www.jalview.org/help.html");
\r
1382 protected void about_actionPerformed(ActionEvent e)
\r
1385 class AboutPanel extends Canvas
\r
1388 public AboutPanel(String version)
\r
1389 { this.version = version; }
\r
1391 public void paint(Graphics g)
\r
1393 g.setColor(Color.white);
\r
1394 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1395 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1396 FontMetrics fm = g.getFontMetrics();
\r
1397 int fh = fm.getHeight();
\r
1399 g.setColor(Color.black);
\r
1400 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1401 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1402 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1403 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1405 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1408 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1410 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1411 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1413 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1417 String version = "test";
\r
1418 java.net.URL url = getClass().getResource("/.build_properties");
\r
1423 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1424 url.openStream()));
\r
1426 while ( (line = reader.readLine()) != null)
\r
1428 if (line.indexOf("VERSION") > -1)
\r
1430 version = line.substring(line.indexOf("=") + 1);
\r
1434 catch (Exception ex)
\r
1436 ex.printStackTrace();
\r
1441 Frame frame = new Frame();
\r
1442 frame.add(new AboutPanel(version));
\r
1443 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1448 * Displays the given URL in a new browser window
\r
1450 * @param url URL to display in browser window.
\r
1451 * <br>New window will be named "HELP_WINDOW"
\r
1453 public void showURL(String url)
\r
1455 showURL(url, "HELP");
\r
1458 public void showURL(String url, String target)
\r
1460 if (applet == null)
\r
1462 System.out.println("Not running as applet - no browser available.");
\r
1468 applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1471 catch (Exception ex)
\r
1473 ex.printStackTrace();
\r
1479 //////////////////////////////////////////////////////////////////////////////////
\r
1480 //JBuilder Graphics here
\r
1482 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1483 protected Menu fileMenu = new Menu();
\r
1484 protected MenuItem closeMenuItem = new MenuItem();
\r
1485 protected Menu editMenu = new Menu();
\r
1486 protected Menu viewMenu = new Menu();
\r
1487 protected Menu colourMenu = new Menu();
\r
1488 protected Menu calculateMenu = new Menu();
\r
1489 protected MenuItem selectAllSequenceMenuItem = new MenuItem();
\r
1490 protected MenuItem deselectAllSequenceMenuItem = new MenuItem();
\r
1491 protected MenuItem invertSequenceMenuItem = new MenuItem();
\r
1492 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1493 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1494 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1495 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1496 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1497 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1498 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1499 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1500 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1501 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1502 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1503 protected MenuItem PCAMenuItem = new MenuItem();
\r
1504 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1505 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1506 BorderLayout borderLayout1 = new BorderLayout();
\r
1507 public Label statusBar = new Label();
\r
1508 protected Menu outputTextboxMenu = new Menu();
\r
1509 protected MenuItem clustalColour = new MenuItem();
\r
1510 protected MenuItem zappoColour = new MenuItem();
\r
1511 protected MenuItem taylorColour = new MenuItem();
\r
1512 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1513 protected MenuItem helixColour = new MenuItem();
