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.jbappletgui.GAlignFrame;
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23 import jalview.schemes.*;
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24 import jalview.datamodel.*;
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25 import jalview.analysis.*;
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26 import jalview.io.*;
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28 import java.awt.event.*;
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30 import java.io.InputStreamReader;
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31 import java.io.BufferedReader;
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32 import java.net.URL;
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34 public class AlignFrame
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37 final AlignmentPanel alignPanel;
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38 final AlignViewport viewport;
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39 int NEW_WINDOW_WIDTH = 700;
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40 int NEW_WINDOW_HEIGHT = 500;
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41 jalview.bin.JalviewLite applet;
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44 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title)
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46 this.applet = applet;
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47 viewport = new AlignViewport(al, applet);
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48 alignPanel = new AlignmentPanel(this, viewport);
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50 alignPanel.validate();
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54 String treeFile = applet.getParameter("treeFile");
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55 if (treeFile != null)
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59 jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
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60 getCodeBase() + treeFile, "URL");
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63 if (fin.getTree() != null)
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65 TreePanel tp = null;
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66 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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67 fin, "FromFile", applet.getCodeBase() + treeFile);
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68 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
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69 addTreeMenuItem(tp, treeFile);
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72 catch (Exception ex)
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74 ex.printStackTrace();
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78 String param = applet.getParameter("sortBy");
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81 if (param.equalsIgnoreCase("Id"))
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82 sortIDMenuItem_actionPerformed(null);
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83 else if (param.equalsIgnoreCase("Pairwise Identity"))
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84 sortPairwiseMenuItem_actionPerformed(null);
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87 param = applet.getParameter("wrap");
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90 if (param.equalsIgnoreCase("true"))
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92 wrapMenuItem.setState(true);
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93 wrapMenuItem_actionPerformed(null);
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99 param = applet.getParameter("windowWidth");
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102 int width = Integer.parseInt(param);
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103 NEW_WINDOW_WIDTH = width;
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105 param = applet.getParameter("windowHeight");
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108 int height = Integer.parseInt(param);
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109 NEW_WINDOW_HEIGHT = height;
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112 catch (Exception ex)
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117 this.addWindowListener(new WindowAdapter()
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119 public void windowClosing(WindowEvent e)
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121 closeMenuItem_actionPerformed(null);
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125 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
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127 public void propertyChange(java.beans.PropertyChangeEvent evt)
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129 if (evt.getPropertyName().equals("alignment"))
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131 alignmentChanged();
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136 jalview.bin.JalviewLite.addFrame(this, title,
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138 NEW_WINDOW_HEIGHT);
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147 * @param String DOCUMENT ME!
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150 public void parseFeaturesFile(String file)
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154 URL url = new URL(file);
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156 BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
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157 SequenceI seq = null;
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158 String line, type, desc, token;
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160 int index, start, end;
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161 StringTokenizer st;
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162 SequenceFeature sf;
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163 FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
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165 while ( (line = in.readLine()) != null)
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168 st = new StringTokenizer(line, "\t");
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169 if (st.countTokens() == 2)
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171 type = st.nextToken();
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172 UserColourScheme ucs = new UserColourScheme(st.nextToken());
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173 fr.setColour(type, ucs.findColour("A"));
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177 while (st.hasMoreElements())
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179 desc = st.nextToken();
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180 token = st.nextToken();
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181 if (!token.equals("ID_NOT_SPECIFIED"))
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183 index = viewport.alignment.findIndex(viewport.alignment.findName(
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189 index = Integer.parseInt(st.nextToken());
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192 start = Integer.parseInt(st.nextToken());
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193 end = Integer.parseInt(st.nextToken());
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195 seq = viewport.alignment.getSequenceAt(index);
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196 start = seq.findIndex(start) - 1;
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197 end = seq.findIndex(end) - 1;
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199 type = st.nextToken();
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201 if(fr.getColour(type)==null)
