1 /********************
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2 * 2004 Jalview Reengineered
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12 package jalview.appletgui;
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14 import jalview.jbappletgui.GAlignFrame;
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15 import jalview.schemes.*;
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16 import jalview.datamodel.*;
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17 import jalview.analysis.*;
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18 import jalview.io.*;
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20 import java.awt.event.*;
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24 public class AlignFrame extends GAlignFrame
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26 final AlignmentPanel alignPanel;
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27 final AlignViewport viewport;
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28 public static final int NEW_WINDOW_WIDTH = 700;
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29 public static final int NEW_WINDOW_HEIGHT = 500;
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30 jalview.bin.JalviewLite applet;
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32 public AlignFrame(AlignmentI al)
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35 viewport = new AlignViewport(al, null);
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36 alignPanel = new AlignmentPanel(this, viewport);
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38 alignPanel.validate();
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41 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)
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43 this.applet = applet;
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44 viewport = new AlignViewport(al, applet);
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45 alignPanel = new AlignmentPanel(this, viewport);
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47 alignPanel.validate();
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49 String treeFile = applet.getParameter("treeFile");
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50 TreePanel treepanel = null;
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51 if (treeFile != null)
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55 treeFile = treeFile;
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56 jalview.io.NewickFile fin = new jalview.io.NewickFile( applet.getCodeBase()+treeFile, "URL");
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59 if (fin.getTree() != null)
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61 TreePanel tp = null;
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62 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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63 fin, "FromFile", applet.getCodeBase()+treeFile);
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64 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
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65 addTreeMenuItem(tp, treeFile);
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68 catch (Exception ex)
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70 ex.printStackTrace();
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77 public void inputText_actionPerformed(ActionEvent e)
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79 CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
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80 Frame frame = new Frame();
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82 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500,500);
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86 protected void outputText_actionPerformed(ActionEvent e)
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88 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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89 Frame frame = new Frame();
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91 jalview.bin.JalviewLite.addFrame(frame,"Alignment output - "+e.getActionCommand(),600, 500);
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92 cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
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95 public void closeMenuItem_actionPerformed(ActionEvent e)
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100 Stack historyList = new Stack();
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101 Stack redoList = new Stack();
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103 void updateEditMenuBar()
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105 if(historyList.size()>0)
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107 undoMenuItem.setEnabled(true);
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108 HistoryItem hi = (HistoryItem)historyList.peek();
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109 undoMenuItem.setLabel("Undo "+hi.getDescription());
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113 undoMenuItem.setEnabled(false);
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114 undoMenuItem.setLabel("Undo");
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117 if(redoList.size()>0)
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119 redoMenuItem.setEnabled(true);
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120 HistoryItem hi = (HistoryItem)redoList.peek();
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121 redoMenuItem.setLabel("Redo "+hi.getDescription());
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125 redoMenuItem.setEnabled(false);
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126 redoMenuItem.setLabel("Redo");
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130 public void addHistoryItem(HistoryItem hi)
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132 historyList.push(hi);
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133 updateEditMenuBar();
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136 protected void undoMenuItem_actionPerformed(ActionEvent e)
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138 HistoryItem hi = (HistoryItem)historyList.pop();
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139 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE));
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140 restoreHistoryItem(hi);
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143 protected void redoMenuItem_actionPerformed(ActionEvent e)
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145 HistoryItem hi = (HistoryItem)redoList.pop();
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146 restoreHistoryItem(hi);
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147 updateEditMenuBar();
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148 viewport.updateConsensus();
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149 alignPanel.repaint();
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150 alignPanel.repaint();
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154 // used by undo and redo
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155 void restoreHistoryItem(HistoryItem hi)
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157 if(hi.getType()== HistoryItem.SORT)
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159 for(int i=0; i<hi.getSequences().size(); i++)
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160 viewport.alignment.getSequences().setElementAt(hi.getSequences().elementAt(i), i);
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164 for (int i = 0; i < hi.getSequences().size(); i++)
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166 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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167 if(restore.getLength()==0)
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169 // log.System.out.println(hi.getHidden().elementAt(i));
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170 restore.setSequence(hi.getHidden().elementAt(i).toString());
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171 viewport.alignment.getSequences().insertElementAt(
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173 hi.getAlignIndex(i));
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176 restore.setSequence(hi.getHidden().elementAt(i).toString());
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178 if(hi.getType()==HistoryItem.PASTE)
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180 for(int i=viewport.alignment.getHeight()-1;i>hi.getSequences().size()-1; i--)
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181 viewport.alignment.deleteSequence(i);
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185 updateEditMenuBar();
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187 viewport.updateConsensus();
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188 viewport.updateConservation();
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189 alignPanel.repaint();
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193 public void moveSelectedSequences(boolean up)
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195 SequenceGroup sg = viewport.getSelectionGroup();
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201 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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203 SequenceI seq = viewport.alignment.getSequenceAt(i);
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204 if (!sg.sequences.contains(seq))
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207 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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208 if (sg.sequences.contains(temp))
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211 viewport.alignment.getSequences().setElementAt(temp, i);
