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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37 alignPanel = new AlignmentPanel(this, viewport);
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38 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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39 fontNameMenuItem.setText(viewport.getFont().getName());
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40 fontSizeMenuItem.setText(viewport.getFont().getSize()+"");
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42 addInternalFrameListener(new InternalFrameAdapter()
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44 public void internalFrameActivated(InternalFrameEvent evt)
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46 javax.swing.SwingUtilities.invokeLater(new Runnable()
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49 { alignPanel.requestFocus(); }
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57 protected void saveAs_actionPerformed(ActionEvent e)
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59 JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
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60 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
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61 chooser.setToolTipText("Save");
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62 int value = chooser.showSaveDialog(this);
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63 if(value == JFileChooser.APPROVE_OPTION)
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65 String choice = chooser.getSelectedFile().getPath();
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66 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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67 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
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69 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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70 out.println(output);
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73 catch(Exception ex){}
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78 protected void outputText_actionPerformed(ActionEvent e)
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80 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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81 JInternalFrame frame = new JInternalFrame();
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82 cap.formatForOutput();
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83 frame.setContentPane(cap);
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84 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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85 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
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88 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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90 HTMLOutput htmlOutput = new HTMLOutput(viewport);
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94 protected void createJPG_actionPerformed(ActionEvent e)
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97 int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;
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98 int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();
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101 if(!viewport.getWrapAlignment())
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103 height = viewport.alignment.getHeight() * viewport.charHeight;
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104 width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;
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107 alignPanel.makeJPG( width, height);
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111 public void printMenuItem_actionPerformed(ActionEvent e)
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113 //Putting in a thread avoids Swing painting problems
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114 PrintThread thread = new PrintThread();
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118 class PrintThread extends Thread
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122 PrinterJob printJob = PrinterJob.getPrinterJob();
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123 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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124 printJob.setPrintable(alignPanel, pf);
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125 if (printJob.printDialog())
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131 catch (Exception PrintException)
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133 PrintException.printStackTrace();
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143 public void closeMenuItem_actionPerformed(ActionEvent e)
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146 this.setClosed(true);
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147 }catch(Exception ex){}
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150 Stack historyList = new Stack();
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151 Stack redoList = new Stack();
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153 void updateEditMenuBar()
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155 if(historyList.size()>0)
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157 undoMenuItem.setEnabled(true);
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158 Object [] history = (Object[])historyList.get(0);
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159 undoMenuItem.setText("Undo "+history[0]);
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163 undoMenuItem.setEnabled(false);
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164 undoMenuItem.setText("Undo");
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167 if(redoList.size()>0)
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169 redoMenuItem.setEnabled(true);
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170 Object [] history = (Object[])redoList.get(0);
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171 redoMenuItem.setText("Redo "+history[0]);
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175 redoMenuItem.setEnabled(false);
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176 redoMenuItem.setText("Redo");
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180 public void addHistoryItem(String type)
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182 // must make sure we add new sequence objects her, not refs to the existing sequences
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184 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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185 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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187 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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188 viewport.getAlignment().getSequenceAt(i).getSequence());
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191 historyList.add(0, new Object[]{type, seq} );
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192 updateEditMenuBar();
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195 protected void undoMenuItem_actionPerformed(ActionEvent e)
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197 Object [] history = (Object[])historyList.remove(0);
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198 // add the redo state before continuing!!
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199 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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200 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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202 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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203 viewport.getAlignment().getSequenceAt(i).
