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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33 public class AlignFrame
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36 final AlignmentPanel alignPanel;
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37 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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45 this.applet = applet;
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46 viewport = new AlignViewport(al, applet);
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47 alignPanel = new AlignmentPanel(this, viewport);
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49 alignPanel.validate();
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53 String treeFile = applet.getParameter("treeFile");
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54 if (treeFile != null)
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58 jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
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59 getCodeBase() + treeFile, "URL");
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62 if (fin.getTree() != null)
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64 TreePanel tp = null;
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65 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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66 fin, "FromFile", applet.getCodeBase() + treeFile);
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67 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
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68 addTreeMenuItem(tp, treeFile);
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71 catch (Exception ex)
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73 ex.printStackTrace();
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77 String param = applet.getParameter("sortBy");
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80 if (param.equalsIgnoreCase("Id"))
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81 sortIDMenuItem_actionPerformed(null);
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82 else if (param.equalsIgnoreCase("Pairwise Identity"))
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83 sortPairwiseMenuItem_actionPerformed(null);
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86 param = applet.getParameter("wrap");
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89 if (param.equalsIgnoreCase("true"))
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91 wrapMenuItem.setState(true);
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92 wrapMenuItem_actionPerformed(null);
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98 param = applet.getParameter("windowWidth");
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101 int width = Integer.parseInt(param);
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102 NEW_WINDOW_WIDTH = width;
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104 param = applet.getParameter("windowHeight");
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107 int height = Integer.parseInt(param);
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108 NEW_WINDOW_HEIGHT = height;
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111 catch (Exception ex)
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116 this.addWindowListener(new WindowAdapter()
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118 public void windowClosing(WindowEvent e)
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120 closeMenuItem_actionPerformed(null);
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124 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
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126 public void propertyChange(java.beans.PropertyChangeEvent evt)
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128 if (evt.getPropertyName().equals("alignment"))
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130 alignmentChanged();
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135 jalview.bin.JalviewLite.addFrame(this, title,
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137 NEW_WINDOW_HEIGHT);
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142 public void inputText_actionPerformed(ActionEvent e)
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144 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);
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145 Frame frame = new Frame();
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147 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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150 protected void outputText_actionPerformed(ActionEvent e)
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152 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);
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153 Frame frame = new Frame();
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155 jalview.bin.JalviewLite.addFrame(frame,
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156 "Alignment output - " + e.getActionCommand(),
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158 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
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159 viewport.getAlignment().
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163 public void closeMenuItem_actionPerformed(ActionEvent e)
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165 PaintRefresher.components.remove(viewport.alignment);
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167 if(PaintRefresher.components.size()==0 && applet==null)
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171 Stack historyList = new Stack();
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172 Stack redoList = new Stack();
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174 void updateEditMenuBar()
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176 if (historyList.size() > 0)
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178 undoMenuItem.setEnabled(true);
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179 HistoryItem hi = (HistoryItem) historyList.peek();
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180 undoMenuItem.setLabel("Undo " + hi.getDescription());
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184 undoMenuItem.setEnabled(false);
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185 undoMenuItem.setLabel("Undo");
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188 if (redoList.size() > 0)
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190 redoMenuItem.setEnabled(true);
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191 HistoryItem hi = (HistoryItem) redoList.peek();
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192 redoMenuItem.setLabel("Redo " + hi.getDescription());
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196 redoMenuItem.setEnabled(false);
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197 redoMenuItem.setLabel("Redo");
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201 public void addHistoryItem(HistoryItem hi)
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203 historyList.push(hi);
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204 updateEditMenuBar();
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207 protected void undoMenuItem_actionPerformed(ActionEvent e)
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209 HistoryItem hi = (HistoryItem) historyList.pop();
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210 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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211 HistoryItem.HIDE));
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212 restoreHistoryItem(hi);
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213 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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216 protected void redoMenuItem_actionPerformed(ActionEvent e)
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218 HistoryItem hi = (HistoryItem) redoList.pop();
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219 restoreHistoryItem(hi);
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220 updateEditMenuBar();
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221 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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224 // used by undo and redo
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225 void restoreHistoryItem(HistoryItem hi)
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227 if (hi.getType() == HistoryItem.SORT)
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229 for (int i = 0; i < hi.getSequences().size(); i++)
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231 viewport.alignment.getSequences().setElementAt(hi.getSequences().
