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", viewport.alignment,
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548 HistoryItem.HIDE));
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555 int start=0, end = viewport.alignment.getWidth();
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557 if(viewport.getSelectionGroup()!=null)
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559 seqs = viewport.getSelectionGroup().sequences;
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560 start = viewport.getSelectionGroup().getStartRes();
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561 end = viewport.getSelectionGroup().getEndRes();
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564 seqs = viewport.alignment.getSequences();
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566 for (int i = 0; i <seqs.size(); i++)
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568 current = (SequenceI)seqs.elementAt(i);
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569 jSize = current.getLength();
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574 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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576 current.deleteCharAt(j);
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585 viewport.updateConservation();
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586 viewport.updateConsensus();
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587 alignPanel.repaint();
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591 public void findMenuItem_actionPerformed(ActionEvent e)
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593 Finder finder = new Finder(alignPanel);
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596 public void font_actionPerformed(ActionEvent e)
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598 Frame frame = new Frame();
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599 FontChooser fc = new FontChooser(alignPanel, frame);
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601 jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);
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605 protected void fullSeqId_actionPerformed(ActionEvent e)
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607 viewport.setShowFullId(fullSeqId.getState());
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608 alignPanel.fontChanged();
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609 alignPanel.repaint();
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612 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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614 viewport.setColourText(colourTextMenuItem.getState());
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615 alignPanel.repaint();
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618 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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620 viewport.setWrapAlignment(wrapMenuItem.getState());
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621 alignPanel.setWrapAlignment(wrapMenuItem.getState());
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622 scaleAbove.setEnabled(wrapMenuItem.getState());
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623 scaleLeft.setEnabled(wrapMenuItem.getState());
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624 scaleRight.setEnabled(wrapMenuItem.getState());
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625 alignPanel.repaint();
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628 protected void scaleAbove_actionPerformed(ActionEvent e)
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630 viewport.setScaleAboveWrapped(scaleAbove.getState());
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631 alignPanel.repaint();
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634 protected void scaleLeft_actionPerformed(ActionEvent e)
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636 viewport.setScaleLeftWrapped(scaleLeft.getState());
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637 alignPanel.repaint();
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640 protected void scaleRight_actionPerformed(ActionEvent e)
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642 viewport.setScaleRightWrapped(scaleRight.getState());
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643 alignPanel.repaint();
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646 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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648 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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649 alignPanel.repaint();
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652 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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654 viewport.setShowText(viewTextMenuItem.getState());
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655 alignPanel.repaint();
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658 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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660 viewport.setRenderGaps(renderGapsMenuItem.getState());
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661 alignPanel.repaint();
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664 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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666 if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
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668 annotationPanelMenuItem.setState(false);
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671 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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672 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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675 public void overviewMenuItem_actionPerformed(ActionEvent e)
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677 if (alignPanel.overviewPanel != null)
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682 Frame frame = new Frame();
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683 OverviewPanel overview = new OverviewPanel(alignPanel);
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684 frame.add(overview);
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685 // +50 must allow for applet frame window
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686 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
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687 overview.preferredSize().width,
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688 overview.preferredSize().height + 50);
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691 frame.addWindowListener(new WindowAdapter()
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693 public void windowClosing(WindowEvent e)
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695 alignPanel.setOverviewPanel(null);
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699 alignPanel.setOverviewPanel(overview);
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703 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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705 changeColour(null);
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708 public void clustalColour_actionPerformed(ActionEvent e)
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710 abovePIDThreshold.setState(false);
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711 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
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712 viewport.alignment.getWidth()));
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715 public void zappoColour_actionPerformed(ActionEvent e)
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717 changeColour(new ZappoColourScheme());
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720 public void taylorColour_actionPerformed(ActionEvent e)
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722 changeColour(new TaylorColourScheme());
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725 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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727 changeColour(new HydrophobicColourScheme());
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730 public void helixColour_actionPerformed(ActionEvent e)
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732 changeColour(new HelixColourScheme());
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735 public void strandColour_actionPerformed(ActionEvent e)
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737 changeColour(new StrandColourScheme());
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740 public void turnColour_actionPerformed(ActionEvent e)
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742 changeColour(new TurnColourScheme());
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745 public void buriedColour_actionPerformed(ActionEvent e)
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747 changeColour(new BuriedColourScheme());
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750 public void nucleotideColour_actionPerformed(ActionEvent e)
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752 changeColour(new NucleotideColourScheme());
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755 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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757 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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760 void changeColour(ColourSchemeI cs)
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764 if (viewport.getAbovePIDThreshold())
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766 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
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768 if (cs instanceof ResidueColourScheme)
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770 ( (ResidueColourScheme) cs).setThreshold(threshold);
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773 viewport.setGlobalColourScheme(cs);
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775 else if (cs instanceof ResidueColourScheme)
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777 ( (ResidueColourScheme) cs).setThreshold(0);
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780 if (viewport.getConservationSelected())
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782 ConservationColourScheme ccs = null;
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784 Alignment al = (Alignment) viewport.alignment;
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785 Conservation c = new Conservation("All",
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786 ResidueProperties.propHash, 3,
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787 al.getSequences(), 0,
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788 al.getWidth() - 1);
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791 c.verdict(false, viewport.ConsPercGaps);
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793 ccs = new ConservationColourScheme(c, cs);
