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 Object [] history = (Object[])historyList.elementAt(0);
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109 undoMenuItem.setLabel("Undo "+history[0]);
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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 Object [] history = (Object[])redoList.elementAt(0);
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121 redoMenuItem.setLabel("Redo "+history[0]);
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125 redoMenuItem.setEnabled(false);
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126 redoMenuItem.setLabel("Redo");
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130 public void addHistoryItem(String type)
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132 // must make sure we add new sequence objects her, not refs to the existing sequences
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133 redoList.removeAllElements();
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134 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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135 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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137 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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138 viewport.getAlignment().getSequenceAt(i).getSequence());
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141 historyList.addElement(new Object[]{type, seq} );
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142 updateEditMenuBar();
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145 protected void undoMenuItem_actionPerformed(ActionEvent e)
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147 Object [] history = (Object[])historyList.elementAt(0);
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148 historyList.removeElementAt(0);
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149 // add the redo state before continuing!!
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150 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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151 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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153 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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154 viewport.getAlignment().getSequenceAt(i).
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159 redoList.addElement(new Object[] {history[0], seq});
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161 seq = (SequenceI[]) history[1];
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163 AlignmentAnnotation[] old = viewport.alignment.getAlignmentAnnotation();
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164 viewport.setAlignment(new Alignment(seq));
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165 updateEditMenuBar();
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166 for (int i = 0; i < old.length; i++)
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167 viewport.alignment.addAnnotation(old[i]);
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169 viewport.updateConservation();
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170 viewport.updateConsensus();
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171 alignPanel.repaint();
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174 public void moveSelectedSequences(boolean up)
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176 SequenceGroup sg = viewport.getSelectionGroup();
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182 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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184 SequenceI seq = viewport.alignment.getSequenceAt(i);
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185 if (!sg.sequences.contains(seq))
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188 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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189 if (sg.sequences.contains(temp))
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192 viewport.alignment.getSequences().setElementAt(temp, i);
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193 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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198 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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200 SequenceI seq = viewport.alignment.getSequenceAt(i);
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201 if (!sg.sequences.contains(seq))
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204 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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205 if (sg.sequences.contains(temp))
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208 viewport.alignment.getSequences().setElementAt(temp, i);
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209 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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213 alignPanel.repaint();
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217 StringBuffer copiedSequences;
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218 protected void copy_actionPerformed(ActionEvent e)
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220 if(viewport.getSelectionGroup()==null)
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223 SequenceGroup sg = viewport.getSelectionGroup();
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224 copiedSequences = new StringBuffer();
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225 Hashtable orderedSeqs = new Hashtable();
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226 for(int i=0; i<sg.getSize(); i++)
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228 SequenceI seq = sg.getSequenceAt(i);
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229 int index = viewport.alignment.findIndex(seq);
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230 orderedSeqs.put(index+"", seq);
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234 for(int i=0; i<sg.getSize(); i++)
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236 SequenceI seq = null;
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237 while( seq == null )
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239 if(orderedSeqs.containsKey(index+""))
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241 seq = (SequenceI) orderedSeqs.get(index + "");
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249 copiedSequences.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
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250 +seq.findPosition( sg.getEndRes() )+ "\t"
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251 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
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257 protected void pasteNew_actionPerformed(ActionEvent e)
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262 protected void pasteThis_actionPerformed(ActionEvent e)
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264 addHistoryItem("Paste");
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268 void paste(boolean newAlignment)
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271 if (copiedSequences == null)
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274 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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275 Vector seqs = new Vector();
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276 while (st.hasMoreElements())
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278 String name = st.nextToken();
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279 int start = Integer.parseInt(st.nextToken());
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280 int end = Integer.parseInt(st.nextToken());
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281 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
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284 viewport.alignment.addSequence(sequence);
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286 seqs.addElement(sequence);
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291 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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292 for(int i=0; i<seqs.size(); i++)
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293 newSeqs[i] = (SequenceI)seqs.elementAt(i);
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295 AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);
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296 String newtitle = new String("Copied sequences");
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297 if( getTitle().startsWith("Copied sequences"))
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298 newtitle = getTitle();
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300 newtitle = newtitle.concat("- from "+getTitle());