\r
1514 protected MenuItem strandColour = new MenuItem();
\r
1515 protected MenuItem turnColour = new MenuItem();
\r
1516 protected MenuItem buriedColour = new MenuItem();
\r
1517 protected MenuItem userDefinedColour = new MenuItem();
\r
1518 protected MenuItem PIDColour = new MenuItem();
\r
1519 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1520 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1521 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1522 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1523 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1524 MenuItem overviewMenuItem = new MenuItem();
\r
1525 protected MenuItem undoMenuItem = new MenuItem();
\r
1526 protected MenuItem redoMenuItem = new MenuItem();
\r
1527 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1528 MenuItem noColourmenuItem = new MenuItem();
\r
1529 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1530 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1531 MenuItem findMenuItem = new MenuItem();
\r
1532 Menu searchMenu = new Menu();
\r
1533 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1534 protected MenuItem nucleotideColour = new MenuItem();
\r
1535 MenuItem deleteGroups = new MenuItem();
\r
1536 MenuItem delete = new MenuItem();
\r
1537 MenuItem copy = new MenuItem();
\r
1538 MenuItem cut = new MenuItem();
\r
1539 Menu Menu1 = new Menu();
\r
1540 MenuItem pasteNew = new MenuItem();
\r
1541 MenuItem pasteThis = new MenuItem();
\r
1542 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
1543 protected MenuItem font = new MenuItem();
\r
1544 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
1545 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
1546 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
1547 MenuItem modifyPID = new MenuItem();
\r
1548 MenuItem modifyConservation = new MenuItem();
\r
1549 protected Menu sortByTreeMenu = new Menu();
\r
1550 Menu sort = new Menu();
\r
1551 Menu calculate = new Menu();
\r
1552 MenuItem inputText = new MenuItem();
\r
1553 Menu helpMenu = new Menu();
\r
1554 MenuItem documentation = new MenuItem();
\r
1555 MenuItem about = new MenuItem();
\r
1556 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
1558 private void jbInit() throws Exception {
\r
1560 setMenuBar(alignFrameMenuBar);
\r
1564 // dynamically fill save as menu with available formats
\r
1565 for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)
\r
1568 item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
\r
1571 item.addActionListener(new java.awt.event.ActionListener()
\r
1573 public void actionPerformed(ActionEvent e)
\r
1575 outputText_actionPerformed(e);
\r
1579 outputTextboxMenu.add(item);
\r
1583 fileMenu.setLabel("File");
\r
1584 closeMenuItem.setLabel("Close");
\r
1585 closeMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1586 public void actionPerformed(ActionEvent e) {
\r
1587 closeMenuItem_actionPerformed(e);
\r
1590 editMenu.setLabel("Edit");
\r
1591 viewMenu.setLabel("View");
\r
1592 colourMenu.setLabel("Colour");
\r
1593 calculateMenu.setLabel("Calculate");
\r
1594 selectAllSequenceMenuItem.setLabel("Select all");
\r
1595 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1596 public void actionPerformed(ActionEvent e) {
\r
1597 selectAllSequenceMenuItem_actionPerformed(e);
\r
1600 deselectAllSequenceMenuItem.setLabel("Deselect All");
\r
1601 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1602 public void actionPerformed(ActionEvent e) {
\r
1603 deselectAllSequenceMenuItem_actionPerformed(e);
\r
1606 invertSequenceMenuItem.setLabel("Invert Selection");
\r
1607 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1608 public void actionPerformed(ActionEvent e) {
\r
1609 invertSequenceMenuItem_actionPerformed(e);
\r
1612 remove2LeftMenuItem.setLabel("Remove Left");
\r
1613 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1614 public void actionPerformed(ActionEvent e) {
\r
1615 remove2LeftMenuItem_actionPerformed(e);
\r
1618 remove2RightMenuItem.setLabel("Remove Right");
