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 static final int NEW_WINDOW_WIDTH = 700;
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34 public static final int NEW_WINDOW_HEIGHT = 500;
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35 public String currentFileFormat = "Jalview";
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37 public AlignFrame(AlignmentI al)
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39 viewport = new AlignViewport(al);
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41 alignPanel = new AlignmentPanel(this, viewport);
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42 alignPanel.annotationPanel.adjustPanelHeight();
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43 alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
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44 alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
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45 alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );
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47 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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49 addInternalFrameListener(new InternalFrameAdapter()
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51 public void internalFrameActivated(InternalFrameEvent evt)
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53 javax.swing.SwingUtilities.invokeLater(new Runnable()
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56 { alignPanel.requestFocus(); }
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64 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
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66 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
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67 , new String[]{"fa, fasta, fastq", "aln", "pfam", "msf", "pir","blc","jar"},
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68 new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"},
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71 chooser.setAcceptAllFileFilterUsed(false);
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72 chooser.setFileView(new JalviewFileView());
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73 chooser.setDialogTitle("Save Alignment to file");
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74 chooser.setToolTipText("Save");
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75 int value = chooser.showSaveDialog(this);
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76 if(value == JalviewFileChooser.APPROVE_OPTION)
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78 currentFileFormat = chooser.getSelectedFormat();
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80 if (currentFileFormat.equals("Jalview"))
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82 String shortName = title.replace('/', '_');
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83 title = title.replace('\\', '_');
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84 String choice = chooser.getSelectedFile().getPath();
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85 Jalview2XML.SaveState(this, System.currentTimeMillis(), shortName,
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87 // USE Jalview2XML to save this file
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91 String choice = chooser.getSelectedFile().getPath();
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92 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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93 String output = FormatAdapter.formatSequences(currentFileFormat, viewport.getAlignment().getSequences());
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95 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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96 out.println(output);
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99 catch(Exception ex){}
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104 protected void outputText_actionPerformed(ActionEvent e)
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106 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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107 JInternalFrame frame = new JInternalFrame();
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108 cap.formatForOutput();
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109 frame.setContentPane(cap);
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110 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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111 cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
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114 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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116 HTMLOutput htmlOutput = new HTMLOutput(viewport);
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120 protected void createPNG_actionPerformed(ActionEvent e)
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122 alignPanel.makePNG();
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125 protected void epsFile_actionPerformed(ActionEvent e)
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127 alignPanel.makeEPS();
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131 public void printMenuItem_actionPerformed(ActionEvent e)
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133 //Putting in a thread avoids Swing painting problems
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134 PrintThread thread = new PrintThread();
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138 class PrintThread extends Thread
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142 PrinterJob printJob = PrinterJob.getPrinterJob();
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143 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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144 printJob.setPrintable(alignPanel, pf);
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145 if (printJob.printDialog())
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151 catch (Exception PrintException)
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153 PrintException.printStackTrace();
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163 public void closeMenuItem_actionPerformed(ActionEvent e)
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166 this.setClosed(true);
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167 }catch(Exception ex){}
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170 Stack historyList = new Stack();
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171 Stack redoList = new Stack();
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173 void updateEditMenuBar()
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175 if(historyList.size()>0)
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177 undoMenuItem.setEnabled(true);
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178 Object [] history = (Object[])historyList.get(0);
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179 undoMenuItem.setText("Undo "+history[0]);
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183 undoMenuItem.setEnabled(false);
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184 undoMenuItem.setText("Undo");
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187 if(redoList.size()>0)
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189 redoMenuItem.setEnabled(true);
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190 Object [] history = (Object[])redoList.get(0);
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191 redoMenuItem.setText("Redo "+history[0]);
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195 redoMenuItem.setEnabled(false);
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196 redoMenuItem.setText("Redo");
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200 public void addHistoryItem(String type)
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202 // must make sure we add new sequence objects her, not refs to the existing sequences
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205 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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206 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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208 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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209 viewport.getAlignment().getSequenceAt(i).getSequence());
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213 historyList.add(0, new Object[]{type, seq} );
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214 updateEditMenuBar();
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217 protected void undoMenuItem_actionPerformed(ActionEvent e)
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219 Object [] history = (Object[])historyList.remove(0);
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220 // add the redo state before continuing!!
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221 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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222 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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224 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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225 viewport.getAlignment().getSequenceAt(i).