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203 // Probably the old style groups file
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204 UserColourScheme ucs = new UserColourScheme(type);
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205 fr.setColour(type, ucs.findColour("A"));
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208 sf = new SequenceFeature(type, desc, "", start, end);
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210 seq.addSequenceFeature(sf);
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214 viewport.showSequenceFeatures = true;
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215 ((Alignment)viewport.alignment).featuresAdded = true;
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217 alignPanel.repaint();
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220 catch (Exception ex)
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222 System.out.println("Error parsing groups file: " + ex);
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227 public void inputText_actionPerformed(ActionEvent e)
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229 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);
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230 Frame frame = new Frame();
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232 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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235 protected void outputText_actionPerformed(ActionEvent e)
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237 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);
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238 Frame frame = new Frame();
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240 jalview.bin.JalviewLite.addFrame(frame,
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241 "Alignment output - " + e.getActionCommand(),
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243 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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244 viewport.getAlignment().getSequences(),
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245 viewport.showDBPrefix,
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246 viewport.showJVSuffix));
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249 public void closeMenuItem_actionPerformed(ActionEvent e)
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251 PaintRefresher.components.remove(viewport.alignment);
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253 if(PaintRefresher.components.size()==0 && applet==null)
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257 Stack historyList = new Stack();
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258 Stack redoList = new Stack();
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260 void updateEditMenuBar()
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262 if (historyList.size() > 0)
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264 undoMenuItem.setEnabled(true);
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265 HistoryItem hi = (HistoryItem) historyList.peek();
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266 undoMenuItem.setLabel("Undo " + hi.getDescription());
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270 undoMenuItem.setEnabled(false);
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271 undoMenuItem.setLabel("Undo");
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274 if (redoList.size() > 0)
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276 redoMenuItem.setEnabled(true);
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277 HistoryItem hi = (HistoryItem) redoList.peek();
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278 redoMenuItem.setLabel("Redo " + hi.getDescription());
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282 redoMenuItem.setEnabled(false);
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283 redoMenuItem.setLabel("Redo");
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287 public void addHistoryItem(HistoryItem hi)
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289 historyList.push(hi);
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290 updateEditMenuBar();
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293 protected void undoMenuItem_actionPerformed(ActionEvent e)
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295 HistoryItem hi = (HistoryItem) historyList.pop();
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296 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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297 HistoryItem.HIDE));
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298 restoreHistoryItem(hi);
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299 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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302 protected void redoMenuItem_actionPerformed(ActionEvent e)
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304 HistoryItem hi = (HistoryItem) redoList.pop();
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305 restoreHistoryItem(hi);
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306 updateEditMenuBar();
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307 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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310 // used by undo and redo
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311 void restoreHistoryItem(HistoryItem hi)
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313 if (hi.getType() == HistoryItem.SORT)
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315 for (int i = 0; i < hi.getSequences().size(); i++)
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317 viewport.alignment.getSequences().setElementAt(hi.getSequences().
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323 for (int i = 0; i < hi.getSequences().size(); i++)
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325 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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326 if (restore.getLength() == 0)
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328 // log.System.out.println(hi.getHidden().elementAt(i));
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329 restore.setSequence(hi.getHidden().elementAt(i).toString());
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330 viewport.alignment.getSequences().insertElementAt(
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332 hi.getAlignIndex(i));
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336 restore.setSequence(hi.getHidden().elementAt(i).toString());
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339 if (hi.getType() == HistoryItem.PASTE)
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341 for (int i = viewport.alignment.getHeight() - 1;
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342 i > hi.getSequences().size() - 1; i--)
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344 viewport.alignment.deleteSequence(i);
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349 updateEditMenuBar();
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351 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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354 public void moveSelectedSequences(boolean up)
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356 SequenceGroup sg = viewport.getSelectionGroup();
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364 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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366 SequenceI seq = viewport.alignment.getSequenceAt(i);
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367 if (!sg.sequences.contains(seq))
