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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45 alignPanel = new AlignmentPanel(this, viewport);
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46 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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48 addInternalFrameListener(new InternalFrameAdapter()
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50 public void internalFrameActivated(InternalFrameEvent evt)
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52 javax.swing.SwingUtilities.invokeLater(new Runnable()
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55 { alignPanel.requestFocus(); }
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63 protected void saveAs_actionPerformed(ActionEvent e)
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65 String suffix [] = null;
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66 if(e.getActionCommand().equals("FASTA"))
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67 suffix = new String[]{"fa", "fasta"};
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68 else if(e.getActionCommand().equals("MSF"))
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69 suffix = new String[]{"msf"};
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70 else if(e.getActionCommand().equals("CLUSTAL"))
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71 suffix = new String[]{"aln"};
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72 else if(e.getActionCommand().equals("BLC"))
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73 suffix = new String[]{"blc"};
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74 else if(e.getActionCommand().equals("PIR"))
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75 suffix = new String[]{"pir"};
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76 else if(e.getActionCommand().equals("PFAM"))
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77 suffix = new String[]{"pfam"};
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79 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
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80 , suffix, e.getActionCommand()+" file");
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81 chooser.setFileView(new JalviewFileView());
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82 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
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83 chooser.setToolTipText("Save");
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84 int value = chooser.showSaveDialog(this);
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85 if(value == JalviewFileChooser.APPROVE_OPTION)
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87 String choice = chooser.getSelectedFile().getPath();
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88 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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89 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
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91 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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92 out.println(output);
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95 catch(Exception ex){}
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100 protected void outputText_actionPerformed(ActionEvent e)
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102 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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103 JInternalFrame frame = new JInternalFrame();
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104 cap.formatForOutput();
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105 frame.setContentPane(cap);
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106 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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107 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
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110 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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112 HTMLOutput htmlOutput = new HTMLOutput(viewport);
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116 protected void createPNG_actionPerformed(ActionEvent e)
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118 alignPanel.makePNG();
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121 protected void epsFile_actionPerformed(ActionEvent e)
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123 alignPanel.makeEPS();
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127 public void printMenuItem_actionPerformed(ActionEvent e)
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129 //Putting in a thread avoids Swing painting problems
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130 PrintThread thread = new PrintThread();
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134 class PrintThread extends Thread
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138 PrinterJob printJob = PrinterJob.getPrinterJob();
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139 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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140 printJob.setPrintable(alignPanel, pf);
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141 if (printJob.printDialog())
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147 catch (Exception PrintException)
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149 PrintException.printStackTrace();
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159 public void closeMenuItem_actionPerformed(ActionEvent e)
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162 this.setClosed(true);
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163 }catch(Exception ex){}
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166 Stack historyList = new Stack();
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167 Stack redoList = new Stack();
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168 JMenuBar jMenuBar1 = new JMenuBar();
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170 void updateEditMenuBar()
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172 if(historyList.size()>0)
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174 undoMenuItem.setEnabled(true);
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175 Object [] history = (Object[])historyList.get(0);
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176 undoMenuItem.setText("Undo "+history[0]);
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180 undoMenuItem.setEnabled(false);
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181 undoMenuItem.setText("Undo");
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184 if(redoList.size()>0)
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186 redoMenuItem.setEnabled(true);
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187 Object [] history = (Object[])redoList.get(0);
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188 redoMenuItem.setText("Redo "+history[0]);
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192 redoMenuItem.setEnabled(false);
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193 redoMenuItem.setText("Redo");
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197 public void addHistoryItem(String type)
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199 // must make sure we add new sequence objects her, not refs to the existing sequences
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201 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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202 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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204 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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205 viewport.getAlignment().getSequenceAt(i).getSequence());
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208 historyList.add(0, new Object[]{type, seq} );
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209 updateEditMenuBar();
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212 protected void undoMenuItem_actionPerformed(ActionEvent e)
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214 Object [] history = (Object[])historyList.remove(0);
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215 // add the redo state before continuing!!
