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 if(e.getActionCommand().equals("XML DUMP"))
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89 XMLStore store = new XMLStore();
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90 store.store(viewport);
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94 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
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95 , suffix, e.getActionCommand()+" file");
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96 chooser.setFileView(new JalviewFileView());
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97 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
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98 chooser.setToolTipText("Save");
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99 int value = chooser.showSaveDialog(this);
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100 if(value == JalviewFileChooser.APPROVE_OPTION)
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102 String choice = chooser.getSelectedFile().getPath();
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103 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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104 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
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106 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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107 out.println(output);
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110 catch(Exception ex){}
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115 protected void outputText_actionPerformed(ActionEvent e)
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117 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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118 JInternalFrame frame = new JInternalFrame();
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119 cap.formatForOutput();
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120 frame.setContentPane(cap);
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121 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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122 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
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125 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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127 HTMLOutput htmlOutput = new HTMLOutput(viewport);
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131 protected void createPNG_actionPerformed(ActionEvent e)
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133 alignPanel.makePNG();
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136 protected void epsFile_actionPerformed(ActionEvent e)
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138 alignPanel.makeEPS();
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142 public void printMenuItem_actionPerformed(ActionEvent e)
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144 //Putting in a thread avoids Swing painting problems
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145 PrintThread thread = new PrintThread();
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149 class PrintThread extends Thread
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153 PrinterJob printJob = PrinterJob.getPrinterJob();
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154 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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155 printJob.setPrintable(alignPanel, pf);
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156 if (printJob.printDialog())
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162 catch (Exception PrintException)
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164 PrintException.printStackTrace();
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174 public void closeMenuItem_actionPerformed(ActionEvent e)
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177 this.setClosed(true);
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178 }catch(Exception ex){}
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181 Stack historyList = new Stack();
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182 Stack redoList = new Stack();
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183 JMenuBar jMenuBar1 = new JMenuBar();
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185 void updateEditMenuBar()
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187 if(historyList.size()>0)
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189 undoMenuItem.setEnabled(true);
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190 Object [] history = (Object[])historyList.get(0);
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191 undoMenuItem.setText("Undo "+history[0]);
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195 undoMenuItem.setEnabled(false);
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196 undoMenuItem.setText("Undo");
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199 if(redoList.size()>0)
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201 redoMenuItem.setEnabled(true);
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202 Object [] history = (Object[])redoList.get(0);
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203 redoMenuItem.setText("Redo "+history[0]);
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207 redoMenuItem.setEnabled(false);
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208 redoMenuItem.setText("Redo");
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212 public void addHistoryItem(String type)
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214 // must make sure we add new sequence objects her, not refs to the existing sequences
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216 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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217 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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219 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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220 viewport.getAlignment().getSequenceAt(i).getSequence());
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223 historyList.add(0, new Object[]{type, seq} );
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224 updateEditMenuBar();
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227 protected void undoMenuItem_actionPerformed(ActionEvent e)
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229 Object [] history = (Object[])historyList.remove(0);
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230 // add the redo state before continuing!!
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231 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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232 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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234 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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235 viewport.getAlignment().getSequenceAt(i).
