1 /********************
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2 * 2004 Jalview Reengineered
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12 package jalview.gui;
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14 import jalview.jbgui.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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19 import jalview.ws.*;
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21 import java.awt.event.*;
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22 import java.awt.print.*;
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23 import javax.swing.*;
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24 import javax.swing.event.*;
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26 import java.awt.datatransfer.*;
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29 public class AlignFrame extends GAlignFrame
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31 final AlignmentPanel alignPanel;
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32 final AlignViewport viewport;
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33 public AlignFrame(AlignmentI al)
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36 viewport = new AlignViewport(al,true,true,true,false);
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38 String fontName = jalview.bin.Cache.getProperty("FONT_NAME");
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39 String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");
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40 String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");
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41 if(fontName!=null && fontStyle!=null && fontSize!=null)
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42 viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );
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46 alignPanel = new AlignmentPanel(this, viewport);
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47 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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49 addInternalFrameListener(new InternalFrameAdapter()
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51 public void internalFrameActivated(InternalFrameEvent evt)
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53 javax.swing.SwingUtilities.invokeLater(new Runnable()
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56 { alignPanel.requestFocus(); }
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64 protected void saveAs_actionPerformed(ActionEvent e)
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66 JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
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67 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
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68 chooser.setToolTipText("Save");
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69 int value = chooser.showSaveDialog(this);
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70 if(value == JFileChooser.APPROVE_OPTION)
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72 String choice = chooser.getSelectedFile().getPath();
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73 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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74 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
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76 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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77 out.println(output);
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80 catch(Exception ex){}
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85 protected void outputText_actionPerformed(ActionEvent e)
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87 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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88 JInternalFrame frame = new JInternalFrame();
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89 cap.formatForOutput();
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90 frame.setContentPane(cap);
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91 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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92 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
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95 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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97 HTMLOutput htmlOutput = new HTMLOutput(viewport);
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101 protected void createJPG_actionPerformed(ActionEvent e)
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104 int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;
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105 int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();
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108 if(!viewport.getWrapAlignment())
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110 height = viewport.alignment.getHeight() * viewport.charHeight;
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111 width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;
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114 alignPanel.makeJPG( width, height);
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118 public void printMenuItem_actionPerformed(ActionEvent e)
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120 //Putting in a thread avoids Swing painting problems
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121 PrintThread thread = new PrintThread();
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125 class PrintThread extends Thread
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129 PrinterJob printJob = PrinterJob.getPrinterJob();
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130 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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131 printJob.setPrintable(alignPanel, pf);
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132 if (printJob.printDialog())
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138 catch (Exception PrintException)
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140 PrintException.printStackTrace();
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150 public void closeMenuItem_actionPerformed(ActionEvent e)
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153 this.setClosed(true);
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154 }catch(Exception ex){}
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157 Stack historyList = new Stack();
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158 Stack redoList = new Stack();
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160 void updateEditMenuBar()
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162 if(historyList.size()>0)
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164 undoMenuItem.setEnabled(true);
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165 Object [] history = (Object[])historyList.get(0);
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166 undoMenuItem.setText("Undo "+history[0]);
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170 undoMenuItem.setEnabled(false);
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171 undoMenuItem.setText("Undo");
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174 if(redoList.size()>0)
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176 redoMenuItem.setEnabled(true);
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177 Object [] history = (Object[])redoList.get(0);
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178 redoMenuItem.setText("Redo "+history[0]);
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182 redoMenuItem.setEnabled(false);
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183 redoMenuItem.setText("Redo");
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187 public void addHistoryItem(String type)
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189 // must make sure we add new sequence objects her, not refs to the existing sequences
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191 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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192 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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194 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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195 viewport.getAlignment().getSequenceAt(i).getSequence());
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198 historyList.add(0, new Object[]{type, seq} );
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199 updateEditMenuBar();
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202 protected void undoMenuItem_actionPerformed(ActionEvent e)
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204 Object [] history = (Object[])historyList.remove(0);
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205 // add the redo state before continuing!!
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206 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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207 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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209 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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210 viewport.getAlignment().getSequenceAt(i).
