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 int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;
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120 int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();
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122 if(!viewport.getWrapAlignment())
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124 height = viewport.alignment.getHeight() * viewport.charHeight;
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125 width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;
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128 alignPanel.makePNG( width, height);
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131 protected void epsFile_actionPerformed(ActionEvent e)
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133 int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;
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134 int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();
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136 if(!viewport.getWrapAlignment())
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138 height = viewport.alignment.getHeight() * viewport.charHeight;
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139 width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;
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142 alignPanel.makeEPS( width, height);
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147 public void printMenuItem_actionPerformed(ActionEvent e)
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149 //Putting in a thread avoids Swing painting problems
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150 PrintThread thread = new PrintThread();
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154 class PrintThread extends Thread
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158 PrinterJob printJob = PrinterJob.getPrinterJob();
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159 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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160 printJob.setPrintable(alignPanel, pf);
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161 if (printJob.printDialog())
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167 catch (Exception PrintException)
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169 PrintException.printStackTrace();
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179 public void closeMenuItem_actionPerformed(ActionEvent e)
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182 this.setClosed(true);
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183 }catch(Exception ex){}
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186 Stack historyList = new Stack();
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187 Stack redoList = new Stack();
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188 JMenuBar jMenuBar1 = new JMenuBar();
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190 void updateEditMenuBar()
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192 if(historyList.size()>0)
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194 undoMenuItem.setEnabled(true);
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195 Object [] history = (Object[])historyList.get(0);
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196 undoMenuItem.setText("Undo "+history[0]);
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200 undoMenuItem.setEnabled(false);
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201 undoMenuItem.setText("Undo");
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204 if(redoList.size()>0)
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206 redoMenuItem.setEnabled(true);
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207 Object [] history = (Object[])redoList.get(0);
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208 redoMenuItem.setText("Redo "+history[0]);
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212 redoMenuItem.setEnabled(false);
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213 redoMenuItem.setText("Redo");
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217 public void addHistoryItem(String type)
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219 // must make sure we add new sequence objects her, not refs to the existing sequences
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221 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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222 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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224 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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225 viewport.getAlignment().getSequenceAt(i).getSequence());
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228 historyList.add(0, new Object[]{type, seq} );
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229 updateEditMenuBar();
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232 protected void undoMenuItem_actionPerformed(ActionEvent e)
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234 Object [] history = (Object[])historyList.remove(0);
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235 // add the redo state before continuing!!
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236 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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237 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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239 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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240 viewport.getAlignment().getSequenceAt(i).
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245 redoList.add(0, new Object[] {history[0], seq});
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247 seq = (SequenceI[]) history[1];
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248 viewport.setAlignment( new Alignment(seq) );
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249 updateEditMenuBar();
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250 alignPanel.RefreshPanels();
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253 public void moveSelectedSequences(boolean up)
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255 SequenceGroup sg = viewport.getSelectionGroup();
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261 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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263 SequenceI seq = viewport.alignment.getSequenceAt(i);
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264 if (!sg.sequences.contains(seq))
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267 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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268 if (sg.sequences.contains(temp))
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271 viewport.alignment.getSequences().setElementAt(temp, i);
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272 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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277 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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279 SequenceI seq = viewport.alignment.getSequenceAt(i);
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280 if (!sg.sequences.contains(seq))
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283 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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284 if (sg.sequences.contains(temp))
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287 viewport.alignment.getSequences().setElementAt(temp, i);
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288 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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292 alignPanel.RefreshPanels();
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297 protected void copy_actionPerformed(ActionEvent e)
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299 if(viewport.getSelectionGroup()==null)
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302 SequenceGroup sg = viewport.getSelectionGroup();
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304 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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305 StringBuffer buffer= new StringBuffer();
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307 for(int i=0; i<sg.getSize(); i++)
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309 SequenceI seq = sg.getSequenceAt(i);
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310 buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
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311 +seq.findPosition( sg.getEndRes() )+ "\t"
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312 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
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314 c.setContents( new StringSelection( buffer.toString()) , null ) ;
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319 protected void pasteNew_actionPerformed(ActionEvent e)
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324 protected void pasteThis_actionPerformed(ActionEvent e)
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326 addHistoryItem("Paste");
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330 void paste(boolean newAlignment)
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333 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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334 Transferable contents = c.getContents(this);
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335 if (contents == null)
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338 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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339 StringTokenizer st = new StringTokenizer(str);
