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.repaint();
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652 PaintRefresher.Refresh(null, viewport.alignment);
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655 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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657 SequenceGroup sg = viewport.getSelectionGroup();
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658 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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660 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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663 PaintRefresher.Refresh(null, viewport.alignment);
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666 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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668 ColumnSelection colSel = viewport.getColumnSelection();
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669 if (colSel.size() > 0)
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671 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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672 HistoryItem.HIDE));
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673 int min = colSel.getMin();
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674 viewport.getAlignment().trimLeft(min);
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675 colSel.compensateForEdit(0, min);
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677 if (viewport.getSelectionGroup() != null)
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679 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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682 Vector groups = viewport.alignment.getGroups();
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683 for (int i = 0; i < groups.size(); i++)
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685 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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686 if (!sg.adjustForRemoveLeft(min))
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688 viewport.alignment.deleteGroup(sg);
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691 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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695 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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697 ColumnSelection colSel = viewport.getColumnSelection();
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698 if (colSel.size() > 0)
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700 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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701 HistoryItem.HIDE));
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702 int max = colSel.getMax();
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703 viewport.getAlignment().trimRight(max);
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704 if (viewport.getSelectionGroup() != null)
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706 viewport.getSelectionGroup().adjustForRemoveRight(max);
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709 Vector groups = viewport.alignment.getGroups();
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710 for (int i = 0; i < groups.size(); i++)
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712 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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713 if (!sg.adjustForRemoveRight(max))
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715 viewport.alignment.deleteGroup(sg);
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718 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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723 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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725 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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726 viewport.alignment,
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727 HistoryItem.HIDE));
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729 //This is to maintain viewport position on first residue
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730 //of first sequence
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731 SequenceI seq = viewport.alignment.getSequenceAt(0);
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732 int startRes = seq.findPosition(viewport.startRes);
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734 viewport.getAlignment().removeGaps();
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736 viewport.setStartRes(seq.findIndex(startRes)-1);
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738 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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741 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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743 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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744 HistoryItem.HIDE));
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746 //This is to maintain viewport position on first residue
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747 //of first sequence
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748 SequenceI seq = viewport.alignment.getSequenceAt(0);
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749 int startRes = seq.findPosition(viewport.startRes);
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756 int start=0, end = viewport.alignment.getWidth();
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758 if (viewport.getSelectionGroup() != null
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759 && viewport.getSelectionGroup().sequences != null
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760 && viewport.getSelectionGroup().sequences.size()>0)
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762 seqs = viewport.getSelectionGroup().sequences;
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763 start = viewport.getSelectionGroup().getStartRes();
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764 end = viewport.getSelectionGroup().getEndRes()+1;
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767 seqs = viewport.alignment.getSequences();
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769 for (int i = 0; i < seqs.size(); i++)
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771 current = (SequenceI) seqs.elementAt(i);
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772 jSize = current.getLength();
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774 // Removing a range is much quicker than removing gaps
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775 // one by one for long sequences
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777 int rangeStart=-1, rangeEnd=-1;
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781 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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798 current.deleteChars(rangeStart, rangeEnd);
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799 j-=rangeEnd-rangeStart;
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800 jSize-=rangeEnd-rangeStart;
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808 while (j < end && j < jSize);
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811 current.deleteChars(rangeStart, rangeEnd);
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814 viewport.setStartRes(seq.findIndex(startRes)-1);
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815 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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818 public void alignmentChanged()
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820 viewport.updateConsensus();
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821 viewport.updateConservation ();
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822 resetAllColourSchemes();
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823 if(alignPanel.overviewPanel!=null)
