1 /********************
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2 * 2004 Jalview Reengineered
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12 package jalview.gui;
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14 import jalview.jbgui.GAlignFrame;
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15 import jalview.schemes.*;
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16 import jalview.datamodel.*;
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17 import jalview.analysis.*;
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18 import jalview.io.*;
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19 import jalview.ws.*;
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21 import java.awt.event.*;
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22 import java.awt.print.*;
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23 import javax.swing.*;
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24 import javax.swing.event.*;
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26 import java.awt.datatransfer.*;
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29 public class AlignFrame extends GAlignFrame
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31 final AlignmentPanel alignPanel;
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32 final AlignViewport viewport;
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33 public AlignFrame(AlignmentI al)
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35 viewport = new AlignViewport(al,true,true,false);
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37 String fontName = jalview.bin.Cache.getProperty("FONT_NAME");
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38 String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");
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39 String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");
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40 if(fontName!=null && fontStyle!=null && fontSize!=null)
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41 viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );
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43 // add conservation graph to alignment
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44 viewport.updateConservation();
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45 viewport.updateConsensus();
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48 alignPanel = new AlignmentPanel(this, viewport);
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50 alignPanel.annotationPanel.adjustPanelHeight();
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51 alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
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52 alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
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54 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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57 addInternalFrameListener(new InternalFrameAdapter()
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59 public void internalFrameActivated(InternalFrameEvent evt)
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61 javax.swing.SwingUtilities.invokeLater(new Runnable()
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64 { alignPanel.requestFocus(); }
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72 protected void saveAs_actionPerformed(ActionEvent e)
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74 String suffix [] = null;
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75 if(e.getActionCommand().equals("FASTA"))
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76 suffix = new String[]{"fa", "fasta"};
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77 else if(e.getActionCommand().equals("MSF"))
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78 suffix = new String[]{"msf"};
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79 else if(e.getActionCommand().equals("CLUSTAL"))
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80 suffix = new String[]{"aln"};
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81 else if(e.getActionCommand().equals("BLC"))
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82 suffix = new String[]{"blc"};
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83 else if(e.getActionCommand().equals("PIR"))
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84 suffix = new String[]{"pir"};
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85 else if(e.getActionCommand().equals("PFAM"))
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86 suffix = new String[]{"pfam"};
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89 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
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90 , suffix, e.getActionCommand()+" file");
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91 chooser.setFileView(new JalviewFileView());
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92 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
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93 chooser.setToolTipText("Save");
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94 int value = chooser.showSaveDialog(this);
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95 if(value == JalviewFileChooser.APPROVE_OPTION)
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97 String choice = chooser.getSelectedFile().getPath();
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98 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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99 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
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101 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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102 out.println(output);
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105 catch(Exception ex){}
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110 protected void outputText_actionPerformed(ActionEvent e)
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112 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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113 JInternalFrame frame = new JInternalFrame();
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114 cap.formatForOutput();
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115 frame.setContentPane(cap);
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116 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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117 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
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120 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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122 HTMLOutput htmlOutput = new HTMLOutput(viewport);
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126 protected void createPNG_actionPerformed(ActionEvent e)
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128 alignPanel.makePNG();
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131 protected void epsFile_actionPerformed(ActionEvent e)
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133 alignPanel.makeEPS();
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137 public void printMenuItem_actionPerformed(ActionEvent e)
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139 //Putting in a thread avoids Swing painting problems
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140 PrintThread thread = new PrintThread();
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144 class PrintThread extends Thread
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148 PrinterJob printJob = PrinterJob.getPrinterJob();
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149 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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150 printJob.setPrintable(alignPanel, pf);
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151 if (printJob.printDialog())
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157 catch (Exception PrintException)
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159 PrintException.printStackTrace();
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169 public void closeMenuItem_actionPerformed(ActionEvent e)
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172 this.setClosed(true);
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173 }catch(Exception ex){}
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176 Stack historyList = new Stack();
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177 Stack redoList = new Stack();
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178 JMenuBar jMenuBar1 = new JMenuBar();
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180 void updateEditMenuBar()
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182 if(historyList.size()>0)
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184 undoMenuItem.setEnabled(true);
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185 Object [] history = (Object[])historyList.get(0);
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186 undoMenuItem.setText("Undo "+history[0]);
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190 undoMenuItem.setEnabled(false);
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191 undoMenuItem.setText("Undo");
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194 if(redoList.size()>0)
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196 redoMenuItem.setEnabled(true);
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197 Object [] history = (Object[])redoList.get(0);
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198 redoMenuItem.setText("Redo "+history[0]);
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202 redoMenuItem.setEnabled(false);
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203 redoMenuItem.setText("Redo");
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207 public void addHistoryItem(String type)
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209 // must make sure we add new sequence objects her, not refs to the existing sequences
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211 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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212 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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214 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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215 viewport.getAlignment().getSequenceAt(i).getSequence());
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218 historyList.add(0, new Object[]{type, seq} );
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219 updateEditMenuBar();
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222 protected void undoMenuItem_actionPerformed(ActionEvent e)
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224 Object [] history = (Object[])historyList.remove(0);
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225 // add the redo state before continuing!!
