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.formatSequences(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.formatSequences(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 AlignmentAnnotation [] old = viewport.alignment.getAlignmentAnnotation();
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236 viewport.setAlignment( new Alignment(seq) );
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237 updateEditMenuBar();
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238 for(int i=0; i<old.length; i++)
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239 viewport.alignment.addAnnotation(old[i]);
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240 viewport.updateConsensus();
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241 viewport.updateConservation();
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242 alignPanel.repaint();
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245 public void moveSelectedSequences(boolean up)
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247 SequenceGroup sg = viewport.getSelectionGroup();
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253 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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255 SequenceI seq = viewport.alignment.getSequenceAt(i);
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256 if (!sg.sequences.contains(seq))
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259 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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260 if (sg.sequences.contains(temp))
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263 viewport.alignment.getSequences().setElementAt(temp, i);
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264 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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269 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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271 SequenceI seq = viewport.alignment.getSequenceAt(i);
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272 if (!sg.sequences.contains(seq))
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275 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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276 if (sg.sequences.contains(temp))
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279 viewport.alignment.getSequences().setElementAt(temp, i);
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280 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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284 alignPanel.repaint();
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289 protected void copy_actionPerformed(ActionEvent e)
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291 if(viewport.getSelectionGroup()==null)
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294 SequenceGroup sg = viewport.getSelectionGroup();
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296 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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297 StringBuffer buffer= new StringBuffer();
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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 buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
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303 +seq.findPosition( sg.getEndRes() )+ "\t"
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304 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
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306 c.setContents( new StringSelection( buffer.toString()) , null ) ;
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311 protected void pasteNew_actionPerformed(ActionEvent e)
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316 protected void pasteThis_actionPerformed(ActionEvent e)
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318 addHistoryItem("Paste");
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322 void paste(boolean newAlignment)
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325 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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326 Transferable contents = c.getContents(this);
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327 if (contents == null)
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330 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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331 StringTokenizer st = new StringTokenizer(str);
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332 ArrayList seqs = new ArrayList();
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333 while (st.hasMoreElements())
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335 String name = st.nextToken();
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336 int start = Integer.parseInt(st.nextToken());
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337 int end = Integer.parseInt(st.nextToken());
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338 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
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341 viewport.alignment.addSequence(sequence);
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343 seqs.add(sequence);
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348 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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349 seqs.toArray(newSeqs);
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350 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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351 Desktop.addInternalFrame(af, "Copied sequences", NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
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355 viewport.setEndSeq(viewport.alignment.getHeight());
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356 viewport.alignment.getWidth();
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357 viewport.updateConservation();
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358 viewport.updateConsensus();
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359 alignPanel.repaint();
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362 }catch(Exception ex){}// could be anything being pasted in here
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367 protected void cut_actionPerformed(ActionEvent e)
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369 copy_actionPerformed(null);
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370 delete_actionPerformed(null);
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373 protected void delete_actionPerformed(ActionEvent e)
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375 addHistoryItem("Delete");
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376 if (viewport.getSelectionGroup() == null)
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379 SequenceGroup sg = viewport.getSelectionGroup();
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380 for (int i=0;i < sg.sequences.size(); i++)
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382 SequenceI seq = sg.getSequenceAt(i);
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383 int index = viewport.getAlignment().findIndex(seq);
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384 seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
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386 if(seq.getSequence().length()<1)
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387 viewport.getAlignment().deleteSequence(seq);
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389 viewport.getAlignment().getSequences().setElementAt(seq, index);
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392 viewport.setSelectionGroup(null);
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393 viewport.alignment.deleteGroup(sg);
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394 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
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395 if(viewport.getAlignment().getHeight()<1)
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398 this.setClosed(true);
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399 }catch(Exception ex){}
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400 viewport.updateConservation();
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401 viewport.updateConsensus();
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402 alignPanel.repaint();