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824 alignPanel.overviewPanel.updateOverviewImage();
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825 alignPanel.repaint();
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828 void resetAllColourSchemes()
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830 ColourSchemeI cs = viewport.globalColourScheme;
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833 if (cs instanceof ClustalxColourScheme)
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835 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
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836 resetClustalX(viewport.alignment.getSequences(),
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837 viewport.alignment.getWidth());
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840 cs.setConsensus(viewport.vconsensus);
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841 if (cs.conservationApplied())
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843 Alignment al = (Alignment) viewport.alignment;
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844 Conservation c = new Conservation("All",
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845 ResidueProperties.propHash, 3,
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846 al.getSequences(), 0,
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847 al.getWidth() - 1);
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849 c.verdict(false, viewport.ConsPercGaps);
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851 cs.setConservation(c);
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855 int s, sSize = viewport.alignment.getGroups().size();
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856 for(s=0; s<sSize; s++)
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858 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
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859 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
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861 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
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863 sg.recalcConservation();
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869 public void findMenuItem_actionPerformed(ActionEvent e)
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871 new Finder(alignPanel);
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874 public void font_actionPerformed(ActionEvent e)
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876 new FontChooser(alignPanel);
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880 public void seqLimits_itemStateChanged(ItemEvent e)
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882 viewport.setShowJVSuffix(seqLimits.getState());
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883 alignPanel.fontChanged();
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884 alignPanel.repaint();
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888 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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890 viewport.setColourText(colourTextMenuItem.getState());
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891 alignPanel.repaint();
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894 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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896 viewport.setWrapAlignment(wrapMenuItem.getState());
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897 alignPanel.setWrapAlignment(wrapMenuItem.getState());
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898 scaleAbove.setEnabled(wrapMenuItem.getState());
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899 scaleLeft.setEnabled(wrapMenuItem.getState());
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900 scaleRight.setEnabled(wrapMenuItem.getState());
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901 alignPanel.repaint();
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904 protected void scaleAbove_actionPerformed(ActionEvent e)
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906 viewport.setScaleAboveWrapped(scaleAbove.getState());
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907 alignPanel.repaint();
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910 protected void scaleLeft_actionPerformed(ActionEvent e)
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912 viewport.setScaleLeftWrapped(scaleLeft.getState());
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913 alignPanel.repaint();
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916 protected void scaleRight_actionPerformed(ActionEvent e)
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918 viewport.setScaleRightWrapped(scaleRight.getState());
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919 alignPanel.repaint();
\r
922 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
924 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
925 alignPanel.repaint();
\r
928 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
930 viewport.setShowText(viewTextMenuItem.getState());
\r
931 alignPanel.repaint();
\r
934 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
936 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
937 alignPanel.repaint();
\r
940 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
942 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
943 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
946 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
948 if (alignPanel.overviewPanel != null)
\r
953 Frame frame = new Frame();
\r
954 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
955 frame.add(overview);
\r
956 // +50 must allow for applet frame window
\r
957 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
958 overview.preferredSize().width,
\r
959 overview.preferredSize().height + 50);
\r
962 frame.addWindowListener(new WindowAdapter()
\r
964 public void windowClosing(WindowEvent e)
\r
966 alignPanel.setOverviewPanel(null);
\r
970 alignPanel.setOverviewPanel(overview);
\r
974 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
976 changeColour(null);
\r
979 public void clustalColour_actionPerformed(ActionEvent e)
\r
981 abovePIDThreshold.setState(false);
\r
982 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
983 viewport.alignment.getWidth()));
\r
986 public void zappoColour_actionPerformed(ActionEvent e)
\r
988 changeColour(new ZappoColourScheme());
\r
991 public void taylorColour_actionPerformed(ActionEvent e)
\r
993 changeColour(new TaylorColourScheme());
\r
996 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
998 changeColour(new HydrophobicColourScheme());
\r
1001 public void helixColour_actionPerformed(ActionEvent e)
\r
1003 changeColour(new HelixColourScheme());
\r
1006 public void strandColour_actionPerformed(ActionEvent e)
\r
1008 changeColour(new StrandColourScheme());
\r
1011 public void turnColour_actionPerformed(ActionEvent e)
\r
1013 changeColour(new TurnColourScheme());
\r
1016 public void buriedColour_actionPerformed(ActionEvent e)
\r
1018 changeColour(new BuriedColourScheme());
\r
1021 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1023 changeColour(new NucleotideColourScheme());
\r
1026 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1028 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1031 void changeColour(ColourSchemeI cs)
\r
1033 int threshold = 0;
\r
1037 if (viewport.getAbovePIDThreshold())
\r
1039 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1041 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1043 viewport.setGlobalColourScheme(cs);
\r
1047 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1050 if (viewport.getConservationSelected())
\r
1053 Alignment al = (Alignment) viewport.alignment;
\r
1054 Conservation c = new Conservation("All",
\r
1055 ResidueProperties.propHash, 3,
\r
1056 al.getSequences(), 0,
\r
1057 al.getWidth() - 1);
\r
1060 c.verdict(false, viewport.ConsPercGaps);
\r
1062 cs.setConservation(c);
\r
1064 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1070 cs.setConservation(null);
\r
1073 cs.setConsensus(viewport.vconsensus);
\r
1076 viewport.setGlobalColourScheme(cs);
\r
1078 if (viewport.getColourAppliesToAllGroups())
\r
