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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51 String treeFile = applet.getParameter("treeFile");
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52 if (treeFile != null)
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56 treeFile = treeFile;
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57 jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
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58 getCodeBase() + treeFile, "URL");
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61 if (fin.getTree() != null)
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63 TreePanel tp = null;
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64 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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65 fin, "FromFile", applet.getCodeBase() + treeFile);
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66 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
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67 addTreeMenuItem(tp, treeFile);
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70 catch (Exception ex)
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72 ex.printStackTrace();
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76 String param = applet.getParameter("sortBy");
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79 if (param.equalsIgnoreCase("Id"))
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80 sortIDMenuItem_actionPerformed(null);
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81 else if (param.equalsIgnoreCase("Pairwise Identity"))
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82 sortPairwiseMenuItem_actionPerformed(null);
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85 this.addWindowListener(new WindowAdapter()
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87 public void windowClosing(WindowEvent e)
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89 closeMenuItem_actionPerformed(null);
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93 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
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95 public void propertyChange(java.beans.PropertyChangeEvent evt)
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97 if (evt.getPropertyName().equals("alignment"))
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105 public void inputText_actionPerformed(ActionEvent e)
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107 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);
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108 Frame frame = new Frame();
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110 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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113 protected void outputText_actionPerformed(ActionEvent e)
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115 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);
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116 Frame frame = new Frame();
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118 jalview.bin.JalviewLite.addFrame(frame,
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119 "Alignment output - " + e.getActionCommand(),
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121 cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
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122 viewport.getAlignment().
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126 public void closeMenuItem_actionPerformed(ActionEvent e)
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128 PaintRefresher.components.remove(viewport.alignment);
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132 Stack historyList = new Stack();
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133 Stack redoList = new Stack();
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135 void updateEditMenuBar()
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137 if (historyList.size() > 0)
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139 undoMenuItem.setEnabled(true);
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140 HistoryItem hi = (HistoryItem) historyList.peek();
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141 undoMenuItem.setLabel("Undo " + hi.getDescription());
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145 undoMenuItem.setEnabled(false);
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146 undoMenuItem.setLabel("Undo");
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149 if (redoList.size() > 0)
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151 redoMenuItem.setEnabled(true);
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152 HistoryItem hi = (HistoryItem) redoList.peek();
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153 redoMenuItem.setLabel("Redo " + hi.getDescription());
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157 redoMenuItem.setEnabled(false);
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158 redoMenuItem.setLabel("Redo");
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162 public void addHistoryItem(HistoryItem hi)
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164 historyList.push(hi);
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165 updateEditMenuBar();
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168 protected void undoMenuItem_actionPerformed(ActionEvent e)
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170 HistoryItem hi = (HistoryItem) historyList.pop();
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171 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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172 HistoryItem.HIDE));
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173 restoreHistoryItem(hi);
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174 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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177 protected void redoMenuItem_actionPerformed(ActionEvent e)
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179 HistoryItem hi = (HistoryItem) redoList.pop();
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180 restoreHistoryItem(hi);
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181 updateEditMenuBar();
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182 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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185 // used by undo and redo
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186 void restoreHistoryItem(HistoryItem hi)
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188 if (hi.getType() == HistoryItem.SORT)
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190 for (int i = 0; i < hi.getSequences().size(); i++)
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192 viewport.alignment.getSequences().setElementAt(hi.getSequences().