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215 redoList.add(0, new Object[] {history[0], seq});
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217 seq = (SequenceI[]) history[1];
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218 viewport.setAlignment( new Alignment(seq) );
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219 updateEditMenuBar();
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220 alignPanel.RefreshPanels();
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223 public void moveSelectedSequences(boolean up)
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225 SequenceGroup sg = viewport.getRubberbandGroup();
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231 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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233 SequenceI seq = viewport.alignment.getSequenceAt(i);
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234 if (!sg.sequences.contains(seq))
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237 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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238 if (sg.sequences.contains(temp))
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241 viewport.alignment.getSequences().setElementAt(temp, i);
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242 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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247 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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249 SequenceI seq = viewport.alignment.getSequenceAt(i);
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250 if (!sg.sequences.contains(seq))
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253 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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254 if (sg.sequences.contains(temp))
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257 viewport.alignment.getSequences().setElementAt(temp, i);
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258 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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262 alignPanel.RefreshPanels();
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267 protected void copy_actionPerformed(ActionEvent e)
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269 if(viewport.getRubberbandGroup()==null)
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272 SequenceGroup sg = viewport.getRubberbandGroup();
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274 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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275 StringBuffer buffer= new StringBuffer();
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277 for(int i=0; i<sg.getSize(); i++)
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279 SequenceI seq = sg.getSequenceAt(i);
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280 buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
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281 +seq.findPosition( sg.getEndRes() )+ "\t"
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282 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
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284 c.setContents( new StringSelection( buffer.toString()) , null ) ;
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289 protected void pasteNew_actionPerformed(ActionEvent e)
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294 protected void pasteThis_actionPerformed(ActionEvent e)
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296 addHistoryItem("Paste");
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300 void paste(boolean newAlignment)
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303 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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304 Transferable contents = c.getContents(this);
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305 if (contents == null)
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308 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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309 StringTokenizer st = new StringTokenizer(str);
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310 ArrayList seqs = new ArrayList();
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311 while (st.hasMoreElements())
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313 String name = st.nextToken();
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314 int start = Integer.parseInt(st.nextToken());
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315 int end = Integer.parseInt(st.nextToken());
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316 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
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319 viewport.alignment.addSequence(sequence);
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321 seqs.add(sequence);
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326 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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327 seqs.toArray(newSeqs);
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328 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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329 int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;
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330 if (newHeight > 500)
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332 Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
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336 viewport.setEndSeq(viewport.alignment.getHeight());
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337 viewport.alignment.getWidth();
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338 alignPanel.RefreshPanels();
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341 }catch(Exception ex){}// could be anything being pasted in here
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346 protected void cut_actionPerformed(ActionEvent e)
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348 copy_actionPerformed(null);
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349 delete_actionPerformed(null);
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352 protected void delete_actionPerformed(ActionEvent e)
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354 addHistoryItem("Delete");
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355 if (viewport.getRubberbandGroup() == null)
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358 SequenceGroup sg = viewport.getRubberbandGroup();
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359 for (int i=0;i < sg.sequences.size(); i++)
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361 SequenceI seq = sg.getSequenceAt(i);
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362 int index = viewport.getAlignment().findIndex(seq);
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363 seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
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365 if(seq.getSequence().length()<1)
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366 viewport.getAlignment().deleteSequence(seq);
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368 viewport.getAlignment().getSequences().setElementAt(seq, index);
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371 viewport.setRubberbandGroup(null);
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372 viewport.alignment.deleteGroup(sg);
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373 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
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374 if(viewport.getAlignment().getHeight()<1)
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377 this.setClosed(true);
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378 }catch(Exception ex){}
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379 alignPanel.RefreshPanels();
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385 protected void redoMenuItem_actionPerformed(ActionEvent e)
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387 Object [] history = (Object[])redoList.remove(0);
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388 SequenceI[] seq = (SequenceI[]) history[1];
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389 viewport.setAlignment( new Alignment(seq) );
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390 updateEditMenuBar();
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391 alignPanel.RefreshPanels();
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395 public void groupsMenuItem_actionPerformed(ActionEvent e)
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397 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
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398 JInternalFrame frame = new JInternalFrame();
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399 frame.setContentPane(geditor);
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400 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
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401 frame.setResizable(false);
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404 protected void deleteGroups_actionPerformed(ActionEvent e)
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406 viewport.alignment.deleteAllGroups();
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407 viewport.getSelection().clear();
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409 alignPanel.RefreshPanels();