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230 redoList.add(0, new Object[] {history[0], seq});
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232 seq = (SequenceI[]) history[1];
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233 AlignmentAnnotation [] old = viewport.alignment.getAlignmentAnnotation();
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234 viewport.setAlignment( new Alignment(seq) );
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235 viewport.alignment.setGapCharacter( Preferences.gapSymbol );
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236 updateEditMenuBar();
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237 for(int i=0; i<old.length; i++)
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238 viewport.alignment.addAnnotation(old[i]);
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239 viewport.updateConsensus();
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240 viewport.updateConservation();
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241 alignPanel.repaint();
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244 public void moveSelectedSequences(boolean up)
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246 SequenceGroup sg = viewport.getSelectionGroup();
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252 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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254 SequenceI seq = viewport.alignment.getSequenceAt(i);
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255 if (!sg.sequences.contains(seq))
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258 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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259 if (sg.sequences.contains(temp))
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262 viewport.alignment.getSequences().setElementAt(temp, i);
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263 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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268 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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270 SequenceI seq = viewport.alignment.getSequenceAt(i);
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271 if (!sg.sequences.contains(seq))
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274 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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275 if (sg.sequences.contains(temp))
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278 viewport.alignment.getSequences().setElementAt(temp, i);
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279 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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283 alignPanel.repaint();
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288 protected void copy_actionPerformed(ActionEvent e)
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290 if(viewport.getSelectionGroup()==null)
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293 SequenceGroup sg = viewport.getSelectionGroup();
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295 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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296 StringBuffer buffer= new StringBuffer();
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298 Hashtable orderedSeqs = new Hashtable();
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299 for(int i=0; i<sg.getSize(); i++)
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301 SequenceI seq = sg.getSequenceAt(i);
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302 int index = viewport.alignment.findIndex(seq);
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303 orderedSeqs.put(index+"", seq);
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307 for(int i=0; i<sg.getSize(); i++)
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309 SequenceI seq = null;
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310 while( seq == null )
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312 if(orderedSeqs.containsKey(index+""))
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314 seq = (SequenceI) orderedSeqs.get(index + "");
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322 buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
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323 +seq.findPosition( sg.getEndRes() )+ "\t"
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324 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
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326 c.setContents( new StringSelection( buffer.toString()) , null ) ;
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331 protected void pasteNew_actionPerformed(ActionEvent e)
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336 protected void pasteThis_actionPerformed(ActionEvent e)
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338 addHistoryItem("Paste");
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342 void paste(boolean newAlignment)
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345 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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346 Transferable contents = c.getContents(this);
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347 if (contents == null)
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350 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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351 StringTokenizer st = new StringTokenizer(str);
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352 ArrayList seqs = new ArrayList();
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353 while (st.hasMoreElements())
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355 String name = st.nextToken();
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356 int start = Integer.parseInt(st.nextToken());
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357 int end = Integer.parseInt(st.nextToken());
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358 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
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361 viewport.alignment.addSequence(sequence);
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363 seqs.add(sequence);
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368 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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369 seqs.toArray(newSeqs);
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370 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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371 String newtitle = new String("Copied sequences");
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372 if( title.startsWith("Copied sequences"))
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375 newtitle = newtitle.concat("- from "+title);
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377 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
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381 viewport.setEndSeq(viewport.alignment.getHeight());
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382 viewport.alignment.getWidth();
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383 viewport.updateConservation();
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384 viewport.updateConsensus();
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385 alignPanel.repaint();
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388 }catch(Exception ex){}// could be anything being pasted in here
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393 protected void cut_actionPerformed(ActionEvent e)
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395 copy_actionPerformed(null);
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396 delete_actionPerformed(null);
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399 protected void delete_actionPerformed(ActionEvent e)
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401 addHistoryItem("Delete");
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402 if (viewport.getSelectionGroup() == null)
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405 SequenceGroup sg = viewport.getSelectionGroup();
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406 for (int i=0;i < sg.sequences.size(); i++)
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408 SequenceI seq = sg.getSequenceAt(i);
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409 int index = viewport.getAlignment().findIndex(seq);
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410 seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
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412 if(seq.getSequence().length()<1)
