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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42 public AlignFrame(AlignmentI al)
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45 viewport = new AlignViewport(al, null);
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46 alignPanel = new AlignmentPanel(this, viewport);
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48 alignPanel.validate();
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50 this.addWindowListener(new WindowAdapter()
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52 public void windowClosing(WindowEvent e)
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54 closeMenuItem_actionPerformed(null);
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61 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)
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63 this.applet = applet;
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64 viewport = new AlignViewport(al, applet);
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65 alignPanel = new AlignmentPanel(this, viewport);
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67 alignPanel.validate();
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69 String treeFile = applet.getParameter("treeFile");
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70 if (treeFile != null)
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74 treeFile = treeFile;
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75 jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
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76 getCodeBase() + treeFile, "URL");
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79 if (fin.getTree() != null)
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81 TreePanel tp = null;
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82 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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83 fin, "FromFile", applet.getCodeBase() + treeFile);
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84 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
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85 addTreeMenuItem(tp, treeFile);
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88 catch (Exception ex)
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90 ex.printStackTrace();
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94 this.addWindowListener(new WindowAdapter()
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96 public void windowClosing(WindowEvent e)
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98 closeMenuItem_actionPerformed(null);
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106 public void inputText_actionPerformed(ActionEvent e)
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108 CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
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109 Frame frame = new Frame();
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111 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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114 protected void outputText_actionPerformed(ActionEvent e)
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116 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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117 Frame frame = new Frame();
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119 jalview.bin.JalviewLite.addFrame(frame,
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120 "Alignment output - " + e.getActionCommand(),
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122 cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
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123 viewport.getAlignment().
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127 public void closeMenuItem_actionPerformed(ActionEvent e)
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129 PaintRefresher.components.remove(viewport.alignment);
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133 Stack historyList = new Stack();
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134 Stack redoList = new Stack();
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136 void updateEditMenuBar()
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138 if (historyList.size() > 0)
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140 undoMenuItem.setEnabled(true);
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141 HistoryItem hi = (HistoryItem) historyList.peek();
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142 undoMenuItem.setLabel("Undo " + hi.getDescription());
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146 undoMenuItem.setEnabled(false);
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147 undoMenuItem.setLabel("Undo");
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150 if (redoList.size() > 0)
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152 redoMenuItem.setEnabled(true);
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153 HistoryItem hi = (HistoryItem) redoList.peek();
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154 redoMenuItem.setLabel("Redo " + hi.getDescription());
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158 redoMenuItem.setEnabled(false);
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159 redoMenuItem.setLabel("Redo");
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163 public void addHistoryItem(HistoryItem hi)
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165 historyList.push(hi);
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166 updateEditMenuBar();
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169 protected void undoMenuItem_actionPerformed(ActionEvent e)
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171 HistoryItem hi = (HistoryItem) historyList.pop();
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172 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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173 HistoryItem.HIDE));
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174 restoreHistoryItem(hi);
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175 resetAllColourSchemes();
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178 protected void redoMenuItem_actionPerformed(ActionEvent e)
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180 HistoryItem hi = (HistoryItem) redoList.pop();
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181 restoreHistoryItem(hi);
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182 updateEditMenuBar();
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183 viewport.updateConsensus();
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184 resetAllColourSchemes();
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185 alignPanel.repaint();
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186 alignPanel.repaint();
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189 // used by undo and redo
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190 void restoreHistoryItem(HistoryItem hi)
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192 if (hi.getType() == HistoryItem.SORT)
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194 for (int i = 0; i < hi.getSequences().size(); i++)
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196 viewport.alignment.getSequences().setElementAt(hi.getSequences().