1080 Vector groups = viewport.alignment.getGroups();
\r
1081 for (int i = 0; i < groups.size(); i++)
\r
1083 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1090 if (cs instanceof ClustalxColourScheme)
\r
1092 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1098 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1100 catch (Exception ex)
\r
1102 ex.printStackTrace();
\r
1107 if (viewport.getAbovePIDThreshold()
\r
1108 || cs instanceof PIDColourScheme
\r
1109 || cs instanceof Blosum62ColourScheme)
\r
1111 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1112 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
1115 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1117 if (viewport.getConservationSelected())
\r
1119 Conservation c = new Conservation("Group",
\r
1120 ResidueProperties.propHash, 3,
\r
1122 viewport.alignment.getWidth() - 1);
\r
1124 c.verdict(false, viewport.ConsPercGaps);
\r
1125 sg.cs.setConservation(c);
\r
1129 sg.cs.setConservation(null);
\r
1130 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1137 if (alignPanel.getOverviewPanel() != null)
\r
1139 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1142 alignPanel.repaint();
\r
1147 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1149 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1151 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1153 SliderPanel.showPIDSlider();
\r
1157 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1159 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1161 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1163 SliderPanel.showConservationSlider();
\r
1167 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1169 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1171 viewport.setAbovePIDThreshold(false);
\r
1172 abovePIDThreshold.setState(false);
\r
1174 changeColour(viewport.getGlobalColourScheme());
\r
1176 modifyConservation_actionPerformed(null);
\r
1179 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1181 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1183 conservationMenuItem.setState(false);
\r
1184 viewport.setConservationSelected(false);
\r
1186 changeColour(viewport.getGlobalColourScheme());
\r
1188 modifyPID_actionPerformed(null);
\r
1191 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1193 new UserDefinedColours(alignPanel, null);
\r
1196 public void PIDColour_actionPerformed(ActionEvent e)
\r
1198 changeColour(new PIDColourScheme());
\r
1201 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1203 changeColour(new Blosum62ColourScheme());
\r
1206 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1208 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1209 HistoryItem.SORT));
\r
1210 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1211 viewport.getAlignment().getSequenceAt(0));
\r
1212 alignPanel.repaint();
\r
1215 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1217 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1218 HistoryItem.SORT));
\r
1219 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1220 alignPanel.repaint();
\r
1223 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1225 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1226 HistoryItem.SORT));
\r
1227 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1228 alignPanel.repaint();
\r
1232 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1234 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
1235 Frame frame = new Frame();
\r
1237 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
1242 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1244 if (viewport.getSelectionGroup().getSize() > 1)
\r
1246 Frame frame = new Frame();
\r
1247 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1248 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1252 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1254 //are the sequences aligned?
\r
1255 if (!viewport.alignment.isAligned())
\r
1257 SequenceI current;
\r
1258 int Width = viewport.getAlignment().getWidth();
\r
1260 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1263 current = viewport.getAlignment().getSequenceAt(i);
\r
1265 if (current.getLength() < Width)
\r
1267 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1270 alignPanel.repaint();
\r
1273 if ( (viewport.getSelectionGroup() != null &&
\r
1274 viewport.getSelectionGroup().getSize() < 4 &&
\r
1275 viewport.getSelectionGroup().getSize() > 0)
\r
1276 || viewport.getAlignment().getHeight() < 4)
\r
1283 new PCAPanel(viewport);
\r
1285 catch (java.lang.OutOfMemoryError ex)
\r
1291 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1293 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1296 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1298 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1301 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1303 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1306 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1308 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1311 void NewTreePanel(String type, String pwType, String title)
\r
1313 //are the sequences aligned?
\r
1314 if (!viewport.alignment.isAligned())
\r
1316 SequenceI current;
\r
1317 int Width = viewport.getAlignment().getWidth();
\r
1319 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1322 current = viewport.getAlignment().getSequenceAt(i);
\r
1324 if (current.getLength() < Width)
\r
1326 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1329 alignPanel.repaint();
\r
1333 final TreePanel tp;
\r
1334 if (viewport.getSelectionGroup() != null &&
\r
1335 viewport.getSelectionGroup().getSize() > 3)
\r
1337 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1339 0, viewport.alignment.getWidth());
\r
1343 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1344 type, pwType, 0, viewport.alignment.getWidth());
\r
1347 addTreeMenuItem(tp, title);
\r
1349 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1352 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1354 final MenuItem item = new MenuItem(title);
\r
1355 sortByTreeMenu.add(item);
\r
1356 item.addActionListener(new java.awt.event.ActionListener()
\r
1358 public void actionPerformed(ActionEvent e)
\r
1360 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1361 HistoryItem.SORT));
\r
1362 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1363 alignPanel.repaint();
\r
1367 treePanel.addWindowListener(new WindowAdapter()
\r
1369 public void windowClosing(WindowEvent e)
\r
1371 sortByTreeMenu.remove(item);
\r
1376 protected void documentation_actionPerformed(ActionEvent e)
\r
1378 showURL("http://www.jalview.org/help.html");
\r
1381 protected void about_actionPerformed(ActionEvent e)
\r
1384 class AboutPanel extends Canvas
\r
1387 public AboutPanel(String version)
\r
1388 { this.version = version; }
\r
1390 public void paint(Graphics g)
\r
1392 g.setColor(Color.white);
\r
1393 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1394 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1395 FontMetrics fm = g.getFontMetrics();
\r
1396 int fh = fm.getHeight();
\r
1398 g.setColor(Color.black);
\r
1399 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1400 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1401 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1402 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1404 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1407 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1409 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1410 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1412 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1416 String version = "test";
\r
1417 java.net.URL url = getClass().getResource("/.build_properties");
\r
1422 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1423 url.openStream()));
\r
1425 while ( (line = reader.readLine()) != null)
\r
1427 if (line.indexOf("VERSION") > -1)
\r
1429 version = line.substring(line.indexOf("=") + 1);
\r
1433 catch (Exception ex)
\r
1435 ex.printStackTrace();
\r
1440 Frame frame = new Frame();
\r
1441 frame.add(new AboutPanel(version));
\r
1442 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1447 * Displays the given URL in a new browser window
\r
1449 * @param url URL to display in browser window.