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212 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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217 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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219 SequenceI seq = viewport.alignment.getSequenceAt(i);
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220 if (!sg.sequences.contains(seq))
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223 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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224 if (sg.sequences.contains(temp))
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227 viewport.alignment.getSequences().setElementAt(temp, i);
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228 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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232 alignPanel.repaint();
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236 StringBuffer copiedSequences;
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237 protected void copy_actionPerformed(ActionEvent e)
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239 if(viewport.getSelectionGroup()==null)
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242 SequenceGroup sg = viewport.getSelectionGroup();
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243 copiedSequences = new StringBuffer();
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244 Hashtable orderedSeqs = new Hashtable();
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245 for(int i=0; i<sg.getSize(); i++)
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247 SequenceI seq = sg.getSequenceAt(i);
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248 int index = viewport.alignment.findIndex(seq);
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249 orderedSeqs.put(index+"", seq);
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253 for(int i=0; i<sg.getSize(); i++)
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255 SequenceI seq = null;
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256 while( seq == null )
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258 if(orderedSeqs.containsKey(index+""))
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260 seq = (SequenceI) orderedSeqs.get(index + "");
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268 copiedSequences.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
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269 +seq.findPosition( sg.getEndRes() )+ "\t"
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270 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
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276 protected void pasteNew_actionPerformed(ActionEvent e)
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281 protected void pasteThis_actionPerformed(ActionEvent e)
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283 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE));
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287 void paste(boolean newAlignment)
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290 if (copiedSequences == null)
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293 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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294 Vector seqs = new Vector();
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295 while (st.hasMoreElements())
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297 String name = st.nextToken();
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298 int start = Integer.parseInt(st.nextToken());
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299 int end = Integer.parseInt(st.nextToken());
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300 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
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303 viewport.alignment.addSequence(sequence);
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305 seqs.addElement(sequence);
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310 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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311 for(int i=0; i<seqs.size(); i++)
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312 newSeqs[i] = (SequenceI)seqs.elementAt(i);
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314 AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);
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315 String newtitle = new String("Copied sequences");
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316 if( getTitle().startsWith("Copied sequences"))
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317 newtitle = getTitle();
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319 newtitle = newtitle.concat("- from "+getTitle());
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320 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
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324 viewport.setEndSeq(viewport.alignment.getHeight());
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325 viewport.alignment.getWidth();
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326 viewport.updateConservation();
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327 viewport.updateConsensus();
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328 alignPanel.repaint();
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331 }catch(Exception ex){}// could be anything being pasted in here
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336 protected void cut_actionPerformed(ActionEvent e)
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338 copy_actionPerformed(null);
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339 delete_actionPerformed(null);
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342 protected void delete_actionPerformed(ActionEvent e)
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344 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
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345 if (viewport.getSelectionGroup() == null)
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348 SequenceGroup sg = viewport.getSelectionGroup();
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349 for (int i=0;i < sg.sequences.size(); i++)
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351 SequenceI seq = sg.getSequenceAt(i);
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352 int index = viewport.getAlignment().findIndex(seq);
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353 seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
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355 if(seq.getSequence().length()<1)
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356 viewport.getAlignment().deleteSequence(seq);
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358 viewport.getAlignment().getSequences().setElementAt(seq, index);
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361 viewport.setSelectionGroup(null);
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362 viewport.alignment.deleteGroup(sg);
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363 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getSize().height);
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364 if(viewport.getAlignment().getHeight()<1)
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367 this.setVisible(false);
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368 }catch(Exception ex){}
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369 viewport.updateConservation();
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370 viewport.updateConsensus();
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371 alignPanel.repaint();
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377 protected void deleteGroups_actionPerformed(ActionEvent e)
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379 viewport.alignment.deleteAllGroups();
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380 viewport.setSelectionGroup(null);
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382 alignPanel.repaint();
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387 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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389 SequenceGroup sg = new SequenceGroup();
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390 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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391 sg.addSequence( viewport.getAlignment().getSequenceAt(i));
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392 sg.setEndRes(viewport.alignment.getWidth());
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393 viewport.setSelectionGroup(sg);
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394 alignPanel.repaint();
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395 PaintRefresher.Refresh(null);
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398 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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400 viewport.setSelectionGroup(null);
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401 viewport.getColumnSelection().clear();
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402 viewport.setSelectionGroup(null);
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403 PaintRefresher.Refresh(null);
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406 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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408 SequenceGroup sg = viewport.getSelectionGroup();
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409 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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410 sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
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412 PaintRefresher.Refresh(null);
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415 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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417 ColumnSelection colSel = viewport.getColumnSelection();
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418 if (colSel.size() > 0)
