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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31 public class AlignFrame
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34 final AlignmentPanel alignPanel;
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35 final AlignViewport viewport;
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36 public static final int NEW_WINDOW_WIDTH = 700;
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37 public static final int NEW_WINDOW_HEIGHT = 500;
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38 jalview.bin.JalviewLite applet;
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40 public AlignFrame(AlignmentI al)
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43 viewport = new AlignViewport(al, null);
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44 alignPanel = new AlignmentPanel(this, viewport);
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46 alignPanel.validate();
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49 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)
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51 this.applet = applet;
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52 viewport = new AlignViewport(al, applet);
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53 alignPanel = new AlignmentPanel(this, viewport);
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55 alignPanel.validate();
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57 String treeFile = applet.getParameter("treeFile");
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58 TreePanel treepanel = null;
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59 if (treeFile != null)
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63 treeFile = treeFile;
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64 jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
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65 getCodeBase() + treeFile, "URL");
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68 if (fin.getTree() != null)
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70 TreePanel tp = null;
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71 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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72 fin, "FromFile", applet.getCodeBase() + treeFile);
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73 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
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74 addTreeMenuItem(tp, treeFile);
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77 catch (Exception ex)
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79 ex.printStackTrace();
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85 public void inputText_actionPerformed(ActionEvent e)
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87 CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
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88 Frame frame = new Frame();
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90 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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93 protected void outputText_actionPerformed(ActionEvent e)
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95 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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96 Frame frame = new Frame();
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98 jalview.bin.JalviewLite.addFrame(frame,
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99 "Alignment output - " + e.getActionCommand(),
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101 cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
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102 viewport.getAlignment().
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106 public void closeMenuItem_actionPerformed(ActionEvent e)
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111 Stack historyList = new Stack();
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112 Stack redoList = new Stack();
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114 void updateEditMenuBar()
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116 if (historyList.size() > 0)
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118 undoMenuItem.setEnabled(true);
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119 HistoryItem hi = (HistoryItem) historyList.peek();
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120 undoMenuItem.setLabel("Undo " + hi.getDescription());
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124 undoMenuItem.setEnabled(false);
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125 undoMenuItem.setLabel("Undo");
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128 if (redoList.size() > 0)
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130 redoMenuItem.setEnabled(true);
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131 HistoryItem hi = (HistoryItem) redoList.peek();
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132 redoMenuItem.setLabel("Redo " + hi.getDescription());
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136 redoMenuItem.setEnabled(false);
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137 redoMenuItem.setLabel("Redo");
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141 public void addHistoryItem(HistoryItem hi)
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143 historyList.push(hi);
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144 updateEditMenuBar();
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147 protected void undoMenuItem_actionPerformed(ActionEvent e)
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149 HistoryItem hi = (HistoryItem) historyList.pop();
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150 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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151 HistoryItem.HIDE));
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152 restoreHistoryItem(hi);
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155 protected void redoMenuItem_actionPerformed(ActionEvent e)
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157 HistoryItem hi = (HistoryItem) redoList.pop();
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158 restoreHistoryItem(hi);
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159 updateEditMenuBar();
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160 viewport.updateConsensus();
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161 alignPanel.repaint();
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162 alignPanel.repaint();
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165 // used by undo and redo
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166 void restoreHistoryItem(HistoryItem hi)
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168 if (hi.getType() == HistoryItem.SORT)
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170 for (int i = 0; i < hi.getSequences().size(); i++)
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172 viewport.alignment.getSequences().setElementAt(hi.getSequences().
