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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36 public AlignFrame(AlignmentI al)
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39 String ip = java.net.InetAddress.getLocalHost().getHostAddress();
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40 if( !ip.startsWith("10."))
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41 webService.setVisible(false);
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43 catch(java.net.UnknownHostException e){}
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44 viewport = new AlignViewport(al);
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47 alignPanel = new AlignmentPanel(this, viewport);
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48 alignPanel.annotationPanel.adjustPanelHeight();
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49 alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
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50 alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
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51 alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );
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53 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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55 addInternalFrameListener(new InternalFrameAdapter()
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57 public void internalFrameActivated(InternalFrameEvent evt)
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59 javax.swing.SwingUtilities.invokeLater(new Runnable()
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62 { alignPanel.requestFocus(); }
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70 protected void saveAs_actionPerformed(ActionEvent e)
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72 String suffix [] = null;
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73 if(e.getActionCommand().equals("FASTA"))
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74 suffix = new String[]{"fa", "fasta"};
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75 else if(e.getActionCommand().equals("MSF"))
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76 suffix = new String[]{"msf"};
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77 else if(e.getActionCommand().equals("CLUSTAL"))
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78 suffix = new String[]{"aln"};
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79 else if(e.getActionCommand().equals("BLC"))
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80 suffix = new String[]{"blc"};
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81 else if(e.getActionCommand().equals("PIR"))
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82 suffix = new String[]{"pir"};
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83 else if(e.getActionCommand().equals("PFAM"))
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84 suffix = new String[]{"pfam"};
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87 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
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88 , suffix, e.getActionCommand()+" file");
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89 chooser.setFileView(new JalviewFileView());
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90 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
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91 chooser.setToolTipText("Save");
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92 int value = chooser.showSaveDialog(this);
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93 if(value == JalviewFileChooser.APPROVE_OPTION)
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95 String choice = chooser.getSelectedFile().getPath();
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96 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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97 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
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99 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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100 out.println(output);
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103 catch(Exception ex){}
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108 protected void outputText_actionPerformed(ActionEvent e)
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110 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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111 JInternalFrame frame = new JInternalFrame();
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112 cap.formatForOutput();
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113 frame.setContentPane(cap);
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114 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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115 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
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118 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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120 HTMLOutput htmlOutput = new HTMLOutput(viewport);
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124 protected void createPNG_actionPerformed(ActionEvent e)
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126 alignPanel.makePNG();
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129 protected void epsFile_actionPerformed(ActionEvent e)
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131 alignPanel.makeEPS();
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135 public void printMenuItem_actionPerformed(ActionEvent e)
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137 //Putting in a thread avoids Swing painting problems
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138 PrintThread thread = new PrintThread();
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142 class PrintThread extends Thread
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146 PrinterJob printJob = PrinterJob.getPrinterJob();
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147 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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148 printJob.setPrintable(alignPanel, pf);
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149 if (printJob.printDialog())
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155 catch (Exception PrintException)
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157 PrintException.printStackTrace();
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167 public void closeMenuItem_actionPerformed(ActionEvent e)
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170 this.setClosed(true);
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171 }catch(Exception ex){}
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174 Stack historyList = new Stack();
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175 Stack redoList = new Stack();
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177 void updateEditMenuBar()
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179 if(historyList.size()>0)
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181 undoMenuItem.setEnabled(true);
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182 Object [] history = (Object[])historyList.get(0);
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183 undoMenuItem.setText("Undo "+history[0]);
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187 undoMenuItem.setEnabled(false);
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188 undoMenuItem.setText("Undo");
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191 if(redoList.size()>0)
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193 redoMenuItem.setEnabled(true);
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194 Object [] history = (Object[])redoList.get(0);
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195 redoMenuItem.setText("Redo "+history[0]);
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199 redoMenuItem.setEnabled(false);
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200 redoMenuItem.setText("Redo");
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204 public void addHistoryItem(String type)
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206 // must make sure we add new sequence objects her, not refs to the existing sequences
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208 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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209 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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211 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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212 viewport.getAlignment().getSequenceAt(i).getSequence());
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215 historyList.add(0, new Object[]{type, seq} );
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216 updateEditMenuBar();
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219 protected void undoMenuItem_actionPerformed(ActionEvent e)
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221 Object [] history = (Object[])historyList.remove(0);
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222 // add the redo state before continuing!!
