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 alignMenu.setVisible(false);
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43 catch(java.net.UnknownHostException e){}
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44 viewport = new AlignViewport(al,true,true,false);
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46 String fontName = jalview.bin.Cache.getProperty("FONT_NAME");
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47 String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");
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48 String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");
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49 if(fontName!=null && fontStyle!=null && fontSize!=null)
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50 viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );
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52 // add conservation graph to alignment
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53 viewport.updateConservation();
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54 viewport.updateConsensus();
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57 alignPanel = new AlignmentPanel(this, viewport);
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59 alignPanel.annotationPanel.adjustPanelHeight();
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60 alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
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61 alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
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63 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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66 addInternalFrameListener(new InternalFrameAdapter()
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68 public void internalFrameActivated(InternalFrameEvent evt)
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70 javax.swing.SwingUtilities.invokeLater(new Runnable()
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73 { alignPanel.requestFocus(); }
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81 protected void saveAs_actionPerformed(ActionEvent e)
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83 String suffix [] = null;
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84 if(e.getActionCommand().equals("FASTA"))
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85 suffix = new String[]{"fa", "fasta"};
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86 else if(e.getActionCommand().equals("MSF"))
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87 suffix = new String[]{"msf"};
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88 else if(e.getActionCommand().equals("CLUSTAL"))
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89 suffix = new String[]{"aln"};
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90 else if(e.getActionCommand().equals("BLC"))
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91 suffix = new String[]{"blc"};
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92 else if(e.getActionCommand().equals("PIR"))
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93 suffix = new String[]{"pir"};
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94 else if(e.getActionCommand().equals("PFAM"))
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95 suffix = new String[]{"pfam"};
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98 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
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99 , suffix, e.getActionCommand()+" file");
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100 chooser.setFileView(new JalviewFileView());
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101 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
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102 chooser.setToolTipText("Save");
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103 int value = chooser.showSaveDialog(this);
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104 if(value == JalviewFileChooser.APPROVE_OPTION)
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106 String choice = chooser.getSelectedFile().getPath();
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107 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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108 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
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110 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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111 out.println(output);
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114 catch(Exception ex){}
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119 protected void outputText_actionPerformed(ActionEvent e)
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121 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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122 JInternalFrame frame = new JInternalFrame();
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123 cap.formatForOutput();
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124 frame.setContentPane(cap);
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125 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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126 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
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129 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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131 HTMLOutput htmlOutput = new HTMLOutput(viewport);
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135 protected void createPNG_actionPerformed(ActionEvent e)
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137 alignPanel.makePNG();
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140 protected void epsFile_actionPerformed(ActionEvent e)
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142 alignPanel.makeEPS();
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146 public void printMenuItem_actionPerformed(ActionEvent e)
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148 //Putting in a thread avoids Swing painting problems
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149 PrintThread thread = new PrintThread();
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153 class PrintThread extends Thread
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157 PrinterJob printJob = PrinterJob.getPrinterJob();
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158 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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159 printJob.setPrintable(alignPanel, pf);
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160 if (printJob.printDialog())
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166 catch (Exception PrintException)
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168 PrintException.printStackTrace();
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178 public void closeMenuItem_actionPerformed(ActionEvent e)
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181 this.setClosed(true);
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182 }catch(Exception ex){}
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185 Stack historyList = new Stack();
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186 Stack redoList = new Stack();
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187 JMenuBar jMenuBar1 = new JMenuBar();
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189 void updateEditMenuBar()
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191 if(historyList.size()>0)
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193 undoMenuItem.setEnabled(true);
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194 Object [] history = (Object[])historyList.get(0);
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195 undoMenuItem.setText("Undo "+history[0]);
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199 undoMenuItem.setEnabled(false);
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200 undoMenuItem.setText("Undo");
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203 if(redoList.size()>0)
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205 redoMenuItem.setEnabled(true);
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206 Object [] history = (Object[])redoList.get(0);
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207 redoMenuItem.setText("Redo "+history[0]);
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211 redoMenuItem.setEnabled(false);
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212 redoMenuItem.setText("Redo");
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216 public void addHistoryItem(String type)
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218 // must make sure we add new sequence objects her, not refs to the existing sequences
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220 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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221 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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223 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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224 viewport.getAlignment().getSequenceAt(i).getSequence());
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227 historyList.add(0, new Object[]{type, seq} );
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228 updateEditMenuBar();
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231 protected void undoMenuItem_actionPerformed(ActionEvent e)
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233 Object [] history = (Object[])historyList.remove(0);
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234 // add the redo state before continuing!!
