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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51 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)
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53 this.applet = applet;
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54 viewport = new AlignViewport(al, applet);
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55 alignPanel = new AlignmentPanel(this, viewport);
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57 alignPanel.validate();
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59 String treeFile = applet.getParameter("treeFile");
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60 TreePanel treepanel = null;
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61 if (treeFile != null)
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65 treeFile = treeFile;
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66 jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
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67 getCodeBase() + treeFile, "URL");
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70 if (fin.getTree() != null)
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72 TreePanel tp = null;
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73 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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74 fin, "FromFile", applet.getCodeBase() + treeFile);
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75 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
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76 addTreeMenuItem(tp, treeFile);
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79 catch (Exception ex)
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81 ex.printStackTrace();
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88 public void inputText_actionPerformed(ActionEvent e)
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90 CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
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91 Frame frame = new Frame();
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93 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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96 protected void outputText_actionPerformed(ActionEvent e)
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98 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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99 Frame frame = new Frame();
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101 jalview.bin.JalviewLite.addFrame(frame,
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102 "Alignment output - " + e.getActionCommand(),
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104 cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
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105 viewport.getAlignment().
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109 public void closeMenuItem_actionPerformed(ActionEvent e)
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114 Stack historyList = new Stack();
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115 Stack redoList = new Stack();
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117 void updateEditMenuBar()
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119 if (historyList.size() > 0)
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121 undoMenuItem.setEnabled(true);
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122 HistoryItem hi = (HistoryItem) historyList.peek();
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123 undoMenuItem.setLabel("Undo " + hi.getDescription());
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127 undoMenuItem.setEnabled(false);
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128 undoMenuItem.setLabel("Undo");
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131 if (redoList.size() > 0)
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133 redoMenuItem.setEnabled(true);
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134 HistoryItem hi = (HistoryItem) redoList.peek();
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135 redoMenuItem.setLabel("Redo " + hi.getDescription());
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139 redoMenuItem.setEnabled(false);
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140 redoMenuItem.setLabel("Redo");
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144 public void addHistoryItem(HistoryItem hi)
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146 historyList.push(hi);
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147 updateEditMenuBar();
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150 protected void undoMenuItem_actionPerformed(ActionEvent e)
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152 HistoryItem hi = (HistoryItem) historyList.pop();
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153 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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154 HistoryItem.HIDE));
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155 restoreHistoryItem(hi);
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158 protected void redoMenuItem_actionPerformed(ActionEvent e)
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160 HistoryItem hi = (HistoryItem) redoList.pop();
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161 restoreHistoryItem(hi);
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162 updateEditMenuBar();
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163 viewport.updateConsensus();
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164 alignPanel.repaint();
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165 alignPanel.repaint();
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168 // used by undo and redo
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169 void restoreHistoryItem(HistoryItem hi)
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171 if (hi.getType() == HistoryItem.SORT)
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173 for (int i = 0; i < hi.getSequences().size(); i++)
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175 viewport.alignment.getSequences().setElementAt(hi.getSequences().
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181 for (int i = 0; i < hi.getSequences().size(); i++)
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183 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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184 if (restore.getLength() == 0)
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186 // log.System.out.println(hi.getHidden().elementAt(i));
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187 restore.setSequence(hi.getHidden().elementAt(i).toString());
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188 viewport.alignment.getSequences().insertElementAt(
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190 hi.getAlignIndex(i));
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194 restore.setSequence(hi.getHidden().elementAt(i).toString());
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197 if (hi.getType() == HistoryItem.PASTE)
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199 for (int i = viewport.alignment.getHeight() - 1;
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200 i > hi.getSequences().size() - 1; i--)
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202 viewport.alignment.deleteSequence(i);
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207 updateEditMenuBar();
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209 viewport.updateConsensus();
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210 viewport.updateConservation();
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211 alignPanel.repaint();
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214 public void moveSelectedSequences(boolean up)
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216 SequenceGroup sg = viewport.getSelectionGroup();
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224 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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226 SequenceI seq = viewport.alignment.getSequenceAt(i);
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227 if (!sg.sequences.contains(seq))
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232 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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233 if (sg.sequences.contains(temp))
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238 viewport.alignment.getSequences().setElementAt(temp, i);
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239 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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244 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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246 SequenceI seq = viewport.alignment.getSequenceAt(i);
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247 if (!sg.sequences.contains(seq))