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414 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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416 Selection sel = viewport.getSelection();
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417 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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418 sel.addElement( viewport.getAlignment().getSequenceAt(i));
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419 PaintRefresher.Refresh(null);
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422 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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424 viewport.setRubberbandGroup(null);
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425 viewport.getSelection().clear();
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426 PaintRefresher.Refresh(null);
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429 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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431 Selection sel = viewport.getSelection();
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432 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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434 if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
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435 sel.removeElement(viewport.getAlignment().getSequenceAt(i));
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437 sel.addElement(viewport.getAlignment().getSequenceAt(i));
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439 PaintRefresher.Refresh(null);
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443 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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445 viewport.getColumnSelection().clear();
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449 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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451 addHistoryItem("delete columns");
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452 ColumnSelection colSel = viewport.getColumnSelection();
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453 if (colSel.size() > 0)
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455 int min = colSel.getMin();
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456 viewport.getAlignment().trimLeft(min);
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457 colSel.compensateForEdit(0,min);
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458 alignPanel.RefreshPanels();
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462 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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464 addHistoryItem("delete columns");
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465 ColumnSelection colSel = viewport.getColumnSelection();
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466 if (colSel.size() > 0)
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468 int max = colSel.getMax();
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470 viewport.getAlignment().trimRight(max);
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472 alignPanel.RefreshPanels();
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477 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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479 addHistoryItem("delete gapped columns");
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480 viewport.getAlignment().removeGaps();
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481 alignPanel.RefreshPanels();
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484 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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486 addHistoryItem("delete all gaps");
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489 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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491 current = viewport.getAlignment().getSequenceAt(i);
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492 jSize = current.getLength();
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493 for (int j=0; j < jSize; j++)
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494 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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496 current.deleteCharAt(j);
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502 alignPanel.RefreshPanels();
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505 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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507 char thisChar = '-';
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508 char nextChar = '.';
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509 if(viewport.getGapCharacter()=='-')
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514 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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515 viewport.setGapCharacter(thisChar);
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516 alignPanel.RefreshPanels();
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519 public void findMenuItem_actionPerformed(ActionEvent e)
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521 JInternalFrame frame = new JInternalFrame();
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522 Finder finder = new Finder(viewport, alignPanel, frame);
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523 frame.setContentPane(finder);
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524 Desktop.addInternalFrame(frame, "Find", 340,110);
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529 public void font_actionPerformed(ActionEvent e)
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531 // JOptionPane op = new JOptionPane();
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532 JInternalFrame frame = new JInternalFrame();
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533 FontChooser fc = new FontChooser( alignPanel, frame );
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534 frame.setContentPane(fc);
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535 Desktop.addInternalFrame(frame, "Change Font", 480,100);
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538 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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540 viewport.setColourText( colourTextMenuItem.isSelected() );
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541 alignPanel.RefreshPanels();
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544 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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546 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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547 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
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551 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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553 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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554 alignPanel.RefreshPanels();
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557 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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559 viewport.setShowText( viewTextMenuItem.isSelected() );
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560 alignPanel.RefreshPanels();
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564 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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566 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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567 alignPanel.RefreshPanels();
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570 public void sequenceFeatures_actionPerformed(ActionEvent evt)
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572 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
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573 if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
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575 AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
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576 ((Alignment)viewport.alignment).featuresAdded = true;
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578 alignPanel.RefreshPanels();
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581 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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583 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
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586 public void overviewMenuItem_actionPerformed(ActionEvent e)
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588 if (alignPanel.overviewPanel != null)
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591 JInternalFrame frame = new JInternalFrame();
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592 OverviewPanel overview = alignPanel.getOverviewPanel();
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594 overview = new OverviewPanel(alignPanel, viewport);
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595 frame.setContentPane(overview);
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596 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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597 frame.getWidth(), frame.getHeight());