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216 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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217 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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219 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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220 viewport.getAlignment().getSequenceAt(i).
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225 redoList.add(0, new Object[] {history[0], seq});
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227 seq = (SequenceI[]) history[1];
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228 viewport.setAlignment( new Alignment(seq) );
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229 updateEditMenuBar();
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230 alignPanel.RefreshPanels();
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233 public void moveSelectedSequences(boolean up)
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235 SequenceGroup sg = viewport.getSelectionGroup();
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241 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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243 SequenceI seq = viewport.alignment.getSequenceAt(i);
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244 if (!sg.sequences.contains(seq))
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247 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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248 if (sg.sequences.contains(temp))
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251 viewport.alignment.getSequences().setElementAt(temp, i);
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252 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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257 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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259 SequenceI seq = viewport.alignment.getSequenceAt(i);
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260 if (!sg.sequences.contains(seq))
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263 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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264 if (sg.sequences.contains(temp))
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267 viewport.alignment.getSequences().setElementAt(temp, i);
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268 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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272 alignPanel.RefreshPanels();
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277 protected void copy_actionPerformed(ActionEvent e)
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279 if(viewport.getSelectionGroup()==null)
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282 SequenceGroup sg = viewport.getSelectionGroup();
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284 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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285 StringBuffer buffer= new StringBuffer();
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287 for(int i=0; i<sg.getSize(); i++)
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289 SequenceI seq = sg.getSequenceAt(i);
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290 buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
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291 +seq.findPosition( sg.getEndRes() )+ "\t"
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292 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
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294 c.setContents( new StringSelection( buffer.toString()) , null ) ;
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299 protected void pasteNew_actionPerformed(ActionEvent e)
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304 protected void pasteThis_actionPerformed(ActionEvent e)
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306 addHistoryItem("Paste");
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310 void paste(boolean newAlignment)
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313 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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314 Transferable contents = c.getContents(this);
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315 if (contents == null)
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318 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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319 StringTokenizer st = new StringTokenizer(str);
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320 ArrayList seqs = new ArrayList();
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321 while (st.hasMoreElements())
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323 String name = st.nextToken();
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324 int start = Integer.parseInt(st.nextToken());
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325 int end = Integer.parseInt(st.nextToken());
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326 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
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329 viewport.alignment.addSequence(sequence);
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331 seqs.add(sequence);
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336 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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337 seqs.toArray(newSeqs);
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338 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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339 int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;
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340 if (newHeight > 500)
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342 Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
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346 viewport.setEndSeq(viewport.alignment.getHeight());
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347 viewport.alignment.getWidth();
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348 alignPanel.RefreshPanels();
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351 }catch(Exception ex){}// could be anything being pasted in here
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356 protected void cut_actionPerformed(ActionEvent e)
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358 copy_actionPerformed(null);
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359 delete_actionPerformed(null);
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362 protected void delete_actionPerformed(ActionEvent e)
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364 addHistoryItem("Delete");
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365 if (viewport.getSelectionGroup() == null)
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368 SequenceGroup sg = viewport.getSelectionGroup();
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369 for (int i=0;i < sg.sequences.size(); i++)
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371 SequenceI seq = sg.getSequenceAt(i);
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372 int index = viewport.getAlignment().findIndex(seq);
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373 seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
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375 if(seq.getSequence().length()<1)
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376 viewport.getAlignment().deleteSequence(seq);
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378 viewport.getAlignment().getSequences().setElementAt(seq, index);
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381 viewport.setSelectionGroup(null);
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382 viewport.alignment.deleteGroup(sg);
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383 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
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384 if(viewport.getAlignment().getHeight()<1)
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387 this.setClosed(true);
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388 }catch(Exception ex){}
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389 alignPanel.RefreshPanels();
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395 protected void redoMenuItem_actionPerformed(ActionEvent e)
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397 Object [] history = (Object[])redoList.remove(0);