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237 for (int i = 0; i < hi.getSequences().size(); i++)
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239 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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240 if (restore.getLength() == 0)
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242 // log.System.out.println(hi.getHidden().elementAt(i));
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243 restore.setSequence(hi.getHidden().elementAt(i).toString());
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244 viewport.alignment.getSequences().insertElementAt(
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246 hi.getAlignIndex(i));
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250 restore.setSequence(hi.getHidden().elementAt(i).toString());
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253 if (hi.getType() == HistoryItem.PASTE)
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255 for (int i = viewport.alignment.getHeight() - 1;
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256 i > hi.getSequences().size() - 1; i--)
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258 viewport.alignment.deleteSequence(i);
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263 updateEditMenuBar();
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265 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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268 public void moveSelectedSequences(boolean up)
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270 SequenceGroup sg = viewport.getSelectionGroup();
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278 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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280 SequenceI seq = viewport.alignment.getSequenceAt(i);
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281 if (!sg.sequences.contains(seq))
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286 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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287 if (sg.sequences.contains(temp))
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292 viewport.alignment.getSequences().setElementAt(temp, i);
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293 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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298 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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300 SequenceI seq = viewport.alignment.getSequenceAt(i);
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301 if (!sg.sequences.contains(seq))
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306 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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307 if (sg.sequences.contains(temp))
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312 viewport.alignment.getSequences().setElementAt(temp, i);
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313 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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317 alignPanel.repaint();
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320 StringBuffer copiedSequences;
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321 protected void copy_actionPerformed(ActionEvent e)
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323 if (viewport.getSelectionGroup() == null)
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328 SequenceGroup sg = viewport.getSelectionGroup();
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329 copiedSequences = new StringBuffer();
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330 Hashtable orderedSeqs = new Hashtable();
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331 for (int i = 0; i < sg.getSize(); i++)
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333 SequenceI seq = sg.getSequenceAt(i);
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334 int index = viewport.alignment.findIndex(seq);
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335 orderedSeqs.put(index + "", seq);
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338 int index = 0, startRes, endRes;
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341 for (int i = 0; i < sg.getSize(); i++)
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343 SequenceI seq = null;
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345 while (seq == null)
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347 if (orderedSeqs.containsKey(index + ""))
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349 seq = (SequenceI) orderedSeqs.get(index + "");
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361 //Returns residue following index if gap
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362 startRes = seq.findPosition(sg.getStartRes());
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365 //Need to find the residue preceeding index if gap
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368 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
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370 ch = seq.getCharAt(j);
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371 if (!jalview.util.Comparison.isGap( (ch)))
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379 endRes += seq.getStart() -1;
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382 copiedSequences.append(seq.getName() + "\t" +
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385 seq.getSequence(sg.getStartRes(),
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386 sg.getEndRes() + 1) + "\n");
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391 protected void pasteNew_actionPerformed(ActionEvent e)
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396 protected void pasteThis_actionPerformed(ActionEvent e)
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398 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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399 HistoryItem.PASTE));
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403 void paste(boolean newAlignment)
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407 if (copiedSequences == null)
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412 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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413 Vector seqs = new Vector();
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414 while (st.hasMoreElements())
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416 String name = st.nextToken();
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417 int start = Integer.parseInt(st.nextToken());
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418 int end = Integer.parseInt(st.nextToken());
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419 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
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423 viewport.alignment.addSequence(sequence);
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427 seqs.addElement(sequence);
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433 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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434 for (int i = 0; i < seqs.size(); i++)
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436 newSeqs[i] = (SequenceI) seqs.elementAt(i);
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439 String newtitle = new String("Copied sequences");
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440 if (getTitle().startsWith("Copied sequences"))
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442 newtitle = getTitle();
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446 newtitle = newtitle.concat("- from " + getTitle());
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448 AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);
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450 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
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451 NEW_WINDOW_HEIGHT);
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455 viewport.setEndSeq(viewport.alignment.getHeight());
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456 viewport.alignment.getWidth();
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457 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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461 catch (Exception ex)
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462 {} // could be anything being pasted in here
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466 protected void cut_actionPerformed(ActionEvent e)
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468 copy_actionPerformed(null);
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469 delete_actionPerformed(null);