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252 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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253 if (sg.sequences.contains(temp))
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258 viewport.alignment.getSequences().setElementAt(temp, i);
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259 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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263 alignPanel.repaint();
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266 StringBuffer copiedSequences;
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267 protected void copy_actionPerformed(ActionEvent e)
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269 if (viewport.getSelectionGroup() == null)
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274 SequenceGroup sg = viewport.getSelectionGroup();
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275 copiedSequences = new StringBuffer();
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276 Hashtable orderedSeqs = new Hashtable();
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277 for (int i = 0; i < sg.getSize(); i++)
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279 SequenceI seq = sg.getSequenceAt(i);
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280 int index = viewport.alignment.findIndex(seq);
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281 orderedSeqs.put(index + "", seq);
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284 int index = 0, startRes, endRes;
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287 for (int i = 0; i < sg.getSize(); i++)
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289 SequenceI seq = null;
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291 while (seq == null)
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293 if (orderedSeqs.containsKey(index + ""))
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295 seq = (SequenceI) orderedSeqs.get(index + "");
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307 //Returns residue following index if gap
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308 startRes = seq.findPosition(sg.getStartRes());
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311 //Need to find the residue preceeding index if gap
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314 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
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316 ch = seq.getCharAt(j);
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317 if (!jalview.util.Comparison.isGap( (ch)))
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325 endRes += seq.getStart() -1;
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328 copiedSequences.append(seq.getName() + "\t" +
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331 seq.getSequence(sg.getStartRes(),
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332 sg.getEndRes() + 1) + "\n");
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337 protected void pasteNew_actionPerformed(ActionEvent e)
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342 protected void pasteThis_actionPerformed(ActionEvent e)
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344 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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345 HistoryItem.PASTE));
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349 void paste(boolean newAlignment)
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353 if (copiedSequences == null)
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358 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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359 Vector seqs = new Vector();
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360 while (st.hasMoreElements())
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362 String name = st.nextToken();
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363 int start = Integer.parseInt(st.nextToken());
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364 int end = Integer.parseInt(st.nextToken());
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365 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
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369 viewport.alignment.addSequence(sequence);
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373 seqs.addElement(sequence);
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379 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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380 for (int i = 0; i < seqs.size(); i++)
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382 newSeqs[i] = (SequenceI) seqs.elementAt(i);
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385 AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);
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386 String newtitle = new String("Copied sequences");
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387 if (getTitle().startsWith("Copied sequences"))
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389 newtitle = getTitle();
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393 newtitle = newtitle.concat("- from " + getTitle());
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395 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
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396 NEW_WINDOW_HEIGHT);
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400 viewport.setEndSeq(viewport.alignment.getHeight());
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401 viewport.alignment.getWidth();
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402 viewport.updateConservation();
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403 viewport.updateConsensus();
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404 alignPanel.repaint();
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408 catch (Exception ex)
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409 {} // could be anything being pasted in here
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413 protected void cut_actionPerformed(ActionEvent e)
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415 copy_actionPerformed(null);
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416 delete_actionPerformed(null);
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419 protected void delete_actionPerformed(ActionEvent e)
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421 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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422 HistoryItem.HIDE));
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423 if (viewport.getSelectionGroup() == null)
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429 SequenceGroup sg = viewport.getSelectionGroup();
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430 boolean allSequences = false;
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431 if(sg.sequences.size()==viewport.alignment.getHeight())
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432 allSequences = true;
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434 for (int i = 0; i < sg.sequences.size(); i++)
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436 SequenceI seq = sg.getSequenceAt(i);
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437 int index = viewport.getAlignment().findIndex(seq);
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438 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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440 // If the cut affects all sequences, remove highlighted columns
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443 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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444 sg.getEndRes() + 1);
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448 if (seq.getSequence().length() < 1)
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450 viewport.getAlignment().deleteSequence(seq);
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454 viewport.getAlignment().getSequences().setElementAt(seq, index);
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458 viewport.setSelectionGroup(null);
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459 viewport.alignment.deleteGroup(sg);
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460 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
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461 if (viewport.getAlignment().getHeight() < 1)
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465 this.setVisible(false);
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467 catch (Exception ex)
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470 viewport.updateConservation();
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471 viewport.updateConsensus();
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472 alignPanel.repaint();
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476 protected void deleteGroups_actionPerformed(ActionEvent e)
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478 viewport.alignment.deleteAllGroups();
