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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401 SequenceGroup sg = viewport.getSelectionGroup();
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402 boolean allSequences = false;
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403 if(sg.sequences.size()==viewport.alignment.getHeight())
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404 allSequences = true;
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406 for (int i = 0; i < sg.sequences.size(); i++)
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408 SequenceI seq = sg.getSequenceAt(i);
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409 int index = viewport.getAlignment().findIndex(seq);
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410 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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412 // If the cut affects all sequences, remove highlighted columns
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415 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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416 sg.getEndRes() + 1);
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420 if (seq.getSequence().length() < 1)
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422 viewport.getAlignment().deleteSequence(seq);
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426 viewport.getAlignment().getSequences().setElementAt(seq, index);
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430 viewport.setSelectionGroup(null);
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431 viewport.alignment.deleteGroup(sg);
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432 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
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433 if (viewport.getAlignment().getHeight() < 1)
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437 this.setVisible(false);
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439 catch (Exception ex)
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442 viewport.updateConservation();
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443 viewport.updateConsensus();
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444 alignPanel.repaint();
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448 protected void deleteGroups_actionPerformed(ActionEvent e)
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450 viewport.alignment.deleteAllGroups();
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451 viewport.setSelectionGroup(null);
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453 alignPanel.repaint();
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456 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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458 SequenceGroup sg = new SequenceGroup();
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459 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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461 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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463 sg.setEndRes(viewport.alignment.getWidth());
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464 viewport.setSelectionGroup(sg);
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465 alignPanel.repaint();
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466 PaintRefresher.Refresh(null);
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469 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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471 viewport.setSelectionGroup(null);
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472 viewport.getColumnSelection().clear();
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473 viewport.setSelectionGroup(null);
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474 PaintRefresher.Refresh(null);
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477 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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479 SequenceGroup sg = viewport.getSelectionGroup();
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480 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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482 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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485 PaintRefresher.Refresh(null);
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488 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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490 ColumnSelection colSel = viewport.getColumnSelection();
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491 if (colSel.size() > 0)
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493 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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494 HistoryItem.HIDE));
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495 int min = colSel.getMin();
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496 viewport.getAlignment().trimLeft(min);
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497 colSel.compensateForEdit(0, min);
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499 if (viewport.getSelectionGroup() != null)
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501 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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504 Vector groups = viewport.alignment.getGroups();
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505 for (int i = 0; i < groups.size(); i++)
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507 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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508 if (!sg.adjustForRemoveLeft(min))
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510 viewport.alignment.deleteGroup(sg);
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514 alignPanel.repaint();
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518 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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520 ColumnSelection colSel = viewport.getColumnSelection();
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521 if (colSel.size() > 0)
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523 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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524 HistoryItem.HIDE));
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525 int max = colSel.getMax();
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526 viewport.getAlignment().trimRight(max);
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527 if (viewport.getSelectionGroup() != null)
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529 viewport.getSelectionGroup().adjustForRemoveRight(max);
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532 Vector groups = viewport.alignment.getGroups();
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533 for (int i = 0; i < groups.size(); i++)
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535 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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536 if (!sg.adjustForRemoveRight(max))
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538 viewport.alignment.deleteGroup(sg);
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542 alignPanel.repaint();
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547 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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549 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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550 viewport.alignment,
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551 HistoryItem.HIDE));
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552 viewport.getAlignment().removeGaps();
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553 viewport.updateConservation();
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554 viewport.updateConsensus();
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555 alignPanel.repaint();
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558 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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560 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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561 HistoryItem.HIDE));
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568 int start=0, end = viewport.alignment.getWidth();
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570 if(viewport.getSelectionGroup()!=null)
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572 seqs = viewport.getSelectionGroup().sequences;
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573 start = viewport.getSelectionGroup().getStartRes();
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574 end = viewport.getSelectionGroup().getEndRes();
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577 seqs = viewport.alignment.getSequences();
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579 for (int i = 0; i <seqs.size(); i++)
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581 current = (SequenceI)seqs.elementAt(i);
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582 jSize = current.getLength();
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587 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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589 current.deleteCharAt(j);
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595 while(j < end && j < jSize) ;
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598 viewport.updateConservation();
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599 viewport.updateConsensus();