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420 addHistoryItem(new HistoryItem("Remove Left",viewport.alignment,
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421 HistoryItem.HIDE));
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422 int min = colSel.getMin();
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423 viewport.getAlignment().trimLeft(min);
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424 colSel.compensateForEdit(0,min);
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426 if(viewport.getSelectionGroup()!=null)
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427 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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429 Vector groups = viewport.alignment.getGroups();
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430 for(int i=0; i<groups.size(); i++)
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432 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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433 if(!sg.adjustForRemoveLeft(min))
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434 viewport.alignment.deleteGroup(sg);
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437 alignPanel.repaint();
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441 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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443 ColumnSelection colSel = viewport.getColumnSelection();
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444 if (colSel.size() > 0)
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446 addHistoryItem(new HistoryItem("Remove Right",viewport.alignment,
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447 HistoryItem.HIDE));
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448 int max = colSel.getMax();
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449 viewport.getAlignment().trimRight(max);
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450 if(viewport.getSelectionGroup()!=null)
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451 viewport.getSelectionGroup().adjustForRemoveRight(max);
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453 Vector groups = viewport.alignment.getGroups();
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454 for(int i=0; i<groups.size(); i++)
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456 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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457 if(!sg.adjustForRemoveRight(max))
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458 viewport.alignment.deleteGroup(sg);
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463 alignPanel.repaint();
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468 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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470 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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471 viewport.alignment,
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472 HistoryItem.HIDE));
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473 viewport.getAlignment().removeGaps();
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474 viewport.updateConservation();
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475 viewport.updateConsensus();
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476 alignPanel.repaint();
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479 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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481 addHistoryItem(new HistoryItem("Remove Gaps",
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482 viewport.alignment,
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483 HistoryItem.HIDE));
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486 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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488 current = viewport.getAlignment().getSequenceAt(i);
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489 jSize = current.getLength();
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490 for (int j=0; j < jSize; j++)
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491 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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493 current.deleteCharAt(j);
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498 viewport.updateConservation();
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499 viewport.updateConsensus();
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500 alignPanel.repaint();
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504 public void findMenuItem_actionPerformed(ActionEvent e)
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506 Finder finder = new Finder(alignPanel);
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510 public void font_actionPerformed(ActionEvent e)
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512 Frame frame = new Frame();
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513 FontChooser fc = new FontChooser( alignPanel, frame);
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515 jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440,100);
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519 protected void fullSeqId_actionPerformed(ActionEvent e)
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521 viewport.setShowFullId( fullSeqId.getState() );
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522 alignPanel.fontChanged();
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523 alignPanel.repaint();
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526 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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528 viewport.setColourText( colourTextMenuItem.getState() );
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529 alignPanel.repaint();
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532 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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534 viewport.setWrapAlignment( wrapMenuItem.getState() );
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535 alignPanel.setWrapAlignment( wrapMenuItem.getState() );
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536 scaleAbove.setEnabled( wrapMenuItem.getState() );
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537 scaleLeft.setEnabled( wrapMenuItem.getState());
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538 scaleRight.setEnabled( wrapMenuItem.getState());
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539 alignPanel.repaint();
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542 protected void scaleAbove_actionPerformed(ActionEvent e)
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544 viewport.setScaleAboveWrapped(scaleAbove.getState());
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545 alignPanel.repaint();
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548 protected void scaleLeft_actionPerformed(ActionEvent e)
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550 viewport.setScaleLeftWrapped(scaleLeft.getState());
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551 alignPanel.repaint();
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554 protected void scaleRight_actionPerformed(ActionEvent e)
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556 viewport.setScaleRightWrapped(scaleRight.getState());
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557 alignPanel.repaint();
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562 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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564 viewport.setShowBoxes( viewBoxesMenuItem.getState() );
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565 alignPanel.repaint();
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568 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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570 viewport.setShowText( viewTextMenuItem.getState() );
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571 alignPanel.repaint();
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575 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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577 viewport.setRenderGaps(renderGapsMenuItem.getState());
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578 alignPanel.repaint();
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582 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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584 if(annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
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586 annotationPanelMenuItem.setState(false);
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589 viewport.setShowAnnotation( annotationPanelMenuItem.getState() );
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590 alignPanel.setAnnotationVisible( annotationPanelMenuItem.getState() );
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593 public void overviewMenuItem_actionPerformed(ActionEvent e)
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595 if (alignPanel.overviewPanel != null)
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598 Frame frame = new Frame();
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599 OverviewPanel overview = new OverviewPanel(alignPanel);
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600 frame.add(overview);
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601 // +50 must allow for applet frame window
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602 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
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603 overview.preferredSize().width, overview.preferredSize().height+50);
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606 frame.addWindowListener(new WindowAdapter()
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607 { public void windowClosing(WindowEvent e)
