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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55 AlignmentUtil.fetchSequenceFeatures(al, alignPanel);
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58 protected void saveAs_actionPerformed(ActionEvent e)
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60 JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
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61 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
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62 chooser.setToolTipText("Save");
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63 int value = chooser.showSaveDialog(this);
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64 if(value == JFileChooser.APPROVE_OPTION)
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66 String choice = chooser.getSelectedFile().getPath();
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67 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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68 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
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70 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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71 out.println(output);
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74 catch(Exception ex){}
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79 protected void outputText_actionPerformed(ActionEvent e)
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81 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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82 JInternalFrame frame = new JInternalFrame();
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83 cap.formatForOutput();
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84 frame.setContentPane(cap);
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85 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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86 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
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89 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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91 HTMLOutput htmlOutput = new HTMLOutput(viewport);
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95 public void printMenuItem_actionPerformed(ActionEvent e)
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97 //Putting in a thread avoids Swing painting problems
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98 PrintThread thread = new PrintThread();
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102 class PrintThread extends Thread
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106 PrinterJob printJob = PrinterJob.getPrinterJob();
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107 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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108 printJob.setPrintable(alignPanel, pf);
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109 if (printJob.printDialog())
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115 catch (Exception PrintException)
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117 PrintException.printStackTrace();
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127 public void closeMenuItem_actionPerformed(ActionEvent e)
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130 this.setClosed(true);
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131 }catch(Exception ex){}
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134 ArrayList historyList = new ArrayList();
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135 ArrayList redoList = new ArrayList();
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137 void updateEditMenuBar()
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139 if(historyList.size()>0)
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141 undoMenuItem.setEnabled(true);
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142 Object [] history = (Object[])historyList.get(0);
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143 undoMenuItem.setText("Undo "+history[0]);
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147 undoMenuItem.setEnabled(false);
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148 undoMenuItem.setText("Undo");
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151 if(redoList.size()>0)
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153 redoMenuItem.setEnabled(true);
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154 Object [] history = (Object[])redoList.get(0);
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155 redoMenuItem.setText("Redo "+history[0]);
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159 redoMenuItem.setEnabled(false);
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160 redoMenuItem.setText("Redo");
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164 public void addHistoryItem(String type)
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166 // must make sure we add new sequence objects her, not refs to the existing sequences
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168 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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169 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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171 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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172 viewport.getAlignment().getSequenceAt(i).getSequence());
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175 historyList.add(0, new Object[]{type, seq} );
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176 updateEditMenuBar();
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179 protected void undoMenuItem_actionPerformed(ActionEvent e)
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181 Object [] history = (Object[])historyList.remove(0);
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182 // add the redo state before continuing!!
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183 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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184 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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186 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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187 viewport.getAlignment().getSequenceAt(i).
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192 redoList.add(0, new Object[] {history[0], seq});
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194 seq = (SequenceI[]) history[1];
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195 viewport.setAlignment( new Alignment(seq) );
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196 updateEditMenuBar();
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197 alignPanel.RefreshPanels();
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200 protected void copy_actionPerformed(ActionEvent e)
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202 if(viewport.getRubberbandGroup()==null)
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205 SequenceGroup sg = viewport.getRubberbandGroup();
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207 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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208 StringBuffer buffer= new StringBuffer();
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210 for(int i=0; i<sg.getSize(); i++)
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212 SequenceI seq = sg.getSequenceAt(i);
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213 buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
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214 +seq.findPosition( sg.getEndRes() )+ "\t"
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215 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
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217 c.setContents( new StringSelection( buffer.toString()) , null ) ;
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222 protected void pasteNew_actionPerformed(ActionEvent e)
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227 protected void pasteThis_actionPerformed(ActionEvent e)
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232 void paste(boolean newAlignment)
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235 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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236 Transferable contents = c.getContents(this);
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237 if (contents == null)
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240 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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241 StringTokenizer st = new StringTokenizer(str);
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242 ArrayList seqs = new ArrayList();
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243 while (st.hasMoreElements())
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245 String name = st.nextToken();
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246 int start = Integer.parseInt(st.nextToken());
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247 int end = Integer.parseInt(st.nextToken());