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398 SequenceI[] seq = (SequenceI[]) history[1];
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399 viewport.setAlignment( new Alignment(seq) );
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400 updateEditMenuBar();
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401 alignPanel.RefreshPanels();
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405 public void groupsMenuItem_actionPerformed(ActionEvent e)
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407 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
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408 JInternalFrame frame = new JInternalFrame();
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409 frame.setContentPane(geditor);
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410 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
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411 frame.setResizable(false);
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414 protected void deleteGroups_actionPerformed(ActionEvent e)
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416 viewport.alignment.deleteAllGroups();
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417 viewport.setSelectionGroup(null);
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419 alignPanel.RefreshPanels();
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424 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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426 SequenceGroup sg = new SequenceGroup();
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427 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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428 sg.addSequence( viewport.getAlignment().getSequenceAt(i));
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429 sg.setEndRes(viewport.alignment.getWidth());
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430 viewport.setSelectionGroup(sg);
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431 PaintRefresher.Refresh(null);
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434 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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436 viewport.setSelectionGroup(null);
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437 PaintRefresher.Refresh(null);
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440 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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442 SequenceGroup sg = viewport.getSelectionGroup();
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443 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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444 sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
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446 PaintRefresher.Refresh(null);
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450 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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452 viewport.getColumnSelection().clear();
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456 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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458 addHistoryItem("delete columns");
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459 ColumnSelection colSel = viewport.getColumnSelection();
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460 if (colSel.size() > 0)
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462 int min = colSel.getMin();
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463 viewport.getAlignment().trimLeft(min);
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464 colSel.compensateForEdit(0,min);
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465 alignPanel.RefreshPanels();
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469 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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471 addHistoryItem("delete columns");
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472 ColumnSelection colSel = viewport.getColumnSelection();
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473 if (colSel.size() > 0)
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475 int max = colSel.getMax();
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477 viewport.getAlignment().trimRight(max);
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479 alignPanel.RefreshPanels();
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484 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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486 addHistoryItem("delete gapped columns");
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487 viewport.getAlignment().removeGaps();
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488 alignPanel.RefreshPanels();
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491 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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493 addHistoryItem("delete all gaps");
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496 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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498 current = viewport.getAlignment().getSequenceAt(i);
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499 jSize = current.getLength();
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500 for (int j=0; j < jSize; j++)
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501 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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503 current.deleteCharAt(j);
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509 alignPanel.RefreshPanels();
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512 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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514 char thisChar = '-';
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515 char nextChar = '.';
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516 if(viewport.getGapCharacter()=='-')
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521 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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522 viewport.setGapCharacter(thisChar);
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523 alignPanel.RefreshPanels();
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526 public void findMenuItem_actionPerformed(ActionEvent e)
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528 JInternalFrame frame = new JInternalFrame();
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529 Finder finder = new Finder(viewport, alignPanel, frame);
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530 frame.setContentPane(finder);
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531 Desktop.addInternalFrame(frame, "Find", 340,110);
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536 public void font_actionPerformed(ActionEvent e)
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538 // JOptionPane op = new JOptionPane();
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539 JInternalFrame frame = new JInternalFrame();
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540 FontChooser fc = new FontChooser( alignPanel, frame );
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541 frame.setContentPane(fc);
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542 Desktop.addInternalFrame(frame, "Change Font", 480,100);
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545 protected void fullSeqId_actionPerformed(ActionEvent e)
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547 viewport.setShowFullId( fullSeqId.isSelected() );
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549 alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
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550 alignPanel.RefreshPanels();
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553 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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555 viewport.setColourText( colourTextMenuItem.isSelected() );
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556 alignPanel.RefreshPanels();
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559 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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561 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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562 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