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223 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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224 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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226 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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227 viewport.getAlignment().getSequenceAt(i).
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232 redoList.add(0, new Object[] {history[0], seq});
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234 seq = (SequenceI[]) history[1];
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235 viewport.setAlignment( new Alignment(seq) );
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236 updateEditMenuBar();
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237 viewport.updateConsensus();
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238 alignPanel.repaint();
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241 public void moveSelectedSequences(boolean up)
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243 SequenceGroup sg = viewport.getSelectionGroup();
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249 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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251 SequenceI seq = viewport.alignment.getSequenceAt(i);
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252 if (!sg.sequences.contains(seq))
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255 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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256 if (sg.sequences.contains(temp))
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259 viewport.alignment.getSequences().setElementAt(temp, i);
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260 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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265 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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267 SequenceI seq = viewport.alignment.getSequenceAt(i);
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268 if (!sg.sequences.contains(seq))
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271 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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272 if (sg.sequences.contains(temp))
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275 viewport.alignment.getSequences().setElementAt(temp, i);
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276 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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280 alignPanel.repaint();
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285 protected void copy_actionPerformed(ActionEvent e)
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287 if(viewport.getSelectionGroup()==null)
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290 SequenceGroup sg = viewport.getSelectionGroup();
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292 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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293 StringBuffer buffer= new StringBuffer();
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295 for(int i=0; i<sg.getSize(); i++)
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297 SequenceI seq = sg.getSequenceAt(i);
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298 buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
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299 +seq.findPosition( sg.getEndRes() )+ "\t"
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300 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
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302 c.setContents( new StringSelection( buffer.toString()) , null ) ;
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307 protected void pasteNew_actionPerformed(ActionEvent e)
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312 protected void pasteThis_actionPerformed(ActionEvent e)
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314 addHistoryItem("Paste");
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318 void paste(boolean newAlignment)
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321 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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322 Transferable contents = c.getContents(this);
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323 if (contents == null)
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326 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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327 StringTokenizer st = new StringTokenizer(str);
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328 ArrayList seqs = new ArrayList();
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329 while (st.hasMoreElements())
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331 String name = st.nextToken();
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332 int start = Integer.parseInt(st.nextToken());
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333 int end = Integer.parseInt(st.nextToken());
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334 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
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337 viewport.alignment.addSequence(sequence);
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339 seqs.add(sequence);
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344 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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345 seqs.toArray(newSeqs);
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346 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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347 Desktop.addInternalFrame(af, "Copied sequences", NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
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351 viewport.setEndSeq(viewport.alignment.getHeight());
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352 viewport.alignment.getWidth();
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353 viewport.updateConservation();
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354 viewport.updateConsensus();
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355 alignPanel.repaint();
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358 }catch(Exception ex){}// could be anything being pasted in here
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363 protected void cut_actionPerformed(ActionEvent e)
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365 copy_actionPerformed(null);
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366 delete_actionPerformed(null);
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369 protected void delete_actionPerformed(ActionEvent e)
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371 addHistoryItem("Delete");
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372 if (viewport.getSelectionGroup() == null)
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375 SequenceGroup sg = viewport.getSelectionGroup();
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376 for (int i=0;i < sg.sequences.size(); i++)
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378 SequenceI seq = sg.getSequenceAt(i);
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379 int index = viewport.getAlignment().findIndex(seq);
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380 seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
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382 if(seq.getSequence().length()<1)
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383 viewport.getAlignment().deleteSequence(seq);
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385 viewport.getAlignment().getSequences().setElementAt(seq, index);
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388 viewport.setSelectionGroup(null);
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389 viewport.alignment.deleteGroup(sg);
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390 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
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391 if(viewport.getAlignment().getHeight()<1)
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394 this.setClosed(true);
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395 }catch(Exception ex){}
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396 viewport.updateConservation();
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397 viewport.updateConsensus();