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248 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
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251 viewport.alignment.addSequence(sequence);
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253 seqs.add(sequence);
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258 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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259 seqs.toArray(newSeqs);
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260 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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261 int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;
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262 if (newHeight > 500)
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264 Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
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268 viewport.setEndSeq(viewport.alignment.getHeight());
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269 viewport.alignment.getWidth();
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270 alignPanel.RefreshPanels();
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273 }catch(Exception ex){}// could be anything being pasted in here
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278 protected void cut_actionPerformed(ActionEvent e)
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280 copy_actionPerformed(null);
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281 delete_actionPerformed(null);
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284 protected void delete_actionPerformed(ActionEvent e)
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286 if (viewport.getRubberbandGroup() == null)
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289 SequenceGroup sg = viewport.getRubberbandGroup();
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290 for (int i=0;i < sg.sequences.size(); i++)
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291 viewport.getAlignment().deleteSequence(sg.getSequenceAt(i));
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293 viewport.alignment.deleteGroup(sg);
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294 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
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295 if(viewport.getAlignment().getHeight()<1)
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298 this.setClosed(true);
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299 }catch(Exception ex){}
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300 alignPanel.RefreshPanels();
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306 protected void redoMenuItem_actionPerformed(ActionEvent e)
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308 Object [] history = (Object[])redoList.remove(0);
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309 SequenceI[] seq = (SequenceI[]) history[1];
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310 viewport.setAlignment( new Alignment(seq) );
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311 updateEditMenuBar();
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312 alignPanel.RefreshPanels();
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316 public void groupsMenuItem_actionPerformed(ActionEvent e)
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318 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
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319 JInternalFrame frame = new JInternalFrame();
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320 frame.setContentPane(geditor);
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321 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
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322 frame.setResizable(false);
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325 protected void deleteGroups_actionPerformed(ActionEvent e)
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327 viewport.alignment.deleteAllGroups();
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328 viewport.getSelection().clear();
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330 alignPanel.RefreshPanels();
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335 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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337 Selection sel = viewport.getSelection();
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338 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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339 sel.addElement( viewport.getAlignment().getSequenceAt(i));
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340 PaintRefresher.Refresh(null);
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343 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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345 viewport.setRubberbandGroup(null);
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346 viewport.getSelection().clear();
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347 PaintRefresher.Refresh(null);
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350 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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352 Selection sel = viewport.getSelection();
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353 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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355 if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
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356 sel.removeElement(viewport.getAlignment().getSequenceAt(i));
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358 sel.addElement(viewport.getAlignment().getSequenceAt(i));
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360 PaintRefresher.Refresh(null);
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364 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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366 viewport.getColumnSelection().clear();
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370 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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372 addHistoryItem("delete columns");
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373 ColumnSelection colSel = viewport.getColumnSelection();
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374 if (colSel.size() > 0)
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376 int min = colSel.getMin();
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377 viewport.getAlignment().trimLeft(min);
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378 colSel.compensateForEdit(0,min);
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379 alignPanel.RefreshPanels();
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383 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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385 addHistoryItem("delete columns");
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386 ColumnSelection colSel = viewport.getColumnSelection();
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387 if (colSel.size() > 0)
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389 int max = colSel.getMax();
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391 viewport.getAlignment().trimRight(max);
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393 alignPanel.RefreshPanels();
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398 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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400 addHistoryItem("delete gapped columns");
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401 viewport.getAlignment().removeGaps();
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402 alignPanel.RefreshPanels();
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405 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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407 addHistoryItem("delete all gaps");
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410 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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412 current = viewport.getAlignment().getSequenceAt(i);
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413 jSize = current.getLength();
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414 for (int j=0; j < jSize; j++)
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415 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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417 current.deleteCharAt(j);
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423 alignPanel.RefreshPanels();
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426 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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428 char thisChar = '-';
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429 char nextChar = '.';
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430 if(viewport.getGapCharacter()=='-')
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435 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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436 viewport.setGapCharacter(thisChar);