\r
1450 * <br>New window will be named "HELP_WINDOW"
\r
1452 public void showURL(String url)
\r
1454 showURL(url, "HELP");
\r
1457 public void showURL(String url, String target)
\r
1459 if (applet == null)
\r
1461 System.out.println("Not running as applet - no browser available.");
\r
1467 applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1470 catch (Exception ex)
\r
1472 ex.printStackTrace();
\r
1478 //////////////////////////////////////////////////////////////////////////////////
\r
1479 //JBuilder Graphics here
\r
1481 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1482 protected Menu fileMenu = new Menu();
\r
1483 protected MenuItem closeMenuItem = new MenuItem();
\r
1484 protected Menu editMenu = new Menu();
\r
1485 protected Menu viewMenu = new Menu();
\r
1486 protected Menu colourMenu = new Menu();
\r
1487 protected Menu calculateMenu = new Menu();
\r
1488 protected MenuItem selectAllSequenceMenuItem = new MenuItem();
\r
1489 protected MenuItem deselectAllSequenceMenuItem = new MenuItem();
\r
1490 protected MenuItem invertSequenceMenuItem = new MenuItem();
\r
1491 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1492 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1493 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1494 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1495 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1496 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1497 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1498 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1499 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1500 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1501 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1502 protected MenuItem PCAMenuItem = new MenuItem();
\r
1503 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1504 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1505 BorderLayout borderLayout1 = new BorderLayout();
\r
1506 public Label statusBar = new Label();
\r
1507 protected Menu outputTextboxMenu = new Menu();
\r
1508 protected MenuItem clustalColour = new MenuItem();
\r
1509 protected MenuItem zappoColour = new MenuItem();
\r
1510 protected MenuItem taylorColour = new MenuItem();
\r
1511 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1512 protected MenuItem helixColour = new MenuItem();
\r
1513 protected MenuItem strandColour = new MenuItem();
\r
1514 protected MenuItem turnColour = new MenuItem();
\r
1515 protected MenuItem buriedColour = new MenuItem();
\r
1516 protected MenuItem userDefinedColour = new MenuItem();
\r
1517 protected MenuItem PIDColour = new MenuItem();
\r
1518 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1519 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1520 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1521 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1522 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1523 MenuItem overviewMenuItem = new MenuItem();
\r
1524 protected MenuItem undoMenuItem = new MenuItem();
\r
1525 protected MenuItem redoMenuItem = new MenuItem();
\r
1526 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1527 MenuItem noColourmenuItem = new MenuItem();
\r
1528 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1529 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1530 MenuItem findMenuItem = new MenuItem();
\r
1531 Menu searchMenu = new Menu();
\r
1532 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1533 protected MenuItem nucleotideColour = new MenuItem();
\r
1534 MenuItem deleteGroups = new MenuItem();
\r
1535 MenuItem delete = new MenuItem();
\r
1536 MenuItem copy = new MenuItem();
\r
1537 MenuItem cut = new MenuItem();
\r
1538 Menu Menu1 = new Menu();
\r
1539 MenuItem pasteNew = new MenuItem();
\r
1540 MenuItem pasteThis = new MenuItem();
\r
1541 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
1542 protected MenuItem font = new MenuItem();
\r
1543 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
1544 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
1545 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
1546 MenuItem modifyPID = new MenuItem();
\r
1547 MenuItem modifyConservation = new MenuItem();
\r
1548 protected Menu sortByTreeMenu = new Menu();
\r
1549 Menu sort = new Menu();
\r
1550 Menu calculate = new Menu();
\r
1551 MenuItem inputText = new MenuItem();
\r
1552 Menu helpMenu = new Menu();
\r
1553 MenuItem documentation = new MenuItem();
\r
1554 MenuItem about = new MenuItem();