\r
1619 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1620 public void actionPerformed(ActionEvent e) {
\r
1621 remove2RightMenuItem_actionPerformed(e);
\r
1624 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
1625 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1626 public void actionPerformed(ActionEvent e) {
\r
1627 removeGappedColumnMenuItem_actionPerformed(e);
\r
1630 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
1631 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1632 public void actionPerformed(ActionEvent e) {
\r
1633 removeAllGapsMenuItem_actionPerformed(e);
\r
1636 viewBoxesMenuItem.setLabel("Boxes");
\r
1637 viewBoxesMenuItem.setState(true);
\r
1638 viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1639 public void itemStateChanged(ItemEvent e) {
\r
1640 viewBoxesMenuItem_actionPerformed(null);
\r
1643 viewTextMenuItem.setLabel("Text");
\r
1644 viewTextMenuItem.setState(true);
\r
1645 viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1646 public void itemStateChanged(ItemEvent e) {
\r
1647 viewTextMenuItem_actionPerformed(null);
\r
1650 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
1651 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1652 public void actionPerformed(ActionEvent e) {
\r
1653 sortPairwiseMenuItem_actionPerformed(e);
\r
1656 sortIDMenuItem.setLabel("by ID");
\r
1657 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1658 public void actionPerformed(ActionEvent e) {
\r
1659 sortIDMenuItem_actionPerformed(e);
\r
1662 sortGroupMenuItem.setLabel("by Group");
\r
1663 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1664 public void actionPerformed(ActionEvent e) {
\r
1665 sortGroupMenuItem_actionPerformed(e);
\r
1668 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
1669 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1670 public void actionPerformed(ActionEvent e) {
\r
1671 removeRedundancyMenuItem_actionPerformed(e);
\r
1674 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
1675 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1676 public void actionPerformed(ActionEvent e) {
\r
1677 pairwiseAlignmentMenuItem_actionPerformed(e);
\r
1680 PCAMenuItem.setLabel("Principal Component Analysis");
\r
1681 PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1682 public void actionPerformed(ActionEvent e) {
\r
1683 PCAMenuItem_actionPerformed(e);
\r
1686 averageDistanceTreeMenuItem.setLabel(
\r
1687 "Average Distance Using % Identity");
\r
1688 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1689 public void actionPerformed(ActionEvent e) {
\r
1690 averageDistanceTreeMenuItem_actionPerformed(e);
\r
1693 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
1694 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1695 public void actionPerformed(ActionEvent e) {
\r
1696 neighbourTreeMenuItem_actionPerformed(e);
\r
1699 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1700 statusBar.setBackground(Color.white);
\r
1701 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1702 statusBar.setText("Status bar");
\r
1703 outputTextboxMenu.setLabel("Output to Textbox");
\r
1704 clustalColour.setLabel("Clustalx");
\r
1706 clustalColour.addActionListener(new java.awt.event.ActionListener() {
\r
1707 public void actionPerformed(ActionEvent e) {
\r
1708 clustalColour_actionPerformed(e);
\r
1711 zappoColour.setLabel("Zappo");
\r
1712 zappoColour.addActionListener(new java.awt.event.ActionListener() {
\r
1713 public void actionPerformed(ActionEvent e) {
\r
1714 zappoColour_actionPerformed(e);
\r
1717 taylorColour.setLabel("Taylor");
\r
1718 taylorColour.addActionListener(new java.awt.event.ActionListener() {
\r
1719 public void actionPerformed(ActionEvent e) {
\r
1720 taylorColour_actionPerformed(e);
\r
1723 hydrophobicityColour.setLabel("Hydrophobicity");
\r
1724 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {
\r
1725 public void actionPerformed(ActionEvent e) {
\r
1726 hydrophobicityColour_actionPerformed(e);
\r
