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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35 viewport = new AlignViewport(al,true,true,false);
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37 String fontName = jalview.bin.Cache.getProperty("FONT_NAME");
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38 String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");
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39 String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");
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40 if(fontName!=null && fontStyle!=null && fontSize!=null)
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41 viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );
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44 alignPanel = new AlignmentPanel(this, viewport);
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45 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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47 // add conservation graph to alignment
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48 viewport.updateConservation();
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49 viewport.updateConsensus();
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51 alignPanel.annotationPanel.adjustPanelHeight();
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52 alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
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53 alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
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56 addInternalFrameListener(new InternalFrameAdapter()
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58 public void internalFrameActivated(InternalFrameEvent evt)
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60 javax.swing.SwingUtilities.invokeLater(new Runnable()
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63 { alignPanel.requestFocus(); }
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71 protected void saveAs_actionPerformed(ActionEvent e)
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73 String suffix [] = null;
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74 if(e.getActionCommand().equals("FASTA"))
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75 suffix = new String[]{"fa", "fasta"};
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76 else if(e.getActionCommand().equals("MSF"))
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77 suffix = new String[]{"msf"};
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78 else if(e.getActionCommand().equals("CLUSTAL"))
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79 suffix = new String[]{"aln"};
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80 else if(e.getActionCommand().equals("BLC"))
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81 suffix = new String[]{"blc"};
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82 else if(e.getActionCommand().equals("PIR"))
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83 suffix = new String[]{"pir"};
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84 else if(e.getActionCommand().equals("PFAM"))
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85 suffix = new String[]{"pfam"};
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87 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
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88 , suffix, e.getActionCommand()+" file");
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89 chooser.setFileView(new JalviewFileView());
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90 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
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91 chooser.setToolTipText("Save");
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92 int value = chooser.showSaveDialog(this);
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93 if(value == JalviewFileChooser.APPROVE_OPTION)
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95 String choice = chooser.getSelectedFile().getPath();
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96 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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97 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
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99 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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100 out.println(output);
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103 catch(Exception ex){}
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108 protected void outputText_actionPerformed(ActionEvent e)
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110 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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111 JInternalFrame frame = new JInternalFrame();
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112 cap.formatForOutput();
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113 frame.setContentPane(cap);
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114 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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115 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
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118 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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120 HTMLOutput htmlOutput = new HTMLOutput(viewport);
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124 protected void createPNG_actionPerformed(ActionEvent e)
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126 alignPanel.makePNG();
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129 protected void epsFile_actionPerformed(ActionEvent e)
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131 alignPanel.makeEPS();
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135 public void printMenuItem_actionPerformed(ActionEvent e)
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137 //Putting in a thread avoids Swing painting problems
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138 PrintThread thread = new PrintThread();
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142 class PrintThread extends Thread
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146 PrinterJob printJob = PrinterJob.getPrinterJob();
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147 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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148 printJob.setPrintable(alignPanel, pf);
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149 if (printJob.printDialog())
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155 catch (Exception PrintException)
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157 PrintException.printStackTrace();
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167 public void closeMenuItem_actionPerformed(ActionEvent e)
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170 this.setClosed(true);
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171 }catch(Exception ex){}
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174 Stack historyList = new Stack();
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175 Stack redoList = new Stack();
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176 JMenuBar jMenuBar1 = new JMenuBar();
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178 void updateEditMenuBar()
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180 if(historyList.size()>0)
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182 undoMenuItem.setEnabled(true);
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183 Object [] history = (Object[])historyList.get(0);
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184 undoMenuItem.setText("Undo "+history[0]);
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188 undoMenuItem.setEnabled(false);
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189 undoMenuItem.setText("Undo");
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192 if(redoList.size()>0)
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194 redoMenuItem.setEnabled(true);
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195 Object [] history = (Object[])redoList.get(0);
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196 redoMenuItem.setText("Redo "+history[0]);
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200 redoMenuItem.setEnabled(false);
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201 redoMenuItem.setText("Redo");
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205 public void addHistoryItem(String type)
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207 // must make sure we add new sequence objects her, not refs to the existing sequences
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209 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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210 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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212 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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213 viewport.getAlignment().getSequenceAt(i).getSequence());
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216 historyList.add(0, new Object[]{type, seq} );
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217 updateEditMenuBar();
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220 protected void undoMenuItem_actionPerformed(ActionEvent e)
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222 Object [] history = (Object[])historyList.remove(0);
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223 // add the redo state before continuing!!
