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,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 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
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67 chooser.setFileView(new JalviewFileView());
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68 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
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69 chooser.setToolTipText("Save");
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70 int value = chooser.showSaveDialog(this);
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71 if(value == JalviewFileChooser.APPROVE_OPTION)
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73 String choice = chooser.getSelectedFile().getPath();
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74 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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75 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
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77 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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78 out.println(output);
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81 catch(Exception ex){}
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86 protected void outputText_actionPerformed(ActionEvent e)
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88 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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89 JInternalFrame frame = new JInternalFrame();
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90 cap.formatForOutput();
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91 frame.setContentPane(cap);
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92 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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93 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
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96 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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98 HTMLOutput htmlOutput = new HTMLOutput(viewport);
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102 protected void createJPG_actionPerformed(ActionEvent e)
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105 int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;
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106 int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();
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109 if(!viewport.getWrapAlignment())
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111 height = viewport.alignment.getHeight() * viewport.charHeight;
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112 width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;
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115 alignPanel.makeJPG( width, height);
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119 public void printMenuItem_actionPerformed(ActionEvent e)
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121 //Putting in a thread avoids Swing painting problems
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122 PrintThread thread = new PrintThread();
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126 class PrintThread extends Thread
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130 PrinterJob printJob = PrinterJob.getPrinterJob();
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131 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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132 printJob.setPrintable(alignPanel, pf);
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133 if (printJob.printDialog())
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139 catch (Exception PrintException)
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141 PrintException.printStackTrace();
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151 public void closeMenuItem_actionPerformed(ActionEvent e)
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154 this.setClosed(true);
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155 }catch(Exception ex){}
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158 Stack historyList = new Stack();
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159 Stack redoList = new Stack();
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161 void updateEditMenuBar()
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163 if(historyList.size()>0)
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165 undoMenuItem.setEnabled(true);
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166 Object [] history = (Object[])historyList.get(0);
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167 undoMenuItem.setText("Undo "+history[0]);
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171 undoMenuItem.setEnabled(false);
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172 undoMenuItem.setText("Undo");
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175 if(redoList.size()>0)
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177 redoMenuItem.setEnabled(true);
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178 Object [] history = (Object[])redoList.get(0);
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179 redoMenuItem.setText("Redo "+history[0]);
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183 redoMenuItem.setEnabled(false);
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184 redoMenuItem.setText("Redo");
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188 public void addHistoryItem(String type)
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190 // must make sure we add new sequence objects her, not refs to the existing sequences
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192 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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193 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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195 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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196 viewport.getAlignment().getSequenceAt(i).getSequence());
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199 historyList.add(0, new Object[]{type, seq} );
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200 updateEditMenuBar();
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203 protected void undoMenuItem_actionPerformed(ActionEvent e)
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205 Object [] history = (Object[])historyList.remove(0);
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206 // add the redo state before continuing!!
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207 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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208 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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210 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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211 viewport.getAlignment().getSequenceAt(i).
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216 redoList.add(0, new Object[] {history[0], seq});
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218 seq = (SequenceI[]) history[1];
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219 viewport.setAlignment( new Alignment(seq) );
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220 updateEditMenuBar();
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221 alignPanel.RefreshPanels();
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224 public void moveSelectedSequences(boolean up)
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226 SequenceGroup sg = viewport.getSelectionGroup();
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232 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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234 SequenceI seq = viewport.alignment.getSequenceAt(i);
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235 if (!sg.sequences.contains(seq))
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238 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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239 if (sg.sequences.contains(temp))
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242 viewport.alignment.getSequences().setElementAt(temp, i);
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243 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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248 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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250 SequenceI seq = viewport.alignment.getSequenceAt(i);
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251 if (!sg.sequences.contains(seq))
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254 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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255 if (sg.sequences.contains(temp))
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258 viewport.alignment.getSequences().setElementAt(temp, i);
