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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189 void updateEditMenuBar()
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191 if(historyList.size()>0)
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193 undoMenuItem.setEnabled(true);
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194 Object [] history = (Object[])historyList.get(0);
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195 undoMenuItem.setText("Undo "+history[0]);
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199 undoMenuItem.setEnabled(false);
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200 undoMenuItem.setText("Undo");
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203 if(redoList.size()>0)
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205 redoMenuItem.setEnabled(true);
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206 Object [] history = (Object[])redoList.get(0);
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207 redoMenuItem.setText("Redo "+history[0]);
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211 redoMenuItem.setEnabled(false);
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212 redoMenuItem.setText("Redo");
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216 public void addHistoryItem(String type)
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218 // must make sure we add new sequence objects her, not refs to the existing sequences
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220 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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221 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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223 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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224 viewport.getAlignment().getSequenceAt(i).getSequence());
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227 historyList.add(0, new Object[]{type, seq} );
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228 updateEditMenuBar();
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231 protected void undoMenuItem_actionPerformed(ActionEvent e)
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233 Object [] history = (Object[])historyList.remove(0);
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234 // add the redo state before continuing!!
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235 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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236 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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238 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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239 viewport.getAlignment().getSequenceAt(i).
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244 redoList.add(0, new Object[] {history[0], seq});
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246 seq = (SequenceI[]) history[1];
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247 viewport.setAlignment( new Alignment(seq) );
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248 updateEditMenuBar();
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249 alignPanel.RefreshPanels();
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252 public void moveSelectedSequences(boolean up)
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254 SequenceGroup sg = viewport.getSelectionGroup();
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260 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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262 SequenceI seq = viewport.alignment.getSequenceAt(i);
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263 if (!sg.sequences.contains(seq))
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266 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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267 if (sg.sequences.contains(temp))
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270 viewport.alignment.getSequences().setElementAt(temp, i);
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271 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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276 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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278 SequenceI seq = viewport.alignment.getSequenceAt(i);
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279 if (!sg.sequences.contains(seq))
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282 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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283 if (sg.sequences.contains(temp))
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286 viewport.alignment.getSequences().setElementAt(temp, i);
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287 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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291 alignPanel.RefreshPanels();
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296 protected void copy_actionPerformed(ActionEvent e)
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298 if(viewport.getSelectionGroup()==null)
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301 SequenceGroup sg = viewport.getSelectionGroup();
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303 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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304 StringBuffer buffer= new StringBuffer();
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306 for(int i=0; i<sg.getSize(); i++)
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308 SequenceI seq = sg.getSequenceAt(i);
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309 buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
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310 +seq.findPosition( sg.getEndRes() )+ "\t"
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311 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
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313 c.setContents( new StringSelection( buffer.toString()) , null ) ;
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318 protected void pasteNew_actionPerformed(ActionEvent e)
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323 protected void pasteThis_actionPerformed(ActionEvent e)
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325 addHistoryItem("Paste");
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329 void paste(boolean newAlignment)
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332 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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333 Transferable contents = c.getContents(this);
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334 if (contents == null)
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337 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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338 StringTokenizer st = new StringTokenizer(str);
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339 ArrayList seqs = new ArrayList();
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340 while (st.hasMoreElements())
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342 String name = st.nextToken();
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343 int start = Integer.parseInt(st.nextToken());
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344 int end = Integer.parseInt(st.nextToken());
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345 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
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348 viewport.alignment.addSequence(sequence);
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350 seqs.add(sequence);
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355 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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356 seqs.toArray(newSeqs);
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357 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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358 int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;
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359 if (newHeight > 500)
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361 Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
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365 viewport.setEndSeq(viewport.alignment.getHeight());
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366 viewport.alignment.getWidth();
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367 alignPanel.RefreshPanels();
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370 }catch(Exception ex){}// could be anything being pasted in here
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375 protected void cut_actionPerformed(ActionEvent e)
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377 copy_actionPerformed(null);
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378 delete_actionPerformed(null);
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381 protected void delete_actionPerformed(ActionEvent e)
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383 addHistoryItem("Delete");
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384 if (viewport.getSelectionGroup() == null)
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387 SequenceGroup sg = viewport.getSelectionGroup();
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388 for (int i=0;i < sg.sequences.size(); i++)
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390 SequenceI seq = sg.getSequenceAt(i);
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391 int index = viewport.getAlignment().findIndex(seq);
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392 seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
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394 if(seq.getSequence().length()<1)
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395 viewport.getAlignment().deleteSequence(seq);
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397 viewport.getAlignment().getSequences().setElementAt(seq, index);
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400 viewport.setSelectionGroup(null);
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401 viewport.alignment.deleteGroup(sg);
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402 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
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403 if(viewport.getAlignment().getHeight()<1)
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406 this.setClosed(true);
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407 }catch(Exception ex){}
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408 alignPanel.RefreshPanels();