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235 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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236 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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238 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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239 viewport.getAlignment().getSequenceAt(i).
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244 redoList.add(0, new Object[] {history[0], seq});
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246 seq = (SequenceI[]) history[1];
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247 viewport.setAlignment( new Alignment(seq) );
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248 updateEditMenuBar();
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249 viewport.updateConsensus();
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250 alignPanel.repaint();
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253 public void moveSelectedSequences(boolean up)
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255 SequenceGroup sg = viewport.getSelectionGroup();
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261 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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263 SequenceI seq = viewport.alignment.getSequenceAt(i);
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264 if (!sg.sequences.contains(seq))
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267 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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268 if (sg.sequences.contains(temp))
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271 viewport.alignment.getSequences().setElementAt(temp, i);
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272 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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277 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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279 SequenceI seq = viewport.alignment.getSequenceAt(i);
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280 if (!sg.sequences.contains(seq))
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283 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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284 if (sg.sequences.contains(temp))
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287 viewport.alignment.getSequences().setElementAt(temp, i);
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288 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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292 alignPanel.repaint();
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297 protected void copy_actionPerformed(ActionEvent e)
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299 if(viewport.getSelectionGroup()==null)
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302 SequenceGroup sg = viewport.getSelectionGroup();
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304 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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305 StringBuffer buffer= new StringBuffer();
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307 for(int i=0; i<sg.getSize(); i++)
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309 SequenceI seq = sg.getSequenceAt(i);
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310 buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
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311 +seq.findPosition( sg.getEndRes() )+ "\t"
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312 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
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314 c.setContents( new StringSelection( buffer.toString()) , null ) ;
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319 protected void pasteNew_actionPerformed(ActionEvent e)
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324 protected void pasteThis_actionPerformed(ActionEvent e)
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326 addHistoryItem("Paste");
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330 void paste(boolean newAlignment)
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333 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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334 Transferable contents = c.getContents(this);
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335 if (contents == null)
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338 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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339 StringTokenizer st = new StringTokenizer(str);
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340 ArrayList seqs = new ArrayList();
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341 while (st.hasMoreElements())
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343 String name = st.nextToken();
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344 int start = Integer.parseInt(st.nextToken());
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345 int end = Integer.parseInt(st.nextToken());
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346 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
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349 viewport.alignment.addSequence(sequence);
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351 seqs.add(sequence);
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356 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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357 seqs.toArray(newSeqs);
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358 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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359 Desktop.addInternalFrame(af, "Copied sequences", NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
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363 viewport.setEndSeq(viewport.alignment.getHeight());
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364 viewport.alignment.getWidth();
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365 viewport.updateConservation();
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366 viewport.updateConsensus();
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367 alignPanel.repaint();
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370 }catch(Exception ex){}// could be anything being pasted in here
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375 protected void cut_actionPerformed(ActionEvent e)
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377 copy_actionPerformed(null);
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378 delete_actionPerformed(null);
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381 protected void delete_actionPerformed(ActionEvent e)
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383 addHistoryItem("Delete");
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384 if (viewport.getSelectionGroup() == null)
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387 SequenceGroup sg = viewport.getSelectionGroup();
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388 for (int i=0;i < sg.sequences.size(); i++)
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390 SequenceI seq = sg.getSequenceAt(i);
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391 int index = viewport.getAlignment().findIndex(seq);
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392 seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
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394 if(seq.getSequence().length()<1)
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395 viewport.getAlignment().deleteSequence(seq);
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397 viewport.getAlignment().getSequences().setElementAt(seq, index);
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400 viewport.setSelectionGroup(null);
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401 viewport.alignment.deleteGroup(sg);
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402 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
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403 if(viewport.getAlignment().getHeight()<1)
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406 this.setClosed(true);
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407 }catch(Exception ex){}
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408 viewport.updateConservation();
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409 viewport.updateConsensus();
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410 alignPanel.repaint();