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408 protected void redoMenuItem_actionPerformed(ActionEvent e)
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410 Object [] history = (Object[])redoList.remove(0);
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411 SequenceI[] seq = (SequenceI[]) history[1];
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412 viewport.setAlignment( new Alignment(seq) );
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413 updateEditMenuBar();
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414 viewport.updateConsensus();
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415 alignPanel.repaint();
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416 alignPanel.repaint();
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420 protected void deleteGroups_actionPerformed(ActionEvent e)
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422 viewport.alignment.deleteAllGroups();
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423 viewport.setSelectionGroup(null);
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425 alignPanel.repaint();
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430 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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432 SequenceGroup sg = new SequenceGroup();
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433 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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434 sg.addSequence( viewport.getAlignment().getSequenceAt(i));
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435 sg.setEndRes(viewport.alignment.getWidth());
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436 viewport.setSelectionGroup(sg);
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437 PaintRefresher.Refresh(null);
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440 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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442 viewport.setSelectionGroup(null);
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443 viewport.getColumnSelection().clear();
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444 viewport.setSelectionGroup(null);
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445 PaintRefresher.Refresh(null);
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448 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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450 SequenceGroup sg = viewport.getSelectionGroup();
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451 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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452 sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
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454 PaintRefresher.Refresh(null);
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457 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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459 addHistoryItem("delete columns");
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460 ColumnSelection colSel = viewport.getColumnSelection();
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461 if (colSel.size() > 0)
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463 int min = colSel.getMin();
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464 viewport.getAlignment().trimLeft(min);
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465 colSel.compensateForEdit(0,min);
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467 if(viewport.getSelectionGroup()!=null)
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468 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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470 Vector groups = viewport.alignment.getGroups();
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471 for(int i=0; i<groups.size(); i++)
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473 SequenceGroup sg = (SequenceGroup) groups.get(i);
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474 if(!sg.adjustForRemoveLeft(min))
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475 viewport.alignment.deleteGroup(sg);
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478 alignPanel.repaint();
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482 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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484 addHistoryItem("delete columns");
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485 ColumnSelection colSel = viewport.getColumnSelection();
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486 if (colSel.size() > 0)
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488 int max = colSel.getMax();
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489 viewport.getAlignment().trimRight(max);
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490 if(viewport.getSelectionGroup()!=null)
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491 viewport.getSelectionGroup().adjustForRemoveRight(max);
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493 Vector groups = viewport.alignment.getGroups();
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494 for(int i=0; i<groups.size(); i++)
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496 SequenceGroup sg = (SequenceGroup) groups.get(i);
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497 if(!sg.adjustForRemoveRight(max))
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498 viewport.alignment.deleteGroup(sg);
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503 alignPanel.repaint();
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508 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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510 addHistoryItem("delete gapped columns");
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511 viewport.getAlignment().removeGaps();
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512 viewport.updateConservation();
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513 viewport.updateConsensus();
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514 alignPanel.repaint();
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517 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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519 addHistoryItem("delete all gaps");
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522 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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524 current = viewport.getAlignment().getSequenceAt(i);
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525 jSize = current.getLength();
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526 for (int j=0; j < jSize; j++)
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527 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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529 current.deleteCharAt(j);
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534 viewport.updateConservation();
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535 viewport.updateConsensus();
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536 alignPanel.repaint();
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540 public void findMenuItem_actionPerformed(ActionEvent e)
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542 JInternalFrame frame = new JInternalFrame();
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543 Finder finder = new Finder(viewport, alignPanel, frame);
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544 frame.setContentPane(finder);
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545 Desktop.addInternalFrame(frame, "Find", 340,110, false);
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546 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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551 public void font_actionPerformed(ActionEvent e)
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553 FontChooser fc = new FontChooser( alignPanel );
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556 protected void fullSeqId_actionPerformed(ActionEvent e)
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558 viewport.setShowFullId( fullSeqId.isSelected() );
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560 alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
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561 alignPanel.repaint();
