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 public static final int NEW_WINDOW_WIDTH = 700;
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39 public static final 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)
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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 treeFile = treeFile;
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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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88 this.addWindowListener(new WindowAdapter()
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90 public void windowClosing(WindowEvent e)
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92 closeMenuItem_actionPerformed(null);
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96 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
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98 public void propertyChange(java.beans.PropertyChangeEvent evt)
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100 if (evt.getPropertyName().equals("alignment"))
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102 alignmentChanged();
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108 public void inputText_actionPerformed(ActionEvent e)
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110 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);
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111 Frame frame = new Frame();
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113 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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116 protected void outputText_actionPerformed(ActionEvent e)
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118 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);
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119 Frame frame = new Frame();
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121 jalview.bin.JalviewLite.addFrame(frame,
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122 "Alignment output - " + e.getActionCommand(),
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124 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
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125 viewport.getAlignment().
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129 public void closeMenuItem_actionPerformed(ActionEvent e)
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131 PaintRefresher.components.remove(viewport.alignment);
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133 if(PaintRefresher.components.size()==0 && applet==null)
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137 Stack historyList = new Stack();
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138 Stack redoList = new Stack();
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140 void updateEditMenuBar()
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142 if (historyList.size() > 0)
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144 undoMenuItem.setEnabled(true);
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145 HistoryItem hi = (HistoryItem) historyList.peek();
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146 undoMenuItem.setLabel("Undo " + hi.getDescription());
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150 undoMenuItem.setEnabled(false);
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151 undoMenuItem.setLabel("Undo");
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154 if (redoList.size() > 0)
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156 redoMenuItem.setEnabled(true);
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157 HistoryItem hi = (HistoryItem) redoList.peek();
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158 redoMenuItem.setLabel("Redo " + hi.getDescription());
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162 redoMenuItem.setEnabled(false);
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163 redoMenuItem.setLabel("Redo");
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167 public void addHistoryItem(HistoryItem hi)
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169 historyList.push(hi);
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170 updateEditMenuBar();
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173 protected void undoMenuItem_actionPerformed(ActionEvent e)
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175 HistoryItem hi = (HistoryItem) historyList.pop();
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176 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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177 HistoryItem.HIDE));
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178 restoreHistoryItem(hi);
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179 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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182 protected void redoMenuItem_actionPerformed(ActionEvent e)
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184 HistoryItem hi = (HistoryItem) redoList.pop();
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185 restoreHistoryItem(hi);
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186 updateEditMenuBar();
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187 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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190 // used by undo and redo
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191 void restoreHistoryItem(HistoryItem hi)
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193 if (hi.getType() == HistoryItem.SORT)
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195 for (int i = 0; i < hi.getSequences().size(); i++)
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197 viewport.alignment.getSequences().setElementAt(hi.getSequences().
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203 for (int i = 0; i < hi.getSequences().size(); i++)
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205 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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206 if (restore.getLength() == 0)
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208 // log.System.out.println(hi.getHidden().elementAt(i));
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209 restore.setSequence(hi.getHidden().elementAt(i).toString());
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210 viewport.alignment.getSequences().insertElementAt(
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212 hi.getAlignIndex(i));
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216 restore.setSequence(hi.getHidden().elementAt(i).toString());
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219 if (hi.getType() == HistoryItem.PASTE)
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221 for (int i = viewport.alignment.getHeight() - 1;
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222 i > hi.getSequences().size() - 1; i--)
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224 viewport.alignment.deleteSequence(i);
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229 updateEditMenuBar();
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231 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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234 public void moveSelectedSequences(boolean up)
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236 SequenceGroup sg = viewport.getSelectionGroup();
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244 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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246 SequenceI seq = viewport.alignment.getSequenceAt(i);
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247 if (!sg.sequences.contains(seq))
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252 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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253 if (sg.sequences.contains(temp))
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258 viewport.alignment.getSequences().setElementAt(temp, i);
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259 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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264 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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266 SequenceI seq = viewport.alignment.getSequenceAt(i);