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340 ArrayList seqs = new ArrayList();
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341 while (st.hasMoreElements())
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343 String name = st.nextToken();
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344 int start = Integer.parseInt(st.nextToken());
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345 int end = Integer.parseInt(st.nextToken());
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346 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
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349 viewport.alignment.addSequence(sequence);
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351 seqs.add(sequence);
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356 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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357 seqs.toArray(newSeqs);
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358 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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359 int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;
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360 if (newHeight > 500)
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362 Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
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366 viewport.setEndSeq(viewport.alignment.getHeight());
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367 viewport.alignment.getWidth();
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368 alignPanel.RefreshPanels();
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371 }catch(Exception ex){}// could be anything being pasted in here
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376 protected void cut_actionPerformed(ActionEvent e)
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378 copy_actionPerformed(null);
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379 delete_actionPerformed(null);
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382 protected void delete_actionPerformed(ActionEvent e)
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384 addHistoryItem("Delete");
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385 if (viewport.getSelectionGroup() == null)
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388 SequenceGroup sg = viewport.getSelectionGroup();
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389 for (int i=0;i < sg.sequences.size(); i++)
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391 SequenceI seq = sg.getSequenceAt(i);
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392 int index = viewport.getAlignment().findIndex(seq);
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393 seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
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395 if(seq.getSequence().length()<1)
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396 viewport.getAlignment().deleteSequence(seq);
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398 viewport.getAlignment().getSequences().setElementAt(seq, index);
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401 viewport.setSelectionGroup(null);
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402 viewport.alignment.deleteGroup(sg);
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403 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
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404 if(viewport.getAlignment().getHeight()<1)
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407 this.setClosed(true);
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408 }catch(Exception ex){}
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409 alignPanel.RefreshPanels();
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415 protected void redoMenuItem_actionPerformed(ActionEvent e)
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417 Object [] history = (Object[])redoList.remove(0);
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418 SequenceI[] seq = (SequenceI[]) history[1];
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419 viewport.setAlignment( new Alignment(seq) );
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420 updateEditMenuBar();
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421 alignPanel.RefreshPanels();
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425 public void groupsMenuItem_actionPerformed(ActionEvent e)
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427 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
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428 JInternalFrame frame = new JInternalFrame();
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429 frame.setContentPane(geditor);
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430 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
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431 frame.setResizable(false);
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434 protected void deleteGroups_actionPerformed(ActionEvent e)
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436 viewport.alignment.deleteAllGroups();
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437 viewport.setSelectionGroup(null);
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439 alignPanel.RefreshPanels();
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444 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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446 SequenceGroup sg = new SequenceGroup();
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447 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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448 sg.addSequence( viewport.getAlignment().getSequenceAt(i));
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449 sg.setEndRes(viewport.alignment.getWidth());
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450 viewport.setSelectionGroup(sg);
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451 PaintRefresher.Refresh(null);
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454 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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456 viewport.setSelectionGroup(null);
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457 PaintRefresher.Refresh(null);
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460 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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462 SequenceGroup sg = viewport.getSelectionGroup();
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463 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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464 sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
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466 PaintRefresher.Refresh(null);
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470 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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472 viewport.getColumnSelection().clear();
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476 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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478 addHistoryItem("delete columns");
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479 ColumnSelection colSel = viewport.getColumnSelection();
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480 if (colSel.size() > 0)
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482 int min = colSel.getMin();
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483 viewport.getAlignment().trimLeft(min);
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484 colSel.compensateForEdit(0,min);
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485 alignPanel.RefreshPanels();
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489 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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491 addHistoryItem("delete columns");
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492 ColumnSelection colSel = viewport.getColumnSelection();
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493 if (colSel.size() > 0)
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495 int max = colSel.getMax();
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497 viewport.getAlignment().trimRight(max);
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499 alignPanel.RefreshPanels();
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504 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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506 addHistoryItem("delete gapped columns");
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507 viewport.getAlignment().removeGaps();
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508 alignPanel.RefreshPanels();
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511 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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513 addHistoryItem("delete all gaps");
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516 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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518 current = viewport.getAlignment().getSequenceAt(i);
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519 jSize = current.getLength();
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520 for (int j=0; j < jSize; j++)
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521 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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523 current.deleteCharAt(j);
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529 alignPanel.RefreshPanels();
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532 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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534 char thisChar = '-';