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202 for (int i = 0; i < hi.getSequences().size(); i++)
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204 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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205 if (restore.getLength() == 0)
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207 // log.System.out.println(hi.getHidden().elementAt(i));
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208 restore.setSequence(hi.getHidden().elementAt(i).toString());
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209 viewport.alignment.getSequences().insertElementAt(
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211 hi.getAlignIndex(i));
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215 restore.setSequence(hi.getHidden().elementAt(i).toString());
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218 if (hi.getType() == HistoryItem.PASTE)
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220 for (int i = viewport.alignment.getHeight() - 1;
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221 i > hi.getSequences().size() - 1; i--)
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223 viewport.alignment.deleteSequence(i);
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228 updateEditMenuBar();
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230 viewport.updateConsensus();
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231 viewport.updateConservation();
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232 alignPanel.repaint();
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235 public void moveSelectedSequences(boolean up)
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237 SequenceGroup sg = viewport.getSelectionGroup();
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245 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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247 SequenceI seq = viewport.alignment.getSequenceAt(i);
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248 if (!sg.sequences.contains(seq))
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253 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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254 if (sg.sequences.contains(temp))
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259 viewport.alignment.getSequences().setElementAt(temp, i);
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260 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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265 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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267 SequenceI seq = viewport.alignment.getSequenceAt(i);
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268 if (!sg.sequences.contains(seq))
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273 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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274 if (sg.sequences.contains(temp))
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279 viewport.alignment.getSequences().setElementAt(temp, i);
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280 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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284 alignPanel.repaint();
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287 StringBuffer copiedSequences;
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288 protected void copy_actionPerformed(ActionEvent e)
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290 if (viewport.getSelectionGroup() == null)
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295 SequenceGroup sg = viewport.getSelectionGroup();
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296 copiedSequences = new StringBuffer();
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297 Hashtable orderedSeqs = new Hashtable();
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298 for (int i = 0; i < sg.getSize(); i++)
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300 SequenceI seq = sg.getSequenceAt(i);
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301 int index = viewport.alignment.findIndex(seq);
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302 orderedSeqs.put(index + "", seq);
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305 int index = 0, startRes, endRes;
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308 for (int i = 0; i < sg.getSize(); i++)
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310 SequenceI seq = null;
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312 while (seq == null)
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314 if (orderedSeqs.containsKey(index + ""))
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316 seq = (SequenceI) orderedSeqs.get(index + "");
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328 //Returns residue following index if gap
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329 startRes = seq.findPosition(sg.getStartRes());
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332 //Need to find the residue preceeding index if gap
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335 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
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337 ch = seq.getCharAt(j);
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338 if (!jalview.util.Comparison.isGap( (ch)))
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346 endRes += seq.getStart() -1;
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349 copiedSequences.append(seq.getName() + "\t" +
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352 seq.getSequence(sg.getStartRes(),
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353 sg.getEndRes() + 1) + "\n");
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358 protected void pasteNew_actionPerformed(ActionEvent e)
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363 protected void pasteThis_actionPerformed(ActionEvent e)
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365 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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366 HistoryItem.PASTE));
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370 void paste(boolean newAlignment)
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374 if (copiedSequences == null)
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379 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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380 Vector seqs = new Vector();
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381 while (st.hasMoreElements())
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383 String name = st.nextToken();
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384 int start = Integer.parseInt(st.nextToken());
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385 int end = Integer.parseInt(st.nextToken());
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386 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
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390 viewport.alignment.addSequence(sequence);
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394 seqs.addElement(sequence);
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400 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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401 for (int i = 0; i < seqs.size(); i++)
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403 newSeqs[i] = (SequenceI) seqs.elementAt(i);
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406 AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);
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407 String newtitle = new String("Copied sequences");
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408 if (getTitle().startsWith("Copied sequences"))
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410 newtitle = getTitle();
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414 newtitle = newtitle.concat("- from " + getTitle());