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198 for (int i = 0; i < hi.getSequences().size(); i++)
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200 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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201 if (restore.getLength() == 0)
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203 // log.System.out.println(hi.getHidden().elementAt(i));
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204 restore.setSequence(hi.getHidden().elementAt(i).toString());
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205 viewport.alignment.getSequences().insertElementAt(
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207 hi.getAlignIndex(i));
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211 restore.setSequence(hi.getHidden().elementAt(i).toString());
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214 if (hi.getType() == HistoryItem.PASTE)
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216 for (int i = viewport.alignment.getHeight() - 1;
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217 i > hi.getSequences().size() - 1; i--)
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219 viewport.alignment.deleteSequence(i);
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224 updateEditMenuBar();
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226 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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229 public void moveSelectedSequences(boolean up)
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231 SequenceGroup sg = viewport.getSelectionGroup();
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239 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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241 SequenceI seq = viewport.alignment.getSequenceAt(i);
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242 if (!sg.sequences.contains(seq))
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247 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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248 if (sg.sequences.contains(temp))
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253 viewport.alignment.getSequences().setElementAt(temp, i);
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254 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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259 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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261 SequenceI seq = viewport.alignment.getSequenceAt(i);
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262 if (!sg.sequences.contains(seq))
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267 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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268 if (sg.sequences.contains(temp))
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273 viewport.alignment.getSequences().setElementAt(temp, i);
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274 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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278 alignPanel.repaint();
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281 StringBuffer copiedSequences;
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282 protected void copy_actionPerformed(ActionEvent e)
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284 if (viewport.getSelectionGroup() == null)
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289 SequenceGroup sg = viewport.getSelectionGroup();
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290 copiedSequences = new StringBuffer();
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291 Hashtable orderedSeqs = new Hashtable();
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292 for (int i = 0; i < sg.getSize(); i++)
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294 SequenceI seq = sg.getSequenceAt(i);
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295 int index = viewport.alignment.findIndex(seq);
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296 orderedSeqs.put(index + "", seq);
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299 int index = 0, startRes, endRes;
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302 for (int i = 0; i < sg.getSize(); i++)
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304 SequenceI seq = null;
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306 while (seq == null)
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308 if (orderedSeqs.containsKey(index + ""))
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310 seq = (SequenceI) orderedSeqs.get(index + "");
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322 //Returns residue following index if gap
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323 startRes = seq.findPosition(sg.getStartRes());
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326 //Need to find the residue preceeding index if gap
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329 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
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331 ch = seq.getCharAt(j);
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332 if (!jalview.util.Comparison.isGap( (ch)))
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340 endRes += seq.getStart() -1;
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343 copiedSequences.append(seq.getName() + "\t" +
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346 seq.getSequence(sg.getStartRes(),
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347 sg.getEndRes() + 1) + "\n");
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352 protected void pasteNew_actionPerformed(ActionEvent e)
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357 protected void pasteThis_actionPerformed(ActionEvent e)
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359 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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360 HistoryItem.PASTE));
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364 void paste(boolean newAlignment)
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368 if (copiedSequences == null)
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373 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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374 Vector seqs = new Vector();
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375 while (st.hasMoreElements())
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377 String name = st.nextToken();
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378 int start = Integer.parseInt(st.nextToken());
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379 int end = Integer.parseInt(st.nextToken());
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380 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
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384 viewport.alignment.addSequence(sequence);
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388 seqs.addElement(sequence);
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394 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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395 for (int i = 0; i < seqs.size(); i++)
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397 newSeqs[i] = (SequenceI) seqs.elementAt(i);
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400 AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);
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401 String newtitle = new String("Copied sequences");
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402 if (getTitle().startsWith("Copied sequences"))
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404 newtitle = getTitle();
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408 newtitle = newtitle.concat("- from " + getTitle());
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410 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