1729 helixColour.setLabel("Helix Propensity");
\r
1730 helixColour.addActionListener(new java.awt.event.ActionListener() {
\r
1731 public void actionPerformed(ActionEvent e) {
\r
1732 helixColour_actionPerformed(e);
\r
1735 strandColour.setLabel("Strand Propensity");
\r
1736 strandColour.addActionListener(new java.awt.event.ActionListener() {
\r
1737 public void actionPerformed(ActionEvent e) {
\r
1738 strandColour_actionPerformed(e);
\r
1741 turnColour.setLabel("Turn Propensity");
\r
1742 turnColour.addActionListener(new java.awt.event.ActionListener() {
\r
1743 public void actionPerformed(ActionEvent e) {
\r
1744 turnColour_actionPerformed(e);
\r
1747 buriedColour.setLabel("Buried Index");
\r
1748 buriedColour.addActionListener(new java.awt.event.ActionListener() {
\r
1749 public void actionPerformed(ActionEvent e) {
\r
1750 buriedColour_actionPerformed(e);
\r
1753 userDefinedColour.setLabel("User Defined...");
\r
1754 userDefinedColour.addActionListener(new java.awt.event.ActionListener() {
\r
1755 public void actionPerformed(ActionEvent e) {
\r
1756 userDefinedColour_actionPerformed(e);
\r
1759 PIDColour.setLabel("Percentage Identity");
\r
1760 PIDColour.addActionListener(new java.awt.event.ActionListener() {
\r
1761 public void actionPerformed(ActionEvent e) {
\r
1762 PIDColour_actionPerformed(e);
\r
1765 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
1766 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {
\r
1767 public void actionPerformed(ActionEvent e) {
\r
1768 BLOSUM62Colour_actionPerformed(e);
\r
1771 avDistanceTreeBlosumMenuItem.setLabel(
\r
1772 "Average Distance Using BLOSUM62");
\r
1773 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1774 public void actionPerformed(ActionEvent e) {
\r
1775 avTreeBlosumMenuItem_actionPerformed(e);
\r
1778 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
1779 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1780 public void actionPerformed(ActionEvent e) {
\r
1781 njTreeBlosumMenuItem_actionPerformed(e);
\r
1784 annotationPanelMenuItem.setActionCommand("");
\r
1785 annotationPanelMenuItem.setState(true);
\r
1786 annotationPanelMenuItem.setLabel("Show Annotations");
\r
1787 annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1788 public void itemStateChanged(ItemEvent e) {
\r
1789 annotationPanelMenuItem_actionPerformed(null);
\r
1792 colourTextMenuItem.setLabel("Colour Text");
\r
1793 colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1794 public void itemStateChanged(ItemEvent e) {
\r
1795 colourTextMenuItem_actionPerformed(null);
\r
1798 overviewMenuItem.setLabel("Overview Window");
\r
1799 overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1800 public void actionPerformed(ActionEvent e) {
\r
1801 overviewMenuItem_actionPerformed(e);
\r
1804 undoMenuItem.setEnabled(false);
\r
1805 undoMenuItem.setLabel("Undo");
\r
1806 undoMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1807 public void actionPerformed(ActionEvent e) {
\r
1808 undoMenuItem_actionPerformed(e);
\r
1811 redoMenuItem.setEnabled(false);
\r
1812 redoMenuItem.setLabel("Redo");
\r
1813 redoMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1814 public void actionPerformed(ActionEvent e) {
\r
1815 redoMenuItem_actionPerformed(e);
\r
1818 conservationMenuItem.setLabel("by Conservation");
\r
1819 conservationMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1820 public void itemStateChanged(ItemEvent e) {
\r
1821 conservationMenuItem_actionPerformed(null);
\r
1824 noColourmenuItem.setLabel("None");
\r
1825 noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1826 public void actionPerformed(ActionEvent e) {
\r
1827 noColourmenuItem_actionPerformed(e);
\r
1830 wrapMenuItem.setLabel("Wrap");
\r
1831 wrapMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1832 public void itemStateChanged(ItemEvent e) {
\r
1833 wrapMenuItem_actionPerformed(null);
\r
1836 renderGapsMenuItem.setLabel("Show Gaps");
\r
1837 renderGapsMenuItem.setState(true);
\r
1838 renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1839 public void itemStateChanged(ItemEvent e) {
