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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67 if(e.getActionCommand().equals("FASTA"))
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69 else if(e.getActionCommand().equals("MSF"))
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71 else if(e.getActionCommand().equals("CLUSTAL"))
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73 else if(e.getActionCommand().equals("BLC"))
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75 else if(e.getActionCommand().equals("PIR"))
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77 else if(e.getActionCommand().equals("PFAM"))
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80 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
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81 , new String[]{suffix}, e.getActionCommand()+" file");
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82 chooser.setFileView(new JalviewFileView());
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83 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
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84 chooser.setToolTipText("Save");
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85 int value = chooser.showSaveDialog(this);
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86 if(value == JalviewFileChooser.APPROVE_OPTION)
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88 String choice = chooser.getSelectedFile().getPath();
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89 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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90 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
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92 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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93 out.println(output);
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96 catch(Exception ex){}
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101 protected void outputText_actionPerformed(ActionEvent e)
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103 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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104 JInternalFrame frame = new JInternalFrame();
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105 cap.formatForOutput();
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106 frame.setContentPane(cap);
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107 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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108 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
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111 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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113 HTMLOutput htmlOutput = new HTMLOutput(viewport);
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117 protected void createPNG_actionPerformed(ActionEvent e)
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119 alignPanel.makePNG();
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122 protected void epsFile_actionPerformed(ActionEvent e)
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124 alignPanel.makeEPS();
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128 public void printMenuItem_actionPerformed(ActionEvent e)
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130 //Putting in a thread avoids Swing painting problems
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131 PrintThread thread = new PrintThread();
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135 class PrintThread extends Thread
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139 PrinterJob printJob = PrinterJob.getPrinterJob();
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140 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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141 printJob.setPrintable(alignPanel, pf);
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142 if (printJob.printDialog())
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148 catch (Exception PrintException)
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150 PrintException.printStackTrace();
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160 public void closeMenuItem_actionPerformed(ActionEvent e)
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163 this.setClosed(true);
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164 }catch(Exception ex){}
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167 Stack historyList = new Stack();
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168 Stack redoList = new Stack();
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169 JMenuBar jMenuBar1 = new JMenuBar();
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171 void updateEditMenuBar()
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173 if(historyList.size()>0)
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175 undoMenuItem.setEnabled(true);
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176 Object [] history = (Object[])historyList.get(0);
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177 undoMenuItem.setText("Undo "+history[0]);
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181 undoMenuItem.setEnabled(false);
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182 undoMenuItem.setText("Undo");
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185 if(redoList.size()>0)
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187 redoMenuItem.setEnabled(true);
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188 Object [] history = (Object[])redoList.get(0);
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189 redoMenuItem.setText("Redo "+history[0]);
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193 redoMenuItem.setEnabled(false);
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194 redoMenuItem.setText("Redo");
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198 public void addHistoryItem(String type)
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200 // must make sure we add new sequence objects her, not refs to the existing sequences
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202 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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203 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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205 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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206 viewport.getAlignment().getSequenceAt(i).getSequence());
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209 historyList.add(0, new Object[]{type, seq} );
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210 updateEditMenuBar();
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213 protected void undoMenuItem_actionPerformed(ActionEvent e)
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215 Object [] history = (Object[])historyList.remove(0);
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216 // add the redo state before continuing!!
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217 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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218 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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220 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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221 viewport.getAlignment().getSequenceAt(i).