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416 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
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417 NEW_WINDOW_HEIGHT);
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421 viewport.setEndSeq(viewport.alignment.getHeight());
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422 viewport.alignment.getWidth();
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423 viewport.updateConservation();
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424 viewport.updateConsensus();
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425 resetAllColourSchemes();
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426 alignPanel.repaint();
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430 catch (Exception ex)
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431 {} // could be anything being pasted in here
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435 protected void cut_actionPerformed(ActionEvent e)
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437 copy_actionPerformed(null);
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438 delete_actionPerformed(null);
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441 protected void delete_actionPerformed(ActionEvent e)
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443 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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444 HistoryItem.HIDE));
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445 if (viewport.getSelectionGroup() == null)
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451 SequenceGroup sg = viewport.getSelectionGroup();
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452 boolean allSequences = false;
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453 if(sg.sequences.size()==viewport.alignment.getHeight())
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454 allSequences = true;
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456 for (int i = 0; i < sg.sequences.size(); i++)
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458 SequenceI seq = sg.getSequenceAt(i);
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459 int index = viewport.getAlignment().findIndex(seq);
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460 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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462 // If the cut affects all sequences, remove highlighted columns
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465 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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466 sg.getEndRes() + 1);
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470 if (seq.getSequence().length() < 1)
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472 viewport.getAlignment().deleteSequence(seq);
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476 viewport.getAlignment().getSequences().setElementAt(seq, index);
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480 viewport.setSelectionGroup(null);
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481 viewport.alignment.deleteGroup(sg);
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482 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
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483 if (viewport.getAlignment().getHeight() < 1)
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487 this.setVisible(false);
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489 catch (Exception ex)
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492 viewport.updateConservation();
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493 viewport.updateConsensus();
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494 resetAllColourSchemes();
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495 alignPanel.repaint();
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499 protected void deleteGroups_actionPerformed(ActionEvent e)
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501 viewport.alignment.deleteAllGroups();
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502 viewport.setSelectionGroup(null);
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504 alignPanel.repaint();
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507 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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509 SequenceGroup sg = new SequenceGroup();
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510 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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512 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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514 sg.setEndRes(viewport.alignment.getWidth()-1);
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515 viewport.setSelectionGroup(sg);
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516 alignPanel.repaint();
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517 PaintRefresher.Refresh(null, viewport.alignment);
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520 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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522 viewport.setSelectionGroup(null);
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523 viewport.getColumnSelection().clear();
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524 viewport.setSelectionGroup(null);
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525 alignPanel.repaint();
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526 PaintRefresher.Refresh(null, viewport.alignment);
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529 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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531 SequenceGroup sg = viewport.getSelectionGroup();
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532 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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534 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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537 PaintRefresher.Refresh(null, viewport.alignment);
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540 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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542 ColumnSelection colSel = viewport.getColumnSelection();
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543 if (colSel.size() > 0)
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545 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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546 HistoryItem.HIDE));
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547 int min = colSel.getMin();
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548 viewport.getAlignment().trimLeft(min);
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549 colSel.compensateForEdit(0, min);
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551 if (viewport.getSelectionGroup() != null)
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553 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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556 Vector groups = viewport.alignment.getGroups();
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557 for (int i = 0; i < groups.size(); i++)
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559 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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560 if (!sg.adjustForRemoveLeft(min))
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562 viewport.alignment.deleteGroup(sg);
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565 resetAllColourSchemes();
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566 alignPanel.repaint();
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570 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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572 ColumnSelection colSel = viewport.getColumnSelection();