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416 protected void redoMenuItem_actionPerformed(ActionEvent e)
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418 Object [] history = (Object[])redoList.remove(0);
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419 SequenceI[] seq = (SequenceI[]) history[1];
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420 viewport.setAlignment( new Alignment(seq) );
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421 updateEditMenuBar();
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422 viewport.updateConsensus();
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423 alignPanel.repaint();
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424 alignPanel.repaint();
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428 protected void deleteGroups_actionPerformed(ActionEvent e)
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430 viewport.alignment.deleteAllGroups();
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431 viewport.setSelectionGroup(null);
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433 alignPanel.repaint();
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438 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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440 SequenceGroup sg = new SequenceGroup();
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441 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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442 sg.addSequence( viewport.getAlignment().getSequenceAt(i));
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443 sg.setEndRes(viewport.alignment.getWidth());
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444 viewport.setSelectionGroup(sg);
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445 PaintRefresher.Refresh(null);
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448 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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450 viewport.setSelectionGroup(null);
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451 PaintRefresher.Refresh(null);
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454 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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456 SequenceGroup sg = viewport.getSelectionGroup();
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457 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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458 sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
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460 PaintRefresher.Refresh(null);
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464 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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466 viewport.getColumnSelection().clear();
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470 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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472 addHistoryItem("delete columns");
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473 ColumnSelection colSel = viewport.getColumnSelection();
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474 if (colSel.size() > 0)
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476 int min = colSel.getMin();
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477 viewport.getAlignment().trimLeft(min);
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478 colSel.compensateForEdit(0,min);
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480 if(viewport.getSelectionGroup()!=null)
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481 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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483 Vector groups = viewport.alignment.getGroups();
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484 for(int i=0; i<groups.size(); i++)
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486 SequenceGroup sg = (SequenceGroup) groups.get(i);
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487 if(!sg.adjustForRemoveLeft(min))
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488 viewport.alignment.deleteGroup(sg);
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491 alignPanel.repaint();
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495 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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497 addHistoryItem("delete columns");
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498 ColumnSelection colSel = viewport.getColumnSelection();
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499 if (colSel.size() > 0)
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501 int max = colSel.getMax();
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502 viewport.getAlignment().trimRight(max);
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503 if(viewport.getSelectionGroup()!=null)
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504 viewport.getSelectionGroup().adjustForRemoveRight(max);
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506 Vector groups = viewport.alignment.getGroups();
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507 for(int i=0; i<groups.size(); i++)
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509 SequenceGroup sg = (SequenceGroup) groups.get(i);
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510 if(!sg.adjustForRemoveRight(max))
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511 viewport.alignment.deleteGroup(sg);
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516 alignPanel.repaint();
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521 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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523 addHistoryItem("delete gapped columns");
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524 viewport.getAlignment().removeGaps();
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525 viewport.updateConservation();
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526 viewport.updateConsensus();
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527 alignPanel.repaint();
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530 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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532 addHistoryItem("delete all gaps");
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535 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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537 current = viewport.getAlignment().getSequenceAt(i);
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538 jSize = current.getLength();
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539 for (int j=0; j < jSize; j++)
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540 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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542 current.deleteCharAt(j);
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547 viewport.updateConservation();
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548 viewport.updateConsensus();
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549 alignPanel.repaint();
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552 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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554 char thisChar = '-';
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555 char nextChar = '.';
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556 if(viewport.getGapCharacter()=='-')
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561 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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562 viewport.setGapCharacter(thisChar);
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563 alignPanel.repaint();
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566 public void findMenuItem_actionPerformed(ActionEvent e)
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568 JInternalFrame frame = new JInternalFrame();
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569 Finder finder = new Finder(viewport, alignPanel, frame);
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570 frame.setContentPane(finder);
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571 Desktop.addInternalFrame(frame, "Find", 340,110, false);
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572 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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577 public void font_actionPerformed(ActionEvent e)
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579 JInternalFrame frame = new JInternalFrame();
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580 FontChooser fc = new FontChooser( alignPanel, frame );