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372 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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373 if (sg.sequences.contains(temp))
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378 viewport.alignment.getSequences().setElementAt(temp, i);
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379 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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384 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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386 SequenceI seq = viewport.alignment.getSequenceAt(i);
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387 if (!sg.sequences.contains(seq))
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392 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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393 if (sg.sequences.contains(temp))
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398 viewport.alignment.getSequences().setElementAt(temp, i);
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399 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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403 alignPanel.repaint();
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406 StringBuffer copiedSequences;
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407 protected void copy_actionPerformed(ActionEvent e)
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409 if (viewport.getSelectionGroup() == null)
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414 SequenceGroup sg = viewport.getSelectionGroup();
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415 copiedSequences = new StringBuffer();
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416 Hashtable orderedSeqs = new Hashtable();
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417 for (int i = 0; i < sg.getSize(); i++)
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419 SequenceI seq = sg.getSequenceAt(i);
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420 int index = viewport.alignment.findIndex(seq);
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421 orderedSeqs.put(index + "", seq);
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424 int index = 0, startRes, endRes;
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427 for (int i = 0; i < sg.getSize(); i++)
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429 SequenceI seq = null;
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431 while (seq == null)
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433 if (orderedSeqs.containsKey(index + ""))
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435 seq = (SequenceI) orderedSeqs.get(index + "");
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447 //Returns residue following index if gap
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448 startRes = seq.findPosition(sg.getStartRes());
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451 //Need to find the residue preceeding index if gap
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454 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
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456 ch = seq.getCharAt(j);
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457 if (!jalview.util.Comparison.isGap( (ch)))
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465 endRes += seq.getStart() -1;
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468 copiedSequences.append(seq.getName() + "\t" +
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471 seq.getSequence(sg.getStartRes(),
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472 sg.getEndRes() + 1) + "\n");
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477 protected void pasteNew_actionPerformed(ActionEvent e)
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482 protected void pasteThis_actionPerformed(ActionEvent e)
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484 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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485 HistoryItem.PASTE));
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489 void paste(boolean newAlignment)
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493 if (copiedSequences == null)
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498 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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499 Vector seqs = new Vector();
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500 while (st.hasMoreElements())
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502 String name = st.nextToken();
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503 int start = Integer.parseInt(st.nextToken());
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504 int end = Integer.parseInt(st.nextToken());
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505 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
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509 viewport.alignment.addSequence(sequence);
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513 seqs.addElement(sequence);
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519 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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520 for (int i = 0; i < seqs.size(); i++)
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522 newSeqs[i] = (SequenceI) seqs.elementAt(i);
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525 String newtitle = new String("Copied sequences");
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526 if (getTitle().startsWith("Copied sequences"))
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528 newtitle = getTitle();
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532 newtitle = newtitle.concat("- from " + getTitle());
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534 AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);
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536 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
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537 NEW_WINDOW_HEIGHT);
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541 viewport.setEndSeq(viewport.alignment.getHeight());
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542 viewport.alignment.getWidth();
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543 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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547 catch (Exception ex)
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548 {} // could be anything being pasted in here
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552 protected void cut_actionPerformed(ActionEvent e)
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554 copy_actionPerformed(null);
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555 delete_actionPerformed(null);
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558 protected void delete_actionPerformed(ActionEvent e)
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560 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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561 HistoryItem.HIDE));
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562 if (viewport.getSelectionGroup() == null)
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568 SequenceGroup sg = viewport.getSelectionGroup();
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569 boolean allSequences = false;
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570 if(sg.sequences.size()==viewport.alignment.getHeight())
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571 allSequences = true;
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573 for (int i = 0; i < sg.sequences.size(); i++)
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575 SequenceI seq = sg.getSequenceAt(i);
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576 int index = viewport.getAlignment().findIndex(seq);