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240 redoList.add(0, new Object[] {history[0], seq});
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242 seq = (SequenceI[]) history[1];
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243 viewport.setAlignment( new Alignment(seq) );
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244 updateEditMenuBar();
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245 viewport.updateConsensus();
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246 alignPanel.RefreshPanels();
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247 alignPanel.RefreshPanels();
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250 public void moveSelectedSequences(boolean up)
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252 SequenceGroup sg = viewport.getSelectionGroup();
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258 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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260 SequenceI seq = viewport.alignment.getSequenceAt(i);
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261 if (!sg.sequences.contains(seq))
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264 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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265 if (sg.sequences.contains(temp))
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268 viewport.alignment.getSequences().setElementAt(temp, i);
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269 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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274 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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276 SequenceI seq = viewport.alignment.getSequenceAt(i);
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277 if (!sg.sequences.contains(seq))
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280 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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281 if (sg.sequences.contains(temp))
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284 viewport.alignment.getSequences().setElementAt(temp, i);
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285 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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289 alignPanel.RefreshPanels();
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294 protected void copy_actionPerformed(ActionEvent e)
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296 if(viewport.getSelectionGroup()==null)
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299 SequenceGroup sg = viewport.getSelectionGroup();
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301 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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302 StringBuffer buffer= new StringBuffer();
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304 for(int i=0; i<sg.getSize(); i++)
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306 SequenceI seq = sg.getSequenceAt(i);
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307 buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
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308 +seq.findPosition( sg.getEndRes() )+ "\t"
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309 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
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311 c.setContents( new StringSelection( buffer.toString()) , null ) ;
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316 protected void pasteNew_actionPerformed(ActionEvent e)
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321 protected void pasteThis_actionPerformed(ActionEvent e)
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323 addHistoryItem("Paste");
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327 void paste(boolean newAlignment)
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330 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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331 Transferable contents = c.getContents(this);
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332 if (contents == null)
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335 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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336 StringTokenizer st = new StringTokenizer(str);
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337 ArrayList seqs = new ArrayList();
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338 while (st.hasMoreElements())
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340 String name = st.nextToken();
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341 int start = Integer.parseInt(st.nextToken());
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342 int end = Integer.parseInt(st.nextToken());
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343 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
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346 viewport.alignment.addSequence(sequence);
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348 seqs.add(sequence);
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353 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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354 seqs.toArray(newSeqs);
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355 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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356 int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;
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357 if (newHeight > 500)
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359 Desktop.addInternalFrame(af, "Copied sequences", 700, 500);
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363 viewport.setEndSeq(viewport.alignment.getHeight());
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364 viewport.alignment.getWidth();
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365 viewport.updateConservation();
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366 viewport.updateConsensus();
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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 viewport.updateConservation();
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409 viewport.updateConsensus();
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410 alignPanel.RefreshPanels();
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416 protected void redoMenuItem_actionPerformed(ActionEvent e)
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418 Object [] history = (Object[])redoList.remove(0);
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419 SequenceI[] seq = (SequenceI[]) history[1];
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420 viewport.setAlignment( new Alignment(seq) );
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421 updateEditMenuBar();
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422 viewport.updateConsensus();
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423 alignPanel.RefreshPanels();
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424 alignPanel.RefreshPanels();
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428 public void groupsMenuItem_actionPerformed(ActionEvent e)
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430 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
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431 JInternalFrame frame = new JInternalFrame();
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432 frame.setContentPane(geditor);
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433 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
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434 frame.setResizable(false);
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437 protected void deleteGroups_actionPerformed(ActionEvent e)
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439 viewport.alignment.deleteAllGroups();
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440 viewport.setSelectionGroup(null);
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442 alignPanel.RefreshPanels();
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447 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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449 SequenceGroup sg = new SequenceGroup();