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267 if (!sg.sequences.contains(seq))
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272 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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273 if (sg.sequences.contains(temp))
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278 viewport.alignment.getSequences().setElementAt(temp, i);
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279 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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283 alignPanel.repaint();
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286 StringBuffer copiedSequences;
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287 protected void copy_actionPerformed(ActionEvent e)
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289 if (viewport.getSelectionGroup() == null)
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294 SequenceGroup sg = viewport.getSelectionGroup();
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295 copiedSequences = new StringBuffer();
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296 Hashtable orderedSeqs = new Hashtable();
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297 for (int i = 0; i < sg.getSize(); i++)
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299 SequenceI seq = sg.getSequenceAt(i);
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300 int index = viewport.alignment.findIndex(seq);
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301 orderedSeqs.put(index + "", seq);
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304 int index = 0, startRes, endRes;
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307 for (int i = 0; i < sg.getSize(); i++)
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309 SequenceI seq = null;
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311 while (seq == null)
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313 if (orderedSeqs.containsKey(index + ""))
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315 seq = (SequenceI) orderedSeqs.get(index + "");
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327 //Returns residue following index if gap
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328 startRes = seq.findPosition(sg.getStartRes());
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331 //Need to find the residue preceeding index if gap
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334 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
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336 ch = seq.getCharAt(j);
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337 if (!jalview.util.Comparison.isGap( (ch)))
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345 endRes += seq.getStart() -1;
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348 copiedSequences.append(seq.getName() + "\t" +
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351 seq.getSequence(sg.getStartRes(),
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352 sg.getEndRes() + 1) + "\n");
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357 protected void pasteNew_actionPerformed(ActionEvent e)
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362 protected void pasteThis_actionPerformed(ActionEvent e)
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364 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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365 HistoryItem.PASTE));
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369 void paste(boolean newAlignment)
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373 if (copiedSequences == null)
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378 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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379 Vector seqs = new Vector();
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380 while (st.hasMoreElements())
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382 String name = st.nextToken();
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383 int start = Integer.parseInt(st.nextToken());
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384 int end = Integer.parseInt(st.nextToken());
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385 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
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389 viewport.alignment.addSequence(sequence);
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393 seqs.addElement(sequence);
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399 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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400 for (int i = 0; i < seqs.size(); i++)
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402 newSeqs[i] = (SequenceI) seqs.elementAt(i);
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405 AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);
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406 String newtitle = new String("Copied sequences");
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407 if (getTitle().startsWith("Copied sequences"))
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409 newtitle = getTitle();
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413 newtitle = newtitle.concat("- from " + getTitle());
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415 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
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416 NEW_WINDOW_HEIGHT);
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420 viewport.setEndSeq(viewport.alignment.getHeight());
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421 viewport.alignment.getWidth();
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422 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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426 catch (Exception ex)
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427 {} // could be anything being pasted in here
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431 protected void cut_actionPerformed(ActionEvent e)
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433 copy_actionPerformed(null);
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434 delete_actionPerformed(null);
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437 protected void delete_actionPerformed(ActionEvent e)
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439 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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440 HistoryItem.HIDE));
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441 if (viewport.getSelectionGroup() == null)
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447 SequenceGroup sg = viewport.getSelectionGroup();
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448 boolean allSequences = false;
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449 if(sg.sequences.size()==viewport.alignment.getHeight())
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450 allSequences = true;
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452 for (int i = 0; i < sg.sequences.size(); i++)
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454 SequenceI seq = sg.getSequenceAt(i);
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455 int index = viewport.getAlignment().findIndex(seq);
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456 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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458 // If the cut affects all sequences, remove highlighted columns
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461 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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462 sg.getEndRes() + 1);
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466 if (seq.getSequence().length() < 1)
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468 viewport.getAlignment().deleteSequence(seq);
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472 viewport.getAlignment().getSequences().setElementAt(seq, index);
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476 viewport.setSelectionGroup(null);
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477 viewport.alignment.deleteGroup(sg);