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208 redoList.add(0, new Object[] {history[0], seq});
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210 seq = (SequenceI[]) history[1];
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211 viewport.setAlignment( new Alignment(seq) );
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212 updateEditMenuBar();
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213 alignPanel.RefreshPanels();
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216 public void moveSelectedSequences(boolean up)
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218 SequenceGroup sg = viewport.getRubberbandGroup();
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224 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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226 SequenceI seq = viewport.alignment.getSequenceAt(i);
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227 if (!sg.sequences.contains(seq))
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230 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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231 if (sg.sequences.contains(temp))
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234 viewport.alignment.getSequences().setElementAt(temp, i);
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235 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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240 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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242 SequenceI seq = viewport.alignment.getSequenceAt(i);
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243 if (!sg.sequences.contains(seq))
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246 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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247 if (sg.sequences.contains(temp))
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250 viewport.alignment.getSequences().setElementAt(temp, i);
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251 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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255 alignPanel.RefreshPanels();
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260 protected void copy_actionPerformed(ActionEvent e)
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262 if(viewport.getRubberbandGroup()==null)
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265 SequenceGroup sg = viewport.getRubberbandGroup();
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267 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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268 StringBuffer buffer= new StringBuffer();
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270 for(int i=0; i<sg.getSize(); i++)
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272 SequenceI seq = sg.getSequenceAt(i);
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273 buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
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274 +seq.findPosition( sg.getEndRes() )+ "\t"
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275 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
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277 c.setContents( new StringSelection( buffer.toString()) , null ) ;
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282 protected void pasteNew_actionPerformed(ActionEvent e)
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287 protected void pasteThis_actionPerformed(ActionEvent e)
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289 addHistoryItem("Paste");
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293 void paste(boolean newAlignment)
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296 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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297 Transferable contents = c.getContents(this);
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298 if (contents == null)
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301 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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302 StringTokenizer st = new StringTokenizer(str);
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303 ArrayList seqs = new ArrayList();
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304 while (st.hasMoreElements())
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306 String name = st.nextToken();
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307 int start = Integer.parseInt(st.nextToken());
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308 int end = Integer.parseInt(st.nextToken());
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309 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
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312 viewport.alignment.addSequence(sequence);
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314 seqs.add(sequence);
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319 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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320 seqs.toArray(newSeqs);
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321 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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322 int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;
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323 if (newHeight > 500)
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325 Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
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329 viewport.setEndSeq(viewport.alignment.getHeight());
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330 viewport.alignment.getWidth();
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331 alignPanel.RefreshPanels();
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334 }catch(Exception ex){}// could be anything being pasted in here
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339 protected void cut_actionPerformed(ActionEvent e)
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341 copy_actionPerformed(null);
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342 delete_actionPerformed(null);
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345 protected void delete_actionPerformed(ActionEvent e)
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347 addHistoryItem("Delete");
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348 if (viewport.getRubberbandGroup() == null)
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351 SequenceGroup sg = viewport.getRubberbandGroup();
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352 for (int i=0;i < sg.sequences.size(); i++)
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353 viewport.getAlignment().deleteSequence(sg.getSequenceAt(i));
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355 viewport.alignment.deleteGroup(sg);
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356 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
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357 if(viewport.getAlignment().getHeight()<1)
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360 this.setClosed(true);
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361 }catch(Exception ex){}
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362 alignPanel.RefreshPanels();
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368 protected void redoMenuItem_actionPerformed(ActionEvent e)
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370 Object [] history = (Object[])redoList.remove(0);
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371 SequenceI[] seq = (SequenceI[]) history[1];
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372 viewport.setAlignment( new Alignment(seq) );
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373 updateEditMenuBar();
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374 alignPanel.RefreshPanels();
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378 public void groupsMenuItem_actionPerformed(ActionEvent e)
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380 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
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381 JInternalFrame frame = new JInternalFrame();
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382 frame.setContentPane(geditor);
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383 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
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384 frame.setResizable(false);
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387 protected void deleteGroups_actionPerformed(ActionEvent e)
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389 viewport.alignment.deleteAllGroups();
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390 viewport.getSelection().clear();
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392 alignPanel.RefreshPanels();
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397 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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399 Selection sel = viewport.getSelection();
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400 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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401 sel.addElement( viewport.getAlignment().getSequenceAt(i));
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402 PaintRefresher.Refresh(null);
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405 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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407 viewport.setRubberbandGroup(null);
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408 viewport.getSelection().clear();
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409 PaintRefresher.Refresh(null);
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412 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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414 Selection sel = viewport.getSelection();
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415 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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417 if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