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472 protected void delete_actionPerformed(ActionEvent e)
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474 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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475 HistoryItem.HIDE));
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476 if (viewport.getSelectionGroup() == null)
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482 SequenceGroup sg = viewport.getSelectionGroup();
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483 boolean allSequences = false;
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484 if(sg.sequences.size()==viewport.alignment.getHeight())
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485 allSequences = true;
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487 for (int i = 0; i < sg.sequences.size(); i++)
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489 SequenceI seq = sg.getSequenceAt(i);
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490 int index = viewport.getAlignment().findIndex(seq);
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491 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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493 // If the cut affects all sequences, remove highlighted columns
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496 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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497 sg.getEndRes() + 1);
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501 if (seq.getSequence().length() < 1)
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503 viewport.getAlignment().deleteSequence(seq);
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507 viewport.getAlignment().getSequences().setElementAt(seq, index);
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511 viewport.setSelectionGroup(null);
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512 viewport.alignment.deleteGroup(sg);
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513 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
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514 if (viewport.getAlignment().getHeight() < 1)
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518 this.setVisible(false);
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520 catch (Exception ex)
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523 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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527 protected void deleteGroups_actionPerformed(ActionEvent e)
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529 viewport.alignment.deleteAllGroups();
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530 viewport.setSelectionGroup(null);
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532 alignPanel.repaint();
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535 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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537 SequenceGroup sg = new SequenceGroup();
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538 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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540 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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542 sg.setEndRes(viewport.alignment.getWidth()-1);
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543 viewport.setSelectionGroup(sg);
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544 alignPanel.repaint();
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545 PaintRefresher.Refresh(null, viewport.alignment);
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548 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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550 viewport.setSelectionGroup(null);
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551 viewport.getColumnSelection().clear();
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552 viewport.setSelectionGroup(null);
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553 alignPanel.repaint();
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554 PaintRefresher.Refresh(null, viewport.alignment);
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557 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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559 SequenceGroup sg = viewport.getSelectionGroup();
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560 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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562 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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565 PaintRefresher.Refresh(null, viewport.alignment);
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568 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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570 ColumnSelection colSel = viewport.getColumnSelection();
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571 if (colSel.size() > 0)
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573 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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574 HistoryItem.HIDE));
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575 int min = colSel.getMin();
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576 viewport.getAlignment().trimLeft(min);
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577 colSel.compensateForEdit(0, min);
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579 if (viewport.getSelectionGroup() != null)
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581 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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584 Vector groups = viewport.alignment.getGroups();
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585 for (int i = 0; i < groups.size(); i++)
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587 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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588 if (!sg.adjustForRemoveLeft(min))
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590 viewport.alignment.deleteGroup(sg);
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593 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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597 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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599 ColumnSelection colSel = viewport.getColumnSelection();
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600 if (colSel.size() > 0)
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602 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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603 HistoryItem.HIDE));
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604 int max = colSel.getMax();
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605 viewport.getAlignment().trimRight(max);
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606 if (viewport.getSelectionGroup() != null)
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608 viewport.getSelectionGroup().adjustForRemoveRight(max);
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611 Vector groups = viewport.alignment.getGroups();
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612 for (int i = 0; i < groups.size(); i++)
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614 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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615 if (!sg.adjustForRemoveRight(max))
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617 viewport.alignment.deleteGroup(sg);
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620 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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625 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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627 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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628 viewport.alignment,
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629 HistoryItem.HIDE));
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631 //This is to maintain viewport position on first residue
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632 //of first sequence
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633 SequenceI seq = viewport.alignment.getSequenceAt(0);
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634 int startRes = seq.findPosition(viewport.startRes);
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636 viewport.getAlignment().removeGaps();
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638 viewport.setStartRes(seq.findIndex(startRes)-1);