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413 viewport.getAlignment().deleteSequence(seq);
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415 viewport.getAlignment().getSequences().setElementAt(seq, index);
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418 viewport.setSelectionGroup(null);
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419 viewport.alignment.deleteGroup(sg);
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420 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
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421 if(viewport.getAlignment().getHeight()<1)
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424 this.setClosed(true);
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425 }catch(Exception ex){}
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426 viewport.updateConservation();
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427 viewport.updateConsensus();
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428 alignPanel.repaint();
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434 protected void redoMenuItem_actionPerformed(ActionEvent e)
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436 Object [] history = (Object[])redoList.remove(0);
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437 SequenceI[] seq = (SequenceI[]) history[1];
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438 viewport.setAlignment( new Alignment(seq) );
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439 viewport.alignment.setGapCharacter( Preferences.gapSymbol );
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440 updateEditMenuBar();
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441 viewport.updateConsensus();
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442 alignPanel.repaint();
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443 alignPanel.repaint();
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447 protected void deleteGroups_actionPerformed(ActionEvent e)
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449 viewport.alignment.deleteAllGroups();
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450 viewport.setSelectionGroup(null);
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451 alignPanel.repaint();
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456 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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458 SequenceGroup sg = new SequenceGroup();
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459 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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460 sg.addSequence( viewport.getAlignment().getSequenceAt(i));
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461 sg.setEndRes(viewport.alignment.getWidth());
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462 viewport.setSelectionGroup(sg);
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463 PaintRefresher.Refresh(null);
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466 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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468 viewport.setSelectionGroup(null);
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469 viewport.getColumnSelection().clear();
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470 viewport.setSelectionGroup(null);
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471 PaintRefresher.Refresh(null);
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474 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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476 SequenceGroup sg = viewport.getSelectionGroup();
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477 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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478 sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
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480 PaintRefresher.Refresh(null);
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483 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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485 addHistoryItem("delete columns");
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486 ColumnSelection colSel = viewport.getColumnSelection();
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487 if (colSel.size() > 0)
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489 int min = colSel.getMin();
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490 viewport.getAlignment().trimLeft(min);
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491 colSel.compensateForEdit(0,min);
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493 if(viewport.getSelectionGroup()!=null)
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494 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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496 Vector groups = viewport.alignment.getGroups();
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497 for(int i=0; i<groups.size(); i++)
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499 SequenceGroup sg = (SequenceGroup) groups.get(i);
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500 if(!sg.adjustForRemoveLeft(min))
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501 viewport.alignment.deleteGroup(sg);
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504 alignPanel.repaint();
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508 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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510 addHistoryItem("delete columns");
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511 ColumnSelection colSel = viewport.getColumnSelection();
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512 if (colSel.size() > 0)
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514 int max = colSel.getMax();
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515 viewport.getAlignment().trimRight(max);
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516 if(viewport.getSelectionGroup()!=null)
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517 viewport.getSelectionGroup().adjustForRemoveRight(max);
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519 Vector groups = viewport.alignment.getGroups();
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520 for(int i=0; i<groups.size(); i++)
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522 SequenceGroup sg = (SequenceGroup) groups.get(i);
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523 if(!sg.adjustForRemoveRight(max))
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524 viewport.alignment.deleteGroup(sg);
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529 alignPanel.repaint();
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534 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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536 addHistoryItem("delete gapped columns");
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537 viewport.getAlignment().removeGaps();
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538 viewport.updateConservation();
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539 viewport.updateConsensus();
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540 alignPanel.repaint();
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543 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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545 addHistoryItem("delete all gaps");
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548 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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550 current = viewport.getAlignment().getSequenceAt(i);
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551 jSize = current.getLength();
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552 for (int j=0; j < jSize; j++)
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553 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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555 current.deleteCharAt(j);
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560 viewport.updateConservation();
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561 viewport.updateConsensus();
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562 alignPanel.repaint();
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566 public void findMenuItem_actionPerformed(ActionEvent e)
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568 JInternalFrame frame = new JInternalFrame();
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569 Finder finder = new Finder(viewport, alignPanel, frame);
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570 frame.setContentPane(finder);