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609 alignPanel.setOverviewPanel(null);
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613 alignPanel.setOverviewPanel( overview );
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618 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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620 changeColour( null );
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624 public void clustalColour_actionPerformed(ActionEvent e)
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626 abovePIDThreshold.setState(false);
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627 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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630 public void zappoColour_actionPerformed(ActionEvent e)
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632 changeColour(new ZappoColourScheme());
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635 public void taylorColour_actionPerformed(ActionEvent e)
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637 changeColour(new TaylorColourScheme());
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641 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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643 changeColour( new HydrophobicColourScheme() );
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646 public void helixColour_actionPerformed(ActionEvent e)
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648 changeColour(new HelixColourScheme() );
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652 public void strandColour_actionPerformed(ActionEvent e)
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654 changeColour(new StrandColourScheme());
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658 public void turnColour_actionPerformed(ActionEvent e)
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660 changeColour(new TurnColourScheme());
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664 public void buriedColour_actionPerformed(ActionEvent e)
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666 changeColour(new BuriedColourScheme() );
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669 public void nucleotideColour_actionPerformed(ActionEvent e)
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671 changeColour(new NucleotideColourScheme());
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675 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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677 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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682 void changeColour(ColourSchemeI cs)
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686 if ( viewport.getAbovePIDThreshold() )
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688 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
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690 if (cs instanceof ResidueColourScheme)
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691 ( (ResidueColourScheme) cs).setThreshold(threshold);
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692 else if (cs instanceof ScoreColourScheme)
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693 ( (ScoreColourScheme) cs).setThreshold(threshold);
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695 viewport.setGlobalColourScheme(cs);
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697 else if (cs instanceof ResidueColourScheme)
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698 ( (ResidueColourScheme) cs).setThreshold(0);
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699 else if (cs instanceof ScoreColourScheme)
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700 ( (ScoreColourScheme) cs).setThreshold(0);
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704 if (viewport.getConservationSelected())
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706 ConservationColourScheme ccs = null;
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708 Alignment al = (Alignment) viewport.alignment;
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709 Conservation c = new Conservation("All",
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710 ResidueProperties.propHash, 3,
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711 al.getSequences(), 0,
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712 al.getWidth() - 1);
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715 c.verdict(false, viewport.ConsPercGaps);
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717 ccs = new ConservationColourScheme(c, cs);
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719 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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720 ccs.setConsensus( viewport.vconsensus );
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721 viewport.setGlobalColourScheme(ccs);
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723 SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
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728 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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730 cs.setConsensus(viewport.vconsensus);
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731 viewport.setGlobalColourScheme(cs);
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735 if(viewport.getColourAppliesToAllGroups())
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737 Vector groups = viewport.alignment.getGroups();
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738 for(int i=0; i<groups.size(); i++)
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740 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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742 if (cs instanceof ClustalxColourScheme)
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744 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
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749 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
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751 catch (Exception ex)
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753 ex.printStackTrace();
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757 if(viewport.getAbovePIDThreshold())
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759 if (sg.cs instanceof ResidueColourScheme)
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760 ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
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761 else if (sg.cs instanceof ScoreColourScheme)
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762 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
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764 sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
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767 if( viewport.getConservationSelected() )
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769 Conservation c = new Conservation("Group",
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770 ResidueProperties.propHash, 3,
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771 sg.sequences, 0, viewport.alignment.getWidth()-1);
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773 c.verdict(false, viewport.ConsPercGaps);
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774 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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776 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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777 ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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782 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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783 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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789 if(alignPanel.getOverviewPanel()!=null)
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790 alignPanel.getOverviewPanel().updateOverviewImage();
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792 alignPanel.repaint();
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795 protected void modifyPID_actionPerformed(ActionEvent e)
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797 if(viewport.getAbovePIDThreshold())
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799 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
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801 SliderPanel.showPIDSlider();
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805 protected void modifyConservation_actionPerformed(ActionEvent e)
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807 if(viewport.getConservationSelected())
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809 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
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811 SliderPanel.showConservationSlider();
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816 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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818 viewport.setConservationSelected(conservationMenuItem.getState());
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820 viewport.setAbovePIDThreshold(false);
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821 abovePIDThreshold.setState(false);
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823 ColourSchemeI cs = viewport.getGlobalColourScheme();
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824 if(cs instanceof ConservationColourScheme )
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825 changeColour( ((ConservationColourScheme)cs).cs );
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827 changeColour( cs );
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829 modifyConservation_actionPerformed(null);
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832 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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834 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