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573 if (colSel.size() > 0)
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575 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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576 HistoryItem.HIDE));
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577 int max = colSel.getMax();
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578 viewport.getAlignment().trimRight(max);
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579 if (viewport.getSelectionGroup() != null)
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581 viewport.getSelectionGroup().adjustForRemoveRight(max);
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584 Vector groups = viewport.alignment.getGroups();
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585 for (int i = 0; i < groups.size(); i++)
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587 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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588 if (!sg.adjustForRemoveRight(max))
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590 viewport.alignment.deleteGroup(sg);
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593 resetAllColourSchemes();
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594 alignPanel.repaint();
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599 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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601 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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602 viewport.alignment,
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603 HistoryItem.HIDE));
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605 //This is to maintain viewport position on first residue
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606 //of first sequence
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607 SequenceI seq = viewport.alignment.getSequenceAt(0);
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608 int startRes = seq.findPosition(viewport.startRes);
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610 viewport.getAlignment().removeGaps();
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612 viewport.setStartRes(seq.findIndex(startRes)-1);
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614 viewport.updateConservation();
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615 viewport.updateConsensus();
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616 resetAllColourSchemes();
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617 alignPanel.repaint();
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620 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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622 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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623 HistoryItem.HIDE));
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625 //This is to maintain viewport position on first residue
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626 //of first sequence
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627 SequenceI seq = viewport.alignment.getSequenceAt(0);
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628 int startRes = seq.findPosition(viewport.startRes);
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635 int start=0, end = viewport.alignment.getWidth();
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637 if (viewport.getSelectionGroup() != null
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638 && viewport.getSelectionGroup().sequences != null
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639 && viewport.getSelectionGroup().sequences.size()>0)
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641 seqs = viewport.getSelectionGroup().sequences;
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642 start = viewport.getSelectionGroup().getStartRes();
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643 end = viewport.getSelectionGroup().getEndRes();
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646 seqs = viewport.alignment.getSequences();
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648 for (int i = 0; i <seqs.size(); i++)
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650 current = (SequenceI)seqs.elementAt(i);
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651 jSize = current.getLength();
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656 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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658 current.deleteCharAt(j);
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664 while(j < end && j < jSize) ;
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667 viewport.setStartRes(seq.findIndex(startRes)-1);
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668 viewport.updateConservation();
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669 viewport.updateConsensus();
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670 resetAllColourSchemes();
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671 alignPanel.repaint();
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674 void resetAllColourSchemes()
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676 ColourSchemeI cs = viewport.globalColourScheme;
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679 cs.setConsensus(viewport.vconsensus);
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680 if(cs.conservationApplied())
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682 Alignment al = (Alignment) viewport.alignment;
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683 Conservation c = new Conservation("All",
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684 ResidueProperties.propHash, 3,
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685 al.getSequences(), 0,
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686 al.getWidth() - 1);
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688 c.verdict(false, viewport.ConsPercGaps);
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690 cs.setConservation(c);
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694 if(viewport.getGlobalColourScheme()!=null
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695 && viewport.getGlobalColourScheme() 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 int s, sSize = viewport.alignment.getGroups().size();
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703 for(s=0; s<sSize; s++)
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705 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
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706 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
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708 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
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711 sg.recalcConservation();
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718 public void findMenuItem_actionPerformed(ActionEvent e)
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720 Finder finder = new Finder(alignPanel);
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723 public void font_actionPerformed(ActionEvent e)
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725 Frame frame = new Frame();
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726 FontChooser fc = new FontChooser(alignPanel, frame);
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728 jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);
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732 protected void fullSeqId_actionPerformed(ActionEvent e)
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734 viewport.setShowFullId(fullSeqId.getState());
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735 alignPanel.fontChanged();
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736 alignPanel.repaint();