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571 Desktop.addInternalFrame(frame, "Find", 340,110);
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572 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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577 public void font_actionPerformed(ActionEvent e)
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579 FontChooser fc = new FontChooser( alignPanel );
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582 protected void fullSeqId_actionPerformed(ActionEvent e)
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584 viewport.setShowFullId( fullSeqId.isSelected() );
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586 alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
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587 alignPanel.repaint();
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590 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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592 viewport.setColourText( colourTextMenuItem.isSelected() );
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593 alignPanel.repaint();
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596 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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598 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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599 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
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600 scaleAbove.setVisible( wrapMenuItem.isSelected() );
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601 scaleLeft.setVisible( wrapMenuItem.isSelected() );
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602 scaleRight.setVisible( wrapMenuItem.isSelected() );
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603 alignPanel.repaint();
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606 protected void scaleAbove_actionPerformed(ActionEvent e)
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608 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
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609 alignPanel.repaint();
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612 protected void scaleLeft_actionPerformed(ActionEvent e)
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614 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
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615 alignPanel.repaint();
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618 protected void scaleRight_actionPerformed(ActionEvent e)
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620 viewport.setScaleRightWrapped(scaleRight.isSelected());
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621 alignPanel.repaint();
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626 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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628 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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629 alignPanel.repaint();
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632 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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634 viewport.setShowText( viewTextMenuItem.isSelected() );
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635 alignPanel.repaint();
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639 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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641 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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642 alignPanel.repaint();
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645 public void sequenceFeatures_actionPerformed(ActionEvent evt)
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647 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
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648 if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
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650 SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);
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651 ((Alignment)viewport.alignment).featuresAdded = true;
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653 alignPanel.repaint();
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656 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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658 if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
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660 annotationPanelMenuItem.setSelected(false);
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663 viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
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664 alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
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667 public void overviewMenuItem_actionPerformed(ActionEvent e)
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669 if (alignPanel.overviewPanel != null)
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672 JInternalFrame frame = new JInternalFrame();
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673 OverviewPanel overview = new OverviewPanel(alignPanel);
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674 frame.setContentPane(overview);
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675 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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676 frame.getWidth(), frame.getHeight());
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678 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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679 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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680 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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682 alignPanel.setOverviewPanel(null);
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686 alignPanel.setOverviewPanel( overview );
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691 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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693 changeColour( null );
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697 public void clustalColour_actionPerformed(ActionEvent e)
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699 abovePIDThreshold.setSelected(false);
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700 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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703 public void zappoColour_actionPerformed(ActionEvent e)
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705 changeColour(new ZappoColourScheme());
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708 public void taylorColour_actionPerformed(ActionEvent e)
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710 changeColour(new TaylorColourScheme());
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714 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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716 changeColour( new HydrophobicColourScheme() );
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719 public void helixColour_actionPerformed(ActionEvent e)
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721 changeColour(new HelixColourScheme() );
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725 public void strandColour_actionPerformed(ActionEvent e)
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727 changeColour(new StrandColourScheme());
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731 public void turnColour_actionPerformed(ActionEvent e)
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733 changeColour(new TurnColourScheme());
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737 public void buriedColour_actionPerformed(ActionEvent e)
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739 changeColour(new BuriedColourScheme() );
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742 public void nucleotideColour_actionPerformed(ActionEvent e)
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744 changeColour(new NucleotideColourScheme());
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748 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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750 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
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755 void changeColour(ColourSchemeI cs)
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759 if ( viewport.getAbovePIDThreshold() )
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761 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