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450 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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451 sg.addSequence( viewport.getAlignment().getSequenceAt(i));
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452 sg.setEndRes(viewport.alignment.getWidth());
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453 viewport.setSelectionGroup(sg);
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454 PaintRefresher.Refresh(null);
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457 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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459 viewport.setSelectionGroup(null);
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460 PaintRefresher.Refresh(null);
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463 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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465 SequenceGroup sg = viewport.getSelectionGroup();
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466 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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467 sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
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469 PaintRefresher.Refresh(null);
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473 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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475 viewport.getColumnSelection().clear();
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479 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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481 addHistoryItem("delete columns");
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482 ColumnSelection colSel = viewport.getColumnSelection();
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483 if (colSel.size() > 0)
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485 int min = colSel.getMin();
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486 viewport.getAlignment().trimLeft(min);
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487 colSel.compensateForEdit(0,min);
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489 if(viewport.getSelectionGroup()!=null)
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490 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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492 Vector groups = viewport.alignment.getGroups();
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493 for(int i=0; i<groups.size(); i++)
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495 SequenceGroup sg = (SequenceGroup) groups.get(i);
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496 if(!sg.adjustForRemoveLeft(min))
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497 viewport.alignment.deleteGroup(sg);
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500 alignPanel.RefreshPanels();
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504 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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506 addHistoryItem("delete columns");
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507 ColumnSelection colSel = viewport.getColumnSelection();
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508 if (colSel.size() > 0)
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510 int max = colSel.getMax();
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511 viewport.getAlignment().trimRight(max);
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512 if(viewport.getSelectionGroup()!=null)
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513 viewport.getSelectionGroup().adjustForRemoveRight(max);
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515 Vector groups = viewport.alignment.getGroups();
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516 for(int i=0; i<groups.size(); i++)
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518 SequenceGroup sg = (SequenceGroup) groups.get(i);
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519 if(!sg.adjustForRemoveRight(max))
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520 viewport.alignment.deleteGroup(sg);
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525 alignPanel.RefreshPanels();
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530 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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532 addHistoryItem("delete gapped columns");
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533 viewport.getAlignment().removeGaps();
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534 viewport.updateConservation();
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535 viewport.updateConsensus();
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536 alignPanel.RefreshPanels();
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539 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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541 addHistoryItem("delete all gaps");
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544 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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546 current = viewport.getAlignment().getSequenceAt(i);
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547 jSize = current.getLength();
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548 for (int j=0; j < jSize; j++)
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549 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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551 current.deleteCharAt(j);
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556 viewport.updateConservation();
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557 viewport.updateConsensus();
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558 alignPanel.RefreshPanels();
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561 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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563 char thisChar = '-';
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564 char nextChar = '.';
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565 if(viewport.getGapCharacter()=='-')
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570 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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571 viewport.setGapCharacter(thisChar);
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572 alignPanel.RefreshPanels();
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575 public void findMenuItem_actionPerformed(ActionEvent e)
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577 JInternalFrame frame = new JInternalFrame();
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578 Finder finder = new Finder(viewport, alignPanel, frame);
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579 frame.setContentPane(finder);
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580 Desktop.addInternalFrame(frame, "Find", 340,110);
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585 public void font_actionPerformed(ActionEvent e)
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587 JInternalFrame frame = new JInternalFrame();
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588 FontChooser fc = new FontChooser( alignPanel, frame );
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589 frame.setContentPane(fc);
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590 Desktop.addInternalFrame(frame, "Change Font", 480,100);
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593 protected void fullSeqId_actionPerformed(ActionEvent e)
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595 viewport.setShowFullId( fullSeqId.isSelected() );
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597 alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
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598 alignPanel.RefreshPanels();
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601 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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603 viewport.setColourText( colourTextMenuItem.isSelected() );
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604 alignPanel.RefreshPanels();