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600 alignPanel.repaint();
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604 public void findMenuItem_actionPerformed(ActionEvent e)
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606 Finder finder = new Finder(alignPanel);
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609 public void font_actionPerformed(ActionEvent e)
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611 Frame frame = new Frame();
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612 FontChooser fc = new FontChooser(alignPanel, frame);
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614 jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);
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618 protected void fullSeqId_actionPerformed(ActionEvent e)
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620 viewport.setShowFullId(fullSeqId.getState());
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621 alignPanel.fontChanged();
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622 alignPanel.repaint();
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625 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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627 viewport.setColourText(colourTextMenuItem.getState());
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628 alignPanel.repaint();
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631 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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633 viewport.setWrapAlignment(wrapMenuItem.getState());
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634 alignPanel.setWrapAlignment(wrapMenuItem.getState());
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635 scaleAbove.setEnabled(wrapMenuItem.getState());
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636 scaleLeft.setEnabled(wrapMenuItem.getState());
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637 scaleRight.setEnabled(wrapMenuItem.getState());
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638 alignPanel.repaint();
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641 protected void scaleAbove_actionPerformed(ActionEvent e)
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643 viewport.setScaleAboveWrapped(scaleAbove.getState());
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644 alignPanel.repaint();
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647 protected void scaleLeft_actionPerformed(ActionEvent e)
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649 viewport.setScaleLeftWrapped(scaleLeft.getState());
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650 alignPanel.repaint();
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653 protected void scaleRight_actionPerformed(ActionEvent e)
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655 viewport.setScaleRightWrapped(scaleRight.getState());
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656 alignPanel.repaint();
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659 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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661 viewport.setShowBoxes(viewBoxesMenuItem.getState());
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662 alignPanel.repaint();
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665 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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667 viewport.setShowText(viewTextMenuItem.getState());
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668 alignPanel.repaint();
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671 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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673 viewport.setRenderGaps(renderGapsMenuItem.getState());
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674 alignPanel.repaint();
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677 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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679 if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
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681 annotationPanelMenuItem.setState(false);
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684 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
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685 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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688 public void overviewMenuItem_actionPerformed(ActionEvent e)
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690 if (alignPanel.overviewPanel != null)
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695 Frame frame = new Frame();
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696 OverviewPanel overview = new OverviewPanel(alignPanel);
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697 frame.add(overview);
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698 // +50 must allow for applet frame window
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699 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
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700 overview.preferredSize().width,
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701 overview.preferredSize().height + 50);
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704 frame.addWindowListener(new WindowAdapter()
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706 public void windowClosing(WindowEvent e)
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708 alignPanel.setOverviewPanel(null);
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712 alignPanel.setOverviewPanel(overview);
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716 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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718 changeColour(null);
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721 public void clustalColour_actionPerformed(ActionEvent e)
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723 abovePIDThreshold.setState(false);
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724 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
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725 viewport.alignment.getWidth()));
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728 public void zappoColour_actionPerformed(ActionEvent e)
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730 changeColour(new ZappoColourScheme());
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733 public void taylorColour_actionPerformed(ActionEvent e)
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735 changeColour(new TaylorColourScheme());
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738 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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740 changeColour(new HydrophobicColourScheme());
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743 public void helixColour_actionPerformed(ActionEvent e)
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745 changeColour(new HelixColourScheme());
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748 public void strandColour_actionPerformed(ActionEvent e)
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750 changeColour(new StrandColourScheme());
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753 public void turnColour_actionPerformed(ActionEvent e)
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755 changeColour(new TurnColourScheme());
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758 public void buriedColour_actionPerformed(ActionEvent e)
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760 changeColour(new BuriedColourScheme());
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763 public void nucleotideColour_actionPerformed(ActionEvent e)
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765 changeColour(new NucleotideColourScheme());
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768 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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770 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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773 void changeColour(ColourSchemeI cs)
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777 if (viewport.getAbovePIDThreshold())
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779 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
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781 if (cs instanceof ResidueColourScheme)
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783 ( (ResidueColourScheme) cs).setThreshold(threshold);
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786 viewport.setGlobalColourScheme(cs);
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788 else if (cs instanceof ResidueColourScheme)
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790 ( (ResidueColourScheme) cs).setThreshold(0);
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793 if (viewport.getConservationSelected())
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795 ConservationColourScheme ccs = null;
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797 Alignment al = (Alignment) viewport.alignment;
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798 Conservation c = new Conservation("All",
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799 ResidueProperties.propHash, 3,
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800 al.getSequences(), 0,
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801 al.getWidth() - 1);
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804 c.verdict(false, viewport.ConsPercGaps);
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806 ccs = new ConservationColourScheme(c, cs);