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437 alignPanel.RefreshPanels();
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440 public void findMenuItem_actionPerformed(ActionEvent e)
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442 JOptionPane op = new JOptionPane();
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443 JInternalFrame frame = op.createInternalFrame(this, "Find");
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444 Finder finder = new Finder(viewport, alignPanel, frame);
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445 frame.setClosable(true);
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446 frame.setContentPane(finder);
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447 frame.setSize(340,110);
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448 frame.setVisible(true);
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453 public void fontNameMenuItem_actionPerformed(ActionEvent e)
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455 String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
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458 String selection = JOptionPane.showInternalInputDialog(this,
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461 JOptionPane.QUESTION_MESSAGE,
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463 ,fontNameMenuItem.getText()).toString();
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464 if(selection!=null)
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466 fontNameMenuItem.setText(selection);
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472 public void fontSizeMenuItem_actionPerformed(ActionEvent e)
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474 String selection = JOptionPane.showInternalInputDialog(this,
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475 "Select font size",
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477 JOptionPane.QUESTION_MESSAGE,
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478 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
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479 ,fontSizeMenuItem.getText()).toString();
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480 if(selection!=null)
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482 fontSizeMenuItem.setText(selection);
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487 public void fontStyleMenuItem_actionPerformed(ActionEvent e)
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489 String selection = JOptionPane.showInternalInputDialog(this,
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490 "Select font style",
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492 JOptionPane.QUESTION_MESSAGE,
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493 null, new String[]{"plain", "bold", "italic"}
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494 ,fontStyleMenuItem.getText()).toString();
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495 if(selection!=null)
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497 fontStyleMenuItem.setText(selection);
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503 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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505 viewport.setColourText( colourTextMenuItem.isSelected() );
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506 alignPanel.RefreshPanels();
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511 int style = java.awt.Font.PLAIN;
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512 if(fontStyleMenuItem.getText().equals("bold"))
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513 style = java.awt.Font.BOLD;
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514 else if(fontStyleMenuItem.getText().equals("italic"))
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515 style = java.awt.Font.ITALIC;
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517 viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
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519 Integer.parseInt(fontSizeMenuItem.getText())));
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520 alignPanel.RefreshPanels();
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524 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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526 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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527 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
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531 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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533 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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534 alignPanel.RefreshPanels();
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537 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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539 viewport.setShowText( viewTextMenuItem.isSelected() );
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540 alignPanel.RefreshPanels();
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544 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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546 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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547 alignPanel.RefreshPanels();
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550 public void sequenceFeatures_actionPerformed(ActionEvent evt)
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552 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
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553 alignPanel.RefreshPanels();
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556 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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558 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
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561 public void overviewMenuItem_actionPerformed(ActionEvent e)
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563 if (alignPanel.overviewPanel != null)
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566 JInternalFrame frame = new JInternalFrame();
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567 OverviewPanel overview = alignPanel.getOverviewPanel();
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569 overview = new OverviewPanel(alignPanel, viewport);
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570 frame.setContentPane(overview);
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571 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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572 frame.getWidth(), frame.getHeight());
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574 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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575 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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577 alignPanel.setOverviewPanel(null);
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580 alignPanel.setOverviewPanel( overview );
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582 }catch(java.lang.OutOfMemoryError ex)
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584 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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585 +"\nTry reducing the font size.",
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586 "Out of memory", JOptionPane.WARNING_MESSAGE);
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592 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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594 viewport.setGlobalColourScheme( null );
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599 public void clustalColour_actionPerformed(ActionEvent e)
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601 viewport.setGlobalColourScheme(
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602 new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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603 abovePIDThreshold.setSelected(false);
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607 public void zappoColour_actionPerformed(ActionEvent e)
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609 viewport.setGlobalColourScheme(new ZappoColourScheme() );
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613 public void taylorColour_actionPerformed(ActionEvent e)
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615 viewport.setGlobalColourScheme(new TaylorColourScheme() );
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620 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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622 viewport.setGlobalColourScheme( new HydrophobicColourScheme() );
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626 public void helixColour_actionPerformed(ActionEvent e)
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628 viewport.setGlobalColourScheme( new HelixColourScheme() );
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633 public void strandColour_actionPerformed(ActionEvent e)
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635 viewport.setGlobalColourScheme(new StrandColourScheme() );