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411 NEW_WINDOW_HEIGHT);
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415 viewport.setEndSeq(viewport.alignment.getHeight());
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416 viewport.alignment.getWidth();
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417 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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421 catch (Exception ex)
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422 {} // could be anything being pasted in here
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426 protected void cut_actionPerformed(ActionEvent e)
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428 copy_actionPerformed(null);
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429 delete_actionPerformed(null);
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432 protected void delete_actionPerformed(ActionEvent e)
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434 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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435 HistoryItem.HIDE));
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436 if (viewport.getSelectionGroup() == null)
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442 SequenceGroup sg = viewport.getSelectionGroup();
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443 boolean allSequences = false;
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444 if(sg.sequences.size()==viewport.alignment.getHeight())
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445 allSequences = true;
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447 for (int i = 0; i < sg.sequences.size(); i++)
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449 SequenceI seq = sg.getSequenceAt(i);
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450 int index = viewport.getAlignment().findIndex(seq);
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451 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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453 // If the cut affects all sequences, remove highlighted columns
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456 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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457 sg.getEndRes() + 1);
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461 if (seq.getSequence().length() < 1)
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463 viewport.getAlignment().deleteSequence(seq);
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467 viewport.getAlignment().getSequences().setElementAt(seq, index);
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471 viewport.setSelectionGroup(null);
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472 viewport.alignment.deleteGroup(sg);
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473 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
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474 if (viewport.getAlignment().getHeight() < 1)
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478 this.setVisible(false);
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480 catch (Exception ex)
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483 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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487 protected void deleteGroups_actionPerformed(ActionEvent e)
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489 viewport.alignment.deleteAllGroups();
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490 viewport.setSelectionGroup(null);
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492 alignPanel.repaint();
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495 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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497 SequenceGroup sg = new SequenceGroup();
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498 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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500 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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502 sg.setEndRes(viewport.alignment.getWidth()-1);
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503 viewport.setSelectionGroup(sg);
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504 alignPanel.repaint();
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505 PaintRefresher.Refresh(null, viewport.alignment);
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508 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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510 viewport.setSelectionGroup(null);
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511 viewport.getColumnSelection().clear();
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512 viewport.setSelectionGroup(null);
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513 alignPanel.repaint();
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514 PaintRefresher.Refresh(null, viewport.alignment);
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517 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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519 SequenceGroup sg = viewport.getSelectionGroup();
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520 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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522 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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525 PaintRefresher.Refresh(null, viewport.alignment);
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528 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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530 ColumnSelection colSel = viewport.getColumnSelection();
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531 if (colSel.size() > 0)
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533 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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534 HistoryItem.HIDE));
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535 int min = colSel.getMin();
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536 viewport.getAlignment().trimLeft(min);
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537 colSel.compensateForEdit(0, min);
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539 if (viewport.getSelectionGroup() != null)
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541 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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544 Vector groups = viewport.alignment.getGroups();
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545 for (int i = 0; i < groups.size(); i++)
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547 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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548 if (!sg.adjustForRemoveLeft(min))
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550 viewport.alignment.deleteGroup(sg);
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553 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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557 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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559 ColumnSelection colSel = viewport.getColumnSelection();
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560 if (colSel.size() > 0)
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562 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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563 HistoryItem.HIDE));
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564 int max = colSel.getMax();
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565 viewport.getAlignment().trimRight(max);
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566 if (viewport.getSelectionGroup() != null)
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568 viewport.getSelectionGroup().adjustForRemoveRight(max);