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398 alignPanel.repaint();
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404 protected void redoMenuItem_actionPerformed(ActionEvent e)
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406 Object [] history = (Object[])redoList.remove(0);
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407 SequenceI[] seq = (SequenceI[]) history[1];
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408 viewport.setAlignment( new Alignment(seq) );
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409 updateEditMenuBar();
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410 viewport.updateConsensus();
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411 alignPanel.repaint();
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412 alignPanel.repaint();
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416 protected void deleteGroups_actionPerformed(ActionEvent e)
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418 viewport.alignment.deleteAllGroups();
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419 viewport.setSelectionGroup(null);
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421 alignPanel.repaint();
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426 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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428 SequenceGroup sg = new SequenceGroup();
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429 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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430 sg.addSequence( viewport.getAlignment().getSequenceAt(i));
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431 sg.setEndRes(viewport.alignment.getWidth());
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432 viewport.setSelectionGroup(sg);
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433 PaintRefresher.Refresh(null);
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436 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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438 viewport.setSelectionGroup(null);
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439 viewport.getColumnSelection().clear();
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440 viewport.setSelectionGroup(null);
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441 PaintRefresher.Refresh(null);
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444 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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446 SequenceGroup sg = viewport.getSelectionGroup();
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447 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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448 sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
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450 PaintRefresher.Refresh(null);
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453 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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455 addHistoryItem("delete columns");
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456 ColumnSelection colSel = viewport.getColumnSelection();
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457 if (colSel.size() > 0)
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459 int min = colSel.getMin();
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460 viewport.getAlignment().trimLeft(min);
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461 colSel.compensateForEdit(0,min);
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463 if(viewport.getSelectionGroup()!=null)
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464 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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466 Vector groups = viewport.alignment.getGroups();
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467 for(int i=0; i<groups.size(); i++)
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469 SequenceGroup sg = (SequenceGroup) groups.get(i);
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470 if(!sg.adjustForRemoveLeft(min))
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471 viewport.alignment.deleteGroup(sg);
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474 alignPanel.repaint();
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478 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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480 addHistoryItem("delete columns");
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481 ColumnSelection colSel = viewport.getColumnSelection();
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482 if (colSel.size() > 0)
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484 int max = colSel.getMax();
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485 viewport.getAlignment().trimRight(max);
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486 if(viewport.getSelectionGroup()!=null)
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487 viewport.getSelectionGroup().adjustForRemoveRight(max);
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489 Vector groups = viewport.alignment.getGroups();
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490 for(int i=0; i<groups.size(); i++)
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492 SequenceGroup sg = (SequenceGroup) groups.get(i);
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493 if(!sg.adjustForRemoveRight(max))
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494 viewport.alignment.deleteGroup(sg);
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499 alignPanel.repaint();
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504 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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506 addHistoryItem("delete gapped columns");
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507 viewport.getAlignment().removeGaps();
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508 viewport.updateConservation();
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509 viewport.updateConsensus();
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510 alignPanel.repaint();
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513 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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515 addHistoryItem("delete all gaps");
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518 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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520 current = viewport.getAlignment().getSequenceAt(i);
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521 jSize = current.getLength();
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522 for (int j=0; j < jSize; j++)
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523 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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525 current.deleteCharAt(j);
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530 viewport.updateConservation();
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531 viewport.updateConsensus();
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532 alignPanel.repaint();
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536 public void findMenuItem_actionPerformed(ActionEvent e)
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538 JInternalFrame frame = new JInternalFrame();
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539 Finder finder = new Finder(viewport, alignPanel, frame);
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540 frame.setContentPane(finder);
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541 Desktop.addInternalFrame(frame, "Find", 340,110, false);
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542 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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547 public void font_actionPerformed(ActionEvent e)
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549 FontChooser fc = new FontChooser( alignPanel );
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552 protected void fullSeqId_actionPerformed(ActionEvent e)
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554 viewport.setShowFullId( fullSeqId.isSelected() );
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556 alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
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557 alignPanel.repaint();
