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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32 public class AlignFrame extends GAlignFrame
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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.getCodeBase()+treeFile, "URL");
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67 if (fin.getTree() != null)
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69 TreePanel tp = null;
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70 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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71 fin, "FromFile", applet.getCodeBase()+treeFile);
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72 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
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73 addTreeMenuItem(tp, treeFile);
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76 catch (Exception ex)
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78 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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94 protected void outputText_actionPerformed(ActionEvent e)
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96 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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97 Frame frame = new Frame();
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99 jalview.bin.JalviewLite.addFrame(frame,"Alignment output - "+e.getActionCommand(),600, 500);
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100 cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
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103 public void closeMenuItem_actionPerformed(ActionEvent e)
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108 Stack historyList = new Stack();
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109 Stack redoList = new Stack();
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111 void updateEditMenuBar()
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113 if(historyList.size()>0)
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115 undoMenuItem.setEnabled(true);
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116 HistoryItem hi = (HistoryItem)historyList.peek();
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117 undoMenuItem.setLabel("Undo "+hi.getDescription());
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121 undoMenuItem.setEnabled(false);
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122 undoMenuItem.setLabel("Undo");
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125 if(redoList.size()>0)
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127 redoMenuItem.setEnabled(true);
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128 HistoryItem hi = (HistoryItem)redoList.peek();
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129 redoMenuItem.setLabel("Redo "+hi.getDescription());
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133 redoMenuItem.setEnabled(false);
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134 redoMenuItem.setLabel("Redo");
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138 public void addHistoryItem(HistoryItem hi)
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140 historyList.push(hi);
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141 updateEditMenuBar();
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144 protected void undoMenuItem_actionPerformed(ActionEvent e)
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146 HistoryItem hi = (HistoryItem)historyList.pop();
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147 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE));
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148 restoreHistoryItem(hi);
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151 protected void redoMenuItem_actionPerformed(ActionEvent e)
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153 HistoryItem hi = (HistoryItem)redoList.pop();
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154 restoreHistoryItem(hi);
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155 updateEditMenuBar();
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156 viewport.updateConsensus();
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157 alignPanel.repaint();
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158 alignPanel.repaint();
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162 // used by undo and redo
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163 void restoreHistoryItem(HistoryItem hi)
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165 if(hi.getType()== HistoryItem.SORT)
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167 for(int i=0; i<hi.getSequences().size(); i++)
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168 viewport.alignment.getSequences().setElementAt(hi.getSequences().elementAt(i), i);
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172 for (int i = 0; i < hi.getSequences().size(); i++)
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174 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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175 if(restore.getLength()==0)
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177 // log.System.out.println(hi.getHidden().elementAt(i));
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178 restore.setSequence(hi.getHidden().elementAt(i).toString());
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179 viewport.alignment.getSequences().insertElementAt(
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181 hi.getAlignIndex(i));
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184 restore.setSequence(hi.getHidden().elementAt(i).toString());
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186 if(hi.getType()==HistoryItem.PASTE)
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188 for(int i=viewport.alignment.getHeight()-1;i>hi.getSequences().size()-1; i--)
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189 viewport.alignment.deleteSequence(i);
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193 updateEditMenuBar();
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195 viewport.updateConsensus();
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196 viewport.updateConservation();
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197 alignPanel.repaint();
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201 public void moveSelectedSequences(boolean up)
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203 SequenceGroup sg = viewport.getSelectionGroup();
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209 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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211 SequenceI seq = viewport.alignment.getSequenceAt(i);
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212 if (!sg.sequences.contains(seq))
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215 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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216 if (sg.sequences.contains(temp))
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219 viewport.alignment.getSequences().setElementAt(temp, i);
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220 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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225 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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227 SequenceI seq = viewport.alignment.getSequenceAt(i);
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228 if (!sg.sequences.contains(seq))
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231 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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232 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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240 alignPanel.repaint();
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244 StringBuffer copiedSequences;
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245 protected void copy_actionPerformed(ActionEvent e)
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247 if(viewport.getSelectionGroup()==null)
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250 SequenceGroup sg = viewport.getSelectionGroup();
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251 copiedSequences = new StringBuffer();
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252 Hashtable orderedSeqs = new Hashtable();
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253 for(int i=0; i<sg.getSize(); i++)
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255 SequenceI seq = sg.getSequenceAt(i);
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256 int index = viewport.alignment.findIndex(seq);
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257 orderedSeqs.put(index+"", seq);
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261 for(int i=0; i<sg.getSize(); i++)
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263 SequenceI seq = null;
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264 while( seq == null )
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266 if(orderedSeqs.containsKey(index+""))
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268 seq = (SequenceI) orderedSeqs.get(index + "");
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276 copiedSequences.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
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277 +seq.findPosition( sg.getEndRes() )+ "\t"