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301 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
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305 viewport.setEndSeq(viewport.alignment.getHeight());
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306 viewport.alignment.getWidth();
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307 viewport.updateConservation();
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308 viewport.updateConsensus();
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309 alignPanel.repaint();
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312 }catch(Exception ex){}// could be anything being pasted in here
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317 protected void cut_actionPerformed(ActionEvent e)
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319 copy_actionPerformed(null);
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320 delete_actionPerformed(null);
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323 protected void delete_actionPerformed(ActionEvent e)
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325 addHistoryItem("Delete");
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326 if (viewport.getSelectionGroup() == null)
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329 SequenceGroup sg = viewport.getSelectionGroup();
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330 for (int i=0;i < sg.sequences.size(); i++)
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332 SequenceI seq = sg.getSequenceAt(i);
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333 int index = viewport.getAlignment().findIndex(seq);
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334 seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
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336 if(seq.getSequence().length()<1)
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337 viewport.getAlignment().deleteSequence(seq);
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339 viewport.getAlignment().getSequences().setElementAt(seq, index);
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342 viewport.setSelectionGroup(null);
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343 viewport.alignment.deleteGroup(sg);
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344 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getSize().height);
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345 if(viewport.getAlignment().getHeight()<1)
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348 this.setVisible(false);
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349 }catch(Exception ex){}
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350 viewport.updateConservation();
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351 viewport.updateConsensus();
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352 alignPanel.repaint();
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358 protected void redoMenuItem_actionPerformed(ActionEvent e)
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360 Object [] history = (Object[])redoList.pop();
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361 SequenceI[] seq = (SequenceI[]) history[1];
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363 AlignmentAnnotation[] old = viewport.alignment.getAlignmentAnnotation();
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364 viewport.setAlignment(new Alignment(seq));
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365 for (int i = 0; i < old.length; i++)
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366 viewport.alignment.addAnnotation(old[i]);
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368 viewport.updateConservation();
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369 viewport.updateConsensus();
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370 updateEditMenuBar();
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371 alignPanel.repaint();
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375 protected void deleteGroups_actionPerformed(ActionEvent e)
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377 viewport.alignment.deleteAllGroups();
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378 viewport.setSelectionGroup(null);
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380 alignPanel.repaint();
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385 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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387 SequenceGroup sg = new SequenceGroup();
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388 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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389 sg.addSequence( viewport.getAlignment().getSequenceAt(i));
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390 sg.setEndRes(viewport.alignment.getWidth());
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391 viewport.setSelectionGroup(sg);
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392 alignPanel.repaint();
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393 PaintRefresher.Refresh(null);
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396 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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398 viewport.setSelectionGroup(null);
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399 viewport.getColumnSelection().clear();
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400 viewport.setSelectionGroup(null);
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401 PaintRefresher.Refresh(null);
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404 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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406 SequenceGroup sg = viewport.getSelectionGroup();
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407 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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408 sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
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410 PaintRefresher.Refresh(null);
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413 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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415 addHistoryItem("delete columns");
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416 ColumnSelection colSel = viewport.getColumnSelection();
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417 if (colSel.size() > 0)
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419 int min = colSel.getMin();
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420 viewport.getAlignment().trimLeft(min);
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421 colSel.compensateForEdit(0,min);
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423 if(viewport.getSelectionGroup()!=null)
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424 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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426 Vector groups = viewport.alignment.getGroups();
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427 for(int i=0; i<groups.size(); i++)
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429 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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430 if(!sg.adjustForRemoveLeft(min))
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431 viewport.alignment.deleteGroup(sg);
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434 alignPanel.repaint();
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438 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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440 addHistoryItem("delete columns");
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441 ColumnSelection colSel = viewport.getColumnSelection();
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442 if (colSel.size() > 0)
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444 int max = colSel.getMax();
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445 viewport.getAlignment().trimRight(max);
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446 if(viewport.getSelectionGroup()!=null)
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447 viewport.getSelectionGroup().adjustForRemoveRight(max);
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449 Vector groups = viewport.alignment.getGroups();
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450 for(int i=0; i<groups.size(); i++)
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452 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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453 if(!sg.adjustForRemoveRight(max))
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454 viewport.alignment.deleteGroup(sg);
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459 alignPanel.repaint();