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414 protected void redoMenuItem_actionPerformed(ActionEvent e)
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416 Object [] history = (Object[])redoList.remove(0);
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417 SequenceI[] seq = (SequenceI[]) history[1];
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418 viewport.setAlignment( new Alignment(seq) );
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419 updateEditMenuBar();
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420 alignPanel.RefreshPanels();
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424 public void groupsMenuItem_actionPerformed(ActionEvent e)
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426 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
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427 JInternalFrame frame = new JInternalFrame();
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428 frame.setContentPane(geditor);
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429 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
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430 frame.setResizable(false);
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433 protected void deleteGroups_actionPerformed(ActionEvent e)
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435 viewport.alignment.deleteAllGroups();
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436 viewport.setSelectionGroup(null);
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438 alignPanel.RefreshPanels();
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443 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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445 SequenceGroup sg = new SequenceGroup();
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446 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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447 sg.addSequence( viewport.getAlignment().getSequenceAt(i));
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448 sg.setEndRes(viewport.alignment.getWidth());
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449 viewport.setSelectionGroup(sg);
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450 PaintRefresher.Refresh(null);
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453 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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455 viewport.setSelectionGroup(null);
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456 PaintRefresher.Refresh(null);
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459 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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461 SequenceGroup sg = viewport.getSelectionGroup();
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462 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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463 sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
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465 PaintRefresher.Refresh(null);
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469 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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471 viewport.getColumnSelection().clear();
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475 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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477 addHistoryItem("delete columns");
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478 ColumnSelection colSel = viewport.getColumnSelection();
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479 if (colSel.size() > 0)
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481 int min = colSel.getMin();
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482 viewport.getAlignment().trimLeft(min);
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483 colSel.compensateForEdit(0,min);
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484 alignPanel.RefreshPanels();
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488 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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490 addHistoryItem("delete columns");
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491 ColumnSelection colSel = viewport.getColumnSelection();
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492 if (colSel.size() > 0)
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494 int max = colSel.getMax();
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496 viewport.getAlignment().trimRight(max);
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498 alignPanel.RefreshPanels();
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503 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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505 addHistoryItem("delete gapped columns");
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506 viewport.getAlignment().removeGaps();
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507 alignPanel.RefreshPanels();
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510 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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512 addHistoryItem("delete all gaps");
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515 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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517 current = viewport.getAlignment().getSequenceAt(i);
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518 jSize = current.getLength();
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519 for (int j=0; j < jSize; j++)
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520 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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522 current.deleteCharAt(j);
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528 alignPanel.RefreshPanels();
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531 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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533 char thisChar = '-';
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534 char nextChar = '.';
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535 if(viewport.getGapCharacter()=='-')
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540 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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541 viewport.setGapCharacter(thisChar);
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542 alignPanel.RefreshPanels();
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545 public void findMenuItem_actionPerformed(ActionEvent e)
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547 JInternalFrame frame = new JInternalFrame();
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548 Finder finder = new Finder(viewport, alignPanel, frame);
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549 frame.setContentPane(finder);
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550 Desktop.addInternalFrame(frame, "Find", 340,110);
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555 public void font_actionPerformed(ActionEvent e)
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557 // JOptionPane op = new JOptionPane();
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558 JInternalFrame frame = new JInternalFrame();
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559 FontChooser fc = new FontChooser( alignPanel, frame );
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560 frame.setContentPane(fc);
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561 Desktop.addInternalFrame(frame, "Change Font", 480,100);
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564 protected void fullSeqId_actionPerformed(ActionEvent e)
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566 viewport.setShowFullId( fullSeqId.isSelected() );
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568 alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
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569 alignPanel.RefreshPanels();
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572 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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574 viewport.setColourText( colourTextMenuItem.isSelected() );
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575 alignPanel.RefreshPanels();
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578 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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580 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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581 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
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585 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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587 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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588 alignPanel.RefreshPanels();
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591 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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593 viewport.setShowText( viewTextMenuItem.isSelected() );
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594 alignPanel.RefreshPanels();
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598 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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600 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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601 alignPanel.RefreshPanels();
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604 public void sequenceFeatures_actionPerformed(ActionEvent evt)
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606 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
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607 if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
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609 AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
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610 ((Alignment)viewport.alignment).featuresAdded = true;
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612 alignPanel.RefreshPanels();
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615 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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617 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
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620 public void overviewMenuItem_actionPerformed(ActionEvent e)
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622 if (alignPanel.overviewPanel != null)
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625 JInternalFrame frame = new JInternalFrame();
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626 OverviewPanel overview = alignPanel.getOverviewPanel();