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640 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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643 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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645 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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646 HistoryItem.HIDE));
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648 //This is to maintain viewport position on first residue
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649 //of first sequence
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650 SequenceI seq = viewport.alignment.getSequenceAt(0);
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651 int startRes = seq.findPosition(viewport.startRes);
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658 int start=0, end = viewport.alignment.getWidth();
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660 if (viewport.getSelectionGroup() != null
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661 && viewport.getSelectionGroup().sequences != null
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662 && viewport.getSelectionGroup().sequences.size()>0)
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664 seqs = viewport.getSelectionGroup().sequences;
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665 start = viewport.getSelectionGroup().getStartRes();
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666 end = viewport.getSelectionGroup().getEndRes()+1;
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669 seqs = viewport.alignment.getSequences();
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671 for (int i = 0; i < seqs.size(); i++)
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673 current = (SequenceI) seqs.elementAt(i);
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674 jSize = current.getLength();
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676 // Removing a range is much quicker than removing gaps
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677 // one by one for long sequences
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679 int rangeStart=-1, rangeEnd=-1;
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683 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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700 current.deleteChars(rangeStart, rangeEnd);
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701 j-=rangeEnd-rangeStart;
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702 jSize-=rangeEnd-rangeStart;
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710 while (j < end && j < jSize);
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713 current.deleteChars(rangeStart, rangeEnd);
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716 viewport.setStartRes(seq.findIndex(startRes)-1);
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717 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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720 public void alignmentChanged()
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722 viewport.updateConsensus();
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723 viewport.updateConservation ();
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724 resetAllColourSchemes();
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725 if(alignPanel.overviewPanel!=null)
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726 alignPanel.overviewPanel.updateOverviewImage();
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727 alignPanel.repaint();
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730 void resetAllColourSchemes()
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732 ColourSchemeI cs = viewport.globalColourScheme;
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735 if (cs instanceof ClustalxColourScheme)
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737 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
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738 resetClustalX(viewport.alignment.getSequences(),
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739 viewport.alignment.getWidth());
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742 cs.setConsensus(viewport.vconsensus);
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743 if (cs.conservationApplied())
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745 Alignment al = (Alignment) viewport.alignment;
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746 Conservation c = new Conservation("All",
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747 ResidueProperties.propHash, 3,
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748 al.getSequences(), 0,
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749 al.getWidth() - 1);
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751 c.verdict(false, viewport.ConsPercGaps);
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753 cs.setConservation(c);
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757 int s, sSize = viewport.alignment.getGroups().size();
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758 for(s=0; s<sSize; s++)
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760 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
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761 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
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763 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
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765 sg.recalcConservation();
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771 public void findMenuItem_actionPerformed(ActionEvent e)
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773 new Finder(alignPanel);
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776 public void font_actionPerformed(ActionEvent e)
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778 new FontChooser(alignPanel);
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781 protected void fullSeqId_actionPerformed(ActionEvent e)
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783 viewport.setShowFullId(fullSeqId.getState());
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784 alignPanel.fontChanged();
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785 alignPanel.repaint();
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788 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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790 viewport.setColourText(colourTextMenuItem.getState());
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791 alignPanel.repaint();
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794 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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796 viewport.setWrapAlignment(wrapMenuItem.getState());
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797 alignPanel.setWrapAlignment(wrapMenuItem.getState());
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798 scaleAbove.setEnabled(wrapMenuItem.getState());
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799 scaleLeft.setEnabled(wrapMenuItem.getState());
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800 scaleRight.setEnabled(wrapMenuItem.getState());
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801 alignPanel.repaint();
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804 protected void scaleAbove_actionPerformed(ActionEvent e)
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806 viewport.setScaleAboveWrapped(scaleAbove.getState());
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807 alignPanel.repaint();
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810 protected void scaleLeft_actionPerformed(ActionEvent e)
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812 viewport.setScaleLeftWrapped(scaleLeft.getState());
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813 alignPanel.repaint();
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816 protected void scaleRight_actionPerformed(ActionEvent e)
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818 viewport.setScaleRightWrapped(scaleRight.getState());
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819 alignPanel.repaint();
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822 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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824 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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825 alignPanel.repaint();
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828 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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830 viewport.setShowText(viewTextMenuItem.getState());