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224 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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225 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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227 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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228 viewport.getAlignment().getSequenceAt(i).
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233 redoList.add(0, new Object[] {history[0], seq});
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235 seq = (SequenceI[]) history[1];
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236 viewport.setAlignment( new Alignment(seq) );
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237 updateEditMenuBar();
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238 viewport.updateConsensus();
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239 alignPanel.RefreshPanels();
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240 alignPanel.RefreshPanels();
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243 public void moveSelectedSequences(boolean up)
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245 SequenceGroup sg = viewport.getSelectionGroup();
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251 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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253 SequenceI seq = viewport.alignment.getSequenceAt(i);
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254 if (!sg.sequences.contains(seq))
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257 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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258 if (sg.sequences.contains(temp))
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261 viewport.alignment.getSequences().setElementAt(temp, i);
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262 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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267 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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269 SequenceI seq = viewport.alignment.getSequenceAt(i);
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270 if (!sg.sequences.contains(seq))
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273 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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274 if (sg.sequences.contains(temp))
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277 viewport.alignment.getSequences().setElementAt(temp, i);
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278 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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282 alignPanel.RefreshPanels();
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287 protected void copy_actionPerformed(ActionEvent e)
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289 if(viewport.getSelectionGroup()==null)
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292 SequenceGroup sg = viewport.getSelectionGroup();
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294 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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295 StringBuffer buffer= new StringBuffer();
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297 for(int i=0; i<sg.getSize(); i++)
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299 SequenceI seq = sg.getSequenceAt(i);
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300 buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
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301 +seq.findPosition( sg.getEndRes() )+ "\t"
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302 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
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304 c.setContents( new StringSelection( buffer.toString()) , null ) ;
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309 protected void pasteNew_actionPerformed(ActionEvent e)
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314 protected void pasteThis_actionPerformed(ActionEvent e)
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316 addHistoryItem("Paste");
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320 void paste(boolean newAlignment)
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323 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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324 Transferable contents = c.getContents(this);
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325 if (contents == null)
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328 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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329 StringTokenizer st = new StringTokenizer(str);
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330 ArrayList seqs = new ArrayList();
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331 while (st.hasMoreElements())
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333 String name = st.nextToken();
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334 int start = Integer.parseInt(st.nextToken());
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335 int end = Integer.parseInt(st.nextToken());
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336 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
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339 viewport.alignment.addSequence(sequence);
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341 seqs.add(sequence);
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346 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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347 seqs.toArray(newSeqs);
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348 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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349 int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;
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350 if (newHeight > 500)
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352 Desktop.addInternalFrame(af, "Copied sequences", 700, 500);
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356 viewport.setEndSeq(viewport.alignment.getHeight());
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357 viewport.alignment.getWidth();
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358 viewport.updateConservation();
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359 viewport.updateConsensus();
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360 alignPanel.RefreshPanels();
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363 }catch(Exception ex){}// could be anything being pasted in here
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368 protected void cut_actionPerformed(ActionEvent e)
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370 copy_actionPerformed(null);
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371 delete_actionPerformed(null);
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374 protected void delete_actionPerformed(ActionEvent e)
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376 addHistoryItem("Delete");
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377 if (viewport.getSelectionGroup() == null)
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380 SequenceGroup sg = viewport.getSelectionGroup();
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381 for (int i=0;i < sg.sequences.size(); i++)
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383 SequenceI seq = sg.getSequenceAt(i);
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384 int index = viewport.getAlignment().findIndex(seq);
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385 seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
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387 if(seq.getSequence().length()<1)
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388 viewport.getAlignment().deleteSequence(seq);
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390 viewport.getAlignment().getSequences().setElementAt(seq, index);
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393 viewport.setSelectionGroup(null);
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394 viewport.alignment.deleteGroup(sg);
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395 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
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396 if(viewport.getAlignment().getHeight()<1)
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399 this.setClosed(true);