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178 for (int i = 0; i < hi.getSequences().size(); i++)
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180 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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181 if (restore.getLength() == 0)
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183 // log.System.out.println(hi.getHidden().elementAt(i));
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184 restore.setSequence(hi.getHidden().elementAt(i).toString());
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185 viewport.alignment.getSequences().insertElementAt(
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187 hi.getAlignIndex(i));
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191 restore.setSequence(hi.getHidden().elementAt(i).toString());
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194 if (hi.getType() == HistoryItem.PASTE)
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196 for (int i = viewport.alignment.getHeight() - 1;
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197 i > hi.getSequences().size() - 1; i--)
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199 viewport.alignment.deleteSequence(i);
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204 updateEditMenuBar();
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206 viewport.updateConsensus();
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207 viewport.updateConservation();
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208 alignPanel.repaint();
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211 public void moveSelectedSequences(boolean up)
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213 SequenceGroup sg = viewport.getSelectionGroup();
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221 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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223 SequenceI seq = viewport.alignment.getSequenceAt(i);
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224 if (!sg.sequences.contains(seq))
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229 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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230 if (sg.sequences.contains(temp))
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235 viewport.alignment.getSequences().setElementAt(temp, i);
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236 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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241 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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243 SequenceI seq = viewport.alignment.getSequenceAt(i);
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244 if (!sg.sequences.contains(seq))
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249 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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250 if (sg.sequences.contains(temp))
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255 viewport.alignment.getSequences().setElementAt(temp, i);
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256 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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260 alignPanel.repaint();
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263 StringBuffer copiedSequences;
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264 protected void copy_actionPerformed(ActionEvent e)
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266 if (viewport.getSelectionGroup() == null)
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271 SequenceGroup sg = viewport.getSelectionGroup();
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272 copiedSequences = new StringBuffer();
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273 Hashtable orderedSeqs = new Hashtable();
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274 for (int i = 0; i < sg.getSize(); i++)
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276 SequenceI seq = sg.getSequenceAt(i);
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277 int index = viewport.alignment.findIndex(seq);
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278 orderedSeqs.put(index + "", seq);
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282 for (int i = 0; i < sg.getSize(); i++)
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284 SequenceI seq = null;
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285 while (seq == null)
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287 if (orderedSeqs.containsKey(index + ""))
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289 seq = (SequenceI) orderedSeqs.get(index + "");
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299 copiedSequences.append(seq.getName() + "\t" +
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300 seq.findPosition(sg.getStartRes()) + "\t"
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301 + seq.findPosition(sg.getEndRes()) + "\t"
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303 sg.getSequenceAt(i).getSequence(sg.getStartRes(),
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304 sg.getEndRes() + 1) + "\n");
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309 protected void pasteNew_actionPerformed(ActionEvent e)
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314 protected void pasteThis_actionPerformed(ActionEvent e)
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316 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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317 HistoryItem.PASTE));
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321 void paste(boolean newAlignment)
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325 if (copiedSequences == null)
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330 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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331 Vector seqs = new Vector();
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332 while (st.hasMoreElements())
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334 String name = st.nextToken();
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335 int start = Integer.parseInt(st.nextToken());
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336 int end = Integer.parseInt(st.nextToken());
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337 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
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341 viewport.alignment.addSequence(sequence);
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345 seqs.addElement(sequence);
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351 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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352 for (int i = 0; i < seqs.size(); i++)
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354 newSeqs[i] = (SequenceI) seqs.elementAt(i);
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357 AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);
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358 String newtitle = new String("Copied sequences");
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359 if (getTitle().startsWith("Copied sequences"))
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361 newtitle = getTitle();
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365 newtitle = newtitle.concat("- from " + getTitle());
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367 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
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368 NEW_WINDOW_HEIGHT);
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372 viewport.setEndSeq(viewport.alignment.getHeight());
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373 viewport.alignment.getWidth();
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374 viewport.updateConservation();
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375 viewport.updateConsensus();
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376 alignPanel.repaint();
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380 catch (Exception ex)
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381 {} // could be anything being pasted in here
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385 protected void cut_actionPerformed(ActionEvent e)
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387 copy_actionPerformed(null);
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388 delete_actionPerformed(null);
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391 protected void delete_actionPerformed(ActionEvent e)
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393 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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394 HistoryItem.HIDE));
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395 if (viewport.getSelectionGroup() == null)
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400 SequenceGroup sg = viewport.getSelectionGroup();
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401 for (int i = 0; i < sg.sequences.size(); i++)
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403 SequenceI seq = sg.getSequenceAt(i);
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404 int index = viewport.getAlignment().findIndex(seq);
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405 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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407 if (seq.getSequence().length() < 1)
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409 viewport.getAlignment().deleteSequence(seq);
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413 viewport.getAlignment().getSequences().setElementAt(seq, index);
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417 viewport.setSelectionGroup(null);
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418 viewport.alignment.deleteGroup(sg);
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419 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
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420 if (viewport.getAlignment().getHeight() < 1)