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808 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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809 ccs.setConsensus(viewport.vconsensus);
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810 viewport.setGlobalColourScheme(ccs);
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812 SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
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817 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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820 cs.setConsensus(viewport.vconsensus);
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822 viewport.setGlobalColourScheme(cs);
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825 if (viewport.getColourAppliesToAllGroups())
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827 Vector groups = viewport.alignment.getGroups();
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828 for (int i = 0; i < groups.size(); i++)
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830 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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837 if (cs instanceof ClustalxColourScheme)
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839 ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
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840 cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());
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847 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
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849 catch (Exception ex)
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851 ex.printStackTrace();
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856 if (viewport.getAbovePIDThreshold())
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858 if (sg.cs instanceof ResidueColourScheme)
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860 ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
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863 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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866 if (viewport.getConservationSelected())
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868 Conservation c = new Conservation("Group",
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869 ResidueProperties.propHash, 3,
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871 viewport.alignment.getWidth() - 1);
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873 c.verdict(false, viewport.ConsPercGaps);
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874 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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876 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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877 ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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882 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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883 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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889 if (alignPanel.getOverviewPanel() != null)
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891 alignPanel.getOverviewPanel().updateOverviewImage();
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894 alignPanel.repaint();
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897 protected void modifyPID_actionPerformed(ActionEvent e)
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899 if (viewport.getAbovePIDThreshold())
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901 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
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903 SliderPanel.showPIDSlider();
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907 protected void modifyConservation_actionPerformed(ActionEvent e)
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909 if (viewport.getConservationSelected())
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911 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
913 SliderPanel.showConservationSlider();
\r
917 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
919 viewport.setConservationSelected(conservationMenuItem.getState());
\r
921 viewport.setAbovePIDThreshold(false);
\r
922 abovePIDThreshold.setState(false);
\r
924 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
925 if (cs instanceof ConservationColourScheme)
\r
927 changeColour( ( (ConservationColourScheme) cs).cs);
\r
934 modifyConservation_actionPerformed(null);
\r
937 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
939 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
941 conservationMenuItem.setState(false);
\r
942 viewport.setConservationSelected(false);
\r
944 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
946 if (cs instanceof ConservationColourScheme)
\r
948 changeColour( ( (ConservationColourScheme) cs).cs);
\r
955 modifyPID_actionPerformed(null);
\r
958 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
960 UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);
\r
963 public void PIDColour_actionPerformed(ActionEvent e)
\r
965 changeColour(new PIDColourScheme());
\r
968 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
970 changeColour(new Blosum62ColourScheme());
\r
973 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
975 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
976 HistoryItem.SORT));
\r
977 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
978 viewport.getAlignment().getSequenceAt(0));
\r
979 alignPanel.repaint();
\r
982 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
984 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
985 HistoryItem.SORT));
\r
986 AlignmentSorter.sortByID(viewport.getAlignment());
\r
987 alignPanel.repaint();
\r
990 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
992 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
993 HistoryItem.SORT));
\r
994 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
995 alignPanel.repaint();
\r
999 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1001 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
1002 Frame frame = new Frame();
\r
1004 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
1009 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1011 if (viewport.getSelectionGroup().getSize() > 1)
\r
1013 Frame frame = new Frame();
\r
1014 frame.add(new PairwiseAlignPanel(viewport));
\r
1015 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1019 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1022 if ( (viewport.getSelectionGroup() != null &&
\r
1023 viewport.getSelectionGroup().getSize() < 4 &&
\r
1024 viewport.getSelectionGroup().getSize() > 0)
\r
1025 || viewport.getAlignment().getHeight() < 4)
\r
1032 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
1033 Frame frame = new Frame();
\r
1034 frame.add(pcaPanel);
\r
1035 jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",
\r
1038 catch (java.lang.OutOfMemoryError ex)
\r
1044 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1046 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1049 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1051 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1054 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1056 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1059 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1061 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1064 void NewTreePanel(String type, String pwType, String title)
\r
1066 //are the sequences aligned?
\r
1067 if (!viewport.alignment.isAligned())
\r
1072 final TreePanel tp;
\r
1073 if (viewport.getSelectionGroup() != null &&
\r
1074 viewport.getSelectionGroup().getSize() > 3)
\r
1076 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1078 0, viewport.alignment.getWidth());
\r
1082 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1083 type, pwType, 0, viewport.alignment.getWidth());
\r
1086 addTreeMenuItem(tp, title);
\r
1088 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1091 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1093 final MenuItem item = new MenuItem(title);
\r
1094 sortByTreeMenu.add(item);
\r
1095 item.addActionListener(new java.awt.event.ActionListener()
\r
1097 public void actionPerformed(ActionEvent e)
\r
1099 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1100 HistoryItem.SORT));
\r
1101 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1102 alignPanel.repaint();
\r
1106 treePanel.addWindowListener(new WindowAdapter()
\r
1108 public void windowClosing(WindowEvent e)
\r
1110 sortByTreeMenu.remove(item);
\r
1115 protected void documentation_actionPerformed(ActionEvent e)
\r
1117 jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");
\r
1120 protected void about_actionPerformed(ActionEvent e)
\r
1125 public void paint(Graphics g)
\r
1127 g.setColor(Color.white);
\r
1128 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1129 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1130 FontMetrics fm = g.getFontMetrics();
\r
1131 int fh = fm.getHeight();
\r
1133 g.setColor(Color.black);
\r
1134 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1135 g.drawString("JalView - Release 2.0", 200, y += fh);
\r
1136 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1137 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1139 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1142 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1144 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1145 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1147 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1151 Frame frame = new Frame();
\r
1152 frame.add(new AboutPanel());
\r
1153 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r