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535 char nextChar = '.';
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536 if(viewport.getGapCharacter()=='-')
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541 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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542 viewport.setGapCharacter(thisChar);
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543 alignPanel.RefreshPanels();
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546 public void findMenuItem_actionPerformed(ActionEvent e)
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548 JInternalFrame frame = new JInternalFrame();
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549 Finder finder = new Finder(viewport, alignPanel, frame);
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550 frame.setContentPane(finder);
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551 Desktop.addInternalFrame(frame, "Find", 340,110);
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556 public void font_actionPerformed(ActionEvent e)
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558 // JOptionPane op = new JOptionPane();
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559 JInternalFrame frame = new JInternalFrame();
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560 FontChooser fc = new FontChooser( alignPanel, frame );
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561 frame.setContentPane(fc);
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562 Desktop.addInternalFrame(frame, "Change Font", 480,100);
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565 protected void fullSeqId_actionPerformed(ActionEvent e)
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567 viewport.setShowFullId( fullSeqId.isSelected() );
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569 alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
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570 alignPanel.RefreshPanels();
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573 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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575 viewport.setColourText( colourTextMenuItem.isSelected() );
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576 alignPanel.RefreshPanels();
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579 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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581 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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582 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
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586 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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588 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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589 alignPanel.RefreshPanels();
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592 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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594 viewport.setShowText( viewTextMenuItem.isSelected() );
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595 alignPanel.RefreshPanels();
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599 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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601 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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602 alignPanel.RefreshPanels();
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605 public void sequenceFeatures_actionPerformed(ActionEvent evt)
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607 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
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608 if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
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610 AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
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611 ((Alignment)viewport.alignment).featuresAdded = true;
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613 alignPanel.RefreshPanels();
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616 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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618 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
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621 public void overviewMenuItem_actionPerformed(ActionEvent e)
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623 if (alignPanel.overviewPanel != null)
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626 JInternalFrame frame = new JInternalFrame();
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627 OverviewPanel overview = alignPanel.getOverviewPanel();
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629 overview = new OverviewPanel(alignPanel, viewport);
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630 frame.setContentPane(overview);
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631 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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632 frame.getWidth(), frame.getHeight());
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634 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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635 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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637 alignPanel.setOverviewPanel(null);
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640 alignPanel.setOverviewPanel( overview );
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642 }catch(java.lang.OutOfMemoryError ex)
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644 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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645 +"\nTry reducing the font size.",
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646 "Out of memory", JOptionPane.WARNING_MESSAGE);
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652 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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654 changeColour( null );
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658 public void clustalColour_actionPerformed(ActionEvent e)
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660 abovePIDThreshold.setSelected(false);
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661 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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664 public void zappoColour_actionPerformed(ActionEvent e)
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666 changeColour(new ZappoColourScheme());
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669 public void taylorColour_actionPerformed(ActionEvent e)
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671 changeColour(new TaylorColourScheme());
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675 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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677 changeColour( new HydrophobicColourScheme() );
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680 public void helixColour_actionPerformed(ActionEvent e)
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682 changeColour(new HelixColourScheme() );
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686 public void strandColour_actionPerformed(ActionEvent e)
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688 changeColour(new StrandColourScheme());
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692 public void turnColour_actionPerformed(ActionEvent e)
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694 changeColour(new TurnColourScheme());
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698 public void buriedColour_actionPerformed(ActionEvent e)
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700 changeColour(new BuriedColourScheme() );
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703 public void nucleotideColour_actionPerformed(ActionEvent e)
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705 changeColour(new NucleotideColourScheme());
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709 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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711 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
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716 void changeColour(ColourSchemeI cs)
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719 if(viewport.getColourAppliesToAllGroups())
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721 Vector groups = viewport.alignment.getGroups();
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722 for(int i=0; i<groups.size(); i++)
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724 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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727 if(abovePIDThreshold.isSelected())
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728 abovePIDThreshold_actionPerformed(null);
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729 else if( viewport.getConservationSelected() )
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731 Conservation c = new Conservation("Group",
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732 ResidueProperties.propHash, 3,
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733 sg.sequences, sg.getStartRes(),
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736 c.verdict(false, 100);
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737 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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746 if ( viewport.getAbovePIDThreshold())
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749 threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