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581 frame.setContentPane(fc);
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582 Desktop.addInternalFrame(frame, "Change Font", 480,100, false);
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583 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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584 if(alignPanel.getOverviewPanel()!=null)
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585 alignPanel.getOverviewPanel().updateOverviewImage();
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588 protected void fullSeqId_actionPerformed(ActionEvent e)
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590 viewport.setShowFullId( fullSeqId.isSelected() );
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592 alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
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593 alignPanel.repaint();
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596 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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598 viewport.setColourText( colourTextMenuItem.isSelected() );
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599 alignPanel.repaint();
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602 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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604 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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605 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
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606 scaleAbove.setVisible( wrapMenuItem.isSelected() );
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607 scaleLeft.setVisible( wrapMenuItem.isSelected() );
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608 scaleRight.setVisible( wrapMenuItem.isSelected() );
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609 alignPanel.repaint();
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612 protected void scaleAbove_actionPerformed(ActionEvent e)
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614 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
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615 alignPanel.repaint();
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618 protected void scaleLeft_actionPerformed(ActionEvent e)
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620 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
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621 alignPanel.repaint();
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624 protected void scaleRight_actionPerformed(ActionEvent e)
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626 viewport.setScaleRightWrapped(scaleRight.isSelected());
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627 alignPanel.repaint();
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632 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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634 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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635 alignPanel.repaint();
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638 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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640 viewport.setShowText( viewTextMenuItem.isSelected() );
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641 alignPanel.repaint();
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645 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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647 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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648 alignPanel.repaint();
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651 public void sequenceFeatures_actionPerformed(ActionEvent evt)
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653 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
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654 if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
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656 AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
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657 ((Alignment)viewport.alignment).featuresAdded = true;
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659 alignPanel.repaint();
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662 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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664 if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
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666 annotationPanelMenuItem.setSelected(false);
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669 viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
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670 alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
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673 public void overviewMenuItem_actionPerformed(ActionEvent e)
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675 if (alignPanel.overviewPanel != null)
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678 JInternalFrame frame = new JInternalFrame();
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679 OverviewPanel overview = new OverviewPanel(alignPanel);
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680 frame.setContentPane(overview);
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681 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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682 frame.getWidth(), frame.getHeight());
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684 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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685 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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686 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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688 alignPanel.setOverviewPanel(null);
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692 alignPanel.setOverviewPanel( overview );
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697 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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699 changeColour( null );
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703 public void clustalColour_actionPerformed(ActionEvent e)
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705 abovePIDThreshold.setSelected(false);
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706 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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709 public void zappoColour_actionPerformed(ActionEvent e)
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711 changeColour(new ZappoColourScheme());
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714 public void taylorColour_actionPerformed(ActionEvent e)
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716 changeColour(new TaylorColourScheme());
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720 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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722 changeColour( new HydrophobicColourScheme() );
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725 public void helixColour_actionPerformed(ActionEvent e)
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727 changeColour(new HelixColourScheme() );
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731 public void strandColour_actionPerformed(ActionEvent e)
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733 changeColour(new StrandColourScheme());
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737 public void turnColour_actionPerformed(ActionEvent e)
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739 changeColour(new TurnColourScheme());
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743 public void buriedColour_actionPerformed(ActionEvent e)
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745 changeColour(new BuriedColourScheme() );
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748 public void nucleotideColour_actionPerformed(ActionEvent e)
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750 changeColour(new NucleotideColourScheme());
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754 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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756 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
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761 void changeColour(ColourSchemeI cs)