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571 Vector groups = viewport.alignment.getGroups();
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572 for (int i = 0; i < groups.size(); i++)
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574 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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575 if (!sg.adjustForRemoveRight(max))
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577 viewport.alignment.deleteGroup(sg);
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580 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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585 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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587 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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588 viewport.alignment,
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589 HistoryItem.HIDE));
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591 //This is to maintain viewport position on first residue
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592 //of first sequence
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593 SequenceI seq = viewport.alignment.getSequenceAt(0);
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594 int startRes = seq.findPosition(viewport.startRes);
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596 viewport.getAlignment().removeGaps();
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598 viewport.setStartRes(seq.findIndex(startRes)-1);
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600 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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603 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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605 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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606 HistoryItem.HIDE));
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608 //This is to maintain viewport position on first residue
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609 //of first sequence
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610 SequenceI seq = viewport.alignment.getSequenceAt(0);
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611 int startRes = seq.findPosition(viewport.startRes);
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618 int start=0, end = viewport.alignment.getWidth();
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620 if (viewport.getSelectionGroup() != null
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621 && viewport.getSelectionGroup().sequences != null
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622 && viewport.getSelectionGroup().sequences.size()>0)
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624 seqs = viewport.getSelectionGroup().sequences;
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625 start = viewport.getSelectionGroup().getStartRes();
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626 end = viewport.getSelectionGroup().getEndRes()+1;
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629 seqs = viewport.alignment.getSequences();
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631 for (int i = 0; i < seqs.size(); i++)
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633 current = (SequenceI) seqs.elementAt(i);
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634 jSize = current.getLength();
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636 // Removing a range is much quicker than removing gaps
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637 // one by one for long sequences
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639 int rangeStart=-1, rangeEnd=-1;
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643 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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660 current.deleteChars(rangeStart, rangeEnd);
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661 j-=rangeEnd-rangeStart;
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662 jSize-=rangeEnd-rangeStart;
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670 while (j < end && j < jSize);
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673 current.deleteChars(rangeStart, rangeEnd);
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676 viewport.setStartRes(seq.findIndex(startRes)-1);
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677 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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680 public void alignmentChanged()
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682 viewport.updateConsensus();
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683 viewport.updateConservation ();
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684 resetAllColourSchemes();
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685 if(alignPanel.overviewPanel!=null)
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686 alignPanel.overviewPanel.updateOverviewImage();
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687 alignPanel.repaint();
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690 void resetAllColourSchemes()
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692 ColourSchemeI cs = viewport.globalColourScheme;
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695 if (cs instanceof ClustalxColourScheme)
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697 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
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698 resetClustalX(viewport.alignment.getSequences(),
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699 viewport.alignment.getWidth());
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702 cs.setConsensus(viewport.vconsensus);
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703 if (cs.conservationApplied())
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705 Alignment al = (Alignment) viewport.alignment;
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706 Conservation c = new Conservation("All",
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707 ResidueProperties.propHash, 3,
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708 al.getSequences(), 0,
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709 al.getWidth() - 1);
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711 c.verdict(false, viewport.ConsPercGaps);
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713 cs.setConservation(c);
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717 int s, sSize = viewport.alignment.getGroups().size();
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718 for(s=0; s<sSize; s++)
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720 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
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721 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
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723 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
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725 sg.recalcConservation();
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731 public void findMenuItem_actionPerformed(ActionEvent e)
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733 Finder finder = new Finder(alignPanel);
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736 public void font_actionPerformed(ActionEvent e)
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738 Frame frame = new Frame();
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739 FontChooser fc = new FontChooser(alignPanel, frame);
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741 jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);
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745 protected void fullSeqId_actionPerformed(ActionEvent e)