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400 }catch(Exception ex){}
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401 viewport.updateConservation();
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402 viewport.updateConsensus();
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403 alignPanel.RefreshPanels();
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409 protected void redoMenuItem_actionPerformed(ActionEvent e)
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411 Object [] history = (Object[])redoList.remove(0);
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412 SequenceI[] seq = (SequenceI[]) history[1];
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413 viewport.setAlignment( new Alignment(seq) );
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414 updateEditMenuBar();
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415 viewport.updateConsensus();
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416 alignPanel.RefreshPanels();
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417 alignPanel.RefreshPanels();
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421 public void groupsMenuItem_actionPerformed(ActionEvent e)
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423 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
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424 JInternalFrame frame = new JInternalFrame();
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425 frame.setContentPane(geditor);
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426 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
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427 frame.setResizable(false);
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430 protected void deleteGroups_actionPerformed(ActionEvent e)
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432 viewport.alignment.deleteAllGroups();
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433 viewport.setSelectionGroup(null);
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435 alignPanel.RefreshPanels();
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440 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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442 SequenceGroup sg = new SequenceGroup();
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443 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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444 sg.addSequence( viewport.getAlignment().getSequenceAt(i));
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445 sg.setEndRes(viewport.alignment.getWidth());
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446 viewport.setSelectionGroup(sg);
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447 PaintRefresher.Refresh(null);
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450 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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452 viewport.setSelectionGroup(null);
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453 PaintRefresher.Refresh(null);
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456 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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458 SequenceGroup sg = viewport.getSelectionGroup();
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459 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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460 sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
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462 PaintRefresher.Refresh(null);
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466 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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468 viewport.getColumnSelection().clear();
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472 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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474 addHistoryItem("delete columns");
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475 ColumnSelection colSel = viewport.getColumnSelection();
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476 if (colSel.size() > 0)
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478 int min = colSel.getMin();
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479 viewport.getAlignment().trimLeft(min);
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480 colSel.compensateForEdit(0,min);
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482 if(viewport.getSelectionGroup()!=null)
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483 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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485 Vector groups = viewport.alignment.getGroups();
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486 for(int i=0; i<groups.size(); i++)
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488 SequenceGroup sg = (SequenceGroup) groups.get(i);
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489 if(!sg.adjustForRemoveLeft(min))
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490 viewport.alignment.deleteGroup(sg);
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493 alignPanel.RefreshPanels();
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497 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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499 addHistoryItem("delete columns");
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500 ColumnSelection colSel = viewport.getColumnSelection();
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501 if (colSel.size() > 0)
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503 int max = colSel.getMax();
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504 viewport.getAlignment().trimRight(max);
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505 if(viewport.getSelectionGroup()!=null)
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506 viewport.getSelectionGroup().adjustForRemoveRight(max);
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508 Vector groups = viewport.alignment.getGroups();
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509 for(int i=0; i<groups.size(); i++)
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511 SequenceGroup sg = (SequenceGroup) groups.get(i);
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512 if(!sg.adjustForRemoveRight(max))
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513 viewport.alignment.deleteGroup(sg);
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518 alignPanel.RefreshPanels();
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523 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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525 addHistoryItem("delete gapped columns");
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526 viewport.getAlignment().removeGaps();
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527 viewport.updateConservation();
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528 viewport.updateConsensus();
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529 alignPanel.RefreshPanels();
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532 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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534 addHistoryItem("delete all gaps");
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537 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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539 current = viewport.getAlignment().getSequenceAt(i);
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540 jSize = current.getLength();
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541 for (int j=0; j < jSize; j++)
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542 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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544 current.deleteCharAt(j);
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549 viewport.updateConservation();
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550 viewport.updateConsensus();
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551 alignPanel.RefreshPanels();
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554 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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556 char thisChar = '-';
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557 char nextChar = '.';
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558 if(viewport.getGapCharacter()=='-')