\r
1555 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
1557 private void jbInit() throws Exception {
\r
1559 setMenuBar(alignFrameMenuBar);
\r
1563 // dynamically fill save as menu with available formats
\r
1564 for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)
\r
1567 item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
\r
1570 item.addActionListener(new java.awt.event.ActionListener()
\r
1572 public void actionPerformed(ActionEvent e)
\r
1574 outputText_actionPerformed(e);
\r
1578 outputTextboxMenu.add(item);
\r
1582 fileMenu.setLabel("File");
\r
1583 closeMenuItem.setLabel("Close");
\r
1584 closeMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1585 public void actionPerformed(ActionEvent e) {
\r
1586 closeMenuItem_actionPerformed(e);
\r
1589 editMenu.setLabel("Edit");
\r
1590 viewMenu.setLabel("View");
\r
1591 colourMenu.setLabel("Colour");
\r
1592 calculateMenu.setLabel("Calculate");
\r
1593 selectAllSequenceMenuItem.setLabel("Select all");
\r
1594 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1595 public void actionPerformed(ActionEvent e) {
\r
1596 selectAllSequenceMenuItem_actionPerformed(e);
\r
1599 deselectAllSequenceMenuItem.setLabel("Deselect All");
\r
1600 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1601 public void actionPerformed(ActionEvent e) {
\r
1602 deselectAllSequenceMenuItem_actionPerformed(e);
\r
1605 invertSequenceMenuItem.setLabel("Invert Selection");
\r
1606 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1607 public void actionPerformed(ActionEvent e) {
\r
1608 invertSequenceMenuItem_actionPerformed(e);
\r
1611 remove2LeftMenuItem.setLabel("Remove Left");
\r
1612 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1613 public void actionPerformed(ActionEvent e) {
\r
1614 remove2LeftMenuItem_actionPerformed(e);
\r
1617 remove2RightMenuItem.setLabel("Remove Right");
\r
1618 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1619 public void actionPerformed(ActionEvent e) {
\r
1620 remove2RightMenuItem_actionPerformed(e);
\r
1623 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
1624 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1625 public void actionPerformed(ActionEvent e) {
\r
1626 removeGappedColumnMenuItem_actionPerformed(e);
\r
1629 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
1630 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1631 public void actionPerformed(ActionEvent e) {
\r
1632 removeAllGapsMenuItem_actionPerformed(e);
\r
1635 viewBoxesMenuItem.setLabel("Boxes");
\r
1636 viewBoxesMenuItem.setState(true);
\r
1637 viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1638 public void itemStateChanged(ItemEvent e) {
\r
1639 viewBoxesMenuItem_actionPerformed(null);
\r
1642 viewTextMenuItem.setLabel("Text");
\r
1643 viewTextMenuItem.setState(true);
\r
1644 viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1645 public void itemStateChanged(ItemEvent e) {
\r
1646 viewTextMenuItem_actionPerformed(null);
\r
1649 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
1650 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1651 public void actionPerformed(ActionEvent e) {
\r
1652 sortPairwiseMenuItem_actionPerformed(e);
\r
1655 sortIDMenuItem.setLabel("by ID");
\r
1656 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1657 public void actionPerformed(ActionEvent e) {
\r
1658 sortIDMenuItem_actionPerformed(e);
\r
1661 sortGroupMenuItem.setLabel("by Group");
\r
1662 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1663 public void actionPerformed(ActionEvent e) {
\r
1664 sortGroupMenuItem_actionPerformed(e);
\r
1667 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
1668 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1669 public void actionPerformed(ActionEvent e) {
\r
1670 removeRedundancyMenuItem_actionPerformed(e);
\r
1673 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
1674 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1675 public void actionPerformed(ActionEvent e) {
\r
1676 pairwiseAlignmentMenuItem_actionPerformed(e);
\r
1679 PCAMenuItem.setLabel("Principal Component Analysis");
\r
1680 PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1681 public void actionPerformed(ActionEvent e) {
\r
1682 PCAMenuItem_actionPerformed(e);
\r
1685 averageDistanceTreeMenuItem.setLabel(
\r
1686 "Average Distance Using % Identity");
\r
1687 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1688 public void actionPerformed(ActionEvent e) {
\r