\r
1840 renderGapsMenuItem_actionPerformed(null);
\r
1843 findMenuItem.setLabel("Find...");
\r
1844 findMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1845 public void actionPerformed(ActionEvent e) {
\r
1846 findMenuItem_actionPerformed(e);
\r
1849 searchMenu.setLabel("Search");
\r
1851 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
1852 abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() {
\r
1853 public void itemStateChanged(ItemEvent e) {
\r
1854 abovePIDThreshold_actionPerformed(null);
\r
1857 nucleotideColour.setLabel("Nucleotide");
\r
1858 nucleotideColour.addActionListener(new java.awt.event.ActionListener() {
\r
1859 public void actionPerformed(ActionEvent e) {
\r
1860 nucleotideColour_actionPerformed(e);
\r
1863 deleteGroups.setLabel("Undefine Groups");
\r
1864 deleteGroups.addActionListener(new java.awt.event.ActionListener() {
\r
1865 public void actionPerformed(ActionEvent e) {
\r
1866 deleteGroups_actionPerformed(e);
\r
1869 copy.setLabel("Copy");
\r
1870 copy.addActionListener(new java.awt.event.ActionListener() {
\r
1871 public void actionPerformed(ActionEvent e) {
\r
1872 copy_actionPerformed(e);
\r
1875 cut.setLabel("Cut");
\r
1876 cut.addActionListener(new java.awt.event.ActionListener() {
\r
1877 public void actionPerformed(ActionEvent e) {
\r
1878 cut_actionPerformed(e);
\r
1881 delete.setLabel("Delete");
\r
1882 delete.addActionListener(new java.awt.event.ActionListener() {
\r
1883 public void actionPerformed(ActionEvent e) {
\r
1884 delete_actionPerformed(e);
\r
1887 Menu1.setLabel("Paste");
\r
1888 pasteNew.setLabel("To New Alignment");
\r
1889 pasteNew.addActionListener(new java.awt.event.ActionListener() {
\r
1890 public void actionPerformed(ActionEvent e) {
\r
1891 pasteNew_actionPerformed(e);
\r
1894 pasteThis.setLabel("Add To This Alignment");
\r
1895 pasteThis.addActionListener(new java.awt.event.ActionListener() {
\r
1896 public void actionPerformed(ActionEvent e) {
\r
1897 pasteThis_actionPerformed(e);
\r
1900 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
1901 applyToAllGroups.setState(true);
\r
1902 applyToAllGroups.addItemListener(new java.awt.event.ItemListener() {
\r
1903 public void itemStateChanged(ItemEvent e) {
\r
1904 applyToAllGroups_actionPerformed(null);
\r
1907 font.setLabel("Font...");
\r
1908 font.addActionListener(new java.awt.event.ActionListener() {
\r
1909 public void actionPerformed(ActionEvent e) {
\r
1910 font_actionPerformed(e);
\r
1913 scaleAbove.setLabel("Scale Above");
\r
1914 scaleAbove.setState(true);
\r
1915 scaleAbove.addItemListener(new java.awt.event.ItemListener() {
\r
1916 public void itemStateChanged(ItemEvent e) {
\r
1917 scaleAbove_actionPerformed(null);
\r
1920 scaleLeft.setEnabled(false);
\r
1921 scaleLeft.setState(true);
\r
1922 scaleLeft.setLabel("Scale Left");
\r
1923 scaleLeft.addItemListener(new java.awt.event.ItemListener() {
\r
1924 public void itemStateChanged(ItemEvent e) {
\r
1925 scaleLeft_actionPerformed(null);
\r
1928 scaleRight.setEnabled(false);
\r
1929 scaleRight.setState(true);
\r
1930 scaleRight.setLabel("Scale Right");
\r
1931 scaleRight.addItemListener(new java.awt.event.ItemListener() {
\r
1932 public void itemStateChanged(ItemEvent e) {
\r
1933 scaleRight_actionPerformed(null);
\r
1936 modifyPID.setLabel("Modify Identity Threshold...");
\r
1937 modifyPID.addActionListener(new java.awt.event.ActionListener() {
\r
1938 public void actionPerformed(ActionEvent e) {
\r
1939 modifyPID_actionPerformed(e);
\r
1942 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
1943 modifyConservation.addActionListener(new java.awt.event.ActionListener() {
\r
1944 public void actionPerformed(ActionEvent e) {
\r
1945 modifyConservation_actionPerformed(e);
\r
1948 sortByTreeMenu.setLabel("By Tree Order");
\r
1949 sort.setLabel("Sort");
\r
1950 calculate.setLabel("Calculate Tree");
\r
1951 inputText.setLabel("Input from textbox");
\r
1952 inputText.addActionListener(new java.awt.event.ActionListener() {