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563 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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564 viewport.setGapCharacter(thisChar);
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565 alignPanel.RefreshPanels();
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568 public void findMenuItem_actionPerformed(ActionEvent e)
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570 JInternalFrame frame = new JInternalFrame();
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571 Finder finder = new Finder(viewport, alignPanel, frame);
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572 frame.setContentPane(finder);
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573 Desktop.addInternalFrame(frame, "Find", 340,110);
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578 public void font_actionPerformed(ActionEvent e)
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580 // JOptionPane op = new JOptionPane();
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581 JInternalFrame frame = new JInternalFrame();
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582 FontChooser fc = new FontChooser( alignPanel, frame );
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583 frame.setContentPane(fc);
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584 Desktop.addInternalFrame(frame, "Change Font", 480,100);
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587 protected void fullSeqId_actionPerformed(ActionEvent e)
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589 viewport.setShowFullId( fullSeqId.isSelected() );
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591 alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
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592 alignPanel.RefreshPanels();
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595 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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597 viewport.setColourText( colourTextMenuItem.isSelected() );
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598 alignPanel.RefreshPanels();
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601 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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603 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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604 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
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608 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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610 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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611 alignPanel.RefreshPanels();
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614 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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616 viewport.setShowText( viewTextMenuItem.isSelected() );
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617 alignPanel.RefreshPanels();
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621 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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623 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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624 alignPanel.RefreshPanels();
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627 public void sequenceFeatures_actionPerformed(ActionEvent evt)
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629 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
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630 if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
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632 AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
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633 ((Alignment)viewport.alignment).featuresAdded = true;
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635 alignPanel.RefreshPanels();
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638 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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640 alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
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643 public void overviewMenuItem_actionPerformed(ActionEvent e)
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645 if (alignPanel.overviewPanel != null)
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648 JInternalFrame frame = new JInternalFrame();
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649 OverviewPanel overview = alignPanel.getOverviewPanel();
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651 overview = new OverviewPanel(alignPanel, viewport);
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652 frame.setContentPane(overview);
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653 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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654 frame.getWidth(), frame.getHeight());
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656 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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657 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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659 alignPanel.setOverviewPanel(null);
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662 alignPanel.setOverviewPanel( overview );
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664 }catch(java.lang.OutOfMemoryError ex)
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666 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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667 +"\nTry reducing the font size.",
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668 "Out of memory", JOptionPane.WARNING_MESSAGE);
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674 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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676 changeColour( null );
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680 public void clustalColour_actionPerformed(ActionEvent e)
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682 abovePIDThreshold.setSelected(false);
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683 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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686 public void zappoColour_actionPerformed(ActionEvent e)
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688 changeColour(new ZappoColourScheme());
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691 public void taylorColour_actionPerformed(ActionEvent e)
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693 changeColour(new TaylorColourScheme());
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697 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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699 changeColour( new HydrophobicColourScheme() );
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702 public void helixColour_actionPerformed(ActionEvent e)
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704 changeColour(new HelixColourScheme() );
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708 public void strandColour_actionPerformed(ActionEvent e)
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710 changeColour(new StrandColourScheme());
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714 public void turnColour_actionPerformed(ActionEvent e)
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716 changeColour(new TurnColourScheme());
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720 public void buriedColour_actionPerformed(ActionEvent e)
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722 changeColour(new BuriedColourScheme() );
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725 public void nucleotideColour_actionPerformed(ActionEvent e)
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727 changeColour(new NucleotideColourScheme());
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731 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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733 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
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738 void changeColour(ColourSchemeI cs)
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741 if(viewport.getColourAppliesToAllGroups())
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743 Vector groups = viewport.alignment.getGroups();
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744 for(int i=0; i<groups.size(); i++)