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424 this.setVisible(false);
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426 catch (Exception ex)
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429 viewport.updateConservation();
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430 viewport.updateConsensus();
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431 alignPanel.repaint();
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435 protected void deleteGroups_actionPerformed(ActionEvent e)
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437 viewport.alignment.deleteAllGroups();
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438 viewport.setSelectionGroup(null);
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440 alignPanel.repaint();
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443 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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445 SequenceGroup sg = new SequenceGroup();
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446 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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448 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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450 sg.setEndRes(viewport.alignment.getWidth());
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451 viewport.setSelectionGroup(sg);
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452 alignPanel.repaint();
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453 PaintRefresher.Refresh(null);
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456 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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458 viewport.setSelectionGroup(null);
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459 viewport.getColumnSelection().clear();
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460 viewport.setSelectionGroup(null);
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461 PaintRefresher.Refresh(null);
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464 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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466 SequenceGroup sg = viewport.getSelectionGroup();
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467 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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469 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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472 PaintRefresher.Refresh(null);
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475 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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477 ColumnSelection colSel = viewport.getColumnSelection();
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478 if (colSel.size() > 0)
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480 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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481 HistoryItem.HIDE));
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482 int min = colSel.getMin();
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483 viewport.getAlignment().trimLeft(min);
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484 colSel.compensateForEdit(0, min);
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486 if (viewport.getSelectionGroup() != null)
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488 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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491 Vector groups = viewport.alignment.getGroups();
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492 for (int i = 0; i < groups.size(); i++)
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494 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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495 if (!sg.adjustForRemoveLeft(min))
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497 viewport.alignment.deleteGroup(sg);
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501 alignPanel.repaint();
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505 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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507 ColumnSelection colSel = viewport.getColumnSelection();
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508 if (colSel.size() > 0)
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510 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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511 HistoryItem.HIDE));
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512 int max = colSel.getMax();
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513 viewport.getAlignment().trimRight(max);
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514 if (viewport.getSelectionGroup() != null)
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516 viewport.getSelectionGroup().adjustForRemoveRight(max);
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519 Vector groups = viewport.alignment.getGroups();
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520 for (int i = 0; i < groups.size(); i++)
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522 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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523 if (!sg.adjustForRemoveRight(max))
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525 viewport.alignment.deleteGroup(sg);
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529 alignPanel.repaint();
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534 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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536 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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537 viewport.alignment,
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538 HistoryItem.HIDE));
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539 viewport.getAlignment().removeGaps();
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540 viewport.updateConservation();
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541 viewport.updateConsensus();
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542 alignPanel.repaint();
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545 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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547 addHistoryItem(new HistoryItem("Remove Gaps",
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548 viewport.alignment,
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549 HistoryItem.HIDE));
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552 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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554 current = viewport.getAlignment().getSequenceAt(i);
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555 jSize = current.getLength();
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556 for (int j = 0; j < jSize; j++)
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558 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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560 current.deleteCharAt(j);
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566 viewport.updateConservation();
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567 viewport.updateConsensus();
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568 alignPanel.repaint();
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571 public void findMenuItem_actionPerformed(ActionEvent e)
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573 Finder finder = new Finder(alignPanel);
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576 public void font_actionPerformed(ActionEvent e)
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578 Frame frame = new Frame();
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579 FontChooser fc = new FontChooser(alignPanel, frame);
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581 jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);
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585 protected void fullSeqId_actionPerformed(ActionEvent e)
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587 viewport.setShowFullId(fullSeqId.getState());
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588 alignPanel.fontChanged();
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589 alignPanel.repaint();
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592 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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594 viewport.setColourText(colourTextMenuItem.getState());
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595 alignPanel.repaint();
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598 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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600 viewport.setWrapAlignment(wrapMenuItem.getState());
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601 alignPanel.setWrapAlignment(wrapMenuItem.getState());
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602 scaleAbove.setEnabled(wrapMenuItem.getState());
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603 scaleLeft.setEnabled(wrapMenuItem.getState());
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604 scaleRight.setEnabled(wrapMenuItem.getState());
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605 alignPanel.repaint();
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608 protected void scaleAbove_actionPerformed(ActionEvent e)
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610 viewport.setScaleAboveWrapped(scaleAbove.getState());
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611 alignPanel.repaint();
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614 protected void scaleLeft_actionPerformed(ActionEvent e)
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616 viewport.setScaleLeftWrapped(scaleLeft.getState());
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617 alignPanel.repaint();
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620 protected void scaleRight_actionPerformed(ActionEvent e)