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278 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
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284 protected void pasteNew_actionPerformed(ActionEvent e)
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289 protected void pasteThis_actionPerformed(ActionEvent e)
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291 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE));
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295 void paste(boolean newAlignment)
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298 if (copiedSequences == null)
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301 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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302 Vector seqs = new Vector();
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303 while (st.hasMoreElements())
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305 String name = st.nextToken();
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306 int start = Integer.parseInt(st.nextToken());
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307 int end = Integer.parseInt(st.nextToken());
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308 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
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311 viewport.alignment.addSequence(sequence);
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313 seqs.addElement(sequence);
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318 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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319 for(int i=0; i<seqs.size(); i++)
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320 newSeqs[i] = (SequenceI)seqs.elementAt(i);
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322 AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);
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323 String newtitle = new String("Copied sequences");
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324 if( getTitle().startsWith("Copied sequences"))
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325 newtitle = getTitle();
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327 newtitle = newtitle.concat("- from "+getTitle());
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328 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
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332 viewport.setEndSeq(viewport.alignment.getHeight());
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333 viewport.alignment.getWidth();
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334 viewport.updateConservation();
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335 viewport.updateConsensus();
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336 alignPanel.repaint();
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339 }catch(Exception ex){}// could be anything being pasted in here
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344 protected void cut_actionPerformed(ActionEvent e)
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346 copy_actionPerformed(null);
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347 delete_actionPerformed(null);
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350 protected void delete_actionPerformed(ActionEvent e)
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352 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
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353 if (viewport.getSelectionGroup() == null)
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356 SequenceGroup sg = viewport.getSelectionGroup();
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357 for (int i=0;i < sg.sequences.size(); i++)
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359 SequenceI seq = sg.getSequenceAt(i);
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360 int index = viewport.getAlignment().findIndex(seq);
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361 seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
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363 if(seq.getSequence().length()<1)
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364 viewport.getAlignment().deleteSequence(seq);
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366 viewport.getAlignment().getSequences().setElementAt(seq, index);
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369 viewport.setSelectionGroup(null);
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370 viewport.alignment.deleteGroup(sg);
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371 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getSize().height);
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372 if(viewport.getAlignment().getHeight()<1)
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375 this.setVisible(false);
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376 }catch(Exception ex){}
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377 viewport.updateConservation();
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378 viewport.updateConsensus();
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379 alignPanel.repaint();
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385 protected void deleteGroups_actionPerformed(ActionEvent e)
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387 viewport.alignment.deleteAllGroups();
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388 viewport.setSelectionGroup(null);
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390 alignPanel.repaint();
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395 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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397 SequenceGroup sg = new SequenceGroup();
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398 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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399 sg.addSequence( viewport.getAlignment().getSequenceAt(i));
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400 sg.setEndRes(viewport.alignment.getWidth());
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401 viewport.setSelectionGroup(sg);
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402 alignPanel.repaint();
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403 PaintRefresher.Refresh(null);
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406 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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408 viewport.setSelectionGroup(null);
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409 viewport.getColumnSelection().clear();
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410 viewport.setSelectionGroup(null);
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411 PaintRefresher.Refresh(null);
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414 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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416 SequenceGroup sg = viewport.getSelectionGroup();
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417 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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418 sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
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420 PaintRefresher.Refresh(null);
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423 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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425 ColumnSelection colSel = viewport.getColumnSelection();
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426 if (colSel.size() > 0)
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428 addHistoryItem(new HistoryItem("Remove Left",viewport.alignment,
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429 HistoryItem.HIDE));
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430 int min = colSel.getMin();
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431 viewport.getAlignment().trimLeft(min);
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432 colSel.compensateForEdit(0,min);
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434 if(viewport.getSelectionGroup()!=null)
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435 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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437 Vector groups = viewport.alignment.getGroups();
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438 for(int i=0; i<groups.size(); i++)
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440 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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441 if(!sg.adjustForRemoveLeft(min))
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442 viewport.alignment.deleteGroup(sg);
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445 alignPanel.repaint();
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449 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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451 ColumnSelection colSel = viewport.getColumnSelection();
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452 if (colSel.size() > 0)
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454 addHistoryItem(new HistoryItem("Remove Right",viewport.alignment,
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455 HistoryItem.HIDE));