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765 if ( viewport.getAbovePIDThreshold() )
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767 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
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769 if (cs instanceof ResidueColourScheme)
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770 ( (ResidueColourScheme) cs).setThreshold(threshold);
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771 else if (cs instanceof ScoreColourScheme)
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772 ( (ScoreColourScheme) cs).setThreshold(threshold);
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774 viewport.setGlobalColourScheme(cs);
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776 else if (cs instanceof ResidueColourScheme)
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777 ( (ResidueColourScheme) cs).setThreshold(0);
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778 else if (cs instanceof ScoreColourScheme)
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779 ( (ScoreColourScheme) cs).setThreshold(0);
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783 if (viewport.getConservationSelected())
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785 ConservationColourScheme ccs = null;
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787 Alignment al = (Alignment) viewport.alignment;
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788 Conservation c = new Conservation("All",
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789 ResidueProperties.propHash, 3,
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790 al.getSequences(), 0,
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791 al.getWidth() - 1);
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794 c.verdict(false, viewport.ConsPercGaps);
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796 ccs = new ConservationColourScheme(c, cs);
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798 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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799 ccs.setConsensus( viewport.vconsensus );
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800 viewport.setGlobalColourScheme(ccs);
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802 SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
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807 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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809 cs.setConsensus(viewport.vconsensus);
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810 viewport.setGlobalColourScheme(cs);
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814 if(viewport.getColourAppliesToAllGroups())
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816 Vector groups = viewport.alignment.getGroups();
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817 for(int i=0; i<groups.size(); i++)
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819 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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821 if (cs instanceof ClustalxColourScheme)
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823 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
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828 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
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830 catch (Exception ex)
\r
832 ex.printStackTrace();
\r
836 if(viewport.getAbovePIDThreshold())
\r
838 if (sg.cs instanceof ResidueColourScheme)
\r
839 ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
\r
840 else if (sg.cs instanceof ScoreColourScheme)
\r
841 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
\r
843 sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
\r
846 if( viewport.getConservationSelected() )
\r
848 Conservation c = new Conservation("Group",
\r
849 ResidueProperties.propHash, 3,
\r
850 sg.sequences, 0, viewport.alignment.getWidth()-1);
\r
852 c.verdict(false, viewport.ConsPercGaps);
\r
853 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
\r
855 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
856 ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
861 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
862 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
868 if(alignPanel.getOverviewPanel()!=null)
\r
869 alignPanel.getOverviewPanel().updateOverviewImage();
\r
870 alignPanel.repaint();
\r
873 protected void modifyPID_actionPerformed(ActionEvent e)
\r
875 if(viewport.getAbovePIDThreshold())
\r
877 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
879 SliderPanel.showPIDSlider();
\r
883 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
885 if(viewport.getConservationSelected())
\r
887 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
889 SliderPanel.showConservationSlider();
\r
894 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
896 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
898 viewport.setAbovePIDThreshold(false);
\r
899 abovePIDThreshold.setSelected(false);
\r
901 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
902 if(cs instanceof ConservationColourScheme )
\r
903 changeColour( ((ConservationColourScheme)cs).cs );
\r
905 changeColour( cs );
\r
907 modifyConservation_actionPerformed(null);
\r
910 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
912 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
914 conservationMenuItem.setSelected(false);
\r
915 viewport.setConservationSelected(false);
\r
917 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
919 if(cs instanceof ConservationColourScheme )
\r
920 changeColour( ((ConservationColourScheme)cs).cs );
\r
922 changeColour( cs );
\r
924 modifyPID_actionPerformed(null);
\r
929 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
931 JInternalFrame frame = new JInternalFrame();
\r
932 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
\r
933 frame.setContentPane(chooser);
\r
934 Desktop.addInternalFrame(frame,"User defined colours", 450,540, false );
\r
937 public void PIDColour_actionPerformed(ActionEvent e)
\r
939 changeColour( new PIDColourScheme() );
\r
943 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
945 changeColour(new Blosum62ColourScheme() );
\r
950 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
952 addHistoryItem("sort");
\r
953 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
\r
954 alignPanel.repaint();
\r
957 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
959 addHistoryItem("sort");
\r
960 AlignmentSorter.sortByID( viewport.getAlignment() );
\r
961 alignPanel.repaint();
\r
964 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
966 addHistoryItem("sort");
\r
967 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
968 AlignmentSorter.sortGroups(viewport.getAlignment());
\r
969 alignPanel.repaint();
\r
972 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
974 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
975 JInternalFrame frame = new JInternalFrame();
\r
976 frame.setContentPane(sp);
\r
977 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
\r
981 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
983 if(viewport.getSelectionGroup().getSize()<2)
\r
984 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
\r
987 JInternalFrame frame = new JInternalFrame();
\r
988 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
989 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
993 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
996 if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
\r
997 || viewport.getAlignment().getHeight()<4)
\r
999 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
\r
1000 +"at least 4 input sequences.",
\r
1001 "Sequence selection insufficient",
\r
1002 JOptionPane.WARNING_MESSAGE);
\r
1007 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
1008 JInternalFrame frame = new JInternalFrame();
\r
1009 frame.setContentPane(pcaPanel);
\r
1010 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
\r
1011 }catch(java.lang.OutOfMemoryError ex)
\r
1013 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
\r
1014 "Out of memory", JOptionPane.WARNING_MESSAGE);
\r
1020 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1022 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1025 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1027 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1031 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1033 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1036 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1038 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1041 void NewTreePanel(String type, String pwType, String title)
\r
1043 //are the sequences aligned?