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418 sel.removeElement(viewport.getAlignment().getSequenceAt(i));
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420 sel.addElement(viewport.getAlignment().getSequenceAt(i));
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422 PaintRefresher.Refresh(null);
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426 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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428 viewport.getColumnSelection().clear();
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432 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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434 addHistoryItem("delete columns");
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435 ColumnSelection colSel = viewport.getColumnSelection();
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436 if (colSel.size() > 0)
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438 int min = colSel.getMin();
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439 viewport.getAlignment().trimLeft(min);
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440 colSel.compensateForEdit(0,min);
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441 alignPanel.RefreshPanels();
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445 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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447 addHistoryItem("delete columns");
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448 ColumnSelection colSel = viewport.getColumnSelection();
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449 if (colSel.size() > 0)
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451 int max = colSel.getMax();
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453 viewport.getAlignment().trimRight(max);
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455 alignPanel.RefreshPanels();
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460 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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462 addHistoryItem("delete gapped columns");
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463 viewport.getAlignment().removeGaps();
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464 alignPanel.RefreshPanels();
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467 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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469 addHistoryItem("delete all gaps");
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472 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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474 current = viewport.getAlignment().getSequenceAt(i);
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475 jSize = current.getLength();
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476 for (int j=0; j < jSize; j++)
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477 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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479 current.deleteCharAt(j);
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485 alignPanel.RefreshPanels();
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488 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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490 char thisChar = '-';
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491 char nextChar = '.';
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492 if(viewport.getGapCharacter()=='-')
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497 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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498 viewport.setGapCharacter(thisChar);
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499 alignPanel.RefreshPanels();
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502 public void findMenuItem_actionPerformed(ActionEvent e)
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504 JOptionPane op = new JOptionPane();
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505 JInternalFrame frame = op.createInternalFrame(this, "Find");
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506 Finder finder = new Finder(viewport, alignPanel, frame);
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507 frame.setClosable(true);
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508 frame.setContentPane(finder);
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509 frame.setSize(340,110);
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510 frame.setVisible(true);
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515 public void fontNameMenuItem_actionPerformed(ActionEvent e)
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517 String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
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520 String selection = JOptionPane.showInternalInputDialog(this,
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523 JOptionPane.QUESTION_MESSAGE,
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525 ,fontNameMenuItem.getText()).toString();
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526 if(selection!=null)
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528 fontNameMenuItem.setText(selection);
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534 public void fontSizeMenuItem_actionPerformed(ActionEvent e)
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536 String selection = JOptionPane.showInternalInputDialog(this,
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537 "Select font size",
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539 JOptionPane.QUESTION_MESSAGE,
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540 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
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541 ,fontSizeMenuItem.getText()).toString();
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542 if(selection!=null)
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544 fontSizeMenuItem.setText(selection);
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549 public void fontStyleMenuItem_actionPerformed(ActionEvent e)
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551 String selection = JOptionPane.showInternalInputDialog(this,
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552 "Select font style",
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554 JOptionPane.QUESTION_MESSAGE,
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555 null, new String[]{"plain", "bold", "italic"}
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556 ,fontStyleMenuItem.getText()).toString();
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557 if(selection!=null)
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559 fontStyleMenuItem.setText(selection);
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565 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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567 viewport.setColourText( colourTextMenuItem.isSelected() );
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568 alignPanel.RefreshPanels();
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573 int style = java.awt.Font.PLAIN;
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574 if(fontStyleMenuItem.getText().equals("bold"))
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575 style = java.awt.Font.BOLD;
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576 else if(fontStyleMenuItem.getText().equals("italic"))
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577 style = java.awt.Font.ITALIC;
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579 viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
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581 Integer.parseInt(fontSizeMenuItem.getText())));
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582 alignPanel.RefreshPanels();
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586 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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588 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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589 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
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593 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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595 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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596 alignPanel.RefreshPanels();
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599 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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601 viewport.setShowText( viewTextMenuItem.isSelected() );
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602 alignPanel.RefreshPanels();
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606 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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608 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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609 alignPanel.RefreshPanels();
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612 public void sequenceFeatures_actionPerformed(ActionEvent evt)
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614 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
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615 if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
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617 AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
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618 ((Alignment)viewport.alignment).featuresAdded = true;
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620 alignPanel.RefreshPanels();
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623 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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625 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
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628 public void overviewMenuItem_actionPerformed(ActionEvent e)