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566 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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568 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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569 alignPanel.RefreshPanels();
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572 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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574 viewport.setShowText( viewTextMenuItem.isSelected() );
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575 alignPanel.RefreshPanels();
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579 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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581 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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582 alignPanel.RefreshPanels();
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585 public void sequenceFeatures_actionPerformed(ActionEvent evt)
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587 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
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588 if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
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590 AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
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591 ((Alignment)viewport.alignment).featuresAdded = true;
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593 alignPanel.RefreshPanels();
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596 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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598 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
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601 public void overviewMenuItem_actionPerformed(ActionEvent e)
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603 if (alignPanel.overviewPanel != null)
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606 JInternalFrame frame = new JInternalFrame();
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607 OverviewPanel overview = alignPanel.getOverviewPanel();
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609 overview = new OverviewPanel(alignPanel, viewport);
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610 frame.setContentPane(overview);
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611 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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612 frame.getWidth(), frame.getHeight());
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614 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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615 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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617 alignPanel.setOverviewPanel(null);
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620 alignPanel.setOverviewPanel( overview );
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622 }catch(java.lang.OutOfMemoryError ex)
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624 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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625 +"\nTry reducing the font size.",
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626 "Out of memory", JOptionPane.WARNING_MESSAGE);
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632 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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634 changeColour( null );
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638 public void clustalColour_actionPerformed(ActionEvent e)
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640 abovePIDThreshold.setSelected(false);
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641 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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644 public void zappoColour_actionPerformed(ActionEvent e)
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646 changeColour(new ZappoColourScheme());
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649 public void taylorColour_actionPerformed(ActionEvent e)
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651 changeColour(new TaylorColourScheme());
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655 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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657 changeColour( new HydrophobicColourScheme() );
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660 public void helixColour_actionPerformed(ActionEvent e)
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662 changeColour(new HelixColourScheme() );
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666 public void strandColour_actionPerformed(ActionEvent e)
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668 changeColour(new StrandColourScheme());
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672 public void turnColour_actionPerformed(ActionEvent e)
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674 changeColour(new TurnColourScheme());
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678 public void buriedColour_actionPerformed(ActionEvent e)
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680 changeColour(new BuriedColourScheme() );
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683 public void nucleotideColour_actionPerformed(ActionEvent e)
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685 changeColour(new NucleotideColourScheme());
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689 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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691 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
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696 void changeColour(ColourSchemeI cs)
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699 if(viewport.getColourAppliesToAllGroups())
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701 Vector groups = viewport.alignment.getGroups();
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702 for(int i=0; i<groups.size(); i++)
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704 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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707 if(abovePIDThreshold.isSelected())
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708 abovePIDThreshold_actionPerformed(null);
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709 else if( viewport.getConservationSelected() )
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711 Conservation c = new Conservation("Group",
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712 ResidueProperties.propHash, 3,
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713 sg.sequences, sg.getStartRes(),
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716 c.verdict(false, 100);
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717 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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726 if ( viewport.getAbovePIDThreshold())
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729 threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
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730 Desktop.hideConservationSlider();
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732 if (cs instanceof ResidueColourScheme)
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733 ( (ResidueColourScheme) cs).setThreshold(threshold);
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734 else if (cs instanceof ScoreColourScheme)
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735 ( (ScoreColourScheme) cs).setThreshold(threshold);
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737 viewport.setGlobalColourScheme(cs);
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741 if (cs instanceof ResidueColourScheme)
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742 ( (ResidueColourScheme) cs).setThreshold(0);
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743 else if (cs instanceof ScoreColourScheme)
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744 ( (ScoreColourScheme) cs).setThreshold(0);
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749 if ( viewport.getConservationSelected() )
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751 ConservationColourScheme ccs = null;
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753 Alignment al = (Alignment) viewport.alignment;
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754 Conservation c = new Conservation("All",
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755 ResidueProperties.propHash, 3,
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756 al.getSequences(), 0,