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479 viewport.setSelectionGroup(null);
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481 alignPanel.repaint();
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484 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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486 SequenceGroup sg = new SequenceGroup();
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487 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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489 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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491 sg.setEndRes(viewport.alignment.getWidth());
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492 viewport.setSelectionGroup(sg);
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493 alignPanel.repaint();
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494 PaintRefresher.Refresh(null, viewport.alignment);
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497 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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499 viewport.setSelectionGroup(null);
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500 viewport.getColumnSelection().clear();
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501 viewport.setSelectionGroup(null);
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502 PaintRefresher.Refresh(null, viewport.alignment);
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505 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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507 SequenceGroup sg = viewport.getSelectionGroup();
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508 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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510 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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513 PaintRefresher.Refresh(null, viewport.alignment);
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516 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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518 ColumnSelection colSel = viewport.getColumnSelection();
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519 if (colSel.size() > 0)
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521 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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522 HistoryItem.HIDE));
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523 int min = colSel.getMin();
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524 viewport.getAlignment().trimLeft(min);
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525 colSel.compensateForEdit(0, min);
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527 if (viewport.getSelectionGroup() != null)
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529 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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532 Vector groups = viewport.alignment.getGroups();
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533 for (int i = 0; i < groups.size(); i++)
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535 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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536 if (!sg.adjustForRemoveLeft(min))
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538 viewport.alignment.deleteGroup(sg);
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542 alignPanel.repaint();
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546 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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548 ColumnSelection colSel = viewport.getColumnSelection();
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549 if (colSel.size() > 0)
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551 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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552 HistoryItem.HIDE));
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553 int max = colSel.getMax();
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554 viewport.getAlignment().trimRight(max);
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555 if (viewport.getSelectionGroup() != null)
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557 viewport.getSelectionGroup().adjustForRemoveRight(max);
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560 Vector groups = viewport.alignment.getGroups();
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561 for (int i = 0; i < groups.size(); i++)
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563 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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564 if (!sg.adjustForRemoveRight(max))
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566 viewport.alignment.deleteGroup(sg);
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570 alignPanel.repaint();
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575 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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577 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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578 viewport.alignment,
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579 HistoryItem.HIDE));
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580 viewport.getAlignment().removeGaps();
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581 viewport.updateConservation();
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582 viewport.updateConsensus();
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583 alignPanel.repaint();
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586 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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588 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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589 HistoryItem.HIDE));
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596 int start=0, end = viewport.alignment.getWidth();
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598 if (viewport.getSelectionGroup() != null
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599 && viewport.getSelectionGroup().sequences != null
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600 && viewport.getSelectionGroup().sequences.size()>0)
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602 seqs = viewport.getSelectionGroup().sequences;
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603 start = viewport.getSelectionGroup().getStartRes();
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604 end = viewport.getSelectionGroup().getEndRes();
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607 seqs = viewport.alignment.getSequences();
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609 for (int i = 0; i <seqs.size(); i++)
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611 current = (SequenceI)seqs.elementAt(i);
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612 jSize = current.getLength();
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617 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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619 current.deleteCharAt(j);
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625 while(j < end && j < jSize) ;
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628 viewport.updateConservation();
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629 viewport.updateConsensus();
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630 alignPanel.repaint();
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634 public void findMenuItem_actionPerformed(ActionEvent e)
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636 Finder finder = new Finder(alignPanel);
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639 public void font_actionPerformed(ActionEvent e)
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641 Frame frame = new Frame();
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642 FontChooser fc = new FontChooser(alignPanel, frame);
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644 jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);
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648 protected void fullSeqId_actionPerformed(ActionEvent e)
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650 viewport.setShowFullId(fullSeqId.getState());
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651 alignPanel.fontChanged();
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652 alignPanel.repaint();
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655 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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657 viewport.setColourText(colourTextMenuItem.getState());
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658 alignPanel.repaint();
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661 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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663 viewport.setWrapAlignment(wrapMenuItem.getState());