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630 if (alignPanel.overviewPanel != null)
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633 JInternalFrame frame = new JInternalFrame();
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634 OverviewPanel overview = alignPanel.getOverviewPanel();
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636 overview = new OverviewPanel(alignPanel, viewport);
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637 frame.setContentPane(overview);
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638 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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639 frame.getWidth(), frame.getHeight());
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641 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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642 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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644 alignPanel.setOverviewPanel(null);
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647 alignPanel.setOverviewPanel( overview );
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649 }catch(java.lang.OutOfMemoryError ex)
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651 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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652 +"\nTry reducing the font size.",
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653 "Out of memory", JOptionPane.WARNING_MESSAGE);
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659 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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661 changeColour( null );
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665 public void clustalColour_actionPerformed(ActionEvent e)
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667 abovePIDThreshold.setSelected(false);
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668 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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671 public void zappoColour_actionPerformed(ActionEvent e)
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673 changeColour(new ZappoColourScheme());
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676 public void taylorColour_actionPerformed(ActionEvent e)
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678 changeColour(new TaylorColourScheme());
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682 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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684 changeColour( new HydrophobicColourScheme() );
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687 public void helixColour_actionPerformed(ActionEvent e)
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689 changeColour(new HelixColourScheme() );
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693 public void strandColour_actionPerformed(ActionEvent e)
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695 changeColour(new StrandColourScheme());
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699 public void turnColour_actionPerformed(ActionEvent e)
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701 changeColour(new TurnColourScheme());
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705 public void buriedColour_actionPerformed(ActionEvent e)
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707 changeColour(new BuriedColourScheme() );
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710 public void nucleotideColour_actionPerformed(ActionEvent e)
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712 changeColour(new NucleotideColourScheme());
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716 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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718 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
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723 void changeColour(ColourSchemeI cs)
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726 if(viewport.getColourAppliesToAllGroups())
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728 Vector groups = viewport.alignment.getGroups();
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729 for(int i=0; i<groups.size(); i++)
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731 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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734 if(abovePIDThreshold.isSelected())
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735 abovePIDThreshold_actionPerformed(null);
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736 else if( viewport.getConservationSelected() )
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738 Conservation c = new Conservation("Group",
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739 ResidueProperties.propHash, 3,
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740 sg.sequences, sg.getStartRes(),
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743 c.verdict(false, 100);
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744 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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753 if ( viewport.getAbovePIDThreshold())
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756 threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
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757 Desktop.hideConservationSlider();
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759 if (cs instanceof ResidueColourScheme)
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760 ( (ResidueColourScheme) cs).setThreshold(threshold);
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761 else if (cs instanceof ScoreColourScheme)
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762 ( (ScoreColourScheme) cs).setThreshold(threshold);
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764 viewport.setGlobalColourScheme(cs);
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768 if (cs instanceof ResidueColourScheme)
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769 ( (ResidueColourScheme) cs).setThreshold(0);
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770 else if (cs instanceof ScoreColourScheme)
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771 ( (ScoreColourScheme) cs).setThreshold(0);
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776 if ( viewport.getConservationSelected() )
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778 ConservationColourScheme ccs = null;
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780 Alignment al = (Alignment) viewport.alignment;
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781 Conservation c = new Conservation("All",
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782 ResidueProperties.propHash, 3,
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783 al.getSequences(), 0,
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787 c.verdict(false, 100);
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789 ccs = new ConservationColourScheme(c, cs);
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791 int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,
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794 ccs.inc = threshold;
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796 viewport.setGlobalColourScheme(ccs);
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800 viewport.setGlobalColourScheme( cs );
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802 alignPanel.RefreshPanels();
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806 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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808 viewport.setConservationSelected(conservationMenuItem.isSelected());
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810 viewport.setAbovePIDThreshold(false);
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811 abovePIDThreshold.setSelected(false);
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812 Desktop.hidePIDSlider();
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813 if(!viewport.getConservationSelected())
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814 Desktop.hideConservationSlider();
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816 ColourSchemeI cs = viewport.getGlobalColourScheme();
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817 if(cs instanceof ConservationColourScheme )
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818 changeColour( ((ConservationColourScheme)cs).cs );
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820 changeColour( cs );
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824 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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826 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
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828 conservationMenuItem.setSelected(false);
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829 viewport.setConservationSelected(false);
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830 Desktop.hideConservationSlider();
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832 if(!viewport.getAbovePIDThreshold())
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833 Desktop.hidePIDSlider();
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836 ColourSchemeI cs = viewport.getGlobalColourScheme();
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837 if(cs instanceof ConservationColourScheme )
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838 changeColour( ((ConservationColourScheme)cs).cs );
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840 changeColour( cs );
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846 public void userDefinedColour_actionPerformed(ActionEvent e)
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848 JInternalFrame frame = new JInternalFrame();
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849 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
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850 frame.setContentPane(chooser);
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851 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