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259 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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263 alignPanel.RefreshPanels();
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268 protected void copy_actionPerformed(ActionEvent e)
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270 if(viewport.getSelectionGroup()==null)
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273 SequenceGroup sg = viewport.getSelectionGroup();
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275 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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276 StringBuffer buffer= new StringBuffer();
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278 for(int i=0; i<sg.getSize(); i++)
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280 SequenceI seq = sg.getSequenceAt(i);
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281 buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
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282 +seq.findPosition( sg.getEndRes() )+ "\t"
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283 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
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285 c.setContents( new StringSelection( buffer.toString()) , null ) ;
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290 protected void pasteNew_actionPerformed(ActionEvent e)
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295 protected void pasteThis_actionPerformed(ActionEvent e)
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297 addHistoryItem("Paste");
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301 void paste(boolean newAlignment)
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304 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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305 Transferable contents = c.getContents(this);
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306 if (contents == null)
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309 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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310 StringTokenizer st = new StringTokenizer(str);
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311 ArrayList seqs = new ArrayList();
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312 while (st.hasMoreElements())
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314 String name = st.nextToken();
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315 int start = Integer.parseInt(st.nextToken());
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316 int end = Integer.parseInt(st.nextToken());
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317 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
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320 viewport.alignment.addSequence(sequence);
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322 seqs.add(sequence);
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327 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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328 seqs.toArray(newSeqs);
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329 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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330 int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;
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331 if (newHeight > 500)
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333 Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
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337 viewport.setEndSeq(viewport.alignment.getHeight());
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338 viewport.alignment.getWidth();
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339 alignPanel.RefreshPanels();
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342 }catch(Exception ex){}// could be anything being pasted in here
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347 protected void cut_actionPerformed(ActionEvent e)
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349 copy_actionPerformed(null);
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350 delete_actionPerformed(null);
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353 protected void delete_actionPerformed(ActionEvent e)
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355 addHistoryItem("Delete");
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356 if (viewport.getSelectionGroup() == null)
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359 SequenceGroup sg = viewport.getSelectionGroup();
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360 for (int i=0;i < sg.sequences.size(); i++)
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362 SequenceI seq = sg.getSequenceAt(i);
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363 int index = viewport.getAlignment().findIndex(seq);
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364 seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
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366 if(seq.getSequence().length()<1)
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367 viewport.getAlignment().deleteSequence(seq);
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369 viewport.getAlignment().getSequences().setElementAt(seq, index);
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372 viewport.setSelectionGroup(null);
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373 viewport.alignment.deleteGroup(sg);
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374 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
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375 if(viewport.getAlignment().getHeight()<1)
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378 this.setClosed(true);
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379 }catch(Exception ex){}
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380 alignPanel.RefreshPanels();
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386 protected void redoMenuItem_actionPerformed(ActionEvent e)
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388 Object [] history = (Object[])redoList.remove(0);
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389 SequenceI[] seq = (SequenceI[]) history[1];
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390 viewport.setAlignment( new Alignment(seq) );
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391 updateEditMenuBar();
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392 alignPanel.RefreshPanels();
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396 public void groupsMenuItem_actionPerformed(ActionEvent e)
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398 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
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399 JInternalFrame frame = new JInternalFrame();
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400 frame.setContentPane(geditor);
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401 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
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402 frame.setResizable(false);
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405 protected void deleteGroups_actionPerformed(ActionEvent e)
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407 viewport.alignment.deleteAllGroups();
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408 viewport.setSelectionGroup(null);
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410 alignPanel.RefreshPanels();
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415 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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417 SequenceGroup sg = new SequenceGroup();
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418 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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419 sg.addSequence( viewport.getAlignment().getSequenceAt(i));
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420 sg.setEndRes(viewport.alignment.getWidth());
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421 viewport.setSelectionGroup(sg);
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422 PaintRefresher.Refresh(null);
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425 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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427 viewport.setSelectionGroup(null);
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428 PaintRefresher.Refresh(null);
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431 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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433 SequenceGroup sg = viewport.getSelectionGroup();
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434 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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435 sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
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437 PaintRefresher.Refresh(null);
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441 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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443 viewport.getColumnSelection().clear();