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739 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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741 viewport.setColourText(colourTextMenuItem.getState());
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742 alignPanel.repaint();
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745 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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747 viewport.setWrapAlignment(wrapMenuItem.getState());
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748 alignPanel.setWrapAlignment(wrapMenuItem.getState());
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749 scaleAbove.setEnabled(wrapMenuItem.getState());
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750 scaleLeft.setEnabled(wrapMenuItem.getState());
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751 scaleRight.setEnabled(wrapMenuItem.getState());
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752 alignPanel.repaint();
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755 protected void scaleAbove_actionPerformed(ActionEvent e)
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757 viewport.setScaleAboveWrapped(scaleAbove.getState());
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758 alignPanel.repaint();
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761 protected void scaleLeft_actionPerformed(ActionEvent e)
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763 viewport.setScaleLeftWrapped(scaleLeft.getState());
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764 alignPanel.repaint();
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767 protected void scaleRight_actionPerformed(ActionEvent e)
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769 viewport.setScaleRightWrapped(scaleRight.getState());
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770 alignPanel.repaint();
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773 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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775 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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776 alignPanel.repaint();
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779 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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781 viewport.setShowText(viewTextMenuItem.getState());
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782 alignPanel.repaint();
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785 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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787 viewport.setRenderGaps(renderGapsMenuItem.getState());
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788 alignPanel.repaint();
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791 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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793 if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
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795 annotationPanelMenuItem.setState(false);
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798 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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799 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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802 public void overviewMenuItem_actionPerformed(ActionEvent e)
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804 if (alignPanel.overviewPanel != null)
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809 Frame frame = new Frame();
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810 OverviewPanel overview = new OverviewPanel(alignPanel);
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811 frame.add(overview);
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812 // +50 must allow for applet frame window
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813 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
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814 overview.preferredSize().width,
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815 overview.preferredSize().height + 50);
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818 frame.addWindowListener(new WindowAdapter()
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820 public void windowClosing(WindowEvent e)
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822 alignPanel.setOverviewPanel(null);
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826 alignPanel.setOverviewPanel(overview);
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830 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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832 changeColour(null);
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835 public void clustalColour_actionPerformed(ActionEvent e)
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837 abovePIDThreshold.setState(false);
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838 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
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839 viewport.alignment.getWidth()));
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842 public void zappoColour_actionPerformed(ActionEvent e)
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844 changeColour(new ZappoColourScheme());
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847 public void taylorColour_actionPerformed(ActionEvent e)
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849 changeColour(new TaylorColourScheme());
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852 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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854 changeColour(new HydrophobicColourScheme());
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857 public void helixColour_actionPerformed(ActionEvent e)
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859 changeColour(new HelixColourScheme());
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862 public void strandColour_actionPerformed(ActionEvent e)
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864 changeColour(new StrandColourScheme());
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867 public void turnColour_actionPerformed(ActionEvent e)
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869 changeColour(new TurnColourScheme());
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872 public void buriedColour_actionPerformed(ActionEvent e)
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874 changeColour(new BuriedColourScheme());
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877 public void nucleotideColour_actionPerformed(ActionEvent e)
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879 changeColour(new NucleotideColourScheme());
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882 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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884 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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887 void changeColour(ColourSchemeI cs)
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893 if (viewport.getAbovePIDThreshold())
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895 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
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897 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
899 viewport.setGlobalColourScheme(cs);
\r
903 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
906 if (viewport.getConservationSelected())
\r
909 Alignment al = (Alignment) viewport.alignment;
\r
910 Conservation c = new Conservation("All",
\r
911 ResidueProperties.propHash, 3,
\r
912 al.getSequences(), 0,
\r
913 al.getWidth() - 1);
\r
916 c.verdict(false, viewport.ConsPercGaps);
\r
918 cs.setConservation(c);
\r
920 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
926 cs.setConservation(null);
\r