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622 viewport.setScaleRightWrapped(scaleRight.getState());
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623 alignPanel.repaint();
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626 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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628 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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629 alignPanel.repaint();
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632 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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634 viewport.setShowText(viewTextMenuItem.getState());
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635 alignPanel.repaint();
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638 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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640 viewport.setRenderGaps(renderGapsMenuItem.getState());
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641 alignPanel.repaint();
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644 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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646 if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
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648 annotationPanelMenuItem.setState(false);
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651 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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652 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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655 public void overviewMenuItem_actionPerformed(ActionEvent e)
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657 if (alignPanel.overviewPanel != null)
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662 Frame frame = new Frame();
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663 OverviewPanel overview = new OverviewPanel(alignPanel);
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664 frame.add(overview);
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665 // +50 must allow for applet frame window
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666 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
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667 overview.preferredSize().width,
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668 overview.preferredSize().height + 50);
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671 frame.addWindowListener(new WindowAdapter()
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673 public void windowClosing(WindowEvent e)
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675 alignPanel.setOverviewPanel(null);
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679 alignPanel.setOverviewPanel(overview);
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683 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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685 changeColour(null);
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688 public void clustalColour_actionPerformed(ActionEvent e)
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690 abovePIDThreshold.setState(false);
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691 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
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692 viewport.alignment.getWidth()));
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695 public void zappoColour_actionPerformed(ActionEvent e)
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697 changeColour(new ZappoColourScheme());
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700 public void taylorColour_actionPerformed(ActionEvent e)
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702 changeColour(new TaylorColourScheme());
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705 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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707 changeColour(new HydrophobicColourScheme());
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710 public void helixColour_actionPerformed(ActionEvent e)
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712 changeColour(new HelixColourScheme());
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715 public void strandColour_actionPerformed(ActionEvent e)
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717 changeColour(new StrandColourScheme());
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720 public void turnColour_actionPerformed(ActionEvent e)
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722 changeColour(new TurnColourScheme());
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725 public void buriedColour_actionPerformed(ActionEvent e)
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727 changeColour(new BuriedColourScheme());
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730 public void nucleotideColour_actionPerformed(ActionEvent e)
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732 changeColour(new NucleotideColourScheme());
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735 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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737 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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740 void changeColour(ColourSchemeI cs)
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744 if (viewport.getAbovePIDThreshold())
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746 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
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748 if (cs instanceof ResidueColourScheme)
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750 ( (ResidueColourScheme) cs).setThreshold(threshold);
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753 viewport.setGlobalColourScheme(cs);
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755 else if (cs instanceof ResidueColourScheme)
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757 ( (ResidueColourScheme) cs).setThreshold(0);
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760 if (viewport.getConservationSelected())
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762 ConservationColourScheme ccs = null;
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764 Alignment al = (Alignment) viewport.alignment;
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765 Conservation c = new Conservation("All",
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766 ResidueProperties.propHash, 3,
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767 al.getSequences(), 0,
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768 al.getWidth() - 1);
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771 c.verdict(false, viewport.ConsPercGaps);
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773 ccs = new ConservationColourScheme(c, cs);
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775 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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776 ccs.setConsensus(viewport.vconsensus);
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777 viewport.setGlobalColourScheme(ccs);
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779 SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
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784 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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787 cs.setConsensus(viewport.vconsensus);
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789 viewport.setGlobalColourScheme(cs);
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792 if (viewport.getColourAppliesToAllGroups())
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794 Vector groups = viewport.alignment.getGroups();
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795 for (int i = 0; i < groups.size(); i++)
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797 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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804 if (cs instanceof ClustalxColourScheme)
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806 ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
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807 cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());
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814 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
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816 catch (Exception ex)
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818 ex.printStackTrace();
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823 if (viewport.getAbovePIDThreshold())
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825 if (sg.cs instanceof ResidueColourScheme)
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827 ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
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830 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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833 if (viewport.getConservationSelected())
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835 Conservation c = new Conservation("Group",
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836 ResidueProperties.propHash, 3,
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838 viewport.alignment.getWidth() - 1);
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840 c.verdict(false, viewport.ConsPercGaps);
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841 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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843 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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844 ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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849 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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850 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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856 if (alignPanel.getOverviewPanel() != null)