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226 redoList.add(0, new Object[] {history[0], seq});
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228 seq = (SequenceI[]) history[1];
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229 viewport.setAlignment( new Alignment(seq) );
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230 updateEditMenuBar();
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231 alignPanel.RefreshPanels();
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234 public void moveSelectedSequences(boolean up)
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236 SequenceGroup sg = viewport.getSelectionGroup();
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242 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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244 SequenceI seq = viewport.alignment.getSequenceAt(i);
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245 if (!sg.sequences.contains(seq))
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248 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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249 if (sg.sequences.contains(temp))
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252 viewport.alignment.getSequences().setElementAt(temp, i);
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253 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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258 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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260 SequenceI seq = viewport.alignment.getSequenceAt(i);
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261 if (!sg.sequences.contains(seq))
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264 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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265 if (sg.sequences.contains(temp))
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268 viewport.alignment.getSequences().setElementAt(temp, i);
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269 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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273 alignPanel.RefreshPanels();
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278 protected void copy_actionPerformed(ActionEvent e)
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280 if(viewport.getSelectionGroup()==null)
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283 SequenceGroup sg = viewport.getSelectionGroup();
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285 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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286 StringBuffer buffer= new StringBuffer();
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288 for(int i=0; i<sg.getSize(); i++)
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290 SequenceI seq = sg.getSequenceAt(i);
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291 buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
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292 +seq.findPosition( sg.getEndRes() )+ "\t"
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293 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
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295 c.setContents( new StringSelection( buffer.toString()) , null ) ;
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300 protected void pasteNew_actionPerformed(ActionEvent e)
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305 protected void pasteThis_actionPerformed(ActionEvent e)
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307 addHistoryItem("Paste");
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311 void paste(boolean newAlignment)
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314 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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315 Transferable contents = c.getContents(this);
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316 if (contents == null)
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319 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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320 StringTokenizer st = new StringTokenizer(str);
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321 ArrayList seqs = new ArrayList();
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322 while (st.hasMoreElements())
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324 String name = st.nextToken();
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325 int start = Integer.parseInt(st.nextToken());
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326 int end = Integer.parseInt(st.nextToken());
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327 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
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330 viewport.alignment.addSequence(sequence);
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332 seqs.add(sequence);
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337 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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338 seqs.toArray(newSeqs);
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339 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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340 int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;
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341 if (newHeight > 500)
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343 Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
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347 viewport.setEndSeq(viewport.alignment.getHeight());
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348 viewport.alignment.getWidth();
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349 alignPanel.RefreshPanels();
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352 }catch(Exception ex){}// could be anything being pasted in here
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357 protected void cut_actionPerformed(ActionEvent e)
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359 copy_actionPerformed(null);
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360 delete_actionPerformed(null);
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363 protected void delete_actionPerformed(ActionEvent e)
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365 addHistoryItem("Delete");
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366 if (viewport.getSelectionGroup() == null)
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369 SequenceGroup sg = viewport.getSelectionGroup();
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370 for (int i=0;i < sg.sequences.size(); i++)
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372 SequenceI seq = sg.getSequenceAt(i);
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373 int index = viewport.getAlignment().findIndex(seq);
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374 seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
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376 if(seq.getSequence().length()<1)
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377 viewport.getAlignment().deleteSequence(seq);
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379 viewport.getAlignment().getSequences().setElementAt(seq, index);
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382 viewport.setSelectionGroup(null);
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383 viewport.alignment.deleteGroup(sg);
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384 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
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385 if(viewport.getAlignment().getHeight()<1)
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388 this.setClosed(true);
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389 }catch(Exception ex){}
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390 alignPanel.RefreshPanels();
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396 protected void redoMenuItem_actionPerformed(ActionEvent e)
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398 Object [] history = (Object[])redoList.remove(0);
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399 SequenceI[] seq = (SequenceI[]) history[1];
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400 viewport.setAlignment( new Alignment(seq) );
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401 updateEditMenuBar();
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402 alignPanel.RefreshPanels();
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406 public void groupsMenuItem_actionPerformed(ActionEvent e)
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408 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
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409 JInternalFrame frame = new JInternalFrame();
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410 frame.setContentPane(geditor);
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411 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
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412 frame.setResizable(false);
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415 protected void deleteGroups_actionPerformed(ActionEvent e)
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417 viewport.alignment.deleteAllGroups();
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418 viewport.setSelectionGroup(null);
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420 alignPanel.RefreshPanels();
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425 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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427 SequenceGroup sg = new SequenceGroup();
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428 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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429 sg.addSequence( viewport.getAlignment().getSequenceAt(i));
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430 sg.setEndRes(viewport.alignment.getWidth());
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431 viewport.setSelectionGroup(sg);
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432 PaintRefresher.Refresh(null);
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435 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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437 viewport.setSelectionGroup(null);
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438 PaintRefresher.Refresh(null);
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441 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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443 SequenceGroup sg = viewport.getSelectionGroup();
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444 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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445 sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
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447 PaintRefresher.Refresh(null);
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451 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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453 viewport.getColumnSelection().clear();
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457 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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459 addHistoryItem("delete columns");