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456 int max = colSel.getMax();
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457 viewport.getAlignment().trimRight(max);
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458 if(viewport.getSelectionGroup()!=null)
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459 viewport.getSelectionGroup().adjustForRemoveRight(max);
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461 Vector groups = viewport.alignment.getGroups();
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462 for(int i=0; i<groups.size(); i++)
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464 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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465 if(!sg.adjustForRemoveRight(max))
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466 viewport.alignment.deleteGroup(sg);
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471 alignPanel.repaint();
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476 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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478 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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479 viewport.alignment,
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480 HistoryItem.HIDE));
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481 viewport.getAlignment().removeGaps();
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482 viewport.updateConservation();
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483 viewport.updateConsensus();
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484 alignPanel.repaint();
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487 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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489 addHistoryItem(new HistoryItem("Remove Gaps",
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490 viewport.alignment,
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491 HistoryItem.HIDE));
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494 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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496 current = viewport.getAlignment().getSequenceAt(i);
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497 jSize = current.getLength();
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498 for (int j=0; j < jSize; j++)
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499 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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501 current.deleteCharAt(j);
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506 viewport.updateConservation();
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507 viewport.updateConsensus();
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508 alignPanel.repaint();
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512 public void findMenuItem_actionPerformed(ActionEvent e)
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514 Finder finder = new Finder(alignPanel);
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518 public void font_actionPerformed(ActionEvent e)
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520 Frame frame = new Frame();
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521 FontChooser fc = new FontChooser( alignPanel, frame);
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523 jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440,100);
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527 protected void fullSeqId_actionPerformed(ActionEvent e)
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529 viewport.setShowFullId( fullSeqId.getState() );
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530 alignPanel.fontChanged();
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531 alignPanel.repaint();
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534 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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536 viewport.setColourText( colourTextMenuItem.getState() );
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537 alignPanel.repaint();
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540 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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542 viewport.setWrapAlignment( wrapMenuItem.getState() );
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543 alignPanel.setWrapAlignment( wrapMenuItem.getState() );
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544 scaleAbove.setEnabled( wrapMenuItem.getState() );
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545 scaleLeft.setEnabled( wrapMenuItem.getState());
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546 scaleRight.setEnabled( wrapMenuItem.getState());
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547 alignPanel.repaint();
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550 protected void scaleAbove_actionPerformed(ActionEvent e)
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552 viewport.setScaleAboveWrapped(scaleAbove.getState());
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553 alignPanel.repaint();
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556 protected void scaleLeft_actionPerformed(ActionEvent e)
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558 viewport.setScaleLeftWrapped(scaleLeft.getState());
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559 alignPanel.repaint();
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562 protected void scaleRight_actionPerformed(ActionEvent e)
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564 viewport.setScaleRightWrapped(scaleRight.getState());
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565 alignPanel.repaint();
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570 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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572 viewport.setShowBoxes( viewBoxesMenuItem.getState() );
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573 alignPanel.repaint();
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576 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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578 viewport.setShowText( viewTextMenuItem.getState() );
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579 alignPanel.repaint();
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583 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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585 viewport.setRenderGaps(renderGapsMenuItem.getState());
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586 alignPanel.repaint();
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590 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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592 if(annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
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594 annotationPanelMenuItem.setState(false);
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597 viewport.setShowAnnotation( annotationPanelMenuItem.getState() );
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598 alignPanel.setAnnotationVisible( annotationPanelMenuItem.getState() );
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601 public void overviewMenuItem_actionPerformed(ActionEvent e)
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603 if (alignPanel.overviewPanel != null)
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606 Frame frame = new Frame();
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607 OverviewPanel overview = new OverviewPanel(alignPanel);
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608 frame.add(overview);
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609 // +50 must allow for applet frame window
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610 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
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611 overview.preferredSize().width, overview.preferredSize().height+50);
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614 frame.addWindowListener(new WindowAdapter()
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615 { public void windowClosing(WindowEvent e)
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617 alignPanel.setOverviewPanel(null);
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621 alignPanel.setOverviewPanel( overview );
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626 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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628 changeColour( null );
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632 public void clustalColour_actionPerformed(ActionEvent e)
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634 abovePIDThreshold.setState(false);
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635 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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638 public void zappoColour_actionPerformed(ActionEvent e)
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640 changeColour(new ZappoColourScheme());
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643 public void taylorColour_actionPerformed(ActionEvent e)
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645 changeColour(new TaylorColourScheme());
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649 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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651 changeColour( new HydrophobicColourScheme() );