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478 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
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479 if (viewport.getAlignment().getHeight() < 1)
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483 this.setVisible(false);
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485 catch (Exception ex)
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488 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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492 protected void deleteGroups_actionPerformed(ActionEvent e)
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494 viewport.alignment.deleteAllGroups();
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495 viewport.setSelectionGroup(null);
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497 alignPanel.repaint();
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500 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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502 SequenceGroup sg = new SequenceGroup();
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503 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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505 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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507 sg.setEndRes(viewport.alignment.getWidth()-1);
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508 viewport.setSelectionGroup(sg);
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509 alignPanel.repaint();
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510 PaintRefresher.Refresh(null, viewport.alignment);
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513 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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515 viewport.setSelectionGroup(null);
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516 viewport.getColumnSelection().clear();
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517 viewport.setSelectionGroup(null);
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518 alignPanel.repaint();
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519 PaintRefresher.Refresh(null, viewport.alignment);
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522 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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524 SequenceGroup sg = viewport.getSelectionGroup();
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525 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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527 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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530 PaintRefresher.Refresh(null, viewport.alignment);
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533 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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535 ColumnSelection colSel = viewport.getColumnSelection();
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536 if (colSel.size() > 0)
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538 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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539 HistoryItem.HIDE));
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540 int min = colSel.getMin();
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541 viewport.getAlignment().trimLeft(min);
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542 colSel.compensateForEdit(0, min);
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544 if (viewport.getSelectionGroup() != null)
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546 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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549 Vector groups = viewport.alignment.getGroups();
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550 for (int i = 0; i < groups.size(); i++)
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552 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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553 if (!sg.adjustForRemoveLeft(min))
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555 viewport.alignment.deleteGroup(sg);
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558 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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562 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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564 ColumnSelection colSel = viewport.getColumnSelection();
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565 if (colSel.size() > 0)
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567 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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568 HistoryItem.HIDE));
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569 int max = colSel.getMax();
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570 viewport.getAlignment().trimRight(max);
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571 if (viewport.getSelectionGroup() != null)
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573 viewport.getSelectionGroup().adjustForRemoveRight(max);
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576 Vector groups = viewport.alignment.getGroups();
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577 for (int i = 0; i < groups.size(); i++)
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579 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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580 if (!sg.adjustForRemoveRight(max))
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582 viewport.alignment.deleteGroup(sg);
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585 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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590 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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592 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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593 viewport.alignment,
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594 HistoryItem.HIDE));
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596 //This is to maintain viewport position on first residue
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597 //of first sequence
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598 SequenceI seq = viewport.alignment.getSequenceAt(0);
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599 int startRes = seq.findPosition(viewport.startRes);
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601 viewport.getAlignment().removeGaps();
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603 viewport.setStartRes(seq.findIndex(startRes)-1);
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605 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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608 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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610 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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611 HistoryItem.HIDE));
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613 //This is to maintain viewport position on first residue
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614 //of first sequence
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615 SequenceI seq = viewport.alignment.getSequenceAt(0);
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616 int startRes = seq.findPosition(viewport.startRes);
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623 int start=0, end = viewport.alignment.getWidth();
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625 if (viewport.getSelectionGroup() != null
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626 && viewport.getSelectionGroup().sequences != null
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627 && viewport.getSelectionGroup().sequences.size()>0)
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629 seqs = viewport.getSelectionGroup().sequences;
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630 start = viewport.getSelectionGroup().getStartRes();
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631 end = viewport.getSelectionGroup().getEndRes()+1;
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634 seqs = viewport.alignment.getSequences();