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460 ColumnSelection colSel = viewport.getColumnSelection();
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461 if (colSel.size() > 0)
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463 int min = colSel.getMin();
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464 viewport.getAlignment().trimLeft(min);
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465 colSel.compensateForEdit(0,min);
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466 alignPanel.RefreshPanels();
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470 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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472 addHistoryItem("delete columns");
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473 ColumnSelection colSel = viewport.getColumnSelection();
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474 if (colSel.size() > 0)
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476 int max = colSel.getMax();
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478 viewport.getAlignment().trimRight(max);
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480 alignPanel.RefreshPanels();
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485 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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487 addHistoryItem("delete gapped columns");
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488 viewport.getAlignment().removeGaps();
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489 alignPanel.RefreshPanels();
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492 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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494 addHistoryItem("delete all gaps");
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497 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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499 current = viewport.getAlignment().getSequenceAt(i);
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500 jSize = current.getLength();
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501 for (int j=0; j < jSize; j++)
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502 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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504 current.deleteCharAt(j);
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510 alignPanel.RefreshPanels();
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513 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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515 char thisChar = '-';
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516 char nextChar = '.';
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517 if(viewport.getGapCharacter()=='-')
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522 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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523 viewport.setGapCharacter(thisChar);
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524 alignPanel.RefreshPanels();
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527 public void findMenuItem_actionPerformed(ActionEvent e)
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529 JInternalFrame frame = new JInternalFrame();
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530 Finder finder = new Finder(viewport, alignPanel, frame);
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531 frame.setContentPane(finder);
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532 Desktop.addInternalFrame(frame, "Find", 340,110);
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537 public void font_actionPerformed(ActionEvent e)
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539 // JOptionPane op = new JOptionPane();
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540 JInternalFrame frame = new JInternalFrame();
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541 FontChooser fc = new FontChooser( alignPanel, frame );
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542 frame.setContentPane(fc);
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543 Desktop.addInternalFrame(frame, "Change Font", 480,100);
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546 protected void fullSeqId_actionPerformed(ActionEvent e)
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548 viewport.setShowFullId( fullSeqId.isSelected() );
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550 alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
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551 alignPanel.RefreshPanels();
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554 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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556 viewport.setColourText( colourTextMenuItem.isSelected() );
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557 alignPanel.RefreshPanels();
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560 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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562 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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563 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
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567 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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569 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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570 alignPanel.RefreshPanels();
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573 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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575 viewport.setShowText( viewTextMenuItem.isSelected() );
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576 alignPanel.RefreshPanels();
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580 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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582 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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583 alignPanel.RefreshPanels();
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586 public void sequenceFeatures_actionPerformed(ActionEvent evt)
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588 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
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589 if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
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591 AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
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592 ((Alignment)viewport.alignment).featuresAdded = true;
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594 alignPanel.RefreshPanels();
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597 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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599 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
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602 public void overviewMenuItem_actionPerformed(ActionEvent e)
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604 if (alignPanel.overviewPanel != null)
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607 JInternalFrame frame = new JInternalFrame();
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608 OverviewPanel overview = alignPanel.getOverviewPanel();
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610 overview = new OverviewPanel(alignPanel, viewport);
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611 frame.setContentPane(overview);
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612 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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613 frame.getWidth(), frame.getHeight());
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615 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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616 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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618 alignPanel.setOverviewPanel(null);
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621 alignPanel.setOverviewPanel( overview );
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623 }catch(java.lang.OutOfMemoryError ex)
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625 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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626 +"\nTry reducing the font size.",
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627 "Out of memory", JOptionPane.WARNING_MESSAGE);
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633 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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635 changeColour( null );
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639 public void clustalColour_actionPerformed(ActionEvent e)
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641 abovePIDThreshold.setSelected(false);
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642 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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645 public void zappoColour_actionPerformed(ActionEvent e)
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647 changeColour(new ZappoColourScheme());
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650 public void taylorColour_actionPerformed(ActionEvent e)
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652 changeColour(new TaylorColourScheme());
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656 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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658 changeColour( new HydrophobicColourScheme() );
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661 public void helixColour_actionPerformed(ActionEvent e)
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663 changeColour(new HelixColourScheme() );
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667 public void strandColour_actionPerformed(ActionEvent e)
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669 changeColour(new StrandColourScheme());
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673 public void turnColour_actionPerformed(ActionEvent e)
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675 changeColour(new TurnColourScheme());
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679 public void buriedColour_actionPerformed(ActionEvent e)
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681 changeColour(new BuriedColourScheme() );
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684 public void nucleotideColour_actionPerformed(ActionEvent e)
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686 changeColour(new NucleotideColourScheme());
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690 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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692 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
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697 void changeColour(ColourSchemeI cs)
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700 if(viewport.getColourAppliesToAllGroups())
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702 Vector groups = viewport.alignment.getGroups();
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703 for(int i=0; i<groups.size(); i++)