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760 c.verdict(false, 100);
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762 ccs = new ConservationColourScheme(c, cs);
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764 int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,
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767 ccs.inc = threshold;
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769 viewport.setGlobalColourScheme(ccs);
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773 viewport.setGlobalColourScheme( cs );
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775 alignPanel.RefreshPanels();
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779 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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781 viewport.setConservationSelected(conservationMenuItem.isSelected());
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782 if(coloursChanging)
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785 coloursChanging = true;
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787 viewport.setAbovePIDThreshold(false);
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788 abovePIDThreshold.setSelected(false);
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789 Desktop.hidePIDSlider();
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790 if(!viewport.getConservationSelected())
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791 Desktop.hideConservationSlider();
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793 ColourSchemeI cs = viewport.getGlobalColourScheme();
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794 if(cs instanceof ConservationColourScheme )
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795 changeColour( ((ConservationColourScheme)cs).cs );
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797 changeColour( cs );
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799 coloursChanging = false;
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802 boolean coloursChanging = false;
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803 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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805 if(coloursChanging)
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808 coloursChanging = true;
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809 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
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811 conservationMenuItem.setSelected(false);
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812 viewport.setConservationSelected(false);
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813 Desktop.hideConservationSlider();
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815 if(!viewport.getAbovePIDThreshold())
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816 Desktop.hidePIDSlider();
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819 ColourSchemeI cs = viewport.getGlobalColourScheme();
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820 if(cs instanceof ConservationColourScheme )
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821 changeColour( ((ConservationColourScheme)cs).cs );
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823 changeColour( cs );
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825 coloursChanging = false;
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830 public void userDefinedColour_actionPerformed(ActionEvent e)
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832 JInternalFrame frame = new JInternalFrame();
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833 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
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834 frame.setContentPane(chooser);
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835 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
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836 frame.setResizable(false);
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837 frame.setIconifiable(false);
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838 frame.setMaximizable(false);
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841 public void PIDColour_actionPerformed(ActionEvent e)
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843 changeColour( new PIDColourScheme() );
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847 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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849 changeColour(new Blosum62ColourScheme(viewport) );
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854 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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856 addHistoryItem("sort");
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857 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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858 alignPanel.RefreshPanels();
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861 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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863 addHistoryItem("sort");
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864 AlignmentSorter.sortByID( viewport.getAlignment() );
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865 alignPanel.RefreshPanels();
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868 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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870 addHistoryItem("sort");
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871 AlignmentSorter.sortByGroup(viewport.getAlignment());
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872 AlignmentSorter.sortGroups(viewport.getAlignment());
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873 alignPanel.RefreshPanels();
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876 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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878 addHistoryItem("sort");
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879 if(viewport.getCurrentTree()==null)
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882 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
\r
883 alignPanel.RefreshPanels();
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886 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
888 RedundancyPanel sp = new RedundancyPanel(alignPanel);
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889 JInternalFrame frame = new JInternalFrame();
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890 frame.setContentPane(sp);
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891 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
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892 frame.setMaximizable(false);
\r
893 frame.setResizable(false);
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897 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
899 if(viewport.getSelectionGroup().getSize()<2)
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900 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
\r
903 JInternalFrame frame = new JInternalFrame();
\r
904 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
905 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
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909 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
912 if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
\r
913 || viewport.getAlignment().getHeight()<4)
\r
915 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
\r
916 +"at least 4 input sequences.",
\r
917 "Sequence selection insufficient",
\r
918 JOptionPane.WARNING_MESSAGE);
\r
923 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
924 JInternalFrame frame = new JInternalFrame();
\r
925 frame.setContentPane(pcaPanel);
\r
926 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
\r
927 }catch(java.lang.OutOfMemoryError ex)
\r
929 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
\r
930 "Out of memory", JOptionPane.WARNING_MESSAGE);
\r
936 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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938 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
941 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
943 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
947 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
949 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
952 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
954 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
957 void NewTreePanel(String type, String pwType, String title)
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959 //are the sequences aligned?