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564 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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566 viewport.setColourText( colourTextMenuItem.isSelected() );
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567 alignPanel.repaint();
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570 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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572 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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573 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
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574 scaleAbove.setVisible( wrapMenuItem.isSelected() );
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575 scaleLeft.setVisible( wrapMenuItem.isSelected() );
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576 scaleRight.setVisible( wrapMenuItem.isSelected() );
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577 alignPanel.repaint();
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580 protected void scaleAbove_actionPerformed(ActionEvent e)
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582 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
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583 alignPanel.repaint();
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586 protected void scaleLeft_actionPerformed(ActionEvent e)
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588 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
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589 alignPanel.repaint();
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592 protected void scaleRight_actionPerformed(ActionEvent e)
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594 viewport.setScaleRightWrapped(scaleRight.isSelected());
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595 alignPanel.repaint();
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600 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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602 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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603 alignPanel.repaint();
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606 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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608 viewport.setShowText( viewTextMenuItem.isSelected() );
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609 alignPanel.repaint();
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613 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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615 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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616 alignPanel.repaint();
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619 public void sequenceFeatures_actionPerformed(ActionEvent evt)
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621 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
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622 if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
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624 SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);
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625 ((Alignment)viewport.alignment).featuresAdded = true;
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627 alignPanel.repaint();
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630 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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632 if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
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634 annotationPanelMenuItem.setSelected(false);
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637 viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
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638 alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
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641 public void overviewMenuItem_actionPerformed(ActionEvent e)
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643 if (alignPanel.overviewPanel != null)
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646 JInternalFrame frame = new JInternalFrame();
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647 OverviewPanel overview = new OverviewPanel(alignPanel);
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648 frame.setContentPane(overview);
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649 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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650 frame.getWidth(), frame.getHeight());
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652 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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653 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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654 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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656 alignPanel.setOverviewPanel(null);
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660 alignPanel.setOverviewPanel( overview );
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665 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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667 changeColour( null );
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671 public void clustalColour_actionPerformed(ActionEvent e)
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673 abovePIDThreshold.setSelected(false);
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674 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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677 public void zappoColour_actionPerformed(ActionEvent e)
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679 changeColour(new ZappoColourScheme());
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682 public void taylorColour_actionPerformed(ActionEvent e)
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684 changeColour(new TaylorColourScheme());
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688 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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690 changeColour( new HydrophobicColourScheme() );
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693 public void helixColour_actionPerformed(ActionEvent e)
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695 changeColour(new HelixColourScheme() );
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699 public void strandColour_actionPerformed(ActionEvent e)
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701 changeColour(new StrandColourScheme());
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705 public void turnColour_actionPerformed(ActionEvent e)
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707 changeColour(new TurnColourScheme());
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711 public void buriedColour_actionPerformed(ActionEvent e)
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713 changeColour(new BuriedColourScheme() );
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716 public void nucleotideColour_actionPerformed(ActionEvent e)
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718 changeColour(new NucleotideColourScheme());
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722 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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724 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
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729 void changeColour(ColourSchemeI cs)
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733 if ( viewport.getAbovePIDThreshold() )
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735 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
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737 if (cs instanceof ResidueColourScheme)
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738 ( (ResidueColourScheme) cs).setThreshold(threshold);
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739 else if (cs instanceof ScoreColourScheme)
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740 ( (ScoreColourScheme) cs).setThreshold(threshold);
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742 viewport.setGlobalColourScheme(cs);
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744 else if (cs instanceof ResidueColourScheme)