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836 conservationMenuItem.setState(false);
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837 viewport.setConservationSelected(false);
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839 ColourSchemeI cs = viewport.getGlobalColourScheme();
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841 if(cs instanceof ConservationColourScheme )
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842 changeColour( ((ConservationColourScheme)cs).cs );
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844 changeColour( cs );
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846 modifyPID_actionPerformed(null);
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851 public void userDefinedColour_actionPerformed(ActionEvent e)
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853 UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
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856 public void PIDColour_actionPerformed(ActionEvent e)
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858 changeColour( new PIDColourScheme() );
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862 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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864 changeColour(new Blosum62ColourScheme() );
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869 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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871 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));
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872 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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873 alignPanel.repaint();
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876 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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878 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));
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879 AlignmentSorter.sortByID( viewport.getAlignment() );
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880 alignPanel.repaint();
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883 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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885 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));
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886 AlignmentSorter.sortByGroup(viewport.getAlignment());
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887 AlignmentSorter.sortGroups(viewport.getAlignment());
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888 alignPanel.repaint();
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891 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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893 RedundancyPanel sp = new RedundancyPanel(alignPanel);
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894 Frame frame = new Frame();
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896 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", 400, 120);
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900 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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902 if(viewport.getSelectionGroup().getSize()>1)
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904 Frame frame = new Frame();
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905 frame.add(new PairwiseAlignPanel(viewport));
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906 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
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910 public void PCAMenuItem_actionPerformed(ActionEvent e)
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913 if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
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914 || viewport.getAlignment().getHeight()<4)
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920 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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921 Frame frame = new Frame();
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922 frame.add(pcaPanel);
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923 jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis", 400, 400);
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924 }catch(java.lang.OutOfMemoryError ex)
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931 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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933 NewTreePanel("AV", "PID", "Average distance tree using PID");
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936 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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938 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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942 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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944 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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947 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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949 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
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952 void NewTreePanel(String type, String pwType, String title)
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954 //are the sequences aligned?
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955 if(!viewport.alignment.isAligned())
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960 final TreePanel tp;
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961 if (viewport.getSelectionGroup() != null &&
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962 viewport.getSelectionGroup().getSize() > 3)
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964 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
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966 0, viewport.alignment.getWidth());
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970 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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971 type, pwType, 0, viewport.alignment.getWidth());
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974 addTreeMenuItem(tp, title);
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976 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
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979 void addTreeMenuItem(final TreePanel treePanel, String title)
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981 final MenuItem item = new MenuItem(title);
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982 sortByTreeMenu.add(item);
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983 item.addActionListener(new java.awt.event.ActionListener()
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985 public void actionPerformed(ActionEvent e)
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987 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
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988 HistoryItem.SORT));
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989 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
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990 alignPanel.repaint();
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994 treePanel.addWindowListener(new WindowAdapter()
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996 public void windowClosing(WindowEvent e)
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998 sortByTreeMenu.remove(item);
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1003 protected void documentation_actionPerformed(ActionEvent e) {
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1005 jalview.bin.JalviewLite.showURL("http://www.jalview.org");
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1009 protected void about_actionPerformed(ActionEvent e)
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1011 class AboutPanel extends Canvas
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1013 public void paint(Graphics g)
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1015 g.setColor(Color.white);
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1016 g.fillRect(0,0,getSize().width, getSize().height);
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1017 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
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1018 FontMetrics fm = g.getFontMetrics();
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1019 int fh = fm.getHeight();
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1021 g.setColor(Color.black);
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1022 g.setFont(new Font("Helvetica", Font.BOLD, 14));
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1023 g.drawString("JalView - Release 2.0", 200,y+=fh);
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1024 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
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1025 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",x,y+=fh*2);
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1026 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",x,y+=fh);
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1027 g.drawString("If you use JalView, please cite:",x,y+=fh+8);
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1028 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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1029 g.drawString("Bioinformatics, 2004 12;426-7.",x,y+=fh);
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1032 Frame frame = new Frame();
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1033 frame.add(new AboutPanel());
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1034 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580,200);
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