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852 frame.setResizable(false);
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853 frame.setIconifiable(false);
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854 frame.setMaximizable(false);
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857 public void PIDColour_actionPerformed(ActionEvent e)
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859 changeColour( new PIDColourScheme() );
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863 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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865 changeColour(new Blosum62ColourScheme(viewport) );
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870 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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872 addHistoryItem("sort");
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873 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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874 alignPanel.RefreshPanels();
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877 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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879 addHistoryItem("sort");
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880 AlignmentSorter.sortByID( viewport.getAlignment() );
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881 alignPanel.RefreshPanels();
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884 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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886 addHistoryItem("sort");
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887 AlignmentSorter.sortByGroup(viewport.getAlignment());
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888 AlignmentSorter.sortGroups(viewport.getAlignment());
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889 alignPanel.RefreshPanels();
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892 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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894 addHistoryItem("sort");
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895 if(viewport.getCurrentTree()==null)
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898 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
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899 alignPanel.RefreshPanels();
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902 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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904 RedundancyPanel sp = new RedundancyPanel(alignPanel);
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905 JInternalFrame frame = new JInternalFrame();
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906 frame.setContentPane(sp);
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907 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
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908 frame.setMaximizable(false);
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909 frame.setResizable(false);
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913 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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915 if(viewport.getSelection().size()<2)
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916 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
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919 JInternalFrame frame = new JInternalFrame();
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920 frame.setContentPane(new PairwiseAlignPanel(viewport));
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921 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
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925 public void PCAMenuItem_actionPerformed(ActionEvent e)
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927 if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
\r
928 || viewport.getAlignment().getHeight()<4)
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930 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
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931 +"at least 4 input sequences.",
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932 "Sequence selection insufficient",
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933 JOptionPane.WARNING_MESSAGE);
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938 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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939 JInternalFrame frame = new JInternalFrame();
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940 frame.setContentPane(pcaPanel);
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941 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
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942 }catch(java.lang.OutOfMemoryError ex)
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944 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
\r
945 "Out of memory", JOptionPane.WARNING_MESSAGE);
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951 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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953 NewTreePanel("AV", "PID", "Average distance tree using PID");
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956 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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958 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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962 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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964 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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967 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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969 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
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972 void NewTreePanel(String type, String pwType, String title)
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974 //are the sequences aligned?
\r
975 if(!viewport.alignment.isAligned())
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977 JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
\r
978 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
\r
983 if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
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985 tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
\r
986 0, viewport.alignment.getWidth());
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990 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
991 type, pwType, 0, viewport.alignment.getWidth());
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994 Desktop.addInternalFrame(tp, title, 600, 500);
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1000 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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1002 JInternalFrame frame = new JInternalFrame();
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1003 ClustalThread ct = new ClustalThread(frame);
\r
1004 Thread t = new Thread(ct);
\r
1006 frame.setContentPane(ct);
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1007 Desktop.addInternalFrame(frame, title, 300, 80);
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1011 class ClustalThread extends JPanel implements Runnable
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1014 int imageIndex = 0;
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1015 boolean webServiceRunning = false;
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1016 JInternalFrame frame;
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1017 public ClustalThread(JInternalFrame frame)
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1019 this.frame = frame;
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1020 image = new Image[9];
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1021 for(int i=0; i<9; i++)
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1023 java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
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1026 image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
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1027 MediaTracker mt = new MediaTracker(this);
\r
1028 mt.addImage(image[i], i);
\r
1029 try{mt.waitForID(i);}
\r
1030 catch(Exception ex){}
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1033 DNATwirler twirler = new DNATwirler();
\r
1035 webServiceRunning = true;
\r
1038 class DNATwirler extends Thread
\r
1042 while(webServiceRunning)
\r
1045 Thread.sleep(100);
\r
1050 catch(Exception ex){}
\r
1056 // Should check to see if the server settings are valid
\r
1057 // Need visual-delay indication here.
\r
1060 jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
\r
1061 Vector sv = viewport.getAlignment().getSequences();
\r
1062 SequenceI[] seqs = new SequenceI[sv.size()];
\r
1067 seqs[i] = (SequenceI) sv.elementAt(i);
\r
1069 while (++i < sv.size());
\r
1071 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
\r
1073 if (alignment != null)
\r
1075 AlignFrame af = new AlignFrame(new Alignment(alignment));
\r
1076 af.clustalColour.setSelected(true);
\r
1077 af.clustalColour_actionPerformed(null);
\r
1078 Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
\r
1079 700, 500); // JBPNote - is there a new window geom. property ?
\r
1082 JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
\r
1083 JOptionPane.WARNING_MESSAGE);
\r
1085 webServiceRunning = false;
\r
1087 frame.setClosed(true);
\r
1088 }catch(Exception ex){}
\r
1091 public void paintComponent(Graphics g)
\r
1093 g.setColor(Color.white);
\r
1094 g.fillRect(0,0,getWidth(), getHeight());
\r
1097 g.drawImage(image[imageIndex],10,10,this);
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1099 g.setFont(new Font("Arial", Font.BOLD, 12));
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1100 g.setColor(Color.black);
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1101 g.drawString("Clustal Alignment Web Service running", 30,30);
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