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447 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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449 addHistoryItem("delete columns");
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450 ColumnSelection colSel = viewport.getColumnSelection();
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451 if (colSel.size() > 0)
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453 int min = colSel.getMin();
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454 viewport.getAlignment().trimLeft(min);
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455 colSel.compensateForEdit(0,min);
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456 alignPanel.RefreshPanels();
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460 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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462 addHistoryItem("delete columns");
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463 ColumnSelection colSel = viewport.getColumnSelection();
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464 if (colSel.size() > 0)
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466 int max = colSel.getMax();
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468 viewport.getAlignment().trimRight(max);
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470 alignPanel.RefreshPanels();
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475 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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477 addHistoryItem("delete gapped columns");
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478 viewport.getAlignment().removeGaps();
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479 alignPanel.RefreshPanels();
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482 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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484 addHistoryItem("delete all gaps");
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487 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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489 current = viewport.getAlignment().getSequenceAt(i);
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490 jSize = current.getLength();
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491 for (int j=0; j < jSize; j++)
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492 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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494 current.deleteCharAt(j);
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500 alignPanel.RefreshPanels();
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503 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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505 char thisChar = '-';
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506 char nextChar = '.';
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507 if(viewport.getGapCharacter()=='-')
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512 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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513 viewport.setGapCharacter(thisChar);
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514 alignPanel.RefreshPanels();
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517 public void findMenuItem_actionPerformed(ActionEvent e)
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519 JInternalFrame frame = new JInternalFrame();
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520 Finder finder = new Finder(viewport, alignPanel, frame);
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521 frame.setContentPane(finder);
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522 Desktop.addInternalFrame(frame, "Find", 340,110);
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527 public void font_actionPerformed(ActionEvent e)
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529 // JOptionPane op = new JOptionPane();
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530 JInternalFrame frame = new JInternalFrame();
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531 FontChooser fc = new FontChooser( alignPanel, frame );
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532 frame.setContentPane(fc);
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533 Desktop.addInternalFrame(frame, "Change Font", 480,100);
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536 protected void fullSeqId_actionPerformed(ActionEvent e)
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538 viewport.setShowFullId( fullSeqId.isSelected() );
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540 alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
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541 alignPanel.RefreshPanels();
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544 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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546 viewport.setColourText( colourTextMenuItem.isSelected() );
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547 alignPanel.RefreshPanels();
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550 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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552 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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553 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
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557 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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559 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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560 alignPanel.RefreshPanels();
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563 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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565 viewport.setShowText( viewTextMenuItem.isSelected() );
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566 alignPanel.RefreshPanels();
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570 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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572 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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573 alignPanel.RefreshPanels();
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576 public void sequenceFeatures_actionPerformed(ActionEvent evt)
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578 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
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579 if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
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581 AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
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582 ((Alignment)viewport.alignment).featuresAdded = true;
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584 alignPanel.RefreshPanels();
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587 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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589 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
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592 public void overviewMenuItem_actionPerformed(ActionEvent e)
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594 if (alignPanel.overviewPanel != null)
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597 JInternalFrame frame = new JInternalFrame();
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598 OverviewPanel overview = alignPanel.getOverviewPanel();
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600 overview = new OverviewPanel(alignPanel, viewport);
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601 frame.setContentPane(overview);
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602 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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603 frame.getWidth(), frame.getHeight());
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605 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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606 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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608 alignPanel.setOverviewPanel(null);
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611 alignPanel.setOverviewPanel( overview );
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613 }catch(java.lang.OutOfMemoryError ex)
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615 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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616 +"\nTry reducing the font size.",
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617 "Out of memory", JOptionPane.WARNING_MESSAGE);
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623 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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625 changeColour( null );
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629 public void clustalColour_actionPerformed(ActionEvent e)
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631 abovePIDThreshold.setSelected(false);