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577 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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579 // If the cut affects all sequences, remove highlighted columns
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582 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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583 sg.getEndRes() + 1);
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587 if (seq.getSequence().length() < 1)
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589 viewport.getAlignment().deleteSequence(seq);
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593 viewport.getAlignment().getSequences().setElementAt(seq, index);
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597 viewport.setSelectionGroup(null);
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598 viewport.alignment.deleteGroup(sg);
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599 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
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600 if (viewport.getAlignment().getHeight() < 1)
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604 this.setVisible(false);
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606 catch (Exception ex)
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609 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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613 protected void deleteGroups_actionPerformed(ActionEvent e)
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615 viewport.alignment.deleteAllGroups();
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616 viewport.setSelectionGroup(null);
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618 alignPanel.repaint();
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621 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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623 SequenceGroup sg = new SequenceGroup();
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624 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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626 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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628 sg.setEndRes(viewport.alignment.getWidth()-1);
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629 viewport.setSelectionGroup(sg);
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630 alignPanel.repaint();
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631 PaintRefresher.Refresh(null, viewport.alignment);
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634 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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636 viewport.setSelectionGroup(null);
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637 viewport.getColumnSelection().clear();
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638 viewport.setSelectionGroup(null);
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639 alignPanel.repaint();
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640 PaintRefresher.Refresh(null, viewport.alignment);
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643 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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645 SequenceGroup sg = viewport.getSelectionGroup();
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646 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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648 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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651 PaintRefresher.Refresh(null, viewport.alignment);
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654 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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656 ColumnSelection colSel = viewport.getColumnSelection();
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657 if (colSel.size() > 0)
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659 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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660 HistoryItem.HIDE));
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661 int min = colSel.getMin();
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662 viewport.getAlignment().trimLeft(min);
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663 colSel.compensateForEdit(0, min);
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665 if (viewport.getSelectionGroup() != null)
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667 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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670 Vector groups = viewport.alignment.getGroups();
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671 for (int i = 0; i < groups.size(); i++)
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673 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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674 if (!sg.adjustForRemoveLeft(min))
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676 viewport.alignment.deleteGroup(sg);
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679 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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683 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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685 ColumnSelection colSel = viewport.getColumnSelection();
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686 if (colSel.size() > 0)
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688 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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689 HistoryItem.HIDE));
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690 int max = colSel.getMax();
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691 viewport.getAlignment().trimRight(max);
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692 if (viewport.getSelectionGroup() != null)
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694 viewport.getSelectionGroup().adjustForRemoveRight(max);
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697 Vector groups = viewport.alignment.getGroups();
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698 for (int i = 0; i < groups.size(); i++)
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700 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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701 if (!sg.adjustForRemoveRight(max))
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703 viewport.alignment.deleteGroup(sg);
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706 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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711 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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713 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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714 viewport.alignment,
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715 HistoryItem.HIDE));
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717 //This is to maintain viewport position on first residue
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718 //of first sequence
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719 SequenceI seq = viewport.alignment.getSequenceAt(0);
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720 int startRes = seq.findPosition(viewport.startRes);
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722 viewport.getAlignment().removeGaps();
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724 viewport.setStartRes(seq.findIndex(startRes)-1);