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747 viewport.setShowFullId(fullSeqId.getState());
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748 alignPanel.fontChanged();
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749 alignPanel.repaint();
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752 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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754 viewport.setColourText(colourTextMenuItem.getState());
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755 alignPanel.repaint();
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758 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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760 viewport.setWrapAlignment(wrapMenuItem.getState());
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761 alignPanel.setWrapAlignment(wrapMenuItem.getState());
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762 scaleAbove.setEnabled(wrapMenuItem.getState());
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763 scaleLeft.setEnabled(wrapMenuItem.getState());
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764 scaleRight.setEnabled(wrapMenuItem.getState());
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765 alignPanel.repaint();
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768 protected void scaleAbove_actionPerformed(ActionEvent e)
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770 viewport.setScaleAboveWrapped(scaleAbove.getState());
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771 alignPanel.repaint();
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774 protected void scaleLeft_actionPerformed(ActionEvent e)
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776 viewport.setScaleLeftWrapped(scaleLeft.getState());
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777 alignPanel.repaint();
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780 protected void scaleRight_actionPerformed(ActionEvent e)
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782 viewport.setScaleRightWrapped(scaleRight.getState());
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783 alignPanel.repaint();
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786 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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788 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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789 alignPanel.repaint();
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792 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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794 viewport.setShowText(viewTextMenuItem.getState());
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795 alignPanel.repaint();
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798 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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800 viewport.setRenderGaps(renderGapsMenuItem.getState());
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801 alignPanel.repaint();
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804 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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806 if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
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808 annotationPanelMenuItem.setState(false);
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811 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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812 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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815 public void overviewMenuItem_actionPerformed(ActionEvent e)
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817 if (alignPanel.overviewPanel != null)
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822 Frame frame = new Frame();
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823 OverviewPanel overview = new OverviewPanel(alignPanel);
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824 frame.add(overview);
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825 // +50 must allow for applet frame window
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826 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
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827 overview.preferredSize().width,
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828 overview.preferredSize().height + 50);
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831 frame.addWindowListener(new WindowAdapter()
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833 public void windowClosing(WindowEvent e)
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835 alignPanel.setOverviewPanel(null);
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839 alignPanel.setOverviewPanel(overview);
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843 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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845 changeColour(null);
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848 public void clustalColour_actionPerformed(ActionEvent e)
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850 abovePIDThreshold.setState(false);
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851 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
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852 viewport.alignment.getWidth()));
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855 public void zappoColour_actionPerformed(ActionEvent e)
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857 changeColour(new ZappoColourScheme());
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860 public void taylorColour_actionPerformed(ActionEvent e)
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862 changeColour(new TaylorColourScheme());
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865 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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867 changeColour(new HydrophobicColourScheme());
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870 public void helixColour_actionPerformed(ActionEvent e)
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872 changeColour(new HelixColourScheme());
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875 public void strandColour_actionPerformed(ActionEvent e)
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877 changeColour(new StrandColourScheme());
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880 public void turnColour_actionPerformed(ActionEvent e)
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882 changeColour(new TurnColourScheme());
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885 public void buriedColour_actionPerformed(ActionEvent e)
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887 changeColour(new BuriedColourScheme());
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890 public void nucleotideColour_actionPerformed(ActionEvent e)
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892 changeColour(new NucleotideColourScheme());
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895 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
897 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
900 void changeColour(ColourSchemeI cs)
\r
906 if (viewport.getAbovePIDThreshold())
\r
908 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
910 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
912 viewport.setGlobalColourScheme(cs);
\r
916 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
919 if (viewport.getConservationSelected())
\r
922 Alignment al = (Alignment) viewport.alignment;
\r
923 Conservation c = new Conservation("All",
\r
924 ResidueProperties.propHash, 3,
\r
925 al.getSequences(), 0,
\r
926 al.getWidth() - 1);
\r
929 c.verdict(false, viewport.ConsPercGaps);
\r
931 cs.setConservation(c);
\r
933 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
939 cs.setConservation(null);
\r