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599 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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600 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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602 alignPanel.setOverviewPanel(null);
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605 alignPanel.setOverviewPanel( overview );
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607 }catch(java.lang.OutOfMemoryError ex)
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609 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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610 +"\nTry reducing the font size.",
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611 "Out of memory", JOptionPane.WARNING_MESSAGE);
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617 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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619 changeColour( null );
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623 public void clustalColour_actionPerformed(ActionEvent e)
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625 abovePIDThreshold.setSelected(false);
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626 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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629 public void zappoColour_actionPerformed(ActionEvent e)
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631 changeColour(new ZappoColourScheme());
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634 public void taylorColour_actionPerformed(ActionEvent e)
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636 changeColour(new TaylorColourScheme());
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640 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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642 changeColour( new HydrophobicColourScheme() );
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645 public void helixColour_actionPerformed(ActionEvent e)
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647 changeColour(new HelixColourScheme() );
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651 public void strandColour_actionPerformed(ActionEvent e)
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653 changeColour(new StrandColourScheme());
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657 public void turnColour_actionPerformed(ActionEvent e)
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659 changeColour(new TurnColourScheme());
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663 public void buriedColour_actionPerformed(ActionEvent e)
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665 changeColour(new BuriedColourScheme() );
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668 public void nucleotideColour_actionPerformed(ActionEvent e)
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670 changeColour(new NucleotideColourScheme());
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674 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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676 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
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681 void changeColour(ColourSchemeI cs)
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684 if(viewport.getColourAppliesToAllGroups())
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686 Vector groups = viewport.alignment.getGroups();
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687 for(int i=0; i<groups.size(); i++)
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689 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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692 if(abovePIDThreshold.isSelected())
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693 abovePIDThreshold_actionPerformed(null);
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694 else if( viewport.getConservationSelected() )
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696 Conservation c = new Conservation("Group",
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697 ResidueProperties.propHash, 3,
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698 sg.sequences, sg.getStartRes(),
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701 c.verdict(false, 100);
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702 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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711 if ( viewport.getAbovePIDThreshold())
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714 threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
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715 Desktop.hideConservationSlider();
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717 if (cs instanceof ResidueColourScheme)
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718 ( (ResidueColourScheme) cs).setThreshold(threshold);
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719 else if (cs instanceof ScoreColourScheme)
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720 ( (ScoreColourScheme) cs).setThreshold(threshold);
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722 viewport.setGlobalColourScheme(cs);
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726 if (cs instanceof ResidueColourScheme)
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727 ( (ResidueColourScheme) cs).setThreshold(0);
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728 else if (cs instanceof ScoreColourScheme)
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729 ( (ScoreColourScheme) cs).setThreshold(0);
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734 if ( viewport.getConservationSelected() )
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736 ConservationColourScheme ccs = null;
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738 Alignment al = (Alignment) viewport.alignment;
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739 Conservation c = new Conservation("All",
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740 ResidueProperties.propHash, 3,
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741 al.getSequences(), 0,
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745 c.verdict(false, 100);
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747 ccs = new ConservationColourScheme(c, cs);
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749 int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,
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752 ccs.inc = threshold;
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754 viewport.setGlobalColourScheme(ccs);
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758 viewport.setGlobalColourScheme( cs );
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760 alignPanel.RefreshPanels();
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764 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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766 viewport.setConservationSelected(conservationMenuItem.isSelected());
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768 viewport.setAbovePIDThreshold(false);
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769 abovePIDThreshold.setSelected(false);
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770 Desktop.hidePIDSlider();
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771 if(!viewport.getConservationSelected())
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772 Desktop.hideConservationSlider();
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774 ColourSchemeI cs = viewport.getGlobalColourScheme();
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775 if(cs instanceof ConservationColourScheme )
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776 changeColour( ((ConservationColourScheme)cs).cs );
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778 changeColour( cs );
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782 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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784 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
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786 conservationMenuItem.setSelected(false);
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787 viewport.setConservationSelected(false);
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788 Desktop.hideConservationSlider();
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790 if(!viewport.getAbovePIDThreshold())
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791 Desktop.hidePIDSlider();
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794 ColourSchemeI cs = viewport.getGlobalColourScheme();
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795 if(cs instanceof ConservationColourScheme )
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796 changeColour( ((ConservationColourScheme)cs).cs );
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798 changeColour( cs );
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804 public void userDefinedColour_actionPerformed(ActionEvent e)
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806 JInternalFrame frame = new JInternalFrame();
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807 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
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808 frame.setContentPane(chooser);
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809 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
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810 frame.setResizable(false);
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811 frame.setIconifiable(false);