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745 ( (ResidueColourScheme) cs).setThreshold(0);
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746 else if (cs instanceof ScoreColourScheme)
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747 ( (ScoreColourScheme) cs).setThreshold(0);
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751 if (viewport.getConservationSelected())
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753 ConservationColourScheme ccs = null;
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755 Alignment al = (Alignment) viewport.alignment;
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756 Conservation c = new Conservation("All",
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757 ResidueProperties.propHash, 3,
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758 al.getSequences(), 0,
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759 al.getWidth() - 1);
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762 c.verdict(false, viewport.ConsPercGaps);
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764 ccs = new ConservationColourScheme(c, cs);
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766 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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767 ccs.setConsensus( viewport.vconsensus );
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768 viewport.setGlobalColourScheme(ccs);
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770 SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
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775 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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777 cs.setConsensus(viewport.vconsensus);
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778 viewport.setGlobalColourScheme(cs);
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782 if(viewport.getColourAppliesToAllGroups())
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784 Vector groups = viewport.alignment.getGroups();
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785 for(int i=0; i<groups.size(); i++)
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787 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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789 if (cs instanceof ClustalxColourScheme)
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791 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
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796 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
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798 catch (Exception ex)
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800 ex.printStackTrace();
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804 if(viewport.getAbovePIDThreshold())
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806 if (sg.cs instanceof ResidueColourScheme)
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807 ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
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808 else if (sg.cs instanceof ScoreColourScheme)
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809 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
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811 sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
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814 if( viewport.getConservationSelected() )
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816 Conservation c = new Conservation("Group",
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817 ResidueProperties.propHash, 3,
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818 sg.sequences, 0, viewport.alignment.getWidth()-1);
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820 c.verdict(false, viewport.ConsPercGaps);
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821 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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823 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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824 ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
829 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
830 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
836 if(alignPanel.getOverviewPanel()!=null)
\r
837 alignPanel.getOverviewPanel().updateOverviewImage();
\r
838 alignPanel.repaint();
\r
841 protected void modifyPID_actionPerformed(ActionEvent e)
\r
843 if(viewport.getAbovePIDThreshold())
\r
845 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
847 SliderPanel.showPIDSlider();
\r
851 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
853 if(viewport.getConservationSelected())
\r
855 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
857 SliderPanel.showConservationSlider();
\r
862 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
864 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
866 viewport.setAbovePIDThreshold(false);
\r
867 abovePIDThreshold.setSelected(false);
\r
869 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
870 if(cs instanceof ConservationColourScheme )
\r
871 changeColour( ((ConservationColourScheme)cs).cs );
\r
873 changeColour( cs );
\r
875 modifyConservation_actionPerformed(null);
\r
878 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
880 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
882 conservationMenuItem.setSelected(false);
\r
883 viewport.setConservationSelected(false);
\r
885 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
887 if(cs instanceof ConservationColourScheme )
\r
888 changeColour( ((ConservationColourScheme)cs).cs );
\r
890 changeColour( cs );
\r
892 modifyPID_actionPerformed(null);
\r
897 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
899 UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
\r
902 public void PIDColour_actionPerformed(ActionEvent e)
\r
904 changeColour( new PIDColourScheme() );
\r
908 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
910 changeColour(new Blosum62ColourScheme() );
\r
915 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
917 addHistoryItem("sort");
\r
918 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
\r
919 alignPanel.repaint();
\r
922 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
924 addHistoryItem("sort");
\r
925 AlignmentSorter.sortByID( viewport.getAlignment() );
\r
926 alignPanel.repaint();
\r
929 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
931 addHistoryItem("sort");
\r
932 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
933 AlignmentSorter.sortGroups(viewport.getAlignment());
\r
934 alignPanel.repaint();
\r
937 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
939 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
940 JInternalFrame frame = new JInternalFrame();
\r
941 frame.setContentPane(sp);
\r
942 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
\r
946 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
948 if(viewport.getSelectionGroup().getSize()<2)
\r
949 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
\r
952 JInternalFrame frame = new JInternalFrame();
\r
953 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
954 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
958 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
961 if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
\r
962 || viewport.getAlignment().getHeight()<4)
\r
964 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
\r
965 +"at least 4 input sequences.",
\r
966 "Sequence selection insufficient",
\r
967 JOptionPane.WARNING_MESSAGE);
\r
972 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
973 JInternalFrame frame = new JInternalFrame();
\r
974 frame.setContentPane(pcaPanel);
\r
975 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
\r
976 }catch(java.lang.OutOfMemoryError ex)
\r
978 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
\r
979 "Out of memory", JOptionPane.WARNING_MESSAGE);
\r
985 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
987 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
990 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
992 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
996 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
998 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1001 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1003 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1006 void NewTreePanel(String type, String pwType, String title)
\r
1008 //are the sequences aligned?