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654 public void helixColour_actionPerformed(ActionEvent e)
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656 changeColour(new HelixColourScheme() );
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660 public void strandColour_actionPerformed(ActionEvent e)
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662 changeColour(new StrandColourScheme());
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666 public void turnColour_actionPerformed(ActionEvent e)
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668 changeColour(new TurnColourScheme());
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672 public void buriedColour_actionPerformed(ActionEvent e)
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674 changeColour(new BuriedColourScheme() );
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677 public void nucleotideColour_actionPerformed(ActionEvent e)
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679 changeColour(new NucleotideColourScheme());
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683 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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685 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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690 void changeColour(ColourSchemeI cs)
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694 if ( viewport.getAbovePIDThreshold() )
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696 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
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698 if (cs instanceof ResidueColourScheme)
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699 ( (ResidueColourScheme) cs).setThreshold(threshold);
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700 else if (cs instanceof ScoreColourScheme)
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701 ( (ScoreColourScheme) cs).setThreshold(threshold);
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703 viewport.setGlobalColourScheme(cs);
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705 else if (cs instanceof ResidueColourScheme)
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706 ( (ResidueColourScheme) cs).setThreshold(0);
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707 else if (cs instanceof ScoreColourScheme)
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708 ( (ScoreColourScheme) cs).setThreshold(0);
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712 if (viewport.getConservationSelected())
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714 ConservationColourScheme ccs = null;
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716 Alignment al = (Alignment) viewport.alignment;
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717 Conservation c = new Conservation("All",
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718 ResidueProperties.propHash, 3,
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719 al.getSequences(), 0,
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720 al.getWidth() - 1);
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723 c.verdict(false, viewport.ConsPercGaps);
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725 ccs = new ConservationColourScheme(c, cs);
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727 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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728 ccs.setConsensus( viewport.vconsensus );
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729 viewport.setGlobalColourScheme(ccs);
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731 SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
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736 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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738 cs.setConsensus(viewport.vconsensus);
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739 viewport.setGlobalColourScheme(cs);
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743 if(viewport.getColourAppliesToAllGroups())
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745 Vector groups = viewport.alignment.getGroups();
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746 for(int i=0; i<groups.size(); i++)
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748 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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750 if (cs instanceof ClustalxColourScheme)
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752 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
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757 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
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759 catch (Exception ex)
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761 ex.printStackTrace();
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765 if(viewport.getAbovePIDThreshold())
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767 if (sg.cs instanceof ResidueColourScheme)
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768 ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
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769 else if (sg.cs instanceof ScoreColourScheme)
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770 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
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772 sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
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775 if( viewport.getConservationSelected() )
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777 Conservation c = new Conservation("Group",
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778 ResidueProperties.propHash, 3,
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779 sg.sequences, 0, viewport.alignment.getWidth()-1);
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781 c.verdict(false, viewport.ConsPercGaps);
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782 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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784 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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785 ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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790 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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791 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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797 if(alignPanel.getOverviewPanel()!=null)
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798 alignPanel.getOverviewPanel().updateOverviewImage();
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800 alignPanel.repaint();
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803 protected void modifyPID_actionPerformed(ActionEvent e)
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805 if(viewport.getAbovePIDThreshold())
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807 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
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809 SliderPanel.showPIDSlider();
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813 protected void modifyConservation_actionPerformed(ActionEvent e)
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815 if(viewport.getConservationSelected())
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817 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
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819 SliderPanel.showConservationSlider();
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824 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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826 viewport.setConservationSelected(conservationMenuItem.getState());
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828 viewport.setAbovePIDThreshold(false);
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829 abovePIDThreshold.setState(false);
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831 ColourSchemeI cs = viewport.getGlobalColourScheme();
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832 if(cs instanceof ConservationColourScheme )
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833 changeColour( ((ConservationColourScheme)cs).cs );
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835 changeColour( cs );
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837 modifyConservation_actionPerformed(null);
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840 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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842 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
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844 conservationMenuItem.setState(false);
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845 viewport.setConservationSelected(false);
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847 ColourSchemeI cs = viewport.getGlobalColourScheme();
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849 if(cs instanceof ConservationColourScheme )
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850 changeColour( ((ConservationColourScheme)cs).cs );
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852 changeColour( cs );
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854 modifyPID_actionPerformed(null);