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831 alignPanel.repaint();
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834 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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836 viewport.setRenderGaps(renderGapsMenuItem.getState());
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837 alignPanel.repaint();
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840 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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842 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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843 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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846 public void overviewMenuItem_actionPerformed(ActionEvent e)
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848 if (alignPanel.overviewPanel != null)
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853 Frame frame = new Frame();
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854 OverviewPanel overview = new OverviewPanel(alignPanel);
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855 frame.add(overview);
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856 // +50 must allow for applet frame window
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857 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
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858 overview.preferredSize().width,
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859 overview.preferredSize().height + 50);
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862 frame.addWindowListener(new WindowAdapter()
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864 public void windowClosing(WindowEvent e)
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866 alignPanel.setOverviewPanel(null);
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870 alignPanel.setOverviewPanel(overview);
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874 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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876 changeColour(null);
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879 public void clustalColour_actionPerformed(ActionEvent e)
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881 abovePIDThreshold.setState(false);
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882 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
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883 viewport.alignment.getWidth()));
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886 public void zappoColour_actionPerformed(ActionEvent e)
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888 changeColour(new ZappoColourScheme());
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891 public void taylorColour_actionPerformed(ActionEvent e)
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893 changeColour(new TaylorColourScheme());
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896 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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898 changeColour(new HydrophobicColourScheme());
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901 public void helixColour_actionPerformed(ActionEvent e)
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903 changeColour(new HelixColourScheme());
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906 public void strandColour_actionPerformed(ActionEvent e)
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908 changeColour(new StrandColourScheme());
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911 public void turnColour_actionPerformed(ActionEvent e)
\r
913 changeColour(new TurnColourScheme());
\r
916 public void buriedColour_actionPerformed(ActionEvent e)
\r
918 changeColour(new BuriedColourScheme());
\r
921 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
923 changeColour(new NucleotideColourScheme());
\r
926 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
928 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
931 void changeColour(ColourSchemeI cs)
\r
937 if (viewport.getAbovePIDThreshold())
\r
939 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
941 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
943 viewport.setGlobalColourScheme(cs);
\r
947 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
950 if (viewport.getConservationSelected())
\r
953 Alignment al = (Alignment) viewport.alignment;
\r
954 Conservation c = new Conservation("All",
\r
955 ResidueProperties.propHash, 3,
\r
956 al.getSequences(), 0,
\r
957 al.getWidth() - 1);
\r
960 c.verdict(false, viewport.ConsPercGaps);
\r
962 cs.setConservation(c);
\r
964 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
970 cs.setConservation(null);
\r
973 cs.setConsensus(viewport.vconsensus);
\r
976 viewport.setGlobalColourScheme(cs);
\r
978 if (viewport.getColourAppliesToAllGroups())
\r
980 Vector groups = viewport.alignment.getGroups();
\r
981 for (int i = 0; i < groups.size(); i++)
\r
983 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
990 if (cs instanceof ClustalxColourScheme)
\r
992 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
998 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1000 catch (Exception ex)
\r
1002 ex.printStackTrace();
\r
1007 if (viewport.getAbovePIDThreshold()
\r
1008 || cs instanceof PIDColourScheme
\r
1009 || cs instanceof Blosum62ColourScheme)
\r
1011 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1012 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
1015 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1017 if (viewport.getConservationSelected())
\r
1019 Conservation c = new Conservation("Group",
\r
1020 ResidueProperties.propHash, 3,
\r
1022 viewport.alignment.getWidth() - 1);
\r
1024 c.verdict(false, viewport.ConsPercGaps);
\r
1025 sg.cs.setConservation(c);
\r
1029 sg.cs.setConservation(null);
\r
1030 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1037 if (alignPanel.getOverviewPanel() != null)
\r
1039 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1042 alignPanel.repaint();
\r
1047 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1049 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1051 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1053 SliderPanel.showPIDSlider();
\r
1057 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1059 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1061 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1063 SliderPanel.showConservationSlider();
\r
1067 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1069 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1071 viewport.setAbovePIDThreshold(false);
\r
1072 abovePIDThreshold.setState(false);
\r
1074 changeColour(viewport.getGlobalColourScheme());
\r
1076 modifyConservation_actionPerformed(null);
\r
1079 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1081 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1083 conservationMenuItem.setState(false);
\r
1084 viewport.setConservationSelected(false);
\r
1086 changeColour(viewport.getGlobalColourScheme());
\r
1088 modifyPID_actionPerformed(null);
\r
1091 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1093 new UserDefinedColours(alignPanel, null);
\r
1096 public void PIDColour_actionPerformed(ActionEvent e)
\r
1098 changeColour(new PIDColourScheme());
\r
1101 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1103 changeColour(new Blosum62ColourScheme());
\r
1106 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1108 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1109 HistoryItem.SORT));
\r
1110 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1111 viewport.getAlignment().getSequenceAt(0));
\r
1112 alignPanel.repaint();
\r
1115 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1117 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1118 HistoryItem.SORT));
\r
1119 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1120 alignPanel.repaint();
\r
1123 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1125 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1126 HistoryItem.SORT));
\r
1127 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1128 alignPanel.repaint();
\r
1132 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1134 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
1135 Frame frame = new Frame();
\r
1137 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
1142 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1144 if (viewport.getSelectionGroup().getSize() > 1)
\r
1146 Frame frame = new Frame();
\r
1147 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1148 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1152 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1154 //are the sequences aligned?