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763 if (cs instanceof ResidueColourScheme)
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764 ( (ResidueColourScheme) cs).setThreshold(threshold);
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765 else if (cs instanceof ScoreColourScheme)
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766 ( (ScoreColourScheme) cs).setThreshold(threshold);
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768 viewport.setGlobalColourScheme(cs);
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770 else if (cs instanceof ResidueColourScheme)
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771 ( (ResidueColourScheme) cs).setThreshold(0);
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772 else if (cs instanceof ScoreColourScheme)
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773 ( (ScoreColourScheme) cs).setThreshold(0);
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777 if (viewport.getConservationSelected())
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779 ConservationColourScheme ccs = null;
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781 Alignment al = (Alignment) viewport.alignment;
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782 Conservation c = new Conservation("All",
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783 ResidueProperties.propHash, 3,
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784 al.getSequences(), 0,
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785 al.getWidth() - 1);
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788 c.verdict(false, viewport.ConsPercGaps);
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790 ccs = new ConservationColourScheme(c, cs);
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792 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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793 ccs.setConsensus( viewport.vconsensus );
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794 viewport.setGlobalColourScheme(ccs);
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796 SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
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801 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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803 cs.setConsensus(viewport.vconsensus);
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804 viewport.setGlobalColourScheme(cs);
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808 if(viewport.getColourAppliesToAllGroups())
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810 Vector groups = viewport.alignment.getGroups();
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811 for(int i=0; i<groups.size(); i++)
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813 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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815 if (cs instanceof ClustalxColourScheme)
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817 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
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822 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
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823 }catch(Exception ex){ex.printStackTrace();}
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826 if(viewport.getAbovePIDThreshold())
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828 if (sg.cs instanceof ResidueColourScheme)
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829 ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
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830 else if (sg.cs instanceof ScoreColourScheme)
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831 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
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833 sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
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836 if( viewport.getConservationSelected() )
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838 Conservation c = new Conservation("Group",
\r
839 ResidueProperties.propHash, 3,
\r
840 sg.sequences, 0, viewport.alignment.getWidth()-1);
\r
842 c.verdict(false, viewport.ConsPercGaps);
\r
843 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
\r
845 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
846 ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
851 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
852 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
858 if(alignPanel.getOverviewPanel()!=null)
\r
859 alignPanel.getOverviewPanel().updateOverviewImage();
\r
860 alignPanel.repaint();
\r
863 protected void modifyPID_actionPerformed(ActionEvent e)
\r
865 if(viewport.getAbovePIDThreshold())
\r
867 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
869 SliderPanel.showPIDSlider();
\r
873 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
875 if(viewport.getConservationSelected())
\r
877 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
879 SliderPanel.showConservationSlider();
\r
884 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
886 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
888 viewport.setAbovePIDThreshold(false);
\r
889 abovePIDThreshold.setSelected(false);
\r
891 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
892 if(cs instanceof ConservationColourScheme )
\r
893 changeColour( ((ConservationColourScheme)cs).cs );
\r
895 changeColour( cs );
\r
897 modifyConservation_actionPerformed(null);
\r
900 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
902 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
904 conservationMenuItem.setSelected(false);
\r
905 viewport.setConservationSelected(false);
\r
907 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
909 if(cs instanceof ConservationColourScheme )
\r
910 changeColour( ((ConservationColourScheme)cs).cs );
\r
912 changeColour( cs );
\r
914 modifyPID_actionPerformed(null);
\r
919 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
921 UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
\r
924 public void PIDColour_actionPerformed(ActionEvent e)
\r
926 changeColour( new PIDColourScheme() );
\r
930 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
932 changeColour(new Blosum62ColourScheme() );
\r
937 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
939 addHistoryItem("sort");
\r
940 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
\r
941 alignPanel.repaint();
\r
944 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
946 addHistoryItem("sort");
\r
947 AlignmentSorter.sortByID( viewport.getAlignment() );
\r
948 alignPanel.repaint();
\r
951 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
953 addHistoryItem("sort");
\r
954 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
955 AlignmentSorter.sortGroups(viewport.getAlignment());
\r
956 alignPanel.repaint();
\r
959 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
961 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
962 JInternalFrame frame = new JInternalFrame();
\r
963 frame.setContentPane(sp);
\r
964 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
\r
968 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
970 if(viewport.getSelectionGroup().getSize()<2)
\r
971 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
\r
974 JInternalFrame frame = new JInternalFrame();
\r
975 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
976 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
980 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
983 if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
\r
984 || viewport.getAlignment().getHeight()<4)
\r
986 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
\r
987 +"at least 4 input sequences.",
\r
988 "Sequence selection insufficient",
\r
989 JOptionPane.WARNING_MESSAGE);
\r
994 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
995 JInternalFrame frame = new JInternalFrame();
\r
996 frame.setContentPane(pcaPanel);
\r
997 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
\r
998 }catch(java.lang.OutOfMemoryError ex)
\r
1000 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
\r
1001 "Out of memory", JOptionPane.WARNING_MESSAGE);
\r
1007 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1009 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1012 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1014 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1018 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1020 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1023 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1025 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1028 void NewTreePanel(String type, String pwType, String title)
\r
1030 //are the sequences aligned?