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628 overview = new OverviewPanel(alignPanel, viewport);
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629 frame.setContentPane(overview);
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630 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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631 frame.getWidth(), frame.getHeight());
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633 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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634 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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636 alignPanel.setOverviewPanel(null);
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639 alignPanel.setOverviewPanel( overview );
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641 }catch(java.lang.OutOfMemoryError ex)
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643 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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644 +"\nTry reducing the font size.",
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645 "Out of memory", JOptionPane.WARNING_MESSAGE);
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651 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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653 changeColour( null );
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657 public void clustalColour_actionPerformed(ActionEvent e)
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659 abovePIDThreshold.setSelected(false);
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660 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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663 public void zappoColour_actionPerformed(ActionEvent e)
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665 changeColour(new ZappoColourScheme());
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668 public void taylorColour_actionPerformed(ActionEvent e)
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670 changeColour(new TaylorColourScheme());
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674 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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676 changeColour( new HydrophobicColourScheme() );
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679 public void helixColour_actionPerformed(ActionEvent e)
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681 changeColour(new HelixColourScheme() );
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685 public void strandColour_actionPerformed(ActionEvent e)
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687 changeColour(new StrandColourScheme());
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691 public void turnColour_actionPerformed(ActionEvent e)
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693 changeColour(new TurnColourScheme());
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697 public void buriedColour_actionPerformed(ActionEvent e)
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699 changeColour(new BuriedColourScheme() );
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702 public void nucleotideColour_actionPerformed(ActionEvent e)
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704 changeColour(new NucleotideColourScheme());
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708 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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710 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
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715 void changeColour(ColourSchemeI cs)
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718 if(viewport.getColourAppliesToAllGroups())
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720 Vector groups = viewport.alignment.getGroups();
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721 for(int i=0; i<groups.size(); i++)
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723 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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726 if(abovePIDThreshold.isSelected())
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727 abovePIDThreshold_actionPerformed(null);
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728 else if( viewport.getConservationSelected() )
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730 Conservation c = new Conservation("Group",
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731 ResidueProperties.propHash, 3,
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732 sg.sequences, sg.getStartRes(),
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735 c.verdict(false, 100);
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736 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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745 if ( viewport.getAbovePIDThreshold())
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748 threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
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749 Desktop.hideConservationSlider();
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751 if (cs instanceof ResidueColourScheme)
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752 ( (ResidueColourScheme) cs).setThreshold(threshold);
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753 else if (cs instanceof ScoreColourScheme)
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754 ( (ScoreColourScheme) cs).setThreshold(threshold);
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756 viewport.setGlobalColourScheme(cs);
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760 if (cs instanceof ResidueColourScheme)
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761 ( (ResidueColourScheme) cs).setThreshold(0);
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762 else if (cs instanceof ScoreColourScheme)
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763 ( (ScoreColourScheme) cs).setThreshold(0);
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768 if ( viewport.getConservationSelected() )
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770 ConservationColourScheme ccs = null;
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772 Alignment al = (Alignment) viewport.alignment;
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773 Conservation c = new Conservation("All",
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774 ResidueProperties.propHash, 3,
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775 al.getSequences(), 0,
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779 c.verdict(false, 100);
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781 ccs = new ConservationColourScheme(c, cs);
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783 int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,
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786 ccs.inc = threshold;
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788 viewport.setGlobalColourScheme(ccs);
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792 viewport.setGlobalColourScheme( cs );
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794 alignPanel.RefreshPanels();
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798 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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800 viewport.setConservationSelected(conservationMenuItem.isSelected());
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802 viewport.setAbovePIDThreshold(false);
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803 abovePIDThreshold.setSelected(false);
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804 Desktop.hidePIDSlider();
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805 if(!viewport.getConservationSelected())
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806 Desktop.hideConservationSlider();
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808 ColourSchemeI cs = viewport.getGlobalColourScheme();
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809 if(cs instanceof ConservationColourScheme )
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810 changeColour( ((ConservationColourScheme)cs).cs );
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812 changeColour( cs );
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816 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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818 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
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820 conservationMenuItem.setSelected(false);
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821 viewport.setConservationSelected(false);
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822 Desktop.hideConservationSlider();
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824 if(!viewport.getAbovePIDThreshold())
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825 Desktop.hidePIDSlider();
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828 ColourSchemeI cs = viewport.getGlobalColourScheme();
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829 if(cs instanceof ConservationColourScheme )
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830 changeColour( ((ConservationColourScheme)cs).cs );
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832 changeColour( cs );
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838 public void userDefinedColour_actionPerformed(ActionEvent e)
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840 JInternalFrame frame = new JInternalFrame();
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841 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
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842 frame.setContentPane(chooser);
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843 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
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844 frame.setResizable(false);
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845 frame.setIconifiable(false);
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846 frame.setMaximizable(false);
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849 public void PIDColour_actionPerformed(ActionEvent e)
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851 changeColour( new PIDColourScheme() );
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855 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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857 changeColour(new Blosum62ColourScheme(viewport) );
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862 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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864 addHistoryItem("sort");
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865 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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866 alignPanel.RefreshPanels();