\r
1155 if (!viewport.alignment.isAligned())
\r
1157 SequenceI current;
\r
1158 int Width = viewport.getAlignment().getWidth();
\r
1160 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1163 current = viewport.getAlignment().getSequenceAt(i);
\r
1165 if (current.getLength() < Width)
\r
1167 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1170 alignPanel.repaint();
\r
1173 if ( (viewport.getSelectionGroup() != null &&
\r
1174 viewport.getSelectionGroup().getSize() < 4 &&
\r
1175 viewport.getSelectionGroup().getSize() > 0)
\r
1176 || viewport.getAlignment().getHeight() < 4)
\r
1183 new PCAPanel(viewport);
\r
1185 catch (java.lang.OutOfMemoryError ex)
\r
1191 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1193 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1196 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1198 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1201 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1203 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1206 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1208 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1211 void NewTreePanel(String type, String pwType, String title)
\r
1213 //are the sequences aligned?
\r
1214 if (!viewport.alignment.isAligned())
\r
1216 SequenceI current;
\r
1217 int Width = viewport.getAlignment().getWidth();
\r
1219 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1222 current = viewport.getAlignment().getSequenceAt(i);
\r
1224 if (current.getLength() < Width)
\r
1226 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1229 alignPanel.repaint();
\r
1233 final TreePanel tp;
\r
1234 if (viewport.getSelectionGroup() != null &&
\r
1235 viewport.getSelectionGroup().getSize() > 3)
\r
1237 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1239 0, viewport.alignment.getWidth());
\r
1243 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1244 type, pwType, 0, viewport.alignment.getWidth());
\r
1247 addTreeMenuItem(tp, title);
\r
1249 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1252 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1254 final MenuItem item = new MenuItem(title);
\r
1255 sortByTreeMenu.add(item);
\r
1256 item.addActionListener(new java.awt.event.ActionListener()
\r
1258 public void actionPerformed(ActionEvent e)
\r
1260 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1261 HistoryItem.SORT));
\r
1262 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1263 alignPanel.repaint();
\r
1267 treePanel.addWindowListener(new WindowAdapter()
\r
1269 public void windowClosing(WindowEvent e)
\r
1271 sortByTreeMenu.remove(item);
\r
1276 protected void documentation_actionPerformed(ActionEvent e)
\r
1278 jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");
\r
1281 protected void about_actionPerformed(ActionEvent e)
\r
1284 class AboutPanel extends Canvas
\r
1287 public AboutPanel(String version)
\r
1288 { this.version = version; }
\r
1290 public void paint(Graphics g)
\r
1292 g.setColor(Color.white);
\r
1293 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1294 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1295 FontMetrics fm = g.getFontMetrics();
\r
1296 int fh = fm.getHeight();
\r
1298 g.setColor(Color.black);
\r
1299 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1300 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1301 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1302 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1304 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1307 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1309 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1310 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1312 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1316 String version = "test";
\r
1317 java.net.URL url = getClass().getResource("/.build_properties");
\r
1322 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1323 url.openStream()));
\r
1325 while ( (line = reader.readLine()) != null)
\r
1327 if (line.indexOf("VERSION") > -1)
\r
1329 version = line.substring(line.indexOf("=") + 1);
\r
1333 catch (Exception ex)
\r
1335 ex.printStackTrace();
\r
1340 Frame frame = new Frame();
\r
1341 frame.add(new AboutPanel(version));
\r
1342 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r