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632 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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635 public void zappoColour_actionPerformed(ActionEvent e)
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637 changeColour(new ZappoColourScheme());
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640 public void taylorColour_actionPerformed(ActionEvent e)
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642 changeColour(new TaylorColourScheme());
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646 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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648 changeColour( new HydrophobicColourScheme() );
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651 public void helixColour_actionPerformed(ActionEvent e)
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653 changeColour(new HelixColourScheme() );
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657 public void strandColour_actionPerformed(ActionEvent e)
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659 changeColour(new StrandColourScheme());
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663 public void turnColour_actionPerformed(ActionEvent e)
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665 changeColour(new TurnColourScheme());
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669 public void buriedColour_actionPerformed(ActionEvent e)
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671 changeColour(new BuriedColourScheme() );
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674 public void nucleotideColour_actionPerformed(ActionEvent e)
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676 changeColour(new NucleotideColourScheme());
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680 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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682 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
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687 void changeColour(ColourSchemeI cs)
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690 if(viewport.getColourAppliesToAllGroups())
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692 Vector groups = viewport.alignment.getGroups();
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693 for(int i=0; i<groups.size(); i++)
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695 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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698 if(abovePIDThreshold.isSelected())
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699 abovePIDThreshold_actionPerformed(null);
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700 else if( viewport.getConservationSelected() )
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702 Conservation c = new Conservation("Group",
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703 ResidueProperties.propHash, 3,
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704 sg.sequences, sg.getStartRes(),
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707 c.verdict(false, 100);
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708 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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717 if ( viewport.getAbovePIDThreshold())
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720 threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
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721 Desktop.hideConservationSlider();
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723 if (cs instanceof ResidueColourScheme)
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724 ( (ResidueColourScheme) cs).setThreshold(threshold);
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725 else if (cs instanceof ScoreColourScheme)
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726 ( (ScoreColourScheme) cs).setThreshold(threshold);
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728 viewport.setGlobalColourScheme(cs);
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732 if (cs instanceof ResidueColourScheme)
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733 ( (ResidueColourScheme) cs).setThreshold(0);
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734 else if (cs instanceof ScoreColourScheme)
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735 ( (ScoreColourScheme) cs).setThreshold(0);
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740 if ( viewport.getConservationSelected() )
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742 ConservationColourScheme ccs = null;
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744 Alignment al = (Alignment) viewport.alignment;
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745 Conservation c = new Conservation("All",
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746 ResidueProperties.propHash, 3,
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747 al.getSequences(), 0,
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751 c.verdict(false, 100);
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753 ccs = new ConservationColourScheme(c, cs);
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755 int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,
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758 ccs.inc = threshold;
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760 viewport.setGlobalColourScheme(ccs);
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764 viewport.setGlobalColourScheme( cs );
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766 alignPanel.RefreshPanels();
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770 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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772 viewport.setConservationSelected(conservationMenuItem.isSelected());
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774 viewport.setAbovePIDThreshold(false);
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775 abovePIDThreshold.setSelected(false);
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776 Desktop.hidePIDSlider();
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777 if(!viewport.getConservationSelected())
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778 Desktop.hideConservationSlider();
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780 ColourSchemeI cs = viewport.getGlobalColourScheme();
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781 if(cs instanceof ConservationColourScheme )
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782 changeColour( ((ConservationColourScheme)cs).cs );
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784 changeColour( cs );
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788 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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790 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
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792 conservationMenuItem.setSelected(false);
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793 viewport.setConservationSelected(false);
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794 Desktop.hideConservationSlider();
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796 if(!viewport.getAbovePIDThreshold())
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797 Desktop.hidePIDSlider();
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800 ColourSchemeI cs = viewport.getGlobalColourScheme();
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801 if(cs instanceof ConservationColourScheme )
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802 changeColour( ((ConservationColourScheme)cs).cs );
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804 changeColour( cs );
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810 public void userDefinedColour_actionPerformed(ActionEvent e)
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812 JInternalFrame frame = new JInternalFrame();
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813 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
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814 frame.setContentPane(chooser);
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815 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
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816 frame.setResizable(false);
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817 frame.setIconifiable(false);
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818 frame.setMaximizable(false);
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821 public void PIDColour_actionPerformed(ActionEvent e)
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823 changeColour( new PIDColourScheme() );
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827 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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829 changeColour(new Blosum62ColourScheme(viewport) );
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834 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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836 addHistoryItem("sort");