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560 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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562 viewport.setColourText( colourTextMenuItem.isSelected() );
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563 alignPanel.repaint();
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566 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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568 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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569 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
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570 scaleAbove.setVisible( wrapMenuItem.isSelected() );
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571 scaleLeft.setVisible( wrapMenuItem.isSelected() );
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572 scaleRight.setVisible( wrapMenuItem.isSelected() );
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573 alignPanel.repaint();
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576 protected void scaleAbove_actionPerformed(ActionEvent e)
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578 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
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579 alignPanel.repaint();
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582 protected void scaleLeft_actionPerformed(ActionEvent e)
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584 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
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585 alignPanel.repaint();
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588 protected void scaleRight_actionPerformed(ActionEvent e)
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590 viewport.setScaleRightWrapped(scaleRight.isSelected());
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591 alignPanel.repaint();
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596 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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598 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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599 alignPanel.repaint();
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602 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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604 viewport.setShowText( viewTextMenuItem.isSelected() );
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605 alignPanel.repaint();
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609 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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611 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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612 alignPanel.repaint();
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615 public void sequenceFeatures_actionPerformed(ActionEvent evt)
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617 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
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618 if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
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620 AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
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621 ((Alignment)viewport.alignment).featuresAdded = true;
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623 alignPanel.repaint();
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626 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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628 if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
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630 annotationPanelMenuItem.setSelected(false);
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633 viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
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634 alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
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637 public void overviewMenuItem_actionPerformed(ActionEvent e)
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639 if (alignPanel.overviewPanel != null)
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642 JInternalFrame frame = new JInternalFrame();
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643 OverviewPanel overview = new OverviewPanel(alignPanel);
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644 frame.setContentPane(overview);
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645 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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646 frame.getWidth(), frame.getHeight());
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648 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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649 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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650 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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652 alignPanel.setOverviewPanel(null);
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656 alignPanel.setOverviewPanel( overview );
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661 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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663 changeColour( null );
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667 public void clustalColour_actionPerformed(ActionEvent e)
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669 abovePIDThreshold.setSelected(false);
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670 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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673 public void zappoColour_actionPerformed(ActionEvent e)
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675 changeColour(new ZappoColourScheme());
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678 public void taylorColour_actionPerformed(ActionEvent e)
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680 changeColour(new TaylorColourScheme());
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684 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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686 changeColour( new HydrophobicColourScheme() );
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689 public void helixColour_actionPerformed(ActionEvent e)
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691 changeColour(new HelixColourScheme() );
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695 public void strandColour_actionPerformed(ActionEvent e)
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697 changeColour(new StrandColourScheme());
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701 public void turnColour_actionPerformed(ActionEvent e)
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703 changeColour(new TurnColourScheme());
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707 public void buriedColour_actionPerformed(ActionEvent e)
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709 changeColour(new BuriedColourScheme() );
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712 public void nucleotideColour_actionPerformed(ActionEvent e)
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714 changeColour(new NucleotideColourScheme());
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718 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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720 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
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725 void changeColour(ColourSchemeI cs)
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729 if ( viewport.getAbovePIDThreshold() )
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731 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
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733 if (cs instanceof ResidueColourScheme)
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734 ( (ResidueColourScheme) cs).setThreshold(threshold);
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735 else if (cs instanceof ScoreColourScheme)
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736 ( (ScoreColourScheme) cs).setThreshold(threshold);
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738 viewport.setGlobalColourScheme(cs);
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740 else if (cs instanceof ResidueColourScheme)
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741 ( (ResidueColourScheme) cs).setThreshold(0);