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750 Desktop.hideConservationSlider();
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752 if (cs instanceof ResidueColourScheme)
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753 ( (ResidueColourScheme) cs).setThreshold(threshold);
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754 else if (cs instanceof ScoreColourScheme)
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755 ( (ScoreColourScheme) cs).setThreshold(threshold);
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757 viewport.setGlobalColourScheme(cs);
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761 if (cs instanceof ResidueColourScheme)
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762 ( (ResidueColourScheme) cs).setThreshold(0);
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763 else if (cs instanceof ScoreColourScheme)
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764 ( (ScoreColourScheme) cs).setThreshold(0);
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769 if ( viewport.getConservationSelected() )
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771 ConservationColourScheme ccs = null;
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773 Alignment al = (Alignment) viewport.alignment;
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774 Conservation c = new Conservation("All",
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775 ResidueProperties.propHash, 3,
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776 al.getSequences(), 0,
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780 c.verdict(false, 100);
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782 ccs = new ConservationColourScheme(c, cs);
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784 int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,
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787 ccs.inc = threshold;
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789 viewport.setGlobalColourScheme(ccs);
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793 viewport.setGlobalColourScheme( cs );
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795 alignPanel.RefreshPanels();
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799 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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801 viewport.setConservationSelected(conservationMenuItem.isSelected());
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803 viewport.setAbovePIDThreshold(false);
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804 abovePIDThreshold.setSelected(false);
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805 Desktop.hidePIDSlider();
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806 if(!viewport.getConservationSelected())
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807 Desktop.hideConservationSlider();
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809 ColourSchemeI cs = viewport.getGlobalColourScheme();
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810 if(cs instanceof ConservationColourScheme )
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811 changeColour( ((ConservationColourScheme)cs).cs );
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813 changeColour( cs );
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817 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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819 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
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821 conservationMenuItem.setSelected(false);
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822 viewport.setConservationSelected(false);
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823 Desktop.hideConservationSlider();
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825 if(!viewport.getAbovePIDThreshold())
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826 Desktop.hidePIDSlider();
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829 ColourSchemeI cs = viewport.getGlobalColourScheme();
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830 if(cs instanceof ConservationColourScheme )
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831 changeColour( ((ConservationColourScheme)cs).cs );
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833 changeColour( cs );
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839 public void userDefinedColour_actionPerformed(ActionEvent e)
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841 JInternalFrame frame = new JInternalFrame();
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842 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
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843 frame.setContentPane(chooser);
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844 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
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845 frame.setResizable(false);
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846 frame.setIconifiable(false);
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847 frame.setMaximizable(false);
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850 public void PIDColour_actionPerformed(ActionEvent e)
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852 changeColour( new PIDColourScheme() );
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856 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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858 changeColour(new Blosum62ColourScheme(viewport) );
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863 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
865 addHistoryItem("sort");
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866 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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867 alignPanel.RefreshPanels();
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870 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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872 addHistoryItem("sort");
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873 AlignmentSorter.sortByID( viewport.getAlignment() );
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874 alignPanel.RefreshPanels();
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877 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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879 addHistoryItem("sort");
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880 AlignmentSorter.sortByGroup(viewport.getAlignment());
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881 AlignmentSorter.sortGroups(viewport.getAlignment());
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882 alignPanel.RefreshPanels();
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885 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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887 addHistoryItem("sort");
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888 if(viewport.getCurrentTree()==null)
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891 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
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892 alignPanel.RefreshPanels();
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895 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
897 RedundancyPanel sp = new RedundancyPanel(alignPanel);
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898 JInternalFrame frame = new JInternalFrame();
\r
899 frame.setContentPane(sp);
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900 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
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901 frame.setMaximizable(false);
\r
902 frame.setResizable(false);
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906 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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908 if(viewport.getSelectionGroup().getSize()<2)
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909 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
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912 JInternalFrame frame = new JInternalFrame();
\r
913 frame.setContentPane(new PairwiseAlignPanel(viewport));
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914 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
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918 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
921 if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
\r
922 || viewport.getAlignment().getHeight()<4)
\r
924 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
\r
925 +"at least 4 input sequences.",
\r
926 "Sequence selection insufficient",
\r
927 JOptionPane.WARNING_MESSAGE);
\r
932 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
933 JInternalFrame frame = new JInternalFrame();
\r
934 frame.setContentPane(pcaPanel);
\r
935 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
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936 }catch(java.lang.OutOfMemoryError ex)
\r
938 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
\r
939 "Out of memory", JOptionPane.WARNING_MESSAGE);
\r
945 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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947 NewTreePanel("AV", "PID", "Average distance tree using PID");
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950 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
952 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
956 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
958 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
961 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
963 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
966 void NewTreePanel(String type, String pwType, String title)
\r
968 //are the sequences aligned?