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746 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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749 if(abovePIDThreshold.isSelected())
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750 abovePIDThreshold_actionPerformed(null);
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751 else if( viewport.getConservationSelected() )
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753 Conservation c = new Conservation("Group",
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754 ResidueProperties.propHash, 3,
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755 sg.sequences, sg.getStartRes(),
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758 c.verdict(false, 100);
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759 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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768 if ( viewport.getAbovePIDThreshold())
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771 threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
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772 Desktop.hideConservationSlider();
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774 if (cs instanceof ResidueColourScheme)
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775 ( (ResidueColourScheme) cs).setThreshold(threshold);
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776 else if (cs instanceof ScoreColourScheme)
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777 ( (ScoreColourScheme) cs).setThreshold(threshold);
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779 viewport.setGlobalColourScheme(cs);
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783 if (cs instanceof ResidueColourScheme)
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784 ( (ResidueColourScheme) cs).setThreshold(0);
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785 else if (cs instanceof ScoreColourScheme)
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786 ( (ScoreColourScheme) cs).setThreshold(0);
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791 if ( viewport.getConservationSelected() )
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793 ConservationColourScheme ccs = null;
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795 Alignment al = (Alignment) viewport.alignment;
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796 Conservation c = new Conservation("All",
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797 ResidueProperties.propHash, 3,
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798 al.getSequences(), 0,
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802 c.verdict(false, 100);
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804 ccs = new ConservationColourScheme(c, cs);
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806 int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,
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809 ccs.inc = threshold;
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811 viewport.setGlobalColourScheme(ccs);
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815 viewport.setGlobalColourScheme( cs );
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817 alignPanel.RefreshPanels();
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821 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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823 viewport.setConservationSelected(conservationMenuItem.isSelected());
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824 if(coloursChanging)
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827 coloursChanging = true;
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829 viewport.setAbovePIDThreshold(false);
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830 abovePIDThreshold.setSelected(false);
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831 Desktop.hidePIDSlider();
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832 if(!viewport.getConservationSelected())
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833 Desktop.hideConservationSlider();
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835 ColourSchemeI cs = viewport.getGlobalColourScheme();
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836 if(cs instanceof ConservationColourScheme )
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837 changeColour( ((ConservationColourScheme)cs).cs );
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839 changeColour( cs );
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841 coloursChanging = false;
\r
844 boolean coloursChanging = false;
\r
845 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
847 if(coloursChanging)
\r
850 coloursChanging = true;
\r
851 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
853 conservationMenuItem.setSelected(false);
\r
854 viewport.setConservationSelected(false);
\r
855 Desktop.hideConservationSlider();
\r
857 if(!viewport.getAbovePIDThreshold())
\r
858 Desktop.hidePIDSlider();
\r
861 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
862 if(cs instanceof ConservationColourScheme )
\r
863 changeColour( ((ConservationColourScheme)cs).cs );
\r
865 changeColour( cs );
\r
867 coloursChanging = false;
\r
872 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
874 JInternalFrame frame = new JInternalFrame();
\r
875 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
\r
876 frame.setContentPane(chooser);
\r
877 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
\r
878 frame.setResizable(false);
\r
879 frame.setIconifiable(false);
\r
880 frame.setMaximizable(false);
\r
883 public void PIDColour_actionPerformed(ActionEvent e)
\r
885 changeColour( new PIDColourScheme() );
\r
889 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
891 changeColour(new Blosum62ColourScheme(viewport) );
\r
896 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
898 addHistoryItem("sort");
\r
899 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
\r
900 alignPanel.RefreshPanels();
\r
903 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
905 addHistoryItem("sort");
\r
906 AlignmentSorter.sortByID( viewport.getAlignment() );
\r
907 alignPanel.RefreshPanels();
\r
910 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
912 addHistoryItem("sort");
\r
913 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
914 AlignmentSorter.sortGroups(viewport.getAlignment());
\r
915 alignPanel.RefreshPanels();
\r
918 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
\r
920 addHistoryItem("sort");
\r
921 if(viewport.getCurrentTree()==null)
\r
924 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
\r
925 alignPanel.RefreshPanels();
\r
928 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
930 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
931 JInternalFrame frame = new JInternalFrame();
\r
932 frame.setContentPane(sp);
\r
933 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
\r
934 frame.setMaximizable(false);
\r
935 frame.setResizable(false);
\r
939 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
941 if(viewport.getSelectionGroup().getSize()<2)
\r
942 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
\r
945 JInternalFrame frame = new JInternalFrame();
\r
946 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
947 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
951 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
954 if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
\r
955 || viewport.getAlignment().getHeight()<4)
\r
957 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
\r
958 +"at least 4 input sequences.",
\r
959 "Sequence selection insufficient",
\r
960 JOptionPane.WARNING_MESSAGE);
\r
965 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
966 JInternalFrame frame = new JInternalFrame();
\r
967 frame.setContentPane(pcaPanel);
\r
968 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
\r
969 }catch(java.lang.OutOfMemoryError ex)
\r
971 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
\r
972 "Out of memory", JOptionPane.WARNING_MESSAGE);
\r
978 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
980 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
983 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
985 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
989 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
991 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
994 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
996 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
999 void NewTreePanel(String type, String pwType, String title)
\r
1001 //are the sequences aligned?