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859 public void userDefinedColour_actionPerformed(ActionEvent e)
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861 UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
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864 public void PIDColour_actionPerformed(ActionEvent e)
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866 changeColour( new PIDColourScheme() );
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870 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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872 changeColour(new Blosum62ColourScheme() );
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877 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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879 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));
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880 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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881 alignPanel.repaint();
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884 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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886 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));
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887 AlignmentSorter.sortByID( viewport.getAlignment() );
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888 alignPanel.repaint();
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891 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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893 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));
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894 AlignmentSorter.sortByGroup(viewport.getAlignment());
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895 AlignmentSorter.sortGroups(viewport.getAlignment());
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896 alignPanel.repaint();
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899 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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901 RedundancyPanel sp = new RedundancyPanel(alignPanel);
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902 Frame frame = new Frame();
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904 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", 400, 120);
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908 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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910 if(viewport.getSelectionGroup().getSize()>1)
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912 Frame frame = new Frame();
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913 frame.add(new PairwiseAlignPanel(viewport));
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914 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
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918 public void PCAMenuItem_actionPerformed(ActionEvent e)
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921 if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
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922 || viewport.getAlignment().getHeight()<4)
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928 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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929 Frame frame = new Frame();
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930 frame.add(pcaPanel);
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931 jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis", 400, 400);
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932 }catch(java.lang.OutOfMemoryError ex)
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939 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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941 NewTreePanel("AV", "PID", "Average distance tree using PID");
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944 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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946 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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950 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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952 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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955 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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957 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
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960 void NewTreePanel(String type, String pwType, String title)
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962 //are the sequences aligned?
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963 if(!viewport.alignment.isAligned())
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968 final TreePanel tp;
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969 if (viewport.getSelectionGroup() != null &&
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970 viewport.getSelectionGroup().getSize() > 3)
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972 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
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974 0, viewport.alignment.getWidth());
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978 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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979 type, pwType, 0, viewport.alignment.getWidth());
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982 addTreeMenuItem(tp, title);
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984 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
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987 void addTreeMenuItem(final TreePanel treePanel, String title)
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989 final MenuItem item = new MenuItem(title);
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990 sortByTreeMenu.add(item);
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991 item.addActionListener(new java.awt.event.ActionListener()
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993 public void actionPerformed(ActionEvent e)
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995 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
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996 HistoryItem.SORT));
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997 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
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998 alignPanel.repaint();
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1002 treePanel.addWindowListener(new WindowAdapter()
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1004 public void windowClosing(WindowEvent e)
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1006 sortByTreeMenu.remove(item);
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1011 protected void documentation_actionPerformed(ActionEvent e) {
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1013 jalview.bin.JalviewLite.showURL("http://www.jalview.org");
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1017 protected void about_actionPerformed(ActionEvent e)
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1019 class AboutPanel extends Canvas
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1021 public void paint(Graphics g)
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1023 g.setColor(Color.white);
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1024 g.fillRect(0,0,getSize().width, getSize().height);
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1025 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
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1026 FontMetrics fm = g.getFontMetrics();
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1027 int fh = fm.getHeight();
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1029 g.setColor(Color.black);
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1030 g.setFont(new Font("Helvetica", Font.BOLD, 14));
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1031 g.drawString("JalView - Release 2.0", 200,y+=fh);
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1032 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
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1033 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",x,y+=fh*2);
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1034 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",x,y+=fh);
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1035 g.drawString("For any issues relating to Jalview, email help@jalview.org", x,y+=fh);
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1036 g.drawString("If you use JalView, please cite:",x,y+=fh+8);
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1037 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",x,y+=fh);
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1038 g.drawString("Bioinformatics, 2004 12;426-7.",x,y+=fh);
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1041 Frame frame = new Frame();
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1042 frame.add(new AboutPanel());
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1043 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580,200);
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