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636 for (int i = 0; i < seqs.size(); i++)
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638 current = (SequenceI) seqs.elementAt(i);
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639 jSize = current.getLength();
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641 // Removing a range is much quicker than removing gaps
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642 // one by one for long sequences
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644 int rangeStart=-1, rangeEnd=-1;
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648 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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665 current.deleteChars(rangeStart, rangeEnd);
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666 j-=rangeEnd-rangeStart;
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667 jSize-=rangeEnd-rangeStart;
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675 while (j < end && j < jSize);
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678 current.deleteChars(rangeStart, rangeEnd);
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681 viewport.setStartRes(seq.findIndex(startRes)-1);
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682 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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685 public void alignmentChanged()
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687 viewport.updateConsensus();
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688 viewport.updateConservation ();
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689 resetAllColourSchemes();
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690 if(alignPanel.overviewPanel!=null)
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691 alignPanel.overviewPanel.updateOverviewImage();
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692 alignPanel.repaint();
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695 void resetAllColourSchemes()
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697 ColourSchemeI cs = viewport.globalColourScheme;
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700 if (cs instanceof ClustalxColourScheme)
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702 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
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703 resetClustalX(viewport.alignment.getSequences(),
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704 viewport.alignment.getWidth());
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707 cs.setConsensus(viewport.vconsensus);
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708 if (cs.conservationApplied())
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710 Alignment al = (Alignment) viewport.alignment;
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711 Conservation c = new Conservation("All",
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712 ResidueProperties.propHash, 3,
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713 al.getSequences(), 0,
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714 al.getWidth() - 1);
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716 c.verdict(false, viewport.ConsPercGaps);
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718 cs.setConservation(c);
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722 int s, sSize = viewport.alignment.getGroups().size();
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723 for(s=0; s<sSize; s++)
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725 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
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726 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
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728 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
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730 sg.recalcConservation();
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736 public void findMenuItem_actionPerformed(ActionEvent e)
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738 Finder finder = new Finder(alignPanel);
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741 public void font_actionPerformed(ActionEvent e)
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743 Frame frame = new Frame();
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744 FontChooser fc = new FontChooser(alignPanel, frame);
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746 jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);
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750 protected void fullSeqId_actionPerformed(ActionEvent e)
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752 viewport.setShowFullId(fullSeqId.getState());
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753 alignPanel.fontChanged();
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754 alignPanel.repaint();
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757 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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759 viewport.setColourText(colourTextMenuItem.getState());
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760 alignPanel.repaint();
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763 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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765 viewport.setWrapAlignment(wrapMenuItem.getState());
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766 alignPanel.setWrapAlignment(wrapMenuItem.getState());
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767 scaleAbove.setEnabled(wrapMenuItem.getState());
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768 scaleLeft.setEnabled(wrapMenuItem.getState());
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769 scaleRight.setEnabled(wrapMenuItem.getState());
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770 alignPanel.repaint();
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773 protected void scaleAbove_actionPerformed(ActionEvent e)
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775 viewport.setScaleAboveWrapped(scaleAbove.getState());
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776 alignPanel.repaint();
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779 protected void scaleLeft_actionPerformed(ActionEvent e)
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781 viewport.setScaleLeftWrapped(scaleLeft.getState());
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782 alignPanel.repaint();
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785 protected void scaleRight_actionPerformed(ActionEvent e)
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787 viewport.setScaleRightWrapped(scaleRight.getState());
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788 alignPanel.repaint();
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791 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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793 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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794 alignPanel.repaint();
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797 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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799 viewport.setShowText(viewTextMenuItem.getState());
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800 alignPanel.repaint();
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803 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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805 viewport.setRenderGaps(renderGapsMenuItem.getState());
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806 alignPanel.repaint();
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809 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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811 if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
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813 annotationPanelMenuItem.setState(false);
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816 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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817 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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820 public void overviewMenuItem_actionPerformed(ActionEvent e)