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607 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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609 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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610 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
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614 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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616 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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617 alignPanel.RefreshPanels();
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620 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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622 viewport.setShowText( viewTextMenuItem.isSelected() );
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623 alignPanel.RefreshPanels();
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627 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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629 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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630 alignPanel.RefreshPanels();
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633 public void sequenceFeatures_actionPerformed(ActionEvent evt)
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635 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
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636 if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
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638 AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
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639 ((Alignment)viewport.alignment).featuresAdded = true;
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641 alignPanel.RefreshPanels();
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644 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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646 if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
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648 annotationPanelMenuItem.setSelected(false);
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651 viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
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652 alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
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655 public void overviewMenuItem_actionPerformed(ActionEvent e)
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657 if (alignPanel.overviewPanel != null)
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660 JInternalFrame frame = new JInternalFrame();
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661 OverviewPanel overview = alignPanel.getOverviewPanel();
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663 overview = new OverviewPanel(alignPanel, viewport);
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664 frame.setContentPane(overview);
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665 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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666 frame.getWidth(), frame.getHeight());
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668 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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669 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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671 alignPanel.setOverviewPanel(null);
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674 alignPanel.setOverviewPanel( overview );
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676 }catch(java.lang.OutOfMemoryError ex)
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678 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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679 +"\nTry reducing the font size.",
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680 "Out of memory", JOptionPane.WARNING_MESSAGE);
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686 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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688 changeColour( null );
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692 public void clustalColour_actionPerformed(ActionEvent e)
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694 abovePIDThreshold.setSelected(false);
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695 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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698 public void zappoColour_actionPerformed(ActionEvent e)
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700 changeColour(new ZappoColourScheme());
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703 public void taylorColour_actionPerformed(ActionEvent e)
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705 changeColour(new TaylorColourScheme());
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709 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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711 changeColour( new HydrophobicColourScheme() );
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714 public void helixColour_actionPerformed(ActionEvent e)
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716 changeColour(new HelixColourScheme() );
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720 public void strandColour_actionPerformed(ActionEvent e)
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722 changeColour(new StrandColourScheme());
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726 public void turnColour_actionPerformed(ActionEvent e)
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728 changeColour(new TurnColourScheme());
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732 public void buriedColour_actionPerformed(ActionEvent e)
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734 changeColour(new BuriedColourScheme() );
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737 public void nucleotideColour_actionPerformed(ActionEvent e)
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739 changeColour(new NucleotideColourScheme());
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743 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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745 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
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750 void changeColour(ColourSchemeI cs)
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753 if(viewport.getColourAppliesToAllGroups())
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755 Vector groups = viewport.alignment.getGroups();
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756 for(int i=0; i<groups.size(); i++)
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758 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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761 if(abovePIDThreshold.isSelected())
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762 abovePIDThreshold_actionPerformed(null);
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763 else if( viewport.getConservationSelected() )
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765 Conservation c = new Conservation("Group",
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766 ResidueProperties.propHash, 3,
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767 sg.sequences, sg.getStartRes(),
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770 c.verdict(false, 100);
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771 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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780 if ( viewport.getAbovePIDThreshold())
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783 threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
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784 Desktop.hideConservationSlider();
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786 if (cs instanceof ResidueColourScheme)
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787 ( (ResidueColourScheme) cs).setThreshold(threshold);
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788 else if (cs instanceof ScoreColourScheme)
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789 ( (ScoreColourScheme) cs).setThreshold(threshold);
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791 viewport.setGlobalColourScheme(cs);