\r
1002 if(!viewport.alignment.isAligned())
\r
1004 JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
\r
1005 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
\r
1009 TreePanel tp=null;
\r
1010 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)
\r
1012 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,
\r
1013 0, viewport.alignment.getWidth());
\r
1017 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1018 type, pwType, 0, viewport.alignment.getWidth());
\r
1021 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1027 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
1029 JInternalFrame frame = new JInternalFrame();
\r
1030 ClustalThread ct = new ClustalThread(frame);
\r
1031 Thread t = new Thread(ct);
\r
1033 frame.setContentPane(ct);
\r
1034 Desktop.addInternalFrame(frame, title, 300, 80);
\r
1038 class ClustalThread extends JPanel implements Runnable
\r
1041 int imageIndex = 0;
\r
1042 boolean webServiceRunning = false;
\r
1043 JInternalFrame frame;
\r
1044 public ClustalThread(JInternalFrame frame)
\r
1046 this.frame = frame;
\r
1047 image = new Image[9];
\r
1048 for(int i=0; i<9; i++)
\r
1050 java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
\r
1053 image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
\r
1054 MediaTracker mt = new MediaTracker(this);
\r
1055 mt.addImage(image[i], i);
\r
1056 try{mt.waitForID(i);}
\r
1057 catch(Exception ex){}
\r
1060 DNATwirler twirler = new DNATwirler();
\r
1062 webServiceRunning = true;
\r
1065 class DNATwirler extends Thread
\r
1069 while(webServiceRunning)
\r
1072 Thread.sleep(100);
\r
1077 catch(Exception ex){}
\r
1083 // Should check to see if the server settings are valid
\r
1084 // Need visual-delay indication here.
\r
1087 jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
\r
1088 Vector sv = viewport.getAlignment().getSequences();
\r
1089 SequenceI[] seqs = new SequenceI[sv.size()];
\r
1094 seqs[i] = (SequenceI) sv.elementAt(i);
\r
1096 while (++i < sv.size());
\r
1098 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
\r
1100 if (alignment != null)
\r
1102 AlignFrame af = new AlignFrame(new Alignment(alignment));
\r
1103 af.clustalColour.setSelected(true);
\r
1104 af.clustalColour_actionPerformed(null);
\r
1105 Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
\r
1106 700, 500); // JBPNote - is there a new window geom. property ?
\r
1109 JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
\r
1110 JOptionPane.WARNING_MESSAGE);
\r
1112 webServiceRunning = false;
\r
1114 frame.setClosed(true);
\r
1115 }catch(Exception ex){}
\r
1118 public void paintComponent(Graphics g)
\r
1120 g.setColor(Color.white);
\r
1121 g.fillRect(0,0,getWidth(), getHeight());
\r
1124 g.drawImage(image[imageIndex],10,10,this);
\r
1126 g.setFont(new Font("Arial", Font.BOLD, 12));
\r
1127 g.setColor(Color.black);
\r
1128 g.drawString("Clustal Alignment Web Service running", 30,30);
\r
1131 protected void jpred_actionPerformed(ActionEvent e)
\r
1134 JInternalFrame frame = new JInternalFrame();
\r
1135 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
\r
1137 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1138 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1139 if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
\r
1141 JPredClient ct = new JPredClient( (SequenceI)
\r
1142 seqs.getSequenceAt(0));
\r
1147 SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
\r
1148 for (int i = 0; i < sz; i++)
\r
1150 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1153 JPredClient ct = new JPredClient(msa);
\r
1159 Vector seqs = viewport.getAlignment().getSequences();
\r
1161 if (seqs.size() == 1 || !viewport.alignment.isAligned())
\r
1163 JPredClient ct = new JPredClient( (SequenceI)
\r
1164 seqs.elementAt(0));
\r
1168 SequenceI[] msa = new SequenceI[seqs.size()];
\r
1169 for (int i = 0; i < seqs.size(); i++)
\r
1171 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1174 JPredClient ct = new JPredClient(msa);
\r
1180 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
\r
1181 // Pick the tree file
\r
1182 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
1183 getProperty("LAST_DIRECTORY"));
\r
1184 chooser.setFileView(new JalviewFileView());
\r
1185 chooser.setDialogTitle("Select a newick-like tree file");
\r
1186 chooser.setToolTipText("Load a tree file");
\r
1187 int value = chooser.showOpenDialog(null);
\r
1188 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
1190 String choice = chooser.getSelectedFile().getPath();
\r
1191 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1192 TreePanel treepanel = null;
\r
1195 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
\r
1198 if (fin.getTree() != null)
\r
1200 TreePanel tp = null;
\r
1201 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1202 fin, "FromFile", choice);
\r
1203 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1206 catch (Exception ex)
\r
1208 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1209 "Problem reading tree file",
\r
1211 JOptionPane.WARNING_MESSAGE);
\r
1212 ex.printStackTrace();
\r