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664 alignPanel.setWrapAlignment(wrapMenuItem.getState());
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665 scaleAbove.setEnabled(wrapMenuItem.getState());
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666 scaleLeft.setEnabled(wrapMenuItem.getState());
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667 scaleRight.setEnabled(wrapMenuItem.getState());
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668 alignPanel.repaint();
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671 protected void scaleAbove_actionPerformed(ActionEvent e)
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673 viewport.setScaleAboveWrapped(scaleAbove.getState());
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674 alignPanel.repaint();
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677 protected void scaleLeft_actionPerformed(ActionEvent e)
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679 viewport.setScaleLeftWrapped(scaleLeft.getState());
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680 alignPanel.repaint();
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683 protected void scaleRight_actionPerformed(ActionEvent e)
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685 viewport.setScaleRightWrapped(scaleRight.getState());
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686 alignPanel.repaint();
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689 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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691 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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692 alignPanel.repaint();
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695 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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697 viewport.setShowText(viewTextMenuItem.getState());
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698 alignPanel.repaint();
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701 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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703 viewport.setRenderGaps(renderGapsMenuItem.getState());
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704 alignPanel.repaint();
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707 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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709 if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
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711 annotationPanelMenuItem.setState(false);
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714 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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715 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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718 public void overviewMenuItem_actionPerformed(ActionEvent e)
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720 if (alignPanel.overviewPanel != null)
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725 Frame frame = new Frame();
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726 OverviewPanel overview = new OverviewPanel(alignPanel);
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727 frame.add(overview);
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728 // +50 must allow for applet frame window
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729 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
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730 overview.preferredSize().width,
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731 overview.preferredSize().height + 50);
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734 frame.addWindowListener(new WindowAdapter()
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736 public void windowClosing(WindowEvent e)
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738 alignPanel.setOverviewPanel(null);
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742 alignPanel.setOverviewPanel(overview);
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746 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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748 changeColour(null);
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751 public void clustalColour_actionPerformed(ActionEvent e)
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753 abovePIDThreshold.setState(false);
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754 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
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755 viewport.alignment.getWidth()));
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758 public void zappoColour_actionPerformed(ActionEvent e)
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760 changeColour(new ZappoColourScheme());
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763 public void taylorColour_actionPerformed(ActionEvent e)
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765 changeColour(new TaylorColourScheme());
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768 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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770 changeColour(new HydrophobicColourScheme());
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773 public void helixColour_actionPerformed(ActionEvent e)
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775 changeColour(new HelixColourScheme());
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778 public void strandColour_actionPerformed(ActionEvent e)
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780 changeColour(new StrandColourScheme());
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783 public void turnColour_actionPerformed(ActionEvent e)
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785 changeColour(new TurnColourScheme());
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788 public void buriedColour_actionPerformed(ActionEvent e)
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790 changeColour(new BuriedColourScheme());
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793 public void nucleotideColour_actionPerformed(ActionEvent e)
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795 changeColour(new NucleotideColourScheme());
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798 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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800 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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803 void changeColour(ColourSchemeI cs)
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807 if (viewport.getAbovePIDThreshold())
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809 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
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811 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
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813 viewport.setGlobalColourScheme(cs);
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817 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
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820 if (viewport.getConservationSelected())
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823 Alignment al = (Alignment) viewport.alignment;
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824 Conservation c = new Conservation("All",
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825 ResidueProperties.propHash, 3,
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826 al.getSequences(), 0,
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827 al.getWidth() - 1);
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830 c.verdict(false, viewport.ConsPercGaps);
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832 cs.setConservation(c);
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834 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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835 cs.setConsensus(viewport.vconsensus);
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836 viewport.setGlobalColourScheme(cs);
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838 SliderPanel.setConservationSlider(alignPanel, cs, "Background");
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843 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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846 cs.setConsensus(viewport.vconsensus);
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848 viewport.setGlobalColourScheme(cs);
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851 if (viewport.getColourAppliesToAllGroups())
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853 Vector groups = viewport.alignment.getGroups();
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854 for (int i = 0; i < groups.size(); i++)
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856 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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863 if (cs instanceof ClustalxColourScheme)