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822 if (alignPanel.overviewPanel != null)
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827 Frame frame = new Frame();
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828 OverviewPanel overview = new OverviewPanel(alignPanel);
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829 frame.add(overview);
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830 // +50 must allow for applet frame window
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831 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
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832 overview.preferredSize().width,
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833 overview.preferredSize().height + 50);
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836 frame.addWindowListener(new WindowAdapter()
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838 public void windowClosing(WindowEvent e)
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840 alignPanel.setOverviewPanel(null);
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844 alignPanel.setOverviewPanel(overview);
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848 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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850 changeColour(null);
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853 public void clustalColour_actionPerformed(ActionEvent e)
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855 abovePIDThreshold.setState(false);
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856 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
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857 viewport.alignment.getWidth()));
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860 public void zappoColour_actionPerformed(ActionEvent e)
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862 changeColour(new ZappoColourScheme());
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865 public void taylorColour_actionPerformed(ActionEvent e)
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867 changeColour(new TaylorColourScheme());
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870 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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872 changeColour(new HydrophobicColourScheme());
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875 public void helixColour_actionPerformed(ActionEvent e)
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877 changeColour(new HelixColourScheme());
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880 public void strandColour_actionPerformed(ActionEvent e)
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882 changeColour(new StrandColourScheme());
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885 public void turnColour_actionPerformed(ActionEvent e)
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887 changeColour(new TurnColourScheme());
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890 public void buriedColour_actionPerformed(ActionEvent e)
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892 changeColour(new BuriedColourScheme());
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895 public void nucleotideColour_actionPerformed(ActionEvent e)
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897 changeColour(new NucleotideColourScheme());
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900 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
902 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
905 void changeColour(ColourSchemeI cs)
\r
911 if (viewport.getAbovePIDThreshold())
\r
913 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
915 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
917 viewport.setGlobalColourScheme(cs);
\r
921 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
924 if (viewport.getConservationSelected())
\r
927 Alignment al = (Alignment) viewport.alignment;
\r
928 Conservation c = new Conservation("All",
\r
929 ResidueProperties.propHash, 3,
\r
930 al.getSequences(), 0,
\r
931 al.getWidth() - 1);
\r
934 c.verdict(false, viewport.ConsPercGaps);
\r
936 cs.setConservation(c);
\r
938 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
944 cs.setConservation(null);
\r
947 cs.setConsensus(viewport.vconsensus);
\r
950 viewport.setGlobalColourScheme(cs);
\r
952 if (viewport.getColourAppliesToAllGroups())
\r
954 Vector groups = viewport.alignment.getGroups();
\r
955 for (int i = 0; i < groups.size(); i++)
\r
957 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
964 if (cs instanceof ClustalxColourScheme)
\r
966 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
972 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
974 catch (Exception ex)
\r
976 ex.printStackTrace();
\r
981 if (viewport.getAbovePIDThreshold()
\r
982 || cs instanceof PIDColourScheme
\r
983 || cs instanceof Blosum62ColourScheme)
\r
985 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
986 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
989 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
991 if (viewport.getConservationSelected())
\r
993 Conservation c = new Conservation("Group",
\r
994 ResidueProperties.propHash, 3,
\r
996 viewport.alignment.getWidth() - 1);
\r
998 c.verdict(false, viewport.ConsPercGaps);
\r
999 sg.cs.setConservation(c);
\r
1003 sg.cs.setConservation(null);
\r
1004 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1011 if (alignPanel.getOverviewPanel() != null)
\r
1013 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1016 alignPanel.repaint();
\r
1021 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1023 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1025 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1027 SliderPanel.showPIDSlider();
\r
1031 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1033 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1035 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1037 SliderPanel.showConservationSlider();
\r
1041 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1043 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1045 viewport.setAbovePIDThreshold(false);
\r
1046 abovePIDThreshold.setState(false);
\r
1048 changeColour(viewport.getGlobalColourScheme());
\r
1050 modifyConservation_actionPerformed(null);
\r
1053 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1055 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1057 conservationMenuItem.setState(false);
\r
1058 viewport.setConservationSelected(false);
\r
1060 changeColour(viewport.getGlobalColourScheme());
\r
1062 modifyPID_actionPerformed(null);
\r
1065 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1067 UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);
\r
1070 public void PIDColour_actionPerformed(ActionEvent e)
\r
1072 changeColour(new PIDColourScheme());
\r
1075 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1077 changeColour(new Blosum62ColourScheme());
\r
1080 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1082 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1083 HistoryItem.SORT));
\r
1084 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1085 viewport.getAlignment().getSequenceAt(0));
\r
1086 alignPanel.repaint();
\r
1089 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1091 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1092 HistoryItem.SORT));
\r
1093 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1094 alignPanel.repaint();
\r
1097 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1099 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1100 HistoryItem.SORT));
\r
1101 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1102 alignPanel.repaint();
\r
1106 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1108 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
1109 Frame frame = new Frame();
\r
1111 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
1116 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1118 if (viewport.getSelectionGroup().getSize() > 1)
\r
1120 Frame frame = new Frame();
\r
1121 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1122 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1126 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1128 //are the sequences aligned?