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464 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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466 addHistoryItem("delete gapped columns");
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467 viewport.getAlignment().removeGaps();
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468 viewport.updateConservation();
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469 viewport.updateConsensus();
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470 alignPanel.repaint();
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473 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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475 addHistoryItem("delete all gaps");
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478 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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480 current = viewport.getAlignment().getSequenceAt(i);
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481 jSize = current.getLength();
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482 for (int j=0; j < jSize; j++)
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483 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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485 current.deleteCharAt(j);
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490 viewport.updateConservation();
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491 viewport.updateConsensus();
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492 alignPanel.repaint();
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496 public void findMenuItem_actionPerformed(ActionEvent e)
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498 Finder finder = new Finder(alignPanel);
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502 public void font_actionPerformed(ActionEvent e)
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504 Frame frame = new Frame();
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505 FontChooser fc = new FontChooser( alignPanel, frame);
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507 jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440,100);
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511 protected void fullSeqId_actionPerformed(ActionEvent e)
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513 viewport.setShowFullId( fullSeqId.getState() );
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514 alignPanel.idPanel.idCanvas.setSize( alignPanel.calculateIdWidth() );
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515 alignPanel.repaint();
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518 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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520 viewport.setColourText( colourTextMenuItem.getState() );
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521 alignPanel.repaint();
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524 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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526 viewport.setWrapAlignment( wrapMenuItem.getState() );
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527 alignPanel.setWrapAlignment( wrapMenuItem.getState() );
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528 scaleAbove.setEnabled( wrapMenuItem.getState() );
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529 scaleLeft.setEnabled( wrapMenuItem.getState());
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530 scaleRight.setEnabled( wrapMenuItem.getState());
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531 alignPanel.repaint();
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534 protected void scaleAbove_actionPerformed(ActionEvent e)
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536 viewport.setScaleAboveWrapped(scaleAbove.getState());
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537 alignPanel.repaint();
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540 protected void scaleLeft_actionPerformed(ActionEvent e)
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542 viewport.setScaleLeftWrapped(scaleLeft.getState());
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543 alignPanel.repaint();
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546 protected void scaleRight_actionPerformed(ActionEvent e)
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548 viewport.setScaleRightWrapped(scaleRight.getState());
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549 alignPanel.repaint();
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554 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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556 viewport.setShowBoxes( viewBoxesMenuItem.getState() );
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557 alignPanel.repaint();
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560 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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562 viewport.setShowText( viewTextMenuItem.getState() );
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563 alignPanel.repaint();
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567 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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569 viewport.setRenderGaps(renderGapsMenuItem.getState());
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570 alignPanel.repaint();
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574 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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576 if(annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
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578 annotationPanelMenuItem.setState(false);
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581 viewport.setShowAnnotation( annotationPanelMenuItem.getState() );
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582 alignPanel.setAnnotationVisible( annotationPanelMenuItem.getState() );
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585 public void overviewMenuItem_actionPerformed(ActionEvent e)
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587 if (alignPanel.overviewPanel != null)
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590 Frame frame = new Frame();
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591 OverviewPanel overview = new OverviewPanel(alignPanel);
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592 frame.add(overview);
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593 // +50 must allow for applet frame window
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594 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
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595 overview.preferredSize().width, overview.preferredSize().height+50);
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598 frame.addWindowListener(new WindowAdapter()
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599 { public void windowClosing(WindowEvent e)
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601 alignPanel.setOverviewPanel(null);
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605 alignPanel.setOverviewPanel( overview );
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610 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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612 changeColour( null );
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616 public void clustalColour_actionPerformed(ActionEvent e)
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618 abovePIDThreshold.setState(false);
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619 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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622 public void zappoColour_actionPerformed(ActionEvent e)
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624 changeColour(new ZappoColourScheme());
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627 public void taylorColour_actionPerformed(ActionEvent e)
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629 changeColour(new TaylorColourScheme());
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633 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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635 changeColour( new HydrophobicColourScheme() );
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638 public void helixColour_actionPerformed(ActionEvent e)
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640 changeColour(new HelixColourScheme() );
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644 public void strandColour_actionPerformed(ActionEvent e)
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646 changeColour(new StrandColourScheme());
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650 public void turnColour_actionPerformed(ActionEvent e)
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652 changeColour(new TurnColourScheme());