942 cs.setConsensus(viewport.vconsensus);
\r
945 viewport.setGlobalColourScheme(cs);
\r
947 if (viewport.getColourAppliesToAllGroups())
\r
949 Vector groups = viewport.alignment.getGroups();
\r
950 for (int i = 0; i < groups.size(); i++)
\r
952 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
959 if (cs instanceof ClustalxColourScheme)
\r
961 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
967 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
969 catch (Exception ex)
\r
971 ex.printStackTrace();
\r
976 if (viewport.getAbovePIDThreshold()
\r
977 || cs instanceof PIDColourScheme
\r
978 || cs instanceof Blosum62ColourScheme)
\r
980 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
981 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
984 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
986 if (viewport.getConservationSelected())
\r
988 Conservation c = new Conservation("Group",
\r
989 ResidueProperties.propHash, 3,
\r
991 viewport.alignment.getWidth() - 1);
\r
993 c.verdict(false, viewport.ConsPercGaps);
\r
994 sg.cs.setConservation(c);
\r
998 sg.cs.setConservation(null);
\r
999 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1006 if (alignPanel.getOverviewPanel() != null)
\r
1008 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1011 alignPanel.repaint();
\r
1016 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1018 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1020 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1022 SliderPanel.showPIDSlider();
\r
1026 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1028 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1030 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1032 SliderPanel.showConservationSlider();
\r
1036 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1038 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1040 viewport.setAbovePIDThreshold(false);
\r
1041 abovePIDThreshold.setState(false);
\r
1043 changeColour(viewport.getGlobalColourScheme());
\r
1045 modifyConservation_actionPerformed(null);
\r
1048 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1050 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1052 conservationMenuItem.setState(false);
\r
1053 viewport.setConservationSelected(false);
\r
1055 changeColour(viewport.getGlobalColourScheme());
\r
1057 modifyPID_actionPerformed(null);
\r
1060 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1062 UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);
\r
1065 public void PIDColour_actionPerformed(ActionEvent e)
\r
1067 changeColour(new PIDColourScheme());
\r
1070 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1072 changeColour(new Blosum62ColourScheme());
\r
1075 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1077 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1078 HistoryItem.SORT));
\r
1079 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1080 viewport.getAlignment().getSequenceAt(0));
\r
1081 alignPanel.repaint();
\r
1084 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1086 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1087 HistoryItem.SORT));
\r
1088 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1089 alignPanel.repaint();
\r
1092 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1094 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1095 HistoryItem.SORT));
\r
1096 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1097 alignPanel.repaint();
\r
1101 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1103 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
1104 Frame frame = new Frame();
\r
1106 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
1111 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1113 if (viewport.getSelectionGroup().getSize() > 1)
\r
1115 Frame frame = new Frame();
\r
1116 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1117 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1121 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1124 if ( (viewport.getSelectionGroup() != null &&
\r
1125 viewport.getSelectionGroup().getSize() < 4 &&
\r
1126 viewport.getSelectionGroup().getSize() > 0)
\r
1127 || viewport.getAlignment().getHeight() < 4)
\r
1134 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
1135 Frame frame = new Frame();
\r
1136 frame.add(pcaPanel);
\r
1137 jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",
\r
1140 catch (java.lang.OutOfMemoryError ex)
\r
1146 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1148 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1151 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1153 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1156 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1158 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1161 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1163 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1166 void NewTreePanel(String type, String pwType, String title)
\r
1168 //are the sequences aligned?
\r
1169 if (!viewport.alignment.isAligned())
\r
1171 SequenceI current;
\r
1172 int Width = viewport.getAlignment().getWidth();
\r
1174 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1177 current = viewport.getAlignment().getSequenceAt(i);
\r
1179 if (current.getLength() < Width)
\r
1181 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1184 alignPanel.repaint();
\r
1188 final TreePanel tp;
\r
1189 if (viewport.getSelectionGroup() != null &&
\r
1190 viewport.getSelectionGroup().getSize() > 3)
\r
1192 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1194 0, viewport.alignment.getWidth());
\r
1198 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1199 type, pwType, 0, viewport.alignment.getWidth());
\r
1202 addTreeMenuItem(tp, title);
\r
1204 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1207 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1209 final MenuItem item = new MenuItem(title);
\r
1210 sortByTreeMenu.add(item);
\r
1211 item.addActionListener(new java.awt.event.ActionListener()
\r
1213 public void actionPerformed(ActionEvent e)
\r
1215 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1216 HistoryItem.SORT));
\r
1217 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1218 alignPanel.repaint();
\r
1222 treePanel.addWindowListener(new WindowAdapter()
\r
1224 public void windowClosing(WindowEvent e)
\r
1226 sortByTreeMenu.remove(item);
\r
1231 protected void documentation_actionPerformed(ActionEvent e)
\r
1233 jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");
\r
1236 protected void about_actionPerformed(ActionEvent e)
\r
1239 class AboutPanel extends Canvas
\r
1242 public AboutPanel(String version)
\r
1243 { this.version = version; }
\r
1245 public void paint(Graphics g)
\r
1247 g.setColor(Color.white);
\r
1248 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1249 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1250 FontMetrics fm = g.getFontMetrics();
\r
1251 int fh = fm.getHeight();
\r
1253 g.setColor(Color.black);
\r
1254 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1255 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1256 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1257 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1259 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1262 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1264 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1265 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1267 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1271 String version = "test";
\r
1272 java.net.URL url = getClass().getResource("/.build_properties");
\r
1277 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1278 url.openStream()));
\r
1280 while ( (line = reader.readLine()) != null)
\r
1282 if (line.indexOf("VERSION") > -1)
\r
1284 version = line.substring(line.indexOf("=") + 1);
\r
1288 catch (Exception ex)
\r
1290 ex.printStackTrace();
\r
1295 Frame frame = new Frame();
\r
1296 frame.add(new AboutPanel(version));
\r
1297 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r