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726 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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729 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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731 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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732 HistoryItem.HIDE));
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734 //This is to maintain viewport position on first residue
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735 //of first sequence
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736 SequenceI seq = viewport.alignment.getSequenceAt(0);
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737 int startRes = seq.findPosition(viewport.startRes);
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744 int start=0, end = viewport.alignment.getWidth();
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746 if (viewport.getSelectionGroup() != null
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747 && viewport.getSelectionGroup().sequences != null
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748 && viewport.getSelectionGroup().sequences.size()>0)
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750 seqs = viewport.getSelectionGroup().sequences;
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751 start = viewport.getSelectionGroup().getStartRes();
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752 end = viewport.getSelectionGroup().getEndRes()+1;
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755 seqs = viewport.alignment.getSequences();
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757 for (int i = 0; i < seqs.size(); i++)
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759 current = (SequenceI) seqs.elementAt(i);
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760 jSize = current.getLength();
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762 // Removing a range is much quicker than removing gaps
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763 // one by one for long sequences
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765 int rangeStart=-1, rangeEnd=-1;
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769 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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786 current.deleteChars(rangeStart, rangeEnd);
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787 j-=rangeEnd-rangeStart;
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788 jSize-=rangeEnd-rangeStart;
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796 while (j < end && j < jSize);
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799 current.deleteChars(rangeStart, rangeEnd);
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802 viewport.setStartRes(seq.findIndex(startRes)-1);
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803 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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806 public void alignmentChanged()
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808 viewport.updateConsensus();
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809 viewport.updateConservation ();
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810 resetAllColourSchemes();
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811 if(alignPanel.overviewPanel!=null)
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812 alignPanel.overviewPanel.updateOverviewImage();
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813 alignPanel.repaint();
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816 void resetAllColourSchemes()
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818 ColourSchemeI cs = viewport.globalColourScheme;
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821 if (cs instanceof ClustalxColourScheme)
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823 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
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824 resetClustalX(viewport.alignment.getSequences(),
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825 viewport.alignment.getWidth());
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828 cs.setConsensus(viewport.vconsensus);
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829 if (cs.conservationApplied())
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831 Alignment al = (Alignment) viewport.alignment;
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832 Conservation c = new Conservation("All",
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833 ResidueProperties.propHash, 3,
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834 al.getSequences(), 0,
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835 al.getWidth() - 1);
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837 c.verdict(false, viewport.ConsPercGaps);
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839 cs.setConservation(c);
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843 int s, sSize = viewport.alignment.getGroups().size();
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844 for(s=0; s<sSize; s++)
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846 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
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847 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
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849 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
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851 sg.recalcConservation();
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857 public void findMenuItem_actionPerformed(ActionEvent e)
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859 new Finder(alignPanel);
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862 public void font_actionPerformed(ActionEvent e)
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864 new FontChooser(alignPanel);
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867 public void dbref_actionPerformed(ItemEvent e)
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869 viewport.showDBPrefix = dbref.getState();
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870 alignPanel.fontChanged();
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871 alignPanel.repaint();
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874 public void seqLimits_itemStateChanged(ItemEvent e)
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876 viewport.setShowJVSuffix(seqLimits.getState());
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877 alignPanel.fontChanged();
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878 alignPanel.repaint();
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882 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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884 viewport.setColourText(colourTextMenuItem.getState());
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885 alignPanel.repaint();
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888 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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890 viewport.setWrapAlignment(wrapMenuItem.getState());
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891 alignPanel.setWrapAlignment(wrapMenuItem.getState());
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892 scaleAbove.setEnabled(wrapMenuItem.getState());
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893 scaleLeft.setEnabled(wrapMenuItem.getState());
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894 scaleRight.setEnabled(wrapMenuItem.getState());
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895 alignPanel.repaint();
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898 protected void scaleAbove_actionPerformed(ActionEvent e)
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900 viewport.setScaleAboveWrapped(scaleAbove.getState());