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705 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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708 if(abovePIDThreshold.isSelected())
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709 abovePIDThreshold_actionPerformed(null);
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710 else if( viewport.getConservationSelected() )
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712 Conservation c = new Conservation("Group",
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713 ResidueProperties.propHash, 3,
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714 sg.sequences, sg.getStartRes(),
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717 c.verdict(false, 100);
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718 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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727 if ( viewport.getAbovePIDThreshold())
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730 threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
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731 Desktop.hideConservationSlider();
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733 if (cs instanceof ResidueColourScheme)
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734 ( (ResidueColourScheme) cs).setThreshold(threshold);
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735 else if (cs instanceof ScoreColourScheme)
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736 ( (ScoreColourScheme) cs).setThreshold(threshold);
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738 viewport.setGlobalColourScheme(cs);
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742 if (cs instanceof ResidueColourScheme)
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743 ( (ResidueColourScheme) cs).setThreshold(0);
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744 else if (cs instanceof ScoreColourScheme)
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745 ( (ScoreColourScheme) cs).setThreshold(0);
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750 if ( viewport.getConservationSelected() )
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752 ConservationColourScheme ccs = null;
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754 Alignment al = (Alignment) viewport.alignment;
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755 Conservation c = new Conservation("All",
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756 ResidueProperties.propHash, 3,
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757 al.getSequences(), 0,
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761 c.verdict(false, 100);
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763 ccs = new ConservationColourScheme(c, cs);
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765 int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,
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768 ccs.inc = threshold;
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770 viewport.setGlobalColourScheme(ccs);
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774 viewport.setGlobalColourScheme( cs );
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776 alignPanel.RefreshPanels();
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780 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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782 viewport.setConservationSelected(conservationMenuItem.isSelected());
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784 viewport.setAbovePIDThreshold(false);
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785 abovePIDThreshold.setSelected(false);
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786 Desktop.hidePIDSlider();
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787 if(!viewport.getConservationSelected())
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788 Desktop.hideConservationSlider();
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790 ColourSchemeI cs = viewport.getGlobalColourScheme();
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791 if(cs instanceof ConservationColourScheme )
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792 changeColour( ((ConservationColourScheme)cs).cs );
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794 changeColour( cs );
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798 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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800 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
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802 conservationMenuItem.setSelected(false);
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803 viewport.setConservationSelected(false);
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804 Desktop.hideConservationSlider();
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806 if(!viewport.getAbovePIDThreshold())
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807 Desktop.hidePIDSlider();
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810 ColourSchemeI cs = viewport.getGlobalColourScheme();
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811 if(cs instanceof ConservationColourScheme )
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812 changeColour( ((ConservationColourScheme)cs).cs );
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814 changeColour( cs );
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820 public void userDefinedColour_actionPerformed(ActionEvent e)
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822 JInternalFrame frame = new JInternalFrame();
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823 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
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824 frame.setContentPane(chooser);
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825 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
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826 frame.setResizable(false);
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827 frame.setIconifiable(false);
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828 frame.setMaximizable(false);
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831 public void PIDColour_actionPerformed(ActionEvent e)
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833 changeColour( new PIDColourScheme() );
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837 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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839 changeColour(new Blosum62ColourScheme(viewport) );
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844 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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846 addHistoryItem("sort");
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847 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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848 alignPanel.RefreshPanels();
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851 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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853 addHistoryItem("sort");
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854 AlignmentSorter.sortByID( viewport.getAlignment() );
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855 alignPanel.RefreshPanels();
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858 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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860 addHistoryItem("sort");
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861 AlignmentSorter.sortByGroup(viewport.getAlignment());
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862 AlignmentSorter.sortGroups(viewport.getAlignment());
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863 alignPanel.RefreshPanels();
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866 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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868 addHistoryItem("sort");
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869 if(viewport.getCurrentTree()==null)
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872 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
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873 alignPanel.RefreshPanels();
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876 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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878 RedundancyPanel sp = new RedundancyPanel(alignPanel);
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879 JInternalFrame frame = new JInternalFrame();
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880 frame.setContentPane(sp);
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881 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
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882 frame.setMaximizable(false);
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883 frame.setResizable(false);
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887 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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889 if(viewport.getSelectionGroup().getSize()<2)
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890 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
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893 JInternalFrame frame = new JInternalFrame();
\r
894 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
895 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
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899 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
902 if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
\r
903 || viewport.getAlignment().getHeight()<4)
\r
905 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
\r
906 +"at least 4 input sequences.",
\r
907 "Sequence selection insufficient",
\r
908 JOptionPane.WARNING_MESSAGE);
\r
913 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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914 JInternalFrame frame = new JInternalFrame();
\r
915 frame.setContentPane(pcaPanel);
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916 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
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917 }catch(java.lang.OutOfMemoryError ex)
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919 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
\r
920 "Out of memory", JOptionPane.WARNING_MESSAGE);
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926 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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928 NewTreePanel("AV", "PID", "Average distance tree using PID");
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931 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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933 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
937 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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939 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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942 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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944 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
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947 void NewTreePanel(String type, String pwType, String title)
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949 //are the sequences aligned?