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795 if (cs instanceof ResidueColourScheme)
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796 ( (ResidueColourScheme) cs).setThreshold(0);
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797 else if (cs instanceof ScoreColourScheme)
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798 ( (ScoreColourScheme) cs).setThreshold(0);
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803 if ( viewport.getConservationSelected() )
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805 ConservationColourScheme ccs = null;
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807 Alignment al = (Alignment) viewport.alignment;
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808 Conservation c = new Conservation("All",
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809 ResidueProperties.propHash, 3,
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810 al.getSequences(), 0,
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814 c.verdict(false, 100);
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816 ccs = new ConservationColourScheme(c, cs);
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818 int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,
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821 ccs.inc = threshold;
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823 viewport.setGlobalColourScheme(ccs);
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827 viewport.setGlobalColourScheme( cs );
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829 alignPanel.RefreshPanels();
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833 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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835 viewport.setConservationSelected(conservationMenuItem.isSelected());
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836 if(coloursChanging)
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839 coloursChanging = true;
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841 viewport.setAbovePIDThreshold(false);
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842 abovePIDThreshold.setSelected(false);
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843 Desktop.hidePIDSlider();
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844 if(!viewport.getConservationSelected())
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845 Desktop.hideConservationSlider();
\r
847 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
848 if(cs instanceof ConservationColourScheme )
\r
849 changeColour( ((ConservationColourScheme)cs).cs );
\r
851 changeColour( cs );
\r
853 coloursChanging = false;
\r
856 boolean coloursChanging = false;
\r
857 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
859 if(coloursChanging)
\r
862 coloursChanging = true;
\r
863 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
865 conservationMenuItem.setSelected(false);
\r
866 viewport.setConservationSelected(false);
\r
867 Desktop.hideConservationSlider();
\r
869 if(!viewport.getAbovePIDThreshold())
\r
870 Desktop.hidePIDSlider();
\r
873 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
874 if(cs instanceof ConservationColourScheme )
\r
875 changeColour( ((ConservationColourScheme)cs).cs );
\r
877 changeColour( cs );
\r
879 coloursChanging = false;
\r
884 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
886 JInternalFrame frame = new JInternalFrame();
\r
887 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
\r
888 frame.setContentPane(chooser);
\r
889 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
\r
890 frame.setResizable(false);
\r
891 frame.setIconifiable(false);
\r
892 frame.setMaximizable(false);
\r
895 public void PIDColour_actionPerformed(ActionEvent e)
\r
897 changeColour( new PIDColourScheme() );
\r
901 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
903 changeColour(new Blosum62ColourScheme(viewport) );
\r
908 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
910 addHistoryItem("sort");
\r
911 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
\r
912 alignPanel.RefreshPanels();
\r
915 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
917 addHistoryItem("sort");
\r
918 AlignmentSorter.sortByID( viewport.getAlignment() );
\r
919 alignPanel.RefreshPanels();
\r
922 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
924 addHistoryItem("sort");
\r
925 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
926 AlignmentSorter.sortGroups(viewport.getAlignment());
\r
927 alignPanel.RefreshPanels();
\r
930 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
\r
932 addHistoryItem("sort");
\r
933 if(viewport.getCurrentTree()==null)
\r
936 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
\r
937 alignPanel.RefreshPanels();
\r
940 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
942 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
943 JInternalFrame frame = new JInternalFrame();
\r
944 frame.setContentPane(sp);
\r
945 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
\r
946 frame.setMaximizable(false);
\r
947 frame.setResizable(false);
\r
951 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
953 if(viewport.getSelectionGroup().getSize()<2)
\r
954 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
\r
957 JInternalFrame frame = new JInternalFrame();
\r
958 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
959 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
963 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
966 if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
\r
967 || viewport.getAlignment().getHeight()<4)
\r
969 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
\r
970 +"at least 4 input sequences.",
\r
971 "Sequence selection insufficient",
\r
972 JOptionPane.WARNING_MESSAGE);
\r
977 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
978 JInternalFrame frame = new JInternalFrame();
\r
979 frame.setContentPane(pcaPanel);
\r
980 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
\r
981 }catch(java.lang.OutOfMemoryError ex)
\r
983 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
\r
984 "Out of memory", JOptionPane.WARNING_MESSAGE);
\r
990 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
992 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
995 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
997 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1001 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1003 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1006 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1008 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1011 void NewTreePanel(String type, String pwType, String title)
\r
1013 //are the sequences aligned?
\r
1014 if(!viewport.alignment.isAligned())
\r
1016 JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
\r
1017 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
\r
1021 TreePanel tp=null;
\r
1022 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)
\r
1024 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,
\r
1025 0, viewport.alignment.getWidth());
\r
1029 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1030 type, pwType, 0, viewport.alignment.getWidth());
\r
1033 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1039 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
1041 JInternalFrame frame = new JInternalFrame();
\r
1042 ClustalThread ct = new ClustalThread(frame);
\r
1043 Thread t = new Thread(ct);
\r
1045 frame.setContentPane(ct);
\r
1046 Desktop.addInternalFrame(frame, title, 300, 80);
\r
1050 class ClustalThread extends JPanel implements Runnable
\r
1053 int imageIndex = 0;
\r
1054 boolean webServiceRunning = false;
\r
1055 JInternalFrame frame;
\r
1056 public ClustalThread(JInternalFrame frame)
\r
1058 this.frame = frame;
\r
1059 image = new Image[9];
\r
1060 for(int i=0; i<9; i++)
\r
1062 java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
\r
1065 image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
\r
1066 MediaTracker mt = new MediaTracker(this);
\r
1067 mt.addImage(image[i], i);
\r
1068 try{mt.waitForID(i);}
\r
1069 catch(Exception ex){}
\r
1072 DNATwirler twirler = new DNATwirler();
\r
1074 webServiceRunning = true;
\r
1077 class DNATwirler extends Thread
\r
1081 while(webServiceRunning)
\r
1084 Thread.sleep(100);
\r
1089 catch(Exception ex){}
\r
1095 // Should check to see if the server settings are valid
\r
1096 // Need visual-delay indication here.