\r
1031 if(!viewport.alignment.isAligned())
\r
1033 JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
\r
1034 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
\r
1038 final TreePanel tp;
\r
1039 if (viewport.getSelectionGroup() != null &&
\r
1040 viewport.getSelectionGroup().getSize() > 3)
\r
1042 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1044 0, viewport.alignment.getWidth());
\r
1048 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1049 type, pwType, 0, viewport.alignment.getWidth());
\r
1052 addTreeMenuItem(tp, title);
\r
1054 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1057 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1059 final JMenuItem item = new JMenuItem(title);
\r
1060 sortByTreeMenu.add(item);
\r
1061 item.addActionListener(new java.awt.event.ActionListener()
\r
1063 public void actionPerformed(ActionEvent e)
\r
1065 addHistoryItem("sort");
\r
1066 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1067 alignPanel.repaint();
\r
1071 treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1073 public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
\r
1075 sortByTreeMenu.remove(item);
\r
1082 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
1084 WebserviceInfo info = new WebserviceInfo("Clustal web service",
\r
1085 "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+
\r
1086 " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
\r
1087 +" Nucleic Acids Research, submitted, June 1994.",
\r
1090 ClustalThread thread = new ClustalThread(info);
\r
1094 class ClustalThread extends Thread
\r
1096 WebserviceInfo info;
\r
1097 public ClustalThread(WebserviceInfo info)
\r
1098 {this.info = info; }
\r
1102 info.setStatus(WebserviceInfo.STATE_RUNNING);
\r
1103 jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
\r
1104 Vector sv = viewport.getAlignment().getSequences();
\r
1105 SequenceI[] seqs = new SequenceI[sv.size()];
\r
1110 seqs[i] = (SequenceI) sv.elementAt(i);
\r
1112 while (++i < sv.size());
\r
1114 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
\r
1115 if (alignment != null)
\r
1117 AlignFrame af = new AlignFrame(new Alignment(alignment));
\r
1118 Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),
\r
1119 NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
\r
1120 af.clustalColour_actionPerformed(null);
\r
1121 af.clustalColour.setSelected(true);
\r
1122 info.setStatus(WebserviceInfo.STATE_STOPPED_OK);
\r
1126 info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
\r
1127 info.appendProgressText("Problem obtaining clustal alignment");
\r
1132 protected void jpred_actionPerformed(ActionEvent e)
\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)seqs.getSequenceAt(0));
\r
1146 SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
\r
1147 for (int i = 0; i < sz; i++)
\r
1149 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1152 JPredClient ct = new JPredClient(msa);
\r
1158 Vector seqs = viewport.getAlignment().getSequences();
\r
1160 if (seqs.size() == 1 || !viewport.alignment.isAligned())
\r
1162 JPredClient ct = new JPredClient( (SequenceI)
\r
1163 seqs.elementAt(0));
\r
1167 SequenceI[] msa = new SequenceI[seqs.size()];
\r
1168 for (int i = 0; i < seqs.size(); i++)
\r
1170 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1173 JPredClient ct = new JPredClient(msa);
\r
1178 protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
\r
1180 // TODO:resolve which menu item was actually selected
\r
1181 // Now, check we have enough sequences
\r
1182 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
\r
1184 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1185 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1187 SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
\r
1188 for (int i = 0; i < sz; i++)
\r
1190 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1193 MsaWSClient ct = new jalview.ws.MsaWSClient(msa);
\r
1197 Vector seqs = viewport.getAlignment().getSequences();
\r
1199 if (seqs.size() > 1) {
\r
1200 SequenceI[] msa = new SequenceI[seqs.size()];
\r
1201 for (int i = 0; i < seqs.size(); i++)
\r
1203 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1206 MsaWSClient ct = new MsaWSClient(msa);
\r
1212 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
\r
1213 // Pick the tree file
\r
1214 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
1215 getProperty("LAST_DIRECTORY"));
\r
1216 chooser.setFileView(new JalviewFileView());
\r
1217 chooser.setDialogTitle("Select a newick-like tree file");
\r
1218 chooser.setToolTipText("Load a tree file");
\r
1219 int value = chooser.showOpenDialog(null);
\r
1220 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
1222 String choice = chooser.getSelectedFile().getPath();
\r
1223 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1226 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
\r
1227 ShowNewickTree(fin, choice);
\r
1229 catch (Exception ex)
\r
1231 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1232 "Problem reading tree file",
\r
1234 JOptionPane.WARNING_MESSAGE);
\r
1235 ex.printStackTrace();
\r
1240 public void ShowNewickTree(NewickFile nf, String title)
\r
1244 if (nf.getTree() != null)
\r
1246 TreePanel tp = new TreePanel(viewport,
\r
1247 viewport.getAlignment().getSequences(),
\r
1248 nf, "FromFile", title);
\r
1249 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1250 addTreeMenuItem(tp, title);
\r
1251 viewport.setCurrentTree(tp.getTree());
\r
1253 }catch(Exception ex){ex.printStackTrace();}
\r