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865 ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
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866 cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());
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873 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
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875 catch (Exception ex)
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877 ex.printStackTrace();
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882 if (viewport.getAbovePIDThreshold()
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883 || cs instanceof PIDColourScheme
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884 || cs instanceof Blosum62ColourScheme)
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886 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
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887 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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890 if (viewport.getConservationSelected())
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892 Conservation c = new Conservation("Group",
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893 ResidueProperties.propHash, 3,
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895 viewport.alignment.getWidth() - 1);
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897 c.verdict(false, viewport.ConsPercGaps);
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899 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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900 cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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905 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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906 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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912 updateCSConsensus();
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914 if (alignPanel.getOverviewPanel() != null)
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916 alignPanel.getOverviewPanel().updateOverviewImage();
\r
919 alignPanel.repaint();
\r
922 public void updateCSConsensus()
\r
924 //Colour schemes must have their consensus updated
\r
928 protected void modifyPID_actionPerformed(ActionEvent e)
\r
930 if (viewport.getAbovePIDThreshold())
\r
932 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
934 SliderPanel.showPIDSlider();
\r
938 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
940 if (viewport.getConservationSelected())
\r
942 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
944 SliderPanel.showConservationSlider();
\r
948 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
950 viewport.setConservationSelected(conservationMenuItem.getState());
\r
952 viewport.setAbovePIDThreshold(false);
\r
953 abovePIDThreshold.setState(false);
\r
955 changeColour(viewport.getGlobalColourScheme());
\r
957 modifyConservation_actionPerformed(null);
\r
960 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
962 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
964 conservationMenuItem.setState(false);
\r
965 viewport.setConservationSelected(false);
\r
967 changeColour(viewport.getGlobalColourScheme());
\r
969 modifyPID_actionPerformed(null);
\r
972 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
974 UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);
\r
977 public void PIDColour_actionPerformed(ActionEvent e)
\r
979 changeColour(new PIDColourScheme());
\r
982 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
984 changeColour(new Blosum62ColourScheme());
\r
987 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
989 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
990 HistoryItem.SORT));
\r
991 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
992 viewport.getAlignment().getSequenceAt(0));
\r
993 alignPanel.repaint();
\r
996 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
998 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
999 HistoryItem.SORT));
\r
1000 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1001 alignPanel.repaint();
\r
1004 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1006 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1007 HistoryItem.SORT));
\r
1008 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1009 alignPanel.repaint();
\r
1013 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1015 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
1016 Frame frame = new Frame();
\r
1018 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
1023 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1025 if (viewport.getSelectionGroup().getSize() > 1)
\r
1027 Frame frame = new Frame();
\r
1028 frame.add(new PairwiseAlignPanel(viewport));
\r
1029 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1033 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1036 if ( (viewport.getSelectionGroup() != null &&
\r
1037 viewport.getSelectionGroup().getSize() < 4 &&
\r
1038 viewport.getSelectionGroup().getSize() > 0)
\r
1039 || viewport.getAlignment().getHeight() < 4)
\r
1046 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
1047 Frame frame = new Frame();
\r
1048 frame.add(pcaPanel);
\r
1049 jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",
\r
1052 catch (java.lang.OutOfMemoryError ex)
\r
1058 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1060 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1063 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1065 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1068 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1070 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1073 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1075 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1078 void NewTreePanel(String type, String pwType, String title)
\r
1080 //are the sequences aligned?
\r
1081 if (!viewport.alignment.isAligned())
\r
1083 SequenceI current;
\r
1084 int Width = viewport.getAlignment().getWidth();
\r
1086 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1089 current = viewport.getAlignment().getSequenceAt(i);
\r
1091 if (current.getLength() < Width)
\r
1093 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1096 alignPanel.repaint();
\r
1100 final TreePanel tp;
\r
1101 if (viewport.getSelectionGroup() != null &&
\r
1102 viewport.getSelectionGroup().getSize() > 3)
\r
1104 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1106 0, viewport.alignment.getWidth());
\r
1110 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1111 type, pwType, 0, viewport.alignment.getWidth());
\r
1114 addTreeMenuItem(tp, title);
\r
1116 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1119 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1121 final MenuItem item = new MenuItem(title);
\r
1122 sortByTreeMenu.add(item);
\r
1123 item.addActionListener(new java.awt.event.ActionListener()
\r
1125 public void actionPerformed(ActionEvent e)
\r
1127 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1128 HistoryItem.SORT));
\r
1129 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1130 alignPanel.repaint();
\r
1134 treePanel.addWindowListener(new WindowAdapter()
\r
1136 public void windowClosing(WindowEvent e)
\r
1138 sortByTreeMenu.remove(item);
\r
1143 protected void documentation_actionPerformed(ActionEvent e)
\r
1145 jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");
\r
1148 protected void about_actionPerformed(ActionEvent e)
\r
1151 class AboutPanel extends Canvas
\r
1154 public AboutPanel(String version)
\r
1155 { this.version = version; }
\r
1157 public void paint(Graphics g)
\r
1159 g.setColor(Color.white);
\r
1160 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1161 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1162 FontMetrics fm = g.getFontMetrics();
\r
1163 int fh = fm.getHeight();
\r
1165 g.setColor(Color.black);
\r
1166 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1167 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1168 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1169 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1171 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1174 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1176 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1177 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1179 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1183 String version = "test";
\r
1184 java.net.URL url = getClass().getResource("/.build_properties");
\r
1189 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1190 url.openStream()));
\r
1192 while ( (line = reader.readLine()) != null)
\r
1194 if (line.indexOf("VERSION") > -1)
\r
1196 version = line.substring(line.indexOf("=") + 1);
\r
1200 catch (Exception ex)
\r
1202 ex.printStackTrace();
\r
1207 Frame frame = new Frame();
\r
1208 frame.add(new AboutPanel(version));
\r
1209 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r