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858 alignPanel.getOverviewPanel().updateOverviewImage();
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861 alignPanel.repaint();
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864 protected void modifyPID_actionPerformed(ActionEvent e)
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866 if (viewport.getAbovePIDThreshold())
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868 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
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870 SliderPanel.showPIDSlider();
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874 protected void modifyConservation_actionPerformed(ActionEvent e)
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876 if (viewport.getConservationSelected())
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878 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
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880 SliderPanel.showConservationSlider();
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884 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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886 viewport.setConservationSelected(conservationMenuItem.getState());
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888 viewport.setAbovePIDThreshold(false);
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889 abovePIDThreshold.setState(false);
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891 ColourSchemeI cs = viewport.getGlobalColourScheme();
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892 if (cs instanceof ConservationColourScheme)
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894 changeColour( ( (ConservationColourScheme) cs).cs);
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901 modifyConservation_actionPerformed(null);
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904 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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906 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
908 conservationMenuItem.setState(false);
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909 viewport.setConservationSelected(false);
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911 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
913 if (cs instanceof ConservationColourScheme)
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915 changeColour( ( (ConservationColourScheme) cs).cs);
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922 modifyPID_actionPerformed(null);
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925 public void userDefinedColour_actionPerformed(ActionEvent e)
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927 UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);
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930 public void PIDColour_actionPerformed(ActionEvent e)
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932 changeColour(new PIDColourScheme());
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935 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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937 changeColour(new Blosum62ColourScheme());
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940 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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942 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
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943 HistoryItem.SORT));
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944 AlignmentSorter.sortByPID(viewport.getAlignment(),
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945 viewport.getAlignment().getSequenceAt(0));
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946 alignPanel.repaint();
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949 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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951 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
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952 HistoryItem.SORT));
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953 AlignmentSorter.sortByID(viewport.getAlignment());
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954 alignPanel.repaint();
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957 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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959 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
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960 HistoryItem.SORT));
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961 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
962 AlignmentSorter.sortGroups(viewport.getAlignment());
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963 alignPanel.repaint();
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966 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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968 RedundancyPanel sp = new RedundancyPanel(alignPanel);
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969 Frame frame = new Frame();
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971 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
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976 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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978 if (viewport.getSelectionGroup().getSize() > 1)
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980 Frame frame = new Frame();
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981 frame.add(new PairwiseAlignPanel(viewport));
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982 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
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986 public void PCAMenuItem_actionPerformed(ActionEvent e)
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989 if ( (viewport.getSelectionGroup() != null &&
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990 viewport.getSelectionGroup().getSize() < 4 &&
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991 viewport.getSelectionGroup().getSize() > 0)
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992 || viewport.getAlignment().getHeight() < 4)
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999 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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1000 Frame frame = new Frame();
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1001 frame.add(pcaPanel);
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1002 jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",
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1005 catch (java.lang.OutOfMemoryError ex)
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1011 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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1013 NewTreePanel("AV", "PID", "Average distance tree using PID");
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1016 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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1018 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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1021 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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1023 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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1026 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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1028 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1031 void NewTreePanel(String type, String pwType, String title)
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1033 //are the sequences aligned?
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1034 if (!viewport.alignment.isAligned())
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1039 final TreePanel tp;
\r
1040 if (viewport.getSelectionGroup() != null &&
\r
1041 viewport.getSelectionGroup().getSize() > 3)
\r
1043 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1045 0, viewport.alignment.getWidth());
\r
1049 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1050 type, pwType, 0, viewport.alignment.getWidth());
\r
1053 addTreeMenuItem(tp, title);
\r
1055 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1058 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1060 final MenuItem item = new MenuItem(title);
\r
1061 sortByTreeMenu.add(item);
\r
1062 item.addActionListener(new java.awt.event.ActionListener()
\r
1064 public void actionPerformed(ActionEvent e)
\r
1066 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1067 HistoryItem.SORT));
\r
1068 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1069 alignPanel.repaint();
\r
1073 treePanel.addWindowListener(new WindowAdapter()
\r
1075 public void windowClosing(WindowEvent e)
\r
1077 sortByTreeMenu.remove(item);
\r
1082 protected void documentation_actionPerformed(ActionEvent e)
\r
1085 jalview.bin.JalviewLite.showURL("http://www.jalview.org");
\r
1089 protected void about_actionPerformed(ActionEvent e)
\r
1094 public void paint(Graphics g)
\r
1096 g.setColor(Color.white);
\r
1097 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1098 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1099 FontMetrics fm = g.getFontMetrics();
\r
1100 int fh = fm.getHeight();
\r
1102 g.setColor(Color.black);
\r
1103 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1104 g.drawString("JalView - Release 2.0", 200, y += fh);
\r
1105 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1106 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1108 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1111 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1113 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1114 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1116 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1120 Frame frame = new Frame();
\r
1121 frame.add(new AboutPanel());
\r
1122 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
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