\r
1129 if (!viewport.alignment.isAligned())
\r
1131 SequenceI current;
\r
1132 int Width = viewport.getAlignment().getWidth();
\r
1134 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1137 current = viewport.getAlignment().getSequenceAt(i);
\r
1139 if (current.getLength() < Width)
\r
1141 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1144 alignPanel.repaint();
\r
1147 if ( (viewport.getSelectionGroup() != null &&
\r
1148 viewport.getSelectionGroup().getSize() < 4 &&
\r
1149 viewport.getSelectionGroup().getSize() > 0)
\r
1150 || viewport.getAlignment().getHeight() < 4)
\r
1157 PCAPanel pcaPanel = new PCAPanel(viewport);
\r
1158 Frame frame = new Frame();
\r
1159 frame.add(pcaPanel);
\r
1160 jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",
\r
1163 catch (java.lang.OutOfMemoryError ex)
\r
1169 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1171 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1174 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1176 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1179 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1181 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1184 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1186 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1189 void NewTreePanel(String type, String pwType, String title)
\r
1191 //are the sequences aligned?
\r
1192 if (!viewport.alignment.isAligned())
\r
1194 SequenceI current;
\r
1195 int Width = viewport.getAlignment().getWidth();
\r
1197 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1200 current = viewport.getAlignment().getSequenceAt(i);
\r
1202 if (current.getLength() < Width)
\r
1204 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1207 alignPanel.repaint();
\r
1211 final TreePanel tp;
\r
1212 if (viewport.getSelectionGroup() != null &&
\r
1213 viewport.getSelectionGroup().getSize() > 3)
\r
1215 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1217 0, viewport.alignment.getWidth());
\r
1221 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1222 type, pwType, 0, viewport.alignment.getWidth());
\r
1225 addTreeMenuItem(tp, title);
\r
1227 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1230 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1232 final MenuItem item = new MenuItem(title);
\r
1233 sortByTreeMenu.add(item);
\r
1234 item.addActionListener(new java.awt.event.ActionListener()
\r
1236 public void actionPerformed(ActionEvent e)
\r
1238 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1239 HistoryItem.SORT));
\r
1240 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1241 alignPanel.repaint();
\r
1245 treePanel.addWindowListener(new WindowAdapter()
\r
1247 public void windowClosing(WindowEvent e)
\r
1249 sortByTreeMenu.remove(item);
\r
1254 protected void documentation_actionPerformed(ActionEvent e)
\r
1256 jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");
\r
1259 protected void about_actionPerformed(ActionEvent e)
\r
1262 class AboutPanel extends Canvas
\r
1265 public AboutPanel(String version)
\r
1266 { this.version = version; }
\r
1268 public void paint(Graphics g)
\r
1270 g.setColor(Color.white);
\r
1271 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1272 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1273 FontMetrics fm = g.getFontMetrics();
\r
1274 int fh = fm.getHeight();
\r
1276 g.setColor(Color.black);
\r
1277 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1278 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1279 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1280 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1282 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1285 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1287 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1288 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1290 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1294 String version = "test";
\r
1295 java.net.URL url = getClass().getResource("/.build_properties");
\r
1300 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1301 url.openStream()));
\r
1303 while ( (line = reader.readLine()) != null)
\r
1305 if (line.indexOf("VERSION") > -1)
\r
1307 version = line.substring(line.indexOf("=") + 1);
\r
1311 catch (Exception ex)
\r
1313 ex.printStackTrace();
\r
1318 Frame frame = new Frame();
\r
1319 frame.add(new AboutPanel(version));
\r
1320 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r