\r
1009 if(!viewport.alignment.isAligned())
\r
1011 JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
\r
1012 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
\r
1016 final TreePanel tp;
\r
1017 if (viewport.getSelectionGroup() != null &&
\r
1018 viewport.getSelectionGroup().getSize() > 3)
\r
1020 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1022 0, viewport.alignment.getWidth());
\r
1026 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1027 type, pwType, 0, viewport.alignment.getWidth());
\r
1030 addTreeMenuItem(tp, title);
\r
1032 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1035 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1037 final JMenuItem item = new JMenuItem(title);
\r
1038 sortByTreeMenu.add(item);
\r
1039 item.addActionListener(new java.awt.event.ActionListener()
\r
1041 public void actionPerformed(ActionEvent e)
\r
1043 addHistoryItem("sort");
\r
1044 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1045 alignPanel.repaint();
\r
1049 treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1051 public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
\r
1053 sortByTreeMenu.remove(item);
\r
1060 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
1062 WebserviceInfo info = new WebserviceInfo("Clustal web service",
\r
1063 "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+
\r
1064 " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
\r
1065 +" Nucleic Acids Research, submitted, June 1994.",
\r
1068 ClustalThread thread = new ClustalThread(info);
\r
1072 class ClustalThread extends Thread
\r
1074 WebserviceInfo info;
\r
1075 public ClustalThread(WebserviceInfo info)
\r
1076 {this.info = info; }
\r
1080 info.setStatus(WebserviceInfo.STATE_RUNNING);
\r
1081 jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
\r
1082 Vector sv = viewport.getAlignment().getSequences();
\r
1083 SequenceI[] seqs = new SequenceI[sv.size()];
\r
1088 seqs[i] = (SequenceI) sv.elementAt(i);
\r
1090 while (++i < sv.size());
\r
1092 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
\r
1093 if (alignment != null)
\r
1095 AlignFrame af = new AlignFrame(new Alignment(alignment));
\r
1096 Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),
\r
1097 NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
\r
1098 af.clustalColour_actionPerformed(null);
\r
1099 af.clustalColour.setSelected(true);
\r
1100 info.setStatus(WebserviceInfo.STATE_STOPPED_OK);
\r
1104 info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
\r
1105 info.appendProgressText("Problem obtaining clustal alignment");
\r
1110 protected void jpred_actionPerformed(ActionEvent e)
\r
1113 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
\r
1115 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1116 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1117 if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
\r
1119 JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));
\r
1124 SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
\r
1125 for (int i = 0; i < sz; i++)
\r
1127 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1130 JPredClient ct = new JPredClient(msa);
\r
1136 Vector seqs = viewport.getAlignment().getSequences();
\r
1138 if (seqs.size() == 1 || !viewport.alignment.isAligned())
\r
1140 JPredClient ct = new JPredClient( (SequenceI)
\r
1141 seqs.elementAt(0));
\r
1145 SequenceI[] msa = new SequenceI[seqs.size()];
\r
1146 for (int i = 0; i < seqs.size(); i++)
\r
1148 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1151 JPredClient ct = new JPredClient(msa);
\r
1156 protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
\r
1158 // TODO:resolve which menu item was actually selected
\r
1159 // Now, check we have enough sequences
\r
1160 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
\r
1162 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1163 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1165 SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
\r
1166 for (int i = 0; i < sz; i++)
\r
1168 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1171 MsaWSClient ct = new jalview.ws.MsaWSClient(msa);
\r
1175 Vector seqs = viewport.getAlignment().getSequences();
\r
1177 if (seqs.size() > 1) {
\r
1178 SequenceI[] msa = new SequenceI[seqs.size()];
\r
1179 for (int i = 0; i < seqs.size(); i++)
\r
1181 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1184 MsaWSClient ct = new MsaWSClient(msa);
\r
1190 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
\r
1191 // Pick the tree file
\r
1192 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
1193 getProperty("LAST_DIRECTORY"));
\r
1194 chooser.setFileView(new JalviewFileView());
\r
1195 chooser.setDialogTitle("Select a newick-like tree file");
\r
1196 chooser.setToolTipText("Load a tree file");
\r
1197 int value = chooser.showOpenDialog(null);
\r
1198 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
1200 String choice = chooser.getSelectedFile().getPath();
\r
1201 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1202 TreePanel treepanel = null;
\r
1205 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
\r
1208 if (fin.getTree() != null)
\r
1210 TreePanel tp = null;
\r
1211 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1212 fin, "FromFile", choice);
\r
1213 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1214 addTreeMenuItem(tp, title);
\r
1217 catch (Exception ex)
\r
1219 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1220 "Problem reading tree file",
\r
1222 JOptionPane.WARNING_MESSAGE);
\r
1223 ex.printStackTrace();
\r