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656 public void buriedColour_actionPerformed(ActionEvent e)
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658 changeColour(new BuriedColourScheme() );
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661 public void nucleotideColour_actionPerformed(ActionEvent e)
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663 changeColour(new NucleotideColourScheme());
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667 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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669 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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674 void changeColour(ColourSchemeI cs)
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678 if ( viewport.getAbovePIDThreshold() )
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680 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
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682 if (cs instanceof ResidueColourScheme)
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683 ( (ResidueColourScheme) cs).setThreshold(threshold);
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684 else if (cs instanceof ScoreColourScheme)
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685 ( (ScoreColourScheme) cs).setThreshold(threshold);
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687 viewport.setGlobalColourScheme(cs);
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689 else if (cs instanceof ResidueColourScheme)
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690 ( (ResidueColourScheme) cs).setThreshold(0);
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691 else if (cs instanceof ScoreColourScheme)
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692 ( (ScoreColourScheme) cs).setThreshold(0);
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696 if (viewport.getConservationSelected())
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698 ConservationColourScheme ccs = null;
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700 Alignment al = (Alignment) viewport.alignment;
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701 Conservation c = new Conservation("All",
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702 ResidueProperties.propHash, 3,
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703 al.getSequences(), 0,
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704 al.getWidth() - 1);
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707 c.verdict(false, viewport.ConsPercGaps);
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709 ccs = new ConservationColourScheme(c, cs);
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711 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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712 ccs.setConsensus( viewport.vconsensus );
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713 viewport.setGlobalColourScheme(ccs);
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715 SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
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720 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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722 cs.setConsensus(viewport.vconsensus);
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723 viewport.setGlobalColourScheme(cs);
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727 if(viewport.getColourAppliesToAllGroups())
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729 Vector groups = viewport.alignment.getGroups();
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730 for(int i=0; i<groups.size(); i++)
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732 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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734 if (cs instanceof ClustalxColourScheme)
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736 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
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741 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
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743 catch (Exception ex)
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745 ex.printStackTrace();
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749 if(viewport.getAbovePIDThreshold())
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751 if (sg.cs instanceof ResidueColourScheme)
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752 ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
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753 else if (sg.cs instanceof ScoreColourScheme)
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754 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
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756 sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
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759 if( viewport.getConservationSelected() )
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761 Conservation c = new Conservation("Group",
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762 ResidueProperties.propHash, 3,
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763 sg.sequences, 0, viewport.alignment.getWidth()-1);
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765 c.verdict(false, viewport.ConsPercGaps);
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766 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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768 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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769 ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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774 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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775 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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781 if(alignPanel.getOverviewPanel()!=null)
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782 alignPanel.getOverviewPanel().updateOverviewImage();
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784 alignPanel.repaint();
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787 protected void modifyPID_actionPerformed(ActionEvent e)
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789 if(viewport.getAbovePIDThreshold())
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791 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
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793 SliderPanel.showPIDSlider();
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797 protected void modifyConservation_actionPerformed(ActionEvent e)
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799 if(viewport.getConservationSelected())
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801 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
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803 SliderPanel.showConservationSlider();
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808 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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810 viewport.setConservationSelected(conservationMenuItem.getState());
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812 viewport.setAbovePIDThreshold(false);
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813 abovePIDThreshold.setState(false);
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815 ColourSchemeI cs = viewport.getGlobalColourScheme();
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816 if(cs instanceof ConservationColourScheme )
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817 changeColour( ((ConservationColourScheme)cs).cs );
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819 changeColour( cs );
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821 modifyConservation_actionPerformed(null);
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824 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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826 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
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828 conservationMenuItem.setState(false);
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829 viewport.setConservationSelected(false);
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831 ColourSchemeI cs = viewport.getGlobalColourScheme();
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833 if(cs instanceof ConservationColourScheme )
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834 changeColour( ((ConservationColourScheme)cs).cs );
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836 changeColour( cs );
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838 modifyPID_actionPerformed(null);
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843 public void userDefinedColour_actionPerformed(ActionEvent e)