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837 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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838 alignPanel.RefreshPanels();
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841 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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843 addHistoryItem("sort");
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844 AlignmentSorter.sortByID( viewport.getAlignment() );
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845 alignPanel.RefreshPanels();
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848 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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850 addHistoryItem("sort");
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851 AlignmentSorter.sortByGroup(viewport.getAlignment());
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852 AlignmentSorter.sortGroups(viewport.getAlignment());
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853 alignPanel.RefreshPanels();
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856 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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858 addHistoryItem("sort");
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859 if(viewport.getCurrentTree()==null)
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862 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
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863 alignPanel.RefreshPanels();
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866 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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868 RedundancyPanel sp = new RedundancyPanel(alignPanel);
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869 JInternalFrame frame = new JInternalFrame();
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870 frame.setContentPane(sp);
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871 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
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872 frame.setMaximizable(false);
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873 frame.setResizable(false);
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877 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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879 if(viewport.getSelectionGroup().getSize()<2)
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880 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
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883 JInternalFrame frame = new JInternalFrame();
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884 frame.setContentPane(new PairwiseAlignPanel(viewport));
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885 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
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889 public void PCAMenuItem_actionPerformed(ActionEvent e)
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892 if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
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893 || viewport.getAlignment().getHeight()<4)
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895 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
\r
896 +"at least 4 input sequences.",
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897 "Sequence selection insufficient",
\r
898 JOptionPane.WARNING_MESSAGE);
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903 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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904 JInternalFrame frame = new JInternalFrame();
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905 frame.setContentPane(pcaPanel);
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906 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
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907 }catch(java.lang.OutOfMemoryError ex)
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909 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
\r
910 "Out of memory", JOptionPane.WARNING_MESSAGE);
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916 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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918 NewTreePanel("AV", "PID", "Average distance tree using PID");
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921 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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923 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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927 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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929 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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932 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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934 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
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937 void NewTreePanel(String type, String pwType, String title)
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939 //are the sequences aligned?
\r
940 if(!viewport.alignment.isAligned())
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942 JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
\r
943 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
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948 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)
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950 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,
\r
951 0, viewport.alignment.getWidth());
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955 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
956 type, pwType, 0, viewport.alignment.getWidth());
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959 Desktop.addInternalFrame(tp, title, 600, 500);
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965 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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967 JInternalFrame frame = new JInternalFrame();
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968 ClustalThread ct = new ClustalThread(frame);
\r
969 Thread t = new Thread(ct);
\r
971 frame.setContentPane(ct);
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972 Desktop.addInternalFrame(frame, title, 300, 80);
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976 class ClustalThread extends JPanel implements Runnable
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979 int imageIndex = 0;
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980 boolean webServiceRunning = false;
\r
981 JInternalFrame frame;
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982 public ClustalThread(JInternalFrame frame)
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984 this.frame = frame;
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985 image = new Image[9];
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986 for(int i=0; i<9; i++)
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988 java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
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991 image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
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992 MediaTracker mt = new MediaTracker(this);
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993 mt.addImage(image[i], i);
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994 try{mt.waitForID(i);}
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995 catch(Exception ex){}
\r
998 DNATwirler twirler = new DNATwirler();
\r
1000 webServiceRunning = true;
\r
1003 class DNATwirler extends Thread
\r
1007 while(webServiceRunning)
\r
1010 Thread.sleep(100);
\r
1015 catch(Exception ex){}
\r
1021 // Should check to see if the server settings are valid
\r
1022 // Need visual-delay indication here.
\r
1025 jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
\r
1026 Vector sv = viewport.getAlignment().getSequences();
\r
1027 SequenceI[] seqs = new SequenceI[sv.size()];
\r
1032 seqs[i] = (SequenceI) sv.elementAt(i);
\r
1034 while (++i < sv.size());
\r
1036 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
\r
1038 if (alignment != null)
\r
1040 AlignFrame af = new AlignFrame(new Alignment(alignment));
\r
1041 af.clustalColour.setSelected(true);
\r
1042 af.clustalColour_actionPerformed(null);
\r
1043 Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
\r
1044 700, 500); // JBPNote - is there a new window geom. property ?
\r
1047 JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
\r
1048 JOptionPane.WARNING_MESSAGE);
\r
1050 webServiceRunning = false;
\r
1052 frame.setClosed(true);
\r
1053 }catch(Exception ex){}
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1056 public void paintComponent(Graphics g)
\r
1058 g.setColor(Color.white);
\r
1059 g.fillRect(0,0,getWidth(), getHeight());
\r
1062 g.drawImage(image[imageIndex],10,10,this);
\r
1064 g.setFont(new Font("Arial", Font.BOLD, 12));
\r
1065 g.setColor(Color.black);
\r
1066 g.drawString("Clustal Alignment Web Service running", 30,30);
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