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640 public void turnColour_actionPerformed(ActionEvent e)
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642 viewport.setGlobalColourScheme(new TurnColourScheme() );
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647 public void buriedColour_actionPerformed(ActionEvent e)
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649 viewport.setGlobalColourScheme( new BuriedColourScheme() );
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653 public void nucleotideColour_actionPerformed(ActionEvent e)
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655 viewport.setGlobalColourScheme( new NucleotideColourScheme() );
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660 void changeColour()
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662 if(abovePIDThreshold.isSelected())
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663 abovePIDThreshold_actionPerformed(null);
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664 else if(conservationMenuItem.isSelected())
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665 conservationMenuItem_actionPerformed(null);
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667 alignPanel.RefreshPanels();
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671 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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673 if(abovePIDThreshold.isSelected())
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675 abovePIDThreshold.setSelected(false);
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676 Desktop.hidePIDSlider();
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679 viewport.setConservationSelected(conservationMenuItem.isSelected());
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681 ColourSchemeI oldCs = viewport.getGlobalColourScheme();
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683 ConservationColourScheme ccs = null;
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684 if (oldCs instanceof ConservationColourScheme)
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685 ccs = (ConservationColourScheme) oldCs;
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687 if (conservationMenuItem.isSelected())
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689 Alignment al = (Alignment) viewport.alignment;
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690 Conservation c = new Conservation("All",
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691 ResidueProperties.propHash, 3,
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692 al.getSequences(), 0,
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696 c.verdict(false, 100);
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699 ccs = new ConservationColourScheme(c, ccs.cs);
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701 ccs = new ConservationColourScheme(c, oldCs);
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704 int threshold = Desktop.setConservationSliderSource(alignPanel, ccs, "Background");
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706 ccs.inc = threshold;
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708 if (ccs.cs instanceof ResidueColourScheme)
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709 ((ResidueColourScheme) ccs.cs).setThreshold(0);
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710 else if (ccs.cs instanceof ScoreColourScheme)
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711 ((ScoreColourScheme)ccs.cs).setThreshold(0);
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713 viewport.setGlobalColourScheme(ccs);
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717 else if (oldCs instanceof ConservationColourScheme)
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719 /// ie, if we remove ConservationColourScheme from backgroundColour
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721 viewport.setGlobalColourScheme(oldCs);
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722 Desktop.hideConservationSlider();
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726 alignPanel.RefreshPanels();
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730 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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732 if(conservationMenuItem.isSelected())
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733 conservationMenuItem.setSelected(false);
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735 ColourSchemeI oldCs = viewport.getGlobalColourScheme();
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737 if (oldCs instanceof ConservationColourScheme)
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739 ConservationColourScheme ccs = (ConservationColourScheme) oldCs;
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743 if(abovePIDThreshold.isSelected())
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745 threshold = Desktop.setPIDSliderSource(alignPanel, oldCs, "Background");
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746 Desktop.hideConservationSlider();
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749 Desktop.hidePIDSlider();
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751 if (oldCs instanceof ResidueColourScheme)
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752 ((ResidueColourScheme) oldCs).setThreshold(threshold);
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753 else if (oldCs instanceof ScoreColourScheme)
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754 ((ScoreColourScheme)oldCs).setThreshold(threshold);
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756 viewport.setGlobalColourScheme(oldCs);
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758 alignPanel.RefreshPanels();
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763 public void userDefinedColour_actionPerformed(ActionEvent e)
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765 JInternalFrame frame = new JInternalFrame();
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766 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
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767 frame.setContentPane(chooser);
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768 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
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769 frame.setResizable(false);
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770 frame.setIconifiable(false);
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771 frame.setMaximizable(false);
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774 public void PIDColour_actionPerformed(ActionEvent e)
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776 viewport.setGlobalColourScheme( new PIDColourScheme() );
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777 alignPanel.setColourScheme( );
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781 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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783 viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport) );
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789 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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791 addHistoryItem("sort");
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792 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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793 alignPanel.RefreshPanels();
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796 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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798 addHistoryItem("sort");
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799 AlignmentSorter.sortByID( viewport.getAlignment() );
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800 alignPanel.RefreshPanels();
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803 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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805 addHistoryItem("sort");
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806 AlignmentSorter.sortByGroup(viewport.getAlignment());
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807 AlignmentSorter.sortGroups(viewport.getAlignment());
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808 alignPanel.RefreshPanels();
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811 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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813 addHistoryItem("sort");
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814 if(viewport.getCurrentTree()==null)
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817 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
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818 alignPanel.RefreshPanels();
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821 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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823 RedundancyPanel sp = new RedundancyPanel(alignPanel);
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824 JInternalFrame frame = new JInternalFrame();
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825 frame.setContentPane(sp);
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826 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
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827 frame.setMaximizable(false);