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845 UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
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848 public void PIDColour_actionPerformed(ActionEvent e)
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850 changeColour( new PIDColourScheme() );
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854 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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856 changeColour(new Blosum62ColourScheme() );
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861 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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863 addHistoryItem("sort");
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864 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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865 alignPanel.repaint();
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868 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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870 addHistoryItem("sort");
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871 AlignmentSorter.sortByID( viewport.getAlignment() );
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872 alignPanel.repaint();
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875 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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877 addHistoryItem("sort");
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878 AlignmentSorter.sortByGroup(viewport.getAlignment());
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879 AlignmentSorter.sortGroups(viewport.getAlignment());
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880 alignPanel.repaint();
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883 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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885 RedundancyPanel sp = new RedundancyPanel(alignPanel);
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886 Frame frame = new Frame();
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888 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", 400, 120);
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892 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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894 if(viewport.getSelectionGroup().getSize()>1)
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896 Frame frame = new Frame();
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897 frame.add(new PairwiseAlignPanel(viewport));
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898 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
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902 public void PCAMenuItem_actionPerformed(ActionEvent e)
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905 if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
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906 || viewport.getAlignment().getHeight()<4)
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912 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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913 Frame frame = new Frame();
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914 frame.add(pcaPanel);
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915 jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis", 400, 400);
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916 }catch(java.lang.OutOfMemoryError ex)
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923 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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925 NewTreePanel("AV", "PID", "Average distance tree using PID");
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928 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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930 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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934 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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936 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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939 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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941 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
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944 void NewTreePanel(String type, String pwType, String title)
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946 //are the sequences aligned?
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947 if(!viewport.alignment.isAligned())
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952 final TreePanel tp;
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953 if (viewport.getSelectionGroup() != null &&
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954 viewport.getSelectionGroup().getSize() > 3)
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956 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
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958 0, viewport.alignment.getWidth());
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962 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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963 type, pwType, 0, viewport.alignment.getWidth());
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966 addTreeMenuItem(tp, title);
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968 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
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971 void addTreeMenuItem(final TreePanel treePanel, String title)
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973 final MenuItem item = new MenuItem(title);
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974 sortByTreeMenu.add(item);
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975 item.addActionListener(new java.awt.event.ActionListener()
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977 public void actionPerformed(ActionEvent e)
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979 addHistoryItem("sort");
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980 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
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981 alignPanel.repaint();
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985 treePanel.addWindowListener(new WindowAdapter()
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987 public void windowClosing(WindowEvent e)
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989 sortByTreeMenu.remove(item);
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994 protected void documentation_actionPerformed(ActionEvent e) {
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996 jalview.bin.JalviewLite.showURL("http://www.jalview.org");
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1000 protected void about_actionPerformed(ActionEvent e)
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1002 class AboutPanel extends Canvas
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1004 public void paint(Graphics g)
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1006 g.setColor(Color.white);
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1007 g.fillRect(0,0,getSize().width, getSize().height);
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1008 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
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1009 FontMetrics fm = g.getFontMetrics();
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1010 int fh = fm.getHeight();
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1012 g.setColor(Color.black);
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1013 g.setFont(new Font("Helvetica", Font.BOLD, 14));
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1014 g.drawString("JalView - Release 2.0", 200,y+=fh);
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1015 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
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1016 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",x,y+=fh*2);
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1017 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",x,y+=fh);
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1018 g.drawString("If you use JalView, please cite:",x,y+=fh+8);
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1019 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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1020 g.drawString("Bioinformatics, 2004 12;426-7.",x,y+=fh);
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1023 Frame frame = new Frame();
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1024 frame.add(new AboutPanel());
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1025 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580,200);
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