\r
1099 jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
\r
1100 Vector sv = viewport.getAlignment().getSequences();
\r
1101 SequenceI[] seqs = new SequenceI[sv.size()];
\r
1106 seqs[i] = (SequenceI) sv.elementAt(i);
\r
1108 while (++i < sv.size());
\r
1110 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
\r
1112 if (alignment != null)
\r
1114 AlignFrame af = new AlignFrame(new Alignment(alignment));
\r
1115 af.clustalColour.setSelected(true);
\r
1116 af.clustalColour_actionPerformed(null);
\r
1117 Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
\r
1118 700, 500); // JBPNote - is there a new window geom. property ?
\r
1121 JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
\r
1122 JOptionPane.WARNING_MESSAGE);
\r
1124 webServiceRunning = false;
\r
1126 frame.setClosed(true);
\r
1127 }catch(Exception ex){}
\r
1130 public void paintComponent(Graphics g)
\r
1132 g.setColor(Color.white);
\r
1133 g.fillRect(0,0,getWidth(), getHeight());
\r
1136 g.drawImage(image[imageIndex],10,10,this);
\r
1138 g.setFont(new Font("Arial", Font.BOLD, 12));
\r
1139 g.setColor(Color.black);
\r
1140 g.drawString("Clustal Alignment Web Service running", 30,30);
\r
1143 protected void jpred_actionPerformed(ActionEvent e)
\r
1146 JInternalFrame frame = new JInternalFrame();
\r
1147 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
\r
1149 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1150 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1151 if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
\r
1153 JPredClient ct = new JPredClient( (SequenceI)
\r
1154 seqs.getSequenceAt(0));
\r
1159 SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
\r
1160 for (int i = 0; i < sz; i++)
\r
1162 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1165 JPredClient ct = new JPredClient(msa);
\r
1171 Vector seqs = viewport.getAlignment().getSequences();
\r
1173 if (seqs.size() == 1 || !viewport.alignment.isAligned())
\r
1175 JPredClient ct = new JPredClient( (SequenceI)
\r
1176 seqs.elementAt(0));
\r
1180 SequenceI[] msa = new SequenceI[seqs.size()];
\r
1181 for (int i = 0; i < seqs.size(); i++)
\r
1183 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1186 JPredClient ct = new JPredClient(msa);
\r
1192 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
\r
1193 // Pick the tree file
\r
1194 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
1195 getProperty("LAST_DIRECTORY"));
\r
1196 chooser.setFileView(new JalviewFileView());
\r
1197 chooser.setDialogTitle("Select a newick-like tree file");
\r
1198 chooser.setToolTipText("Load a tree file");
\r
1199 int value = chooser.showOpenDialog(null);
\r
1200 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
1202 String choice = chooser.getSelectedFile().getPath();
\r
1203 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1204 TreePanel treepanel = null;
\r
1207 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
\r
1210 if (fin.getTree() != null)
\r
1212 TreePanel tp = null;
\r
1213 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1214 fin, "FromFile", choice);
\r
1215 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1218 catch (Exception ex)
\r
1220 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1221 "Problem reading tree file",
\r
1223 JOptionPane.WARNING_MESSAGE);
\r
1224 ex.printStackTrace();
\r