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901 alignPanel.repaint();
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904 protected void scaleLeft_actionPerformed(ActionEvent e)
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906 viewport.setScaleLeftWrapped(scaleLeft.getState());
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907 alignPanel.repaint();
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910 protected void scaleRight_actionPerformed(ActionEvent e)
\r
912 viewport.setScaleRightWrapped(scaleRight.getState());
\r
913 alignPanel.repaint();
\r
916 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
918 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
919 alignPanel.repaint();
\r
922 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
924 viewport.setShowText(viewTextMenuItem.getState());
\r
925 alignPanel.repaint();
\r
928 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
930 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
931 alignPanel.repaint();
\r
934 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
936 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
937 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
940 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
942 if (alignPanel.overviewPanel != null)
\r
947 Frame frame = new Frame();
\r
948 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
949 frame.add(overview);
\r
950 // +50 must allow for applet frame window
\r
951 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
952 overview.preferredSize().width,
\r
953 overview.preferredSize().height + 50);
\r
956 frame.addWindowListener(new WindowAdapter()
\r
958 public void windowClosing(WindowEvent e)
\r
960 alignPanel.setOverviewPanel(null);
\r
964 alignPanel.setOverviewPanel(overview);
\r
968 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
970 changeColour(null);
\r
973 public void clustalColour_actionPerformed(ActionEvent e)
\r
975 abovePIDThreshold.setState(false);
\r
976 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
977 viewport.alignment.getWidth()));
\r
980 public void zappoColour_actionPerformed(ActionEvent e)
\r
982 changeColour(new ZappoColourScheme());
\r
985 public void taylorColour_actionPerformed(ActionEvent e)
\r
987 changeColour(new TaylorColourScheme());
\r
990 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
992 changeColour(new HydrophobicColourScheme());
\r
995 public void helixColour_actionPerformed(ActionEvent e)
\r
997 changeColour(new HelixColourScheme());
\r
1000 public void strandColour_actionPerformed(ActionEvent e)
\r
1002 changeColour(new StrandColourScheme());
\r
1005 public void turnColour_actionPerformed(ActionEvent e)
\r
1007 changeColour(new TurnColourScheme());
\r
1010 public void buriedColour_actionPerformed(ActionEvent e)
\r
1012 changeColour(new BuriedColourScheme());
\r
1015 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1017 changeColour(new NucleotideColourScheme());
\r
1020 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1022 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1025 void changeColour(ColourSchemeI cs)
\r
1027 int threshold = 0;
\r
1031 if (viewport.getAbovePIDThreshold())
\r
1033 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1035 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1037 viewport.setGlobalColourScheme(cs);
\r
1041 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1044 if (viewport.getConservationSelected())
\r
1047 Alignment al = (Alignment) viewport.alignment;
\r
1048 Conservation c = new Conservation("All",
\r
1049 ResidueProperties.propHash, 3,
\r
1050 al.getSequences(), 0,
\r
1051 al.getWidth() - 1);
\r
1054 c.verdict(false, viewport.ConsPercGaps);
\r
1056 cs.setConservation(c);
\r
1058 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1064 cs.setConservation(null);
\r
1067 cs.setConsensus(viewport.vconsensus);
\r
1070 viewport.setGlobalColourScheme(cs);
\r
1072 if (viewport.getColourAppliesToAllGroups())
\r
1074 Vector groups = viewport.alignment.getGroups();
\r
1075 for (int i = 0; i < groups.size(); i++)
\r
1077 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1084 if (cs instanceof ClustalxColourScheme)
\r
1086 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1092 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1094 catch (Exception ex)
\r
1096 ex.printStackTrace();
\r
1101 if (viewport.getAbovePIDThreshold()
\r
1102 || cs instanceof PIDColourScheme
\r
1103 || cs instanceof Blosum62ColourScheme)
\r
1105 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1106 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
1109 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1111 if (viewport.getConservationSelected())
\r
1113 Conservation c = new Conservation("Group",
\r
1114 ResidueProperties.propHash, 3,
\r
1116 viewport.alignment.getWidth() - 1);
\r
1118 c.verdict(false, viewport.ConsPercGaps);
\r
1119 sg.cs.setConservation(c);
\r
1123 sg.cs.setConservation(null);
\r
1124 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1131 if (alignPanel.getOverviewPanel() != null)
\r
1133 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1136 alignPanel.repaint();
\r
1141 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1143 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1145 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1147 SliderPanel.showPIDSlider();
\r
1151 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1153 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1155 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1157 SliderPanel.showConservationSlider();
\r
1161 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1163 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1165 viewport.setAbovePIDThreshold(false);
\r
1166 abovePIDThreshold.setState(false);
\r
1168 changeColour(viewport.getGlobalColourScheme());
\r
1170 modifyConservation_actionPerformed(null);
\r
1173 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1175 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1177 conservationMenuItem.setState(false);
\r
1178 viewport.setConservationSelected(false);
\r
1180 changeColour(viewport.getGlobalColourScheme());
\r
1182 modifyPID_actionPerformed(null);
\r
1185 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1187 new UserDefinedColours(alignPanel, null);
\r
1190 public void PIDColour_actionPerformed(ActionEvent e)
\r
1192 changeColour(new PIDColourScheme());
\r
1195 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1197 changeColour(new Blosum62ColourScheme());
\r
1200 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1202 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1203 HistoryItem.SORT));
\r
1204 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1205 viewport.getAlignment().getSequenceAt(0));
\r
1206 alignPanel.repaint();
\r
1209 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1211 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1212 HistoryItem.SORT));
\r
1213 AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);
\r
1214 alignPanel.repaint();
\r
1217 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1219 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1220 HistoryItem.SORT));
\r
1221 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1222 alignPanel.repaint();
\r
1226 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1228 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
1229 Frame frame = new Frame();
\r
1231 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
1236 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1238 if (viewport.getSelectionGroup().getSize() > 1)
\r
1240 Frame frame = new Frame();
\r
1241 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1242 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1246 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1248 //are the sequences aligned?