\r
950 if(!viewport.alignment.isAligned())
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952 JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
\r
953 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
\r
958 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)
\r
960 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,
\r
961 0, viewport.alignment.getWidth());
\r
965 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
966 type, pwType, 0, viewport.alignment.getWidth());
\r
969 Desktop.addInternalFrame(tp, title, 600, 500);
\r
975 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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977 JInternalFrame frame = new JInternalFrame();
\r
978 ClustalThread ct = new ClustalThread(frame);
\r
979 Thread t = new Thread(ct);
\r
981 frame.setContentPane(ct);
\r
982 Desktop.addInternalFrame(frame, title, 300, 80);
\r
986 class ClustalThread extends JPanel implements Runnable
\r
989 int imageIndex = 0;
\r
990 boolean webServiceRunning = false;
\r
991 JInternalFrame frame;
\r
992 public ClustalThread(JInternalFrame frame)
\r
994 this.frame = frame;
\r
995 image = new Image[9];
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996 for(int i=0; i<9; i++)
\r
998 java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
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1001 image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
\r
1002 MediaTracker mt = new MediaTracker(this);
\r
1003 mt.addImage(image[i], i);
\r
1004 try{mt.waitForID(i);}
\r
1005 catch(Exception ex){}
\r
1008 DNATwirler twirler = new DNATwirler();
\r
1010 webServiceRunning = true;
\r
1013 class DNATwirler extends Thread
\r
1017 while(webServiceRunning)
\r
1020 Thread.sleep(100);
\r
1025 catch(Exception ex){}
\r
1031 // Should check to see if the server settings are valid
\r
1032 // Need visual-delay indication here.
\r
1035 /* jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
\r
1036 Vector sv = viewport.getAlignment().getSequences();
\r
1037 SequenceI[] seqs = new SequenceI[sv.size()];
\r
1042 seqs[i] = (SequenceI) sv.elementAt(i);
\r
1044 while (++i < sv.size());
\r
1046 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
\r
1048 if (alignment != null)
\r
1050 AlignFrame af = new AlignFrame(new Alignment(alignment));
\r
1051 af.clustalColour.setSelected(true);
\r
1052 af.clustalColour_actionPerformed(null);
\r
1053 Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
\r
1054 700, 500); // JBPNote - is there a new window geom. property ?
\r
1057 JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
\r
1058 JOptionPane.WARNING_MESSAGE);
\r
1060 webServiceRunning = false;
\r
1062 frame.setClosed(true);
\r
1063 }catch(Exception ex){}
\r
1066 public void paintComponent(Graphics g)
\r
1068 g.setColor(Color.white);
\r
1069 g.fillRect(0,0,getWidth(), getHeight());
\r
1072 g.drawImage(image[imageIndex],10,10,this);
\r
1074 g.setFont(new Font("Arial", Font.BOLD, 12));
\r
1075 g.setColor(Color.black);
\r
1076 g.drawString("Clustal Alignment Web Service running", 30,30);
\r
1079 public void jpredMenuItem_actionPerformed(ActionEvent e)
\r
1081 // JInternalFrame frame = new JInternalFrame();
\r
1082 // JPredClient ct = new JPredClient((SequenceI)
\r
1083 /// viewport.getAlignment().getSequences().elementAt(0));
\r
1087 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
\r
1088 // Pick the tree file
\r
1089 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
1090 getProperty("LAST_DIRECTORY"));
\r
1091 chooser.setFileView(new JalviewFileView());
\r
1092 chooser.setDialogTitle("Select a newick-like tree file");
\r
1093 chooser.setToolTipText("Load a tree file");
\r
1094 int value = chooser.showOpenDialog(null);
\r
1095 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
1097 String choice = chooser.getSelectedFile().getPath();
\r
1098 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1099 TreePanel treepanel = null;
\r
1102 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
\r
1105 if (fin.getTree() != null)
\r
1107 TreePanel tp = null;
\r
1108 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1109 fin, "FromFile", choice);
\r
1110 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1113 catch (Exception ex)
\r
1115 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1116 "Problem reading tree file",
\r
1118 JOptionPane.WARNING_MESSAGE);
\r
1119 ex.printStackTrace();
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