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828 frame.setResizable(false);
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832 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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834 if(viewport.getSelection().size()<2)
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835 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
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838 JInternalFrame frame = new JInternalFrame();
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839 frame.setContentPane(new PairwiseAlignPanel(viewport));
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840 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
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844 public void PCAMenuItem_actionPerformed(ActionEvent e)
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846 if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
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847 || viewport.getAlignment().getHeight()<4)
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849 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
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850 +"at least 4 input sequences.",
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851 "Sequence selection insufficient",
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852 JOptionPane.WARNING_MESSAGE);
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857 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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858 JInternalFrame frame = new JInternalFrame();
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859 frame.setContentPane(pcaPanel);
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860 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
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861 }catch(java.lang.OutOfMemoryError ex)
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863 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
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864 "Out of memory", JOptionPane.WARNING_MESSAGE);
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870 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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872 NewTreePanel("AV", "PID", "Average distance tree using PID");
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875 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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877 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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881 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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883 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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886 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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888 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
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891 void NewTreePanel(String type, String pwType, String title)
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893 //are the sequences aligned?
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894 if(!viewport.alignment.isAligned())
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896 JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
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897 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
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901 JInternalFrame frame = new javax.swing.JInternalFrame();
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903 if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
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905 tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
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906 viewport.getStartRes(), viewport.getEndRes());
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910 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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911 type, pwType, viewport.getStartRes(),
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912 viewport.getEndRes());
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915 frame.setContentPane(tp);
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916 Desktop.addInternalFrame(frame, title, 600, 500);
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922 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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924 JInternalFrame frame = new JInternalFrame();
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925 ClustalThread ct = new ClustalThread(frame);
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926 Thread t = new Thread(ct);
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928 frame.setContentPane(ct);
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929 Desktop.addInternalFrame(frame, title, 300, 80);
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933 class ClustalThread extends JPanel implements Runnable
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936 int imageIndex = 0;
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937 boolean webServiceRunning = false;
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938 JInternalFrame frame;
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939 public ClustalThread(JInternalFrame frame)
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941 this.frame = frame;
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942 image = new Image[9];
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943 for(int i=0; i<9; i++)
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945 java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");
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948 image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
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949 MediaTracker mt = new MediaTracker(this);
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950 mt.addImage(image[i], i);
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951 try{mt.waitForID(i);}
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952 catch(Exception ex){}
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955 DNATwirler twirler = new DNATwirler();
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957 webServiceRunning = true;
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960 class DNATwirler extends Thread
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964 while(webServiceRunning)
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972 catch(Exception ex){}
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978 // Should check to see if the server settings are valid
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979 // Need visual-delay indication here.
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982 jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
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983 Vector sv = viewport.getAlignment().getSequences();
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984 SequenceI[] seqs = new SequenceI[sv.size()];
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989 seqs[i] = (SequenceI) sv.elementAt(i);
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991 while (++i < sv.size());
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993 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
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995 if (alignment != null)
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997 AlignFrame af = new AlignFrame(new Alignment(alignment));
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998 af.clustalColour.setSelected(true);
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999 af.clustalColour_actionPerformed(null);
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1000 Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
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1001 700, 500); // JBPNote - is there a new window geom. property ?
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1004 JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
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1005 JOptionPane.WARNING_MESSAGE);
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1007 webServiceRunning = false;
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1009 frame.setClosed(true);
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1010 }catch(Exception ex){}
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1013 public void paintComponent(Graphics g)
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1015 g.setColor(Color.white);
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1016 g.fillRect(0,0,getWidth(), getHeight());
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1019 g.drawImage(image[imageIndex],10,10,this);
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1021 g.setFont(new Font("Arial", Font.BOLD, 12));
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1022 g.setColor(Color.black);
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1023 g.drawString("Clustal Alignment Web Service running", 30,30);
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