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812 frame.setMaximizable(false);
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815 public void PIDColour_actionPerformed(ActionEvent e)
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817 changeColour( new PIDColourScheme() );
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821 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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823 changeColour(new Blosum62ColourScheme(viewport) );
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828 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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830 addHistoryItem("sort");
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831 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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832 alignPanel.RefreshPanels();
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835 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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837 addHistoryItem("sort");
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838 AlignmentSorter.sortByID( viewport.getAlignment() );
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839 alignPanel.RefreshPanels();
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842 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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844 addHistoryItem("sort");
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845 AlignmentSorter.sortByGroup(viewport.getAlignment());
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846 AlignmentSorter.sortGroups(viewport.getAlignment());
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847 alignPanel.RefreshPanels();
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850 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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852 addHistoryItem("sort");
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853 if(viewport.getCurrentTree()==null)
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856 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
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857 alignPanel.RefreshPanels();
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860 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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862 RedundancyPanel sp = new RedundancyPanel(alignPanel);
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863 JInternalFrame frame = new JInternalFrame();
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864 frame.setContentPane(sp);
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865 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
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866 frame.setMaximizable(false);
\r
867 frame.setResizable(false);
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871 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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873 if(viewport.getSelection().size()<2)
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874 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
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877 JInternalFrame frame = new JInternalFrame();
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878 frame.setContentPane(new PairwiseAlignPanel(viewport));
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879 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
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883 public void PCAMenuItem_actionPerformed(ActionEvent e)
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885 if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
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886 || viewport.getAlignment().getHeight()<4)
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888 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
\r
889 +"at least 4 input sequences.",
\r
890 "Sequence selection insufficient",
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891 JOptionPane.WARNING_MESSAGE);
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896 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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897 JInternalFrame frame = new JInternalFrame();
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898 frame.setContentPane(pcaPanel);
\r
899 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
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900 }catch(java.lang.OutOfMemoryError ex)
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902 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
\r
903 "Out of memory", JOptionPane.WARNING_MESSAGE);
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909 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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911 NewTreePanel("AV", "PID", "Average distance tree using PID");
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914 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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916 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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920 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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922 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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925 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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927 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
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930 void NewTreePanel(String type, String pwType, String title)
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932 //are the sequences aligned?
\r
933 if(!viewport.alignment.isAligned())
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935 JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
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936 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
\r
941 if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
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943 tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
\r
944 0, viewport.alignment.getWidth());
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948 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
949 type, pwType, 0, viewport.alignment.getWidth());
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952 Desktop.addInternalFrame(tp, title, 600, 500);
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958 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
960 JInternalFrame frame = new JInternalFrame();
\r
961 ClustalThread ct = new ClustalThread(frame);
\r
962 Thread t = new Thread(ct);
\r
964 frame.setContentPane(ct);
\r
965 Desktop.addInternalFrame(frame, title, 300, 80);
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969 class ClustalThread extends JPanel implements Runnable
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972 int imageIndex = 0;
\r
973 boolean webServiceRunning = false;
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974 JInternalFrame frame;
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975 public ClustalThread(JInternalFrame frame)
\r
977 this.frame = frame;
\r
978 image = new Image[9];
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979 for(int i=0; i<9; i++)
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981 java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
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984 image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
\r
985 MediaTracker mt = new MediaTracker(this);
\r
986 mt.addImage(image[i], i);
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987 try{mt.waitForID(i);}
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988 catch(Exception ex){}
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991 DNATwirler twirler = new DNATwirler();
\r
993 webServiceRunning = true;
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996 class DNATwirler extends Thread
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1000 while(webServiceRunning)
\r
1003 Thread.sleep(100);
\r
1008 catch(Exception ex){}
\r
1014 // Should check to see if the server settings are valid
\r
1015 // Need visual-delay indication here.
\r
1018 jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
\r
1019 Vector sv = viewport.getAlignment().getSequences();
\r
1020 SequenceI[] seqs = new SequenceI[sv.size()];
\r
1025 seqs[i] = (SequenceI) sv.elementAt(i);
\r
1027 while (++i < sv.size());
\r
1029 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
\r
1031 if (alignment != null)
\r
1033 AlignFrame af = new AlignFrame(new Alignment(alignment));
\r
1034 af.clustalColour.setSelected(true);
\r
1035 af.clustalColour_actionPerformed(null);
\r
1036 Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
\r
1037 700, 500); // JBPNote - is there a new window geom. property ?
\r
1040 JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
\r
1041 JOptionPane.WARNING_MESSAGE);
\r
1043 webServiceRunning = false;
\r
1045 frame.setClosed(true);
\r
1046 }catch(Exception ex){}
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1049 public void paintComponent(Graphics g)
\r
1051 g.setColor(Color.white);
\r
1052 g.fillRect(0,0,getWidth(), getHeight());
\r
1055 g.drawImage(image[imageIndex],10,10,this);
\r
1057 g.setFont(new Font("Arial", Font.BOLD, 12));
\r
1058 g.setColor(Color.black);
\r
1059 g.drawString("Clustal Alignment Web Service running", 30,30);
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