\r
1249 if (!viewport.alignment.isAligned())
\r
1251 SequenceI current;
\r
1252 int Width = viewport.getAlignment().getWidth();
\r
1254 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1257 current = viewport.getAlignment().getSequenceAt(i);
\r
1259 if (current.getLength() < Width)
\r
1261 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1264 alignPanel.repaint();
\r
1267 if ( (viewport.getSelectionGroup() != null &&
\r
1268 viewport.getSelectionGroup().getSize() < 4 &&
\r
1269 viewport.getSelectionGroup().getSize() > 0)
\r
1270 || viewport.getAlignment().getHeight() < 4)
\r
1277 new PCAPanel(viewport);
\r
1279 catch (java.lang.OutOfMemoryError ex)
\r
1285 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1287 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1290 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1292 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1295 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1297 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1300 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1302 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1305 void NewTreePanel(String type, String pwType, String title)
\r
1307 //are the sequences aligned?
\r
1308 if (!viewport.alignment.isAligned())
\r
1310 SequenceI current;
\r
1311 int Width = viewport.getAlignment().getWidth();
\r
1313 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1316 current = viewport.getAlignment().getSequenceAt(i);
\r
1318 if (current.getLength() < Width)
\r
1320 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1323 alignPanel.repaint();
\r
1327 final TreePanel tp;
\r
1328 if (viewport.getSelectionGroup() != null &&
\r
1329 viewport.getSelectionGroup().getSize() > 3)
\r
1331 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1333 0, viewport.alignment.getWidth());
\r
1337 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1338 type, pwType, 0, viewport.alignment.getWidth());
\r
1341 addTreeMenuItem(tp, title);
\r
1343 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1346 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1348 final MenuItem item = new MenuItem(title);
\r
1349 sortByTreeMenu.add(item);
\r
1350 item.addActionListener(new java.awt.event.ActionListener()
\r
1352 public void actionPerformed(ActionEvent e)
\r
1354 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1355 HistoryItem.SORT));
\r
1356 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1357 alignPanel.repaint();
\r
1361 treePanel.addWindowListener(new WindowAdapter()
\r
1363 public void windowClosing(WindowEvent e)
\r
1365 sortByTreeMenu.remove(item);
\r
1370 protected void documentation_actionPerformed(ActionEvent e)
\r
1372 showURL("http://www.jalview.org/help.html");
\r
1375 protected void about_actionPerformed(ActionEvent e)
\r
1378 class AboutPanel extends Canvas
\r
1381 public AboutPanel(String version)
\r
1382 { this.version = version; }
\r
1384 public void paint(Graphics g)
\r
1386 g.setColor(Color.white);
\r
1387 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1388 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1389 FontMetrics fm = g.getFontMetrics();
\r
1390 int fh = fm.getHeight();
\r
1392 g.setColor(Color.black);
\r
1393 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1394 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1395 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1396 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1398 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1401 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1403 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1404 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1406 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1410 String version = "test";
\r
1411 java.net.URL url = getClass().getResource("/.build_properties");
\r
1416 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1417 url.openStream()));
\r
1419 while ( (line = reader.readLine()) != null)
\r
1421 if (line.indexOf("VERSION") > -1)
\r
1423 version = line.substring(line.indexOf("=") + 1);
\r
1427 catch (Exception ex)
\r
1429 ex.printStackTrace();
\r
1434 Frame frame = new Frame();
\r
1435 frame.add(new AboutPanel(version));
\r
1436 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1441 * Displays the given URL in a new browser window
\r
1443 * @param url URL to display in browser window.
\r
1444 * <br>New window will be named "HELP_WINDOW"
\r
1446 public void showURL(String url)
\r
1448 showURL(url, "HELP");
\r
1451 public void showURL(String url, String target)
\r
1453 if (applet == null)
\r
1455 System.out.println("Not running as applet - no browser available.");
\r
1461 applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1464 catch (Exception ex)
\r
1466 ex.printStackTrace();
\r