1689 averageDistanceTreeMenuItem_actionPerformed(e);
\r
1692 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
1693 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1694 public void actionPerformed(ActionEvent e) {
\r
1695 neighbourTreeMenuItem_actionPerformed(e);
\r
1698 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1699 statusBar.setBackground(Color.white);
\r
1700 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1701 statusBar.setText("Status bar");
\r
1702 outputTextboxMenu.setLabel("Output to Textbox");
\r
1703 clustalColour.setLabel("Clustalx");
\r
1705 clustalColour.addActionListener(new java.awt.event.ActionListener() {
\r
1706 public void actionPerformed(ActionEvent e) {
\r
1707 clustalColour_actionPerformed(e);
\r
1710 zappoColour.setLabel("Zappo");
\r
1711 zappoColour.addActionListener(new java.awt.event.ActionListener() {
\r
1712 public void actionPerformed(ActionEvent e) {
\r
1713 zappoColour_actionPerformed(e);
\r
1716 taylorColour.setLabel("Taylor");
\r
1717 taylorColour.addActionListener(new java.awt.event.ActionListener() {
\r
1718 public void actionPerformed(ActionEvent e) {
\r
1719 taylorColour_actionPerformed(e);
\r
1722 hydrophobicityColour.setLabel("Hydrophobicity");
\r
1723 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {
\r
1724 public void actionPerformed(ActionEvent e) {
\r
1725 hydrophobicityColour_actionPerformed(e);
\r
1728 helixColour.setLabel("Helix Propensity");
\r
1729 helixColour.addActionListener(new java.awt.event.ActionListener() {
\r
1730 public void actionPerformed(ActionEvent e) {
\r
1731 helixColour_actionPerformed(e);
\r
1734 strandColour.setLabel("Strand Propensity");
\r
1735 strandColour.addActionListener(new java.awt.event.ActionListener() {
\r
1736 public void actionPerformed(ActionEvent e) {
\r
1737 strandColour_actionPerformed(e);
\r
1740 turnColour.setLabel("Turn Propensity");
\r
1741 turnColour.addActionListener(new java.awt.event.ActionListener() {
\r
1742 public void actionPerformed(ActionEvent e) {
\r
1743 turnColour_actionPerformed(e);
\r
1746 buriedColour.setLabel("Buried Index");
\r
1747 buriedColour.addActionListener(new java.awt.event.ActionListener() {
\r
1748 public void actionPerformed(ActionEvent e) {
\r
1749 buriedColour_actionPerformed(e);
\r
1752 userDefinedColour.setLabel("User Defined...");
\r
1753 userDefinedColour.addActionListener(new java.awt.event.ActionListener() {
\r
1754 public void actionPerformed(ActionEvent e) {
\r
1755 userDefinedColour_actionPerformed(e);
\r
1758 PIDColour.setLabel("Percentage Identity");
\r
1759 PIDColour.addActionListener(new java.awt.event.ActionListener() {
\r
1760 public void actionPerformed(ActionEvent e) {
\r
1761 PIDColour_actionPerformed(e);
\r
1764 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
1765 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {
\r
1766 public void actionPerformed(ActionEvent e) {
\r
1767 BLOSUM62Colour_actionPerformed(e);
\r
1770 avDistanceTreeBlosumMenuItem.setLabel(
\r
1771 "Average Distance Using BLOSUM62");
\r
1772 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1773 public void actionPerformed(ActionEvent e) {
\r
1774 avTreeBlosumMenuItem_actionPerformed(e);
\r
1777 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
1778 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1779 public void actionPerformed(ActionEvent e) {
\r
1780 njTreeBlosumMenuItem_actionPerformed(e);
\r
1783 annotationPanelMenuItem.setActionCommand("");
\r
1784 annotationPanelMenuItem.setState(true);
\r
1785 annotationPanelMenuItem.setLabel("Show Annotations");
\r
1786 annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1787 public void itemStateChanged(ItemEvent e) {
\r
1788 annotationPanelMenuItem_actionPerformed(null);
\r
1791 colourTextMenuItem.setLabel("Colour Text");
\r
1792 colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1793 public void itemStateChanged(ItemEvent e) {
\r
1794 colourTextMenuItem_actionPerformed(null);
\r
1797 overviewMenuItem.setLabel("Overview Window");
\r
1798 overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1799 public void actionPerformed(ActionEvent e) {
\r
1800 overviewMenuItem_actionPerformed(e);
\r
1803 undoMenuItem.setEnabled(false);
\r
1804 undoMenuItem.setLabel("Undo");
\r
1805 undoMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1806 public void actionPerformed(ActionEvent e) {
\r
1807 undoMenuItem_actionPerformed(e);
\r
1810 redoMenuItem.setEnabled(false);
\r
1811 redoMenuItem.setLabel("Redo");
\r