\r
1953 public void actionPerformed(ActionEvent e) {
\r
1954 inputText_actionPerformed(e);
\r
1958 helpMenu.setLabel("Help");
\r
1959 documentation.setLabel("Documentation");
\r
1960 documentation.addActionListener(new java.awt.event.ActionListener() {
\r
1961 public void actionPerformed(ActionEvent e) {
\r
1962 documentation_actionPerformed(e);
\r
1966 about.setLabel("About...");
\r
1967 about.addActionListener(new java.awt.event.ActionListener() {
\r
1968 public void actionPerformed(ActionEvent e) {
\r
1969 about_actionPerformed(e);
\r
1972 seqLimits.setState(true);
\r
1973 seqLimits.setLabel("Show Sequence Limits");
\r
1974 seqLimits.addItemListener(new ItemListener()
\r
1976 public void itemStateChanged(ItemEvent e)
\r
1978 seqLimits_itemStateChanged(e);
\r
1982 alignFrameMenuBar.add(fileMenu);
\r
1983 alignFrameMenuBar.add(editMenu);
\r
1984 alignFrameMenuBar.add(searchMenu);
\r
1985 alignFrameMenuBar.add(viewMenu);
\r
1986 alignFrameMenuBar.add(colourMenu);
\r
1987 alignFrameMenuBar.add(calculateMenu);
\r
1988 alignFrameMenuBar.add(helpMenu);
\r
1989 fileMenu.add(inputText);
\r
1990 fileMenu.add(outputTextboxMenu);
\r
1991 fileMenu.addSeparator();
\r
1992 fileMenu.add(closeMenuItem);
\r
1993 editMenu.add(undoMenuItem);
\r
1994 editMenu.add(redoMenuItem);
\r
1995 editMenu.add(cut);
\r
1996 editMenu.add(copy);
\r
1997 editMenu.add(Menu1);
\r
1998 editMenu.add(delete);
\r
1999 editMenu.addSeparator();
\r
2000 editMenu.add(selectAllSequenceMenuItem);
\r
2001 editMenu.add(deselectAllSequenceMenuItem);
\r
2002 editMenu.add(invertSequenceMenuItem);
\r
2003 editMenu.add(deleteGroups);
\r
2004 editMenu.addSeparator();
\r
2005 editMenu.add(remove2LeftMenuItem);
\r
2006 editMenu.add(remove2RightMenuItem);
\r
2007 editMenu.add(removeGappedColumnMenuItem);
\r
2008 editMenu.add(removeAllGapsMenuItem);
\r
2009 editMenu.add(removeRedundancyMenuItem);
\r
2010 searchMenu.add(findMenuItem);
\r
2011 viewMenu.add(font);
\r
2012 viewMenu.addSeparator();
\r
2013 viewMenu.add(seqLimits);
\r
2014 viewMenu.addSeparator();
\r
2015 viewMenu.add(wrapMenuItem);
\r
2016 viewMenu.add(scaleAbove);
\r
2017 viewMenu.add(scaleLeft);
\r
2018 viewMenu.add(scaleRight);
\r
2019 viewMenu.addSeparator();
\r
2020 viewMenu.add(viewBoxesMenuItem);
\r
2021 viewMenu.add(viewTextMenuItem);
\r
2022 viewMenu.add(colourTextMenuItem);
\r
2023 viewMenu.add(renderGapsMenuItem);
\r
2024 viewMenu.add(annotationPanelMenuItem);
\r
2025 viewMenu.addSeparator();
\r
2026 viewMenu.add(overviewMenuItem);
\r
2027 colourMenu.add(applyToAllGroups);
\r
2028 colourMenu.addSeparator();
\r
2029 colourMenu.add(noColourmenuItem);
\r
2030 colourMenu.add(clustalColour);
\r
2031 colourMenu.add(BLOSUM62Colour);
\r
2032 colourMenu.add(PIDColour);
\r
2033 colourMenu.add(zappoColour);
\r
2034 colourMenu.add(taylorColour);
\r
2035 colourMenu.add(hydrophobicityColour);
\r
2036 colourMenu.add(helixColour);
\r
2037 colourMenu.add(strandColour);
\r
2038 colourMenu.add(turnColour);
\r
2039 colourMenu.add(buriedColour);
\r
2040 colourMenu.add(nucleotideColour);
\r
2041 colourMenu.add(userDefinedColour);
\r
2042 colourMenu.addSeparator();
\r
2043 colourMenu.add(conservationMenuItem);
\r
2044 colourMenu.add(modifyConservation);
\r
2045 colourMenu.add(abovePIDThreshold);
\r
2046 colourMenu.add(modifyPID);
\r
2047 calculateMenu.add(sort);
\r
2048 calculateMenu.add(calculate);
\r
2049 calculateMenu.addSeparator();
\r
2050 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2051 calculateMenu.add(PCAMenuItem);
\r
2052 this.add(statusBar, BorderLayout.SOUTH);
\r
2053 Menu1.add(pasteNew);
\r
2054 Menu1.add(pasteThis);
\r
2055 sort.add(sortIDMenuItem);
\r
2056 sort.add(sortByTreeMenu);
\r
2057 sort.add(sortGroupMenuItem);
\r
2058 sort.add(sortPairwiseMenuItem);
\r
2059 calculate.add(averageDistanceTreeMenuItem);
\r
2060 calculate.add(neighbourTreeMenuItem);
\r
2061 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2062 calculate.add(njTreeBlosumMenuItem);
\r
2063 helpMenu.add(documentation);
\r
2064 helpMenu.add(about);
\r