\r
1044 if(!viewport.alignment.isAligned())
\r
1046 JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
\r
1047 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
\r
1051 final TreePanel tp;
\r
1052 if (viewport.getSelectionGroup() != null &&
\r
1053 viewport.getSelectionGroup().getSize() > 3)
\r
1055 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1057 0, viewport.alignment.getWidth());
\r
1061 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1062 type, pwType, 0, viewport.alignment.getWidth());
\r
1065 addTreeMenuItem(tp, title);
\r
1067 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1070 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1072 final JMenuItem item = new JMenuItem(title);
\r
1073 sortByTreeMenu.add(item);
\r
1074 item.addActionListener(new java.awt.event.ActionListener()
\r
1076 public void actionPerformed(ActionEvent e)
\r
1078 addHistoryItem("sort");
\r
1079 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1080 alignPanel.repaint();
\r
1084 treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1086 public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
\r
1088 sortByTreeMenu.remove(item);
\r
1095 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
1097 WebserviceInfo info = new WebserviceInfo("Clustal web service",
\r
1098 "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+
\r
1099 " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
\r
1100 +" Nucleic Acids Research, submitted, June 1994.",
\r
1103 ClustalThread thread = new ClustalThread(info);
\r
1107 class ClustalThread extends Thread
\r
1109 WebserviceInfo info;
\r
1110 public ClustalThread(WebserviceInfo info)
\r
1111 {this.info = info; }
\r
1115 info.setStatus(WebserviceInfo.STATE_RUNNING);
\r
1116 jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
\r
1117 Vector sv = viewport.getAlignment().getSequences();
\r
1118 SequenceI[] seqs = new SequenceI[sv.size()];
\r
1123 seqs[i] = (SequenceI) sv.elementAt(i);
\r
1125 while (++i < sv.size());
\r
1127 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
\r
1128 if (alignment != null)
\r
1130 AlignFrame af = new AlignFrame(new Alignment(alignment));
\r
1131 Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),
\r
1132 NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
\r
1133 af.clustalColour_actionPerformed(null);
\r
1134 af.clustalColour.setSelected(true);
\r
1135 info.setStatus(WebserviceInfo.STATE_STOPPED_OK);
\r
1139 info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
\r
1140 info.appendProgressText("Problem obtaining clustal alignment");
\r
1145 protected void jpred_actionPerformed(ActionEvent e)
\r
1148 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
\r
1150 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1151 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1152 if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
\r
1154 JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));
\r
1159 SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
\r
1160 for (int i = 0; i < sz; i++)
\r
1162 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1165 JPredClient ct = new JPredClient(msa);
\r
1171 Vector seqs = viewport.getAlignment().getSequences();
\r
1173 if (seqs.size() == 1 || !viewport.alignment.isAligned())
\r
1175 JPredClient ct = new JPredClient( (SequenceI)
\r
1176 seqs.elementAt(0));
\r
1180 SequenceI[] msa = new SequenceI[seqs.size()];
\r
1181 for (int i = 0; i < seqs.size(); i++)
\r
1183 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1186 JPredClient ct = new JPredClient(msa);
\r
1191 protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
\r
1193 // TODO:resolve which menu item was actually selected
\r
1194 // Now, check we have enough sequences
\r
1195 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
\r
1197 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1198 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1200 SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
\r
1201 for (int i = 0; i < sz; i++)
\r
1203 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1206 MsaWSClient ct = new jalview.ws.MsaWSClient(msa);
\r
1210 Vector seqs = viewport.getAlignment().getSequences();
\r
1212 if (seqs.size() > 1) {
\r
1213 SequenceI[] msa = new SequenceI[seqs.size()];
\r
1214 for (int i = 0; i < seqs.size(); i++)
\r
1216 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1219 MsaWSClient ct = new MsaWSClient(msa);
\r
1225 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
\r
1226 // Pick the tree file
\r
1227 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
1228 getProperty("LAST_DIRECTORY"));
\r
1229 chooser.setFileView(new JalviewFileView());
\r
1230 chooser.setDialogTitle("Select a newick-like tree file");
\r
1231 chooser.setToolTipText("Load a tree file");
\r
1232 int value = chooser.showOpenDialog(null);
\r
1233 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
1235 String choice = chooser.getSelectedFile().getPath();
\r
1236 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1237 TreePanel treepanel = null;
\r
1240 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
\r
1243 if (fin.getTree() != null)
\r
1245 TreePanel tp = null;
\r
1246 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1247 fin, "FromFile", choice);
\r
1248 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1249 addTreeMenuItem(tp, title);
\r
1252 catch (Exception ex)
\r
1254 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1255 "Problem reading tree file",
\r
1257 JOptionPane.WARNING_MESSAGE);
\r
1258 ex.printStackTrace();
\r