1812 redoMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1813 public void actionPerformed(ActionEvent e) {
\r
1814 redoMenuItem_actionPerformed(e);
\r
1817 conservationMenuItem.setLabel("by Conservation");
\r
1818 conservationMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1819 public void itemStateChanged(ItemEvent e) {
\r
1820 conservationMenuItem_actionPerformed(null);
\r
1823 noColourmenuItem.setLabel("None");
\r
1824 noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1825 public void actionPerformed(ActionEvent e) {
\r
1826 noColourmenuItem_actionPerformed(e);
\r
1829 wrapMenuItem.setLabel("Wrap");
\r
1830 wrapMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1831 public void itemStateChanged(ItemEvent e) {
\r
1832 wrapMenuItem_actionPerformed(null);
\r
1835 renderGapsMenuItem.setLabel("Show Gaps");
\r
1836 renderGapsMenuItem.setState(true);
\r
1837 renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1838 public void itemStateChanged(ItemEvent e) {
\r
1839 renderGapsMenuItem_actionPerformed(null);
\r
1842 findMenuItem.setLabel("Find...");
\r
1843 findMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1844 public void actionPerformed(ActionEvent e) {
\r
1845 findMenuItem_actionPerformed(e);
\r
1848 searchMenu.setLabel("Search");
\r
1850 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
1851 abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() {
\r
1852 public void itemStateChanged(ItemEvent e) {
\r
1853 abovePIDThreshold_actionPerformed(null);
\r
1856 nucleotideColour.setLabel("Nucleotide");
\r
1857 nucleotideColour.addActionListener(new java.awt.event.ActionListener() {
\r
1858 public void actionPerformed(ActionEvent e) {
\r
1859 nucleotideColour_actionPerformed(e);
\r
1862 deleteGroups.setLabel("Undefine Groups");
\r
1863 deleteGroups.addActionListener(new java.awt.event.ActionListener() {
\r
1864 public void actionPerformed(ActionEvent e) {
\r
1865 deleteGroups_actionPerformed(e);
\r
1868 copy.setLabel("Copy");
\r
1869 copy.addActionListener(new java.awt.event.ActionListener() {
\r
1870 public void actionPerformed(ActionEvent e) {
\r
1871 copy_actionPerformed(e);
\r
1874 cut.setLabel("Cut");
\r
1875 cut.addActionListener(new java.awt.event.ActionListener() {
\r
1876 public void actionPerformed(ActionEvent e) {
\r
1877 cut_actionPerformed(e);
\r
1880 delete.setLabel("Delete");
\r
1881 delete.addActionListener(new java.awt.event.ActionListener() {
\r
1882 public void actionPerformed(ActionEvent e) {
\r
1883 delete_actionPerformed(e);
\r
1886 Menu1.setLabel("Paste");
\r
1887 pasteNew.setLabel("To New Alignment");
\r
1888 pasteNew.addActionListener(new java.awt.event.ActionListener() {
\r
1889 public void actionPerformed(ActionEvent e) {
\r
1890 pasteNew_actionPerformed(e);
\r
1893 pasteThis.setLabel("Add To This Alignment");
\r
1894 pasteThis.addActionListener(new java.awt.event.ActionListener() {
\r
1895 public void actionPerformed(ActionEvent e) {
\r
1896 pasteThis_actionPerformed(e);
\r
1899 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
1900 applyToAllGroups.setState(true);
\r
1901 applyToAllGroups.addItemListener(new java.awt.event.ItemListener() {
\r
1902 public void itemStateChanged(ItemEvent e) {
\r
1903 applyToAllGroups_actionPerformed(null);
\r
1906 font.setLabel("Font...");
\r
1907 font.addActionListener(new java.awt.event.ActionListener() {
\r
1908 public void actionPerformed(ActionEvent e) {
\r
1909 font_actionPerformed(e);
\r
1912 scaleAbove.setLabel("Scale Above");
\r
1913 scaleAbove.setState(true);
\r
1914 scaleAbove.addItemListener(new java.awt.event.ItemListener() {
\r
1915 public void itemStateChanged(ItemEvent e) {
\r
1916 scaleAbove_actionPerformed(null);
\r
1919 scaleLeft.setEnabled(false);
\r
1920 scaleLeft.setState(true);
\r
1921 scaleLeft.setLabel("Scale Left");
\r
1922 scaleLeft.addItemListener(new java.awt.event.ItemListener() {
\r
1923 public void itemStateChanged(ItemEvent e) {
\r
1924 scaleLeft_actionPerformed(null);
\r
1927 scaleRight.setEnabled(false);
\r
1928 scaleRight.setState(true);
\r
1929 scaleRight.setLabel("Scale Right");
\r
1930 scaleRight.addItemListener(new java.awt.event.ItemListener() {
\r
1931 public void itemStateChanged(ItemEvent e) {
\r
1932 scaleRight_actionPerformed(null);
\r
1935 modifyPID.setLabel("Modify Identity Threshold...");
\r
1936 modifyPID.addActionListener(new java.awt.event.ActionListener() {
\r
1937 public void actionPerformed(ActionEvent e) {
\r
1938 modifyPID_actionPerformed(e);
\r