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742 else if (cs instanceof ScoreColourScheme)
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743 ( (ScoreColourScheme) cs).setThreshold(0);
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747 if (viewport.getConservationSelected())
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749 ConservationColourScheme ccs = null;
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751 Alignment al = (Alignment) viewport.alignment;
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752 Conservation c = new Conservation("All",
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753 ResidueProperties.propHash, 3,
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754 al.getSequences(), 0,
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755 al.getWidth() - 1);
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758 c.verdict(false, viewport.ConsPercGaps);
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760 ccs = new ConservationColourScheme(c, cs);
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762 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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763 ccs.setConsensus( viewport.vconsensus );
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764 viewport.setGlobalColourScheme(ccs);
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766 SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
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771 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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773 cs.setConsensus(viewport.vconsensus);
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774 viewport.setGlobalColourScheme(cs);
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778 if(viewport.getColourAppliesToAllGroups())
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780 Vector groups = viewport.alignment.getGroups();
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781 for(int i=0; i<groups.size(); i++)
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783 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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785 if (cs instanceof ClustalxColourScheme)
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787 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
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792 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
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794 catch (Exception ex)
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796 ex.printStackTrace();
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800 if(viewport.getAbovePIDThreshold())
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802 if (sg.cs instanceof ResidueColourScheme)
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803 ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
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804 else if (sg.cs instanceof ScoreColourScheme)
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805 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
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807 sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
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810 if( viewport.getConservationSelected() )
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812 Conservation c = new Conservation("Group",
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813 ResidueProperties.propHash, 3,
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814 sg.sequences, 0, viewport.alignment.getWidth()-1);
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816 c.verdict(false, viewport.ConsPercGaps);
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817 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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819 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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820 ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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825 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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826 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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832 if(alignPanel.getOverviewPanel()!=null)
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833 alignPanel.getOverviewPanel().updateOverviewImage();
\r
834 alignPanel.repaint();
\r
837 protected void modifyPID_actionPerformed(ActionEvent e)
\r
839 if(viewport.getAbovePIDThreshold())
\r
841 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
843 SliderPanel.showPIDSlider();
\r
847 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
849 if(viewport.getConservationSelected())
\r
851 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
853 SliderPanel.showConservationSlider();
\r
858 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
860 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
862 viewport.setAbovePIDThreshold(false);
\r
863 abovePIDThreshold.setSelected(false);
\r
865 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
866 if(cs instanceof ConservationColourScheme )
\r
867 changeColour( ((ConservationColourScheme)cs).cs );
\r
869 changeColour( cs );
\r
871 modifyConservation_actionPerformed(null);
\r
874 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
876 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
878 conservationMenuItem.setSelected(false);
\r
879 viewport.setConservationSelected(false);
\r
881 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
883 if(cs instanceof ConservationColourScheme )
\r
884 changeColour( ((ConservationColourScheme)cs).cs );
\r
886 changeColour( cs );
\r
888 modifyPID_actionPerformed(null);
\r
893 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
895 UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
\r
898 public void PIDColour_actionPerformed(ActionEvent e)
\r
900 changeColour( new PIDColourScheme() );
\r
904 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
906 changeColour(new Blosum62ColourScheme() );
\r
911 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
913 addHistoryItem("sort");
\r
914 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
\r
915 alignPanel.repaint();
\r
918 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
920 addHistoryItem("sort");
\r
921 AlignmentSorter.sortByID( viewport.getAlignment() );
\r
922 alignPanel.repaint();
\r
925 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
927 addHistoryItem("sort");
\r
928 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
929 AlignmentSorter.sortGroups(viewport.getAlignment());
\r
930 alignPanel.repaint();
\r
933 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
935 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
936 JInternalFrame frame = new JInternalFrame();
\r
937 frame.setContentPane(sp);
\r
938 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
\r
942 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
944 if(viewport.getSelectionGroup().getSize()<2)
\r
945 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
\r
948 JInternalFrame frame = new JInternalFrame();
\r
949 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
950 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
954 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
957 if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
\r
958 || viewport.getAlignment().getHeight()<4)
\r
960 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
\r
961 +"at least 4 input sequences.",
\r
962 "Sequence selection insufficient",
\r
963 JOptionPane.WARNING_MESSAGE);
\r
968 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
969 JInternalFrame frame = new JInternalFrame();
\r
970 frame.setContentPane(pcaPanel);
\r
971 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
\r
972 }catch(java.lang.OutOfMemoryError ex)
\r
974 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
\r
975 "Out of memory", JOptionPane.WARNING_MESSAGE);
\r
981 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
983 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
986 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
988 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
992 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
994 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
997 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
999 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1002 void NewTreePanel(String type, String pwType, String title)
\r
1004 //are the sequences aligned?