\r
969 if(!viewport.alignment.isAligned())
\r
971 JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
\r
972 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
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977 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)
\r
979 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,
\r
980 0, viewport.alignment.getWidth());
\r
984 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
985 type, pwType, 0, viewport.alignment.getWidth());
\r
988 Desktop.addInternalFrame(tp, title, 600, 500);
\r
994 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
996 JInternalFrame frame = new JInternalFrame();
\r
997 ClustalThread ct = new ClustalThread(frame);
\r
998 Thread t = new Thread(ct);
\r
1000 frame.setContentPane(ct);
\r
1001 Desktop.addInternalFrame(frame, title, 300, 80);
\r
1005 class ClustalThread extends JPanel implements Runnable
\r
1008 int imageIndex = 0;
\r
1009 boolean webServiceRunning = false;
\r
1010 JInternalFrame frame;
\r
1011 public ClustalThread(JInternalFrame frame)
\r
1013 this.frame = frame;
\r
1014 image = new Image[9];
\r
1015 for(int i=0; i<9; i++)
\r
1017 java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
\r
1020 image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
\r
1021 MediaTracker mt = new MediaTracker(this);
\r
1022 mt.addImage(image[i], i);
\r
1023 try{mt.waitForID(i);}
\r
1024 catch(Exception ex){}
\r
1027 DNATwirler twirler = new DNATwirler();
\r
1029 webServiceRunning = true;
\r
1032 class DNATwirler extends Thread
\r
1036 while(webServiceRunning)
\r
1039 Thread.sleep(100);
\r
1044 catch(Exception ex){}
\r
1050 // Should check to see if the server settings are valid
\r
1051 // Need visual-delay indication here.
\r
1054 jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
\r
1055 Vector sv = viewport.getAlignment().getSequences();
\r
1056 SequenceI[] seqs = new SequenceI[sv.size()];
\r
1061 seqs[i] = (SequenceI) sv.elementAt(i);
\r
1063 while (++i < sv.size());
\r
1065 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
\r
1067 if (alignment != null)
\r
1069 AlignFrame af = new AlignFrame(new Alignment(alignment));
\r
1070 af.clustalColour.setSelected(true);
\r
1071 af.clustalColour_actionPerformed(null);
\r
1072 Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
\r
1073 700, 500); // JBPNote - is there a new window geom. property ?
\r
1076 JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
\r
1077 JOptionPane.WARNING_MESSAGE);
\r
1079 webServiceRunning = false;
\r
1081 frame.setClosed(true);
\r
1082 }catch(Exception ex){}
\r
1085 public void paintComponent(Graphics g)
\r
1087 g.setColor(Color.white);
\r
1088 g.fillRect(0,0,getWidth(), getHeight());
\r
1091 g.drawImage(image[imageIndex],10,10,this);
\r
1093 g.setFont(new Font("Arial", Font.BOLD, 12));
\r
1094 g.setColor(Color.black);
\r
1095 g.drawString("Clustal Alignment Web Service running", 30,30);
\r
1098 public void jpredMenuItem_actionPerformed(ActionEvent e)
\r
1100 JInternalFrame frame = new JInternalFrame();
\r
1101 JPredClient ct = new JPredClient((SequenceI)
\r
1102 viewport.getAlignment().getSequences().elementAt(0));
\r
1106 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
\r
1107 // Pick the tree file
\r
1108 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
1109 getProperty("LAST_DIRECTORY"));
\r
1110 chooser.setFileView(new JalviewFileView());
\r
1111 chooser.setDialogTitle("Select a newick-like tree file");
\r
1112 chooser.setToolTipText("Load a tree file");
\r
1113 int value = chooser.showOpenDialog(null);
\r
1114 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
1116 String choice = chooser.getSelectedFile().getPath();
\r
1117 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1118 TreePanel treepanel = null;
\r
1121 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
\r
1124 if (fin.getTree() != null)
\r
1126 TreePanel tp = null;
\r
1127 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1128 fin, "FromFile", choice);
\r
1129 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1132 catch (Exception ex)
\r
1134 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1135 "Problem reading tree file",
\r
1137 JOptionPane.WARNING_MESSAGE);
\r
1138 ex.printStackTrace();
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