1941 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
1942 modifyConservation.addActionListener(new java.awt.event.ActionListener() {
\r
1943 public void actionPerformed(ActionEvent e) {
\r
1944 modifyConservation_actionPerformed(e);
\r
1947 sortByTreeMenu.setLabel("By Tree Order");
\r
1948 sort.setLabel("Sort");
\r
1949 calculate.setLabel("Calculate Tree");
\r
1950 inputText.setLabel("Input from textbox");
\r
1951 inputText.addActionListener(new java.awt.event.ActionListener() {
\r
1952 public void actionPerformed(ActionEvent e) {
\r
1953 inputText_actionPerformed(e);
\r
1957 helpMenu.setLabel("Help");
\r
1958 documentation.setLabel("Documentation");
\r
1959 documentation.addActionListener(new java.awt.event.ActionListener() {
\r
1960 public void actionPerformed(ActionEvent e) {
\r
1961 documentation_actionPerformed(e);
\r
1965 about.setLabel("About...");
\r
1966 about.addActionListener(new java.awt.event.ActionListener() {
\r
1967 public void actionPerformed(ActionEvent e) {
\r
1968 about_actionPerformed(e);
\r
1971 seqLimits.setState(true);
\r
1972 seqLimits.setLabel("Show Sequence Limits");
\r
1973 seqLimits.addItemListener(new ItemListener()
\r
1975 public void itemStateChanged(ItemEvent e)
\r
1977 seqLimits_itemStateChanged(e);
\r
1981 alignFrameMenuBar.add(fileMenu);
\r
1982 alignFrameMenuBar.add(editMenu);
\r
1983 alignFrameMenuBar.add(searchMenu);
\r
1984 alignFrameMenuBar.add(viewMenu);
\r
1985 alignFrameMenuBar.add(colourMenu);
\r
1986 alignFrameMenuBar.add(calculateMenu);
\r
1987 alignFrameMenuBar.add(helpMenu);
\r
1988 fileMenu.add(inputText);
\r
1989 fileMenu.add(outputTextboxMenu);
\r
1990 fileMenu.addSeparator();
\r
1991 fileMenu.add(closeMenuItem);
\r
1992 editMenu.add(undoMenuItem);
\r
1993 editMenu.add(redoMenuItem);
\r
1994 editMenu.add(cut);
\r
1995 editMenu.add(copy);
\r
1996 editMenu.add(Menu1);
\r
1997 editMenu.add(delete);
\r
1998 editMenu.addSeparator();
\r
1999 editMenu.add(selectAllSequenceMenuItem);
\r
2000 editMenu.add(deselectAllSequenceMenuItem);
\r
2001 editMenu.add(invertSequenceMenuItem);
\r
2002 editMenu.add(deleteGroups);
\r
2003 editMenu.addSeparator();
\r
2004 editMenu.add(remove2LeftMenuItem);
\r
2005 editMenu.add(remove2RightMenuItem);
\r
2006 editMenu.add(removeGappedColumnMenuItem);
\r
2007 editMenu.add(removeAllGapsMenuItem);
\r
2008 editMenu.add(removeRedundancyMenuItem);
\r
2009 searchMenu.add(findMenuItem);
\r
2010 viewMenu.add(font);
\r
2011 viewMenu.addSeparator();
\r
2012 viewMenu.add(seqLimits);
\r
2013 viewMenu.addSeparator();
\r
2014 viewMenu.add(wrapMenuItem);
\r
2015 viewMenu.add(scaleAbove);
\r
2016 viewMenu.add(scaleLeft);
\r
2017 viewMenu.add(scaleRight);
\r
2018 viewMenu.addSeparator();
\r
2019 viewMenu.add(viewBoxesMenuItem);
\r
2020 viewMenu.add(viewTextMenuItem);
\r
2021 viewMenu.add(colourTextMenuItem);
\r
2022 viewMenu.add(renderGapsMenuItem);
\r
2023 viewMenu.add(annotationPanelMenuItem);
\r
2024 viewMenu.addSeparator();
\r
2025 viewMenu.add(overviewMenuItem);
\r
2026 colourMenu.add(applyToAllGroups);
\r
2027 colourMenu.addSeparator();
\r
2028 colourMenu.add(noColourmenuItem);
\r
2029 colourMenu.add(clustalColour);
\r
2030 colourMenu.add(BLOSUM62Colour);
\r
2031 colourMenu.add(PIDColour);
\r
2032 colourMenu.add(zappoColour);
\r
2033 colourMenu.add(taylorColour);
\r
2034 colourMenu.add(hydrophobicityColour);
\r
2035 colourMenu.add(helixColour);
\r
2036 colourMenu.add(strandColour);
\r
2037 colourMenu.add(turnColour);
\r
2038 colourMenu.add(buriedColour);
\r
2039 colourMenu.add(nucleotideColour);
\r
2040 colourMenu.add(userDefinedColour);
\r
2041 colourMenu.addSeparator();
\r
2042 colourMenu.add(conservationMenuItem);
\r
2043 colourMenu.add(modifyConservation);
\r
2044 colourMenu.add(abovePIDThreshold);
\r
2045 colourMenu.add(modifyPID);
\r
2046 calculateMenu.add(sort);
\r
2047 calculateMenu.add(calculate);
\r
2048 calculateMenu.addSeparator();
\r
2049 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2050 calculateMenu.add(PCAMenuItem);
\r
2051 this.add(statusBar, BorderLayout.SOUTH);
\r
2052 Menu1.add(pasteNew);
\r
2053 Menu1.add(pasteThis);
\r
2054 sort.add(sortIDMenuItem);
\r
2055 sort.add(sortByTreeMenu);
\r
2056 sort.add(sortGroupMenuItem);
\r
2057 sort.add(sortPairwiseMenuItem);
\r
2058 calculate.add(averageDistanceTreeMenuItem);
\r
2059 calculate.add(neighbourTreeMenuItem);
\r
2060 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2061 calculate.add(njTreeBlosumMenuItem);
\r
2062 helpMenu.add(documentation);
\r
2063 helpMenu.add(about);
\r