929 cs.setConsensus(viewport.vconsensus);
\r
932 viewport.setGlobalColourScheme(cs);
\r
934 if (viewport.getColourAppliesToAllGroups())
\r
936 Vector groups = viewport.alignment.getGroups();
\r
937 for (int i = 0; i < groups.size(); i++)
\r
939 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
946 if (cs instanceof ClustalxColourScheme)
\r
948 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
954 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
956 catch (Exception ex)
\r
958 ex.printStackTrace();
\r
963 if (viewport.getAbovePIDThreshold()
\r
964 || cs instanceof PIDColourScheme
\r
965 || cs instanceof Blosum62ColourScheme)
\r
967 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
968 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
971 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
973 if (viewport.getConservationSelected())
\r
975 Conservation c = new Conservation("Group",
\r
976 ResidueProperties.propHash, 3,
\r
978 viewport.alignment.getWidth() - 1);
\r
980 c.verdict(false, viewport.ConsPercGaps);
\r
981 sg.cs.setConservation(c);
\r
985 sg.cs.setConservation(null);
\r
986 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
993 if (alignPanel.getOverviewPanel() != null)
\r
995 alignPanel.getOverviewPanel().updateOverviewImage();
\r
998 alignPanel.repaint();
\r
1003 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1005 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1007 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1009 SliderPanel.showPIDSlider();
\r
1013 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1015 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1017 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1019 SliderPanel.showConservationSlider();
\r
1023 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1025 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1027 viewport.setAbovePIDThreshold(false);
\r
1028 abovePIDThreshold.setState(false);
\r
1030 changeColour(viewport.getGlobalColourScheme());
\r
1032 modifyConservation_actionPerformed(null);
\r
1035 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1037 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1039 conservationMenuItem.setState(false);
\r
1040 viewport.setConservationSelected(false);
\r
1042 changeColour(viewport.getGlobalColourScheme());
\r
1044 modifyPID_actionPerformed(null);
\r
1047 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1049 UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);
\r
1052 public void PIDColour_actionPerformed(ActionEvent e)
\r
1054 changeColour(new PIDColourScheme());
\r
1057 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1059 changeColour(new Blosum62ColourScheme());
\r
1062 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1064 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1065 HistoryItem.SORT));
\r
1066 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1067 viewport.getAlignment().getSequenceAt(0));
\r
1068 alignPanel.repaint();
\r
1071 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1073 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1074 HistoryItem.SORT));
\r
1075 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1076 alignPanel.repaint();
\r
1079 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1081 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1082 HistoryItem.SORT));
\r
1083 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1084 alignPanel.repaint();
\r
1088 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1090 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
1091 Frame frame = new Frame();
\r
1093 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
1098 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1100 if (viewport.getSelectionGroup().getSize() > 1)
\r
1102 Frame frame = new Frame();
\r
1103 frame.add(new PairwiseAlignPanel(viewport));
\r
1104 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1108 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1111 if ( (viewport.getSelectionGroup() != null &&
\r
1112 viewport.getSelectionGroup().getSize() < 4 &&
\r
1113 viewport.getSelectionGroup().getSize() > 0)
\r
1114 || viewport.getAlignment().getHeight() < 4)
\r
1121 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
1122 Frame frame = new Frame();
\r
1123 frame.add(pcaPanel);
\r
1124 jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",
\r
1127 catch (java.lang.OutOfMemoryError ex)
\r
1133 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1135 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1138 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1140 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1143 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1145 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1148 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1150 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1153 void NewTreePanel(String type, String pwType, String title)
\r
1155 //are the sequences aligned?
\r
1156 if (!viewport.alignment.isAligned())
\r
1158 SequenceI current;
\r
1159 int Width = viewport.getAlignment().getWidth();
\r
1161 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1164 current = viewport.getAlignment().getSequenceAt(i);
\r
1166 if (current.getLength() < Width)
\r
1168 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1171 alignPanel.repaint();
\r
1175 final TreePanel tp;
\r
1176 if (viewport.getSelectionGroup() != null &&
\r
1177 viewport.getSelectionGroup().getSize() > 3)
\r
1179 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1181 0, viewport.alignment.getWidth());
\r
1185 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1186 type, pwType, 0, viewport.alignment.getWidth());
\r
1189 addTreeMenuItem(tp, title);
\r
1191 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1194 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1196 final MenuItem item = new MenuItem(title);
\r
1197 sortByTreeMenu.add(item);
\r
1198 item.addActionListener(new java.awt.event.ActionListener()
\r
1200 public void actionPerformed(ActionEvent e)
\r
1202 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1203 HistoryItem.SORT));
\r
1204 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1205 alignPanel.repaint();
\r
1209 treePanel.addWindowListener(new WindowAdapter()
\r
1211 public void windowClosing(WindowEvent e)
\r
1213 sortByTreeMenu.remove(item);
\r
1218 protected void documentation_actionPerformed(ActionEvent e)
\r
1220 jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");
\r
1223 protected void about_actionPerformed(ActionEvent e)
\r
1226 class AboutPanel extends Canvas
\r
1229 public AboutPanel(String version)
\r
1230 { this.version = version; }
\r
1232 public void paint(Graphics g)
\r
1234 g.setColor(Color.white);
\r
1235 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1236 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1237 FontMetrics fm = g.getFontMetrics();
\r
1238 int fh = fm.getHeight();
\r
1240 g.setColor(Color.black);
\r
1241 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1242 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1243 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1244 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1246 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1249 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1251 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1252 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1254 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1258 String version = "test";
\r
1259 java.net.URL url = getClass().getResource("/.build_properties");
\r
1264 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1265 url.openStream()));
\r
1267 while ( (line = reader.readLine()) != null)
\r
1269 if (line.indexOf("VERSION") > -1)
\r
1271 version = line.substring(line.indexOf("=") + 1);
\r
1275 catch (Exception ex)
\r
1277 ex.printStackTrace();
\r
1282 Frame frame = new Frame();
\r
1283 frame.add(new AboutPanel(version));
\r
1284 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r