\r
1005 if(!viewport.alignment.isAligned())
\r
1007 JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
\r
1008 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
\r
1012 final TreePanel tp;
\r
1013 if (viewport.getSelectionGroup() != null &&
\r
1014 viewport.getSelectionGroup().getSize() > 3)
\r
1016 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1018 0, viewport.alignment.getWidth());
\r
1022 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1023 type, pwType, 0, viewport.alignment.getWidth());
\r
1026 addTreeMenuItem(tp, title);
\r
1028 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1031 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1033 final JMenuItem item = new JMenuItem(title);
\r
1034 sortByTreeMenu.add(item);
\r
1035 item.addActionListener(new java.awt.event.ActionListener()
\r
1037 public void actionPerformed(ActionEvent e)
\r
1039 addHistoryItem("sort");
\r
1040 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1041 alignPanel.repaint();
\r
1045 treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1047 public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
\r
1049 sortByTreeMenu.remove(item);
\r
1056 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
1058 WebserviceInfo info = new WebserviceInfo("Clustal web service",
\r
1059 "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+
\r
1060 " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
\r
1061 +" Nucleic Acids Research, submitted, June 1994.",
\r
1064 ClustalThread thread = new ClustalThread(info);
\r
1068 class ClustalThread extends Thread
\r
1070 WebserviceInfo info;
\r
1071 public ClustalThread(WebserviceInfo info)
\r
1072 {this.info = info; }
\r
1076 info.setStatus(WebserviceInfo.STATE_RUNNING);
\r
1077 jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
\r
1078 Vector sv = viewport.getAlignment().getSequences();
\r
1079 SequenceI[] seqs = new SequenceI[sv.size()];
\r
1084 seqs[i] = (SequenceI) sv.elementAt(i);
\r
1086 while (++i < sv.size());
\r
1088 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
\r
1089 if (alignment != null)
\r
1091 AlignFrame af = new AlignFrame(new Alignment(alignment));
\r
1092 Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),
\r
1093 NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
\r
1094 af.clustalColour_actionPerformed(null);
\r
1095 af.clustalColour.setSelected(true);
\r
1096 info.setStatus(WebserviceInfo.STATE_STOPPED_OK);
\r
1100 info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
\r
1101 info.appendProgressText("Problem obtaining clustal alignment");
\r
1106 protected void jpred_actionPerformed(ActionEvent e)
\r
1109 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
\r
1111 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1112 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1113 if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
\r
1115 JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));
\r
1120 SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
\r
1121 for (int i = 0; i < sz; i++)
\r
1123 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1126 JPredClient ct = new JPredClient(msa);
\r
1132 Vector seqs = viewport.getAlignment().getSequences();
\r
1134 if (seqs.size() == 1 || !viewport.alignment.isAligned())
\r
1136 JPredClient ct = new JPredClient( (SequenceI)
\r
1137 seqs.elementAt(0));
\r
1141 SequenceI[] msa = new SequenceI[seqs.size()];
\r
1142 for (int i = 0; i < seqs.size(); i++)
\r
1144 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1147 JPredClient ct = new JPredClient(msa);
\r
1152 protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
\r
1154 // TODO:resolve which menu item was actually selected
\r
1155 // Now, check we have enough sequences
\r
1156 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
\r
1158 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1159 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1161 SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
\r
1162 for (int i = 0; i < sz; i++)
\r
1164 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1167 MsaWSClient ct = new jalview.ws.MsaWSClient(msa);
\r
1171 Vector seqs = viewport.getAlignment().getSequences();
\r
1173 if (seqs.size() > 1) {
\r
1174 SequenceI[] msa = new SequenceI[seqs.size()];
\r
1175 for (int i = 0; i < seqs.size(); i++)
\r
1177 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1180 MsaWSClient ct = new MsaWSClient(msa);
\r
1186 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
\r
1187 // Pick the tree file
\r
1188 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
1189 getProperty("LAST_DIRECTORY"));
\r
1190 chooser.setFileView(new JalviewFileView());
\r
1191 chooser.setDialogTitle("Select a newick-like tree file");
\r
1192 chooser.setToolTipText("Load a tree file");
\r
1193 int value = chooser.showOpenDialog(null);
\r
1194 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
1196 String choice = chooser.getSelectedFile().getPath();
\r
1197 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1198 TreePanel treepanel = null;
\r
1201 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
\r
1204 if (fin.getTree() != null)
\r
1206 TreePanel tp = null;
\r
1207 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1208 fin, "FromFile", choice);
\r
1209 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1210 addTreeMenuItem(tp, title);
\r
1213 catch (Exception ex)
\r
1215 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1216 "Problem reading tree file",
\r
1218 JOptionPane.WARNING_MESSAGE);
\r
1219 ex.printStackTrace();
\r