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869 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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871 addHistoryItem("sort");
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872 AlignmentSorter.sortByID( viewport.getAlignment() );
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873 alignPanel.RefreshPanels();
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876 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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878 addHistoryItem("sort");
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879 AlignmentSorter.sortByGroup(viewport.getAlignment());
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880 AlignmentSorter.sortGroups(viewport.getAlignment());
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881 alignPanel.RefreshPanels();
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884 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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886 addHistoryItem("sort");
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887 if(viewport.getCurrentTree()==null)
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890 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
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891 alignPanel.RefreshPanels();
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894 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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896 RedundancyPanel sp = new RedundancyPanel(alignPanel);
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897 JInternalFrame frame = new JInternalFrame();
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898 frame.setContentPane(sp);
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899 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
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900 frame.setMaximizable(false);
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901 frame.setResizable(false);
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905 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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907 if(viewport.getSelectionGroup().getSize()<2)
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908 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
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911 JInternalFrame frame = new JInternalFrame();
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912 frame.setContentPane(new PairwiseAlignPanel(viewport));
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913 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
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917 public void PCAMenuItem_actionPerformed(ActionEvent e)
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920 if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
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921 || viewport.getAlignment().getHeight()<4)
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923 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
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924 +"at least 4 input sequences.",
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925 "Sequence selection insufficient",
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926 JOptionPane.WARNING_MESSAGE);
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931 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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932 JInternalFrame frame = new JInternalFrame();
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933 frame.setContentPane(pcaPanel);
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934 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
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935 }catch(java.lang.OutOfMemoryError ex)
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937 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
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938 "Out of memory", JOptionPane.WARNING_MESSAGE);
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944 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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946 NewTreePanel("AV", "PID", "Average distance tree using PID");
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949 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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951 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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955 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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957 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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960 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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962 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
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965 void NewTreePanel(String type, String pwType, String title)
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967 //are the sequences aligned?
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968 if(!viewport.alignment.isAligned())
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970 JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
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971 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
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976 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)
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978 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,
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979 0, viewport.alignment.getWidth());
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983 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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984 type, pwType, 0, viewport.alignment.getWidth());
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987 Desktop.addInternalFrame(tp, title, 600, 500);
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993 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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995 JInternalFrame frame = new JInternalFrame();
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996 ClustalThread ct = new ClustalThread(frame);
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997 Thread t = new Thread(ct);
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999 frame.setContentPane(ct);
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1000 Desktop.addInternalFrame(frame, title, 300, 80);
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1004 class ClustalThread extends JPanel implements Runnable
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1007 int imageIndex = 0;
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1008 boolean webServiceRunning = false;
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1009 JInternalFrame frame;
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1010 public ClustalThread(JInternalFrame frame)
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1012 this.frame = frame;
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1013 image = new Image[9];
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1014 for(int i=0; i<9; i++)
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1016 java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
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1019 image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
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1020 MediaTracker mt = new MediaTracker(this);
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1021 mt.addImage(image[i], i);
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1022 try{mt.waitForID(i);}
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1023 catch(Exception ex){}
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1026 DNATwirler twirler = new DNATwirler();
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1028 webServiceRunning = true;
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1031 class DNATwirler extends Thread
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1035 while(webServiceRunning)
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1038 Thread.sleep(100);
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1043 catch(Exception ex){}
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1049 // Should check to see if the server settings are valid
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1050 // Need visual-delay indication here.
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1053 jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
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1054 Vector sv = viewport.getAlignment().getSequences();
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1055 SequenceI[] seqs = new SequenceI[sv.size()];
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1060 seqs[i] = (SequenceI) sv.elementAt(i);
\r
1062 while (++i < sv.size());
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1064 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
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1066 if (alignment != null)
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1068 AlignFrame af = new AlignFrame(new Alignment(alignment));
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1069 af.clustalColour.setSelected(true);
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1070 af.clustalColour_actionPerformed(null);
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1071 Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
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1072 700, 500); // JBPNote - is there a new window geom. property ?
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1075 JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
\r
1076 JOptionPane.WARNING_MESSAGE);
\r
1078 webServiceRunning = false;
\r
1080 frame.setClosed(true);
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1081 }catch(Exception ex){}
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1084 public void paintComponent(Graphics g)
\r
1086 g.setColor(Color.white);
\r
1087 g.fillRect(0,0,getWidth(), getHeight());
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1090 g.drawImage(image[imageIndex],10,10,this);
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1092 g.setFont(new Font("Arial", Font.BOLD, 12));
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1093 g.setColor(Color.black);
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1094 g.drawString("Clustal Alignment Web Service running", 30,30);
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