\r
960 if(!viewport.alignment.isAligned())
\r
962 JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
\r
963 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
\r
968 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)
\r
970 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,
\r
971 0, viewport.alignment.getWidth());
\r
975 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
976 type, pwType, 0, viewport.alignment.getWidth());
\r
979 Desktop.addInternalFrame(tp, title, 600, 500);
\r
985 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
987 JInternalFrame frame = new JInternalFrame();
\r
988 ClustalThread ct = new ClustalThread(frame);
\r
989 Thread t = new Thread(ct);
\r
991 frame.setContentPane(ct);
\r
992 Desktop.addInternalFrame(frame, title, 300, 80);
\r
996 class ClustalThread extends JPanel implements Runnable
\r
999 int imageIndex = 0;
\r
1000 boolean webServiceRunning = false;
\r
1001 JInternalFrame frame;
\r
1002 public ClustalThread(JInternalFrame frame)
\r
1004 this.frame = frame;
\r
1005 image = new Image[9];
\r
1006 for(int i=0; i<9; i++)
\r
1008 java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
\r
1011 image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
\r
1012 MediaTracker mt = new MediaTracker(this);
\r
1013 mt.addImage(image[i], i);
\r
1014 try{mt.waitForID(i);}
\r
1015 catch(Exception ex){}
\r
1018 DNATwirler twirler = new DNATwirler();
\r
1020 webServiceRunning = true;
\r
1023 class DNATwirler extends Thread
\r
1027 while(webServiceRunning)
\r
1030 Thread.sleep(100);
\r
1035 catch(Exception ex){}
\r
1041 // Should check to see if the server settings are valid
\r
1042 // Need visual-delay indication here.
\r
1045 jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
\r
1046 Vector sv = viewport.getAlignment().getSequences();
\r
1047 SequenceI[] seqs = new SequenceI[sv.size()];
\r
1052 seqs[i] = (SequenceI) sv.elementAt(i);
\r
1054 while (++i < sv.size());
\r
1056 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
\r
1058 if (alignment != null)
\r
1060 AlignFrame af = new AlignFrame(new Alignment(alignment));
\r
1061 af.clustalColour.setSelected(true);
\r
1062 af.clustalColour_actionPerformed(null);
\r
1063 Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
\r
1064 700, 500); // JBPNote - is there a new window geom. property ?
\r
1067 JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
\r
1068 JOptionPane.WARNING_MESSAGE);
\r
1070 webServiceRunning = false;
\r
1072 frame.setClosed(true);
\r
1073 }catch(Exception ex){}
\r
1076 public void paintComponent(Graphics g)
\r
1078 g.setColor(Color.white);
\r
1079 g.fillRect(0,0,getWidth(), getHeight());
\r
1082 g.drawImage(image[imageIndex],10,10,this);
\r
1084 g.setFont(new Font("Arial", Font.BOLD, 12));
\r
1085 g.setColor(Color.black);
\r
1086 g.drawString("Clustal Alignment Web Service running", 30,30);
\r
1089 public void jpredMenuItem_actionPerformed(ActionEvent e)
\r
1091 // JInternalFrame frame = new JInternalFrame();
\r
1092 // JPredClient ct = new JPredClient((SequenceI)
\r
1093 /// viewport.getAlignment().getSequences().elementAt(0));
\r
1096 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
\r
1097 // Pick the tree file
\r
1098 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
1099 getProperty("LAST_DIRECTORY"));
\r
1100 chooser.setFileView(new JalviewFileView());
\r
1101 chooser.setDialogTitle("Select a newick-like tree file");
\r
1102 chooser.setToolTipText("Load a tree file");
\r
1103 int value = chooser.showOpenDialog(null);
\r
1104 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
1106 String choice = chooser.getSelectedFile().getPath();
\r
1107 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1108 TreePanel treepanel = null;
\r
1111 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
\r
1114 if (fin.getTree() != null)
\r
1116 TreePanel tp = null;
\r
1117 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1118 fin, "FromFile", choice);
\r
1119 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1122 catch (Exception ex)
\r
1124 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1125 "Problem reading tree file",
\r
1127 JOptionPane.WARNING_MESSAGE);
\r
1128 ex.printStackTrace();
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