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795 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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796 ccs.setConsensus(viewport.vconsensus);
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797 viewport.setGlobalColourScheme(ccs);
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799 SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
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804 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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807 cs.setConsensus(viewport.vconsensus);
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809 viewport.setGlobalColourScheme(cs);
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812 if (viewport.getColourAppliesToAllGroups())
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814 Vector groups = viewport.alignment.getGroups();
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815 for (int i = 0; i < groups.size(); i++)
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817 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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824 if (cs instanceof ClustalxColourScheme)
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826 ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
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827 cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());
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834 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
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836 catch (Exception ex)
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838 ex.printStackTrace();
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843 if (viewport.getAbovePIDThreshold())
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845 if (sg.cs instanceof ResidueColourScheme)
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847 ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
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850 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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853 if (viewport.getConservationSelected())
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855 Conservation c = new Conservation("Group",
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856 ResidueProperties.propHash, 3,
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858 viewport.alignment.getWidth() - 1);
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860 c.verdict(false, viewport.ConsPercGaps);
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861 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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863 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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864 ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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869 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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870 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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876 if (alignPanel.getOverviewPanel() != null)
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878 alignPanel.getOverviewPanel().updateOverviewImage();
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881 alignPanel.repaint();
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884 protected void modifyPID_actionPerformed(ActionEvent e)
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886 if (viewport.getAbovePIDThreshold())
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888 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
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890 SliderPanel.showPIDSlider();
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894 protected void modifyConservation_actionPerformed(ActionEvent e)
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896 if (viewport.getConservationSelected())
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898 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
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900 SliderPanel.showConservationSlider();
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904 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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906 viewport.setConservationSelected(conservationMenuItem.getState());
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908 viewport.setAbovePIDThreshold(false);
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909 abovePIDThreshold.setState(false);
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911 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
912 if (cs instanceof ConservationColourScheme)
\r
914 changeColour( ( (ConservationColourScheme) cs).cs);
\r
921 modifyConservation_actionPerformed(null);
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924 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
926 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
928 conservationMenuItem.setState(false);
\r
929 viewport.setConservationSelected(false);
\r
931 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
933 if (cs instanceof ConservationColourScheme)
\r
935 changeColour( ( (ConservationColourScheme) cs).cs);
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942 modifyPID_actionPerformed(null);
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945 public void userDefinedColour_actionPerformed(ActionEvent e)
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947 UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);
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950 public void PIDColour_actionPerformed(ActionEvent e)
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952 changeColour(new PIDColourScheme());
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955 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
957 changeColour(new Blosum62ColourScheme());
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960 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
962 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
963 HistoryItem.SORT));
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964 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
965 viewport.getAlignment().getSequenceAt(0));
\r
966 alignPanel.repaint();
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969 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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971 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
972 HistoryItem.SORT));
\r
973 AlignmentSorter.sortByID(viewport.getAlignment());
\r
974 alignPanel.repaint();
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977 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
979 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
980 HistoryItem.SORT));
\r
981 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
982 alignPanel.repaint();
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986 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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988 RedundancyPanel sp = new RedundancyPanel(alignPanel);
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989 Frame frame = new Frame();
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991 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
996 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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998 if (viewport.getSelectionGroup().getSize() > 1)
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1000 Frame frame = new Frame();
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1001 frame.add(new PairwiseAlignPanel(viewport));
\r
1002 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1006 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1009 if ( (viewport.getSelectionGroup() != null &&
\r
1010 viewport.getSelectionGroup().getSize() < 4 &&
\r
1011 viewport.getSelectionGroup().getSize() > 0)
\r
1012 || viewport.getAlignment().getHeight() < 4)
\r
1019 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
1020 Frame frame = new Frame();
\r
1021 frame.add(pcaPanel);
\r
1022 jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",
\r
1025 catch (java.lang.OutOfMemoryError ex)
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1031 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1033 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1036 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1038 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1041 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1043 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1046 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1048 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1051 void NewTreePanel(String type, String pwType, String title)
\r
1053 //are the sequences aligned?
\r
1054 if (!viewport.alignment.isAligned())
\r
1059 final TreePanel tp;
\r
1060 if (viewport.getSelectionGroup() != null &&
\r
1061 viewport.getSelectionGroup().getSize() > 3)
\r
1063 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1065 0, viewport.alignment.getWidth());
\r
1069 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1070 type, pwType, 0, viewport.alignment.getWidth());
\r
1073 addTreeMenuItem(tp, title);
\r
1075 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1078 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1080 final MenuItem item = new MenuItem(title);
\r
1081 sortByTreeMenu.add(item);
\r
1082 item.addActionListener(new java.awt.event.ActionListener()
\r
1084 public void actionPerformed(ActionEvent e)
\r
1086 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1087 HistoryItem.SORT));
\r
1088 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1089 alignPanel.repaint();
\r
1093 treePanel.addWindowListener(new WindowAdapter()
\r
1095 public void windowClosing(WindowEvent e)
\r
1097 sortByTreeMenu.remove(item);
\r
1102 protected void documentation_actionPerformed(ActionEvent e)
\r
1105 jalview.bin.JalviewLite.showURL("http://www.jalview.org");
\r
1109 protected void about_actionPerformed(ActionEvent e)
\r
1114 public void paint(Graphics g)
\r
1116 g.setColor(Color.white);
\r
1117 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1118 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1119 FontMetrics fm = g.getFontMetrics();
\r
1120 int fh = fm.getHeight();
\r
1122 g.setColor(Color.black);
\r
1123 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1124 g.drawString("JalView - Release 2.0", 200, y += fh);
\r
1125 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1126 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1128 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1131 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1133 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1134 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1136 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1140 Frame frame = new Frame();
\r
1141 frame.add(new AboutPanel());
\r
1142 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
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