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226 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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227 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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229 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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230 viewport.getAlignment().getSequenceAt(i).
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235 redoList.add(0, new Object[] {history[0], seq});
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237 seq = (SequenceI[]) history[1];
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238 viewport.setAlignment( new Alignment(seq) );
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239 updateEditMenuBar();
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240 viewport.updateConsensus();
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241 alignPanel.RefreshPanels();
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242 alignPanel.RefreshPanels();
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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.RefreshPanels();
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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 int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;
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352 if (newHeight > 500)
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354 Desktop.addInternalFrame(af, "Copied sequences", 700, 500);
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358 viewport.setEndSeq(viewport.alignment.getHeight());
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359 viewport.alignment.getWidth();
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360 viewport.updateConservation();
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361 viewport.updateConsensus();
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362 alignPanel.RefreshPanels();
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365 }catch(Exception ex){}// could be anything being pasted in here
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370 protected void cut_actionPerformed(ActionEvent e)
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372 copy_actionPerformed(null);
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373 delete_actionPerformed(null);
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376 protected void delete_actionPerformed(ActionEvent e)
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378 addHistoryItem("Delete");
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379 if (viewport.getSelectionGroup() == null)
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382 SequenceGroup sg = viewport.getSelectionGroup();
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383 for (int i=0;i < sg.sequences.size(); i++)
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385 SequenceI seq = sg.getSequenceAt(i);
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386 int index = viewport.getAlignment().findIndex(seq);
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387 seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
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389 if(seq.getSequence().length()<1)
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390 viewport.getAlignment().deleteSequence(seq);
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392 viewport.getAlignment().getSequences().setElementAt(seq, index);
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395 viewport.setSelectionGroup(null);
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396 viewport.alignment.deleteGroup(sg);
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397 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
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398 if(viewport.getAlignment().getHeight()<1)
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401 this.setClosed(true);
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402 }catch(Exception ex){}
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403 viewport.updateConservation();
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404 viewport.updateConsensus();
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405 alignPanel.RefreshPanels();
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411 protected void redoMenuItem_actionPerformed(ActionEvent e)
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413 Object [] history = (Object[])redoList.remove(0);
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414 SequenceI[] seq = (SequenceI[]) history[1];
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415 viewport.setAlignment( new Alignment(seq) );
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416 updateEditMenuBar();
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417 viewport.updateConsensus();
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418 alignPanel.RefreshPanels();
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419 alignPanel.RefreshPanels();
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423 protected void deleteGroups_actionPerformed(ActionEvent e)
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425 viewport.alignment.deleteAllGroups();
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426 viewport.setSelectionGroup(null);
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428 alignPanel.RefreshPanels();
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433 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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435 SequenceGroup sg = new SequenceGroup();
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436 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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437 sg.addSequence( viewport.getAlignment().getSequenceAt(i));
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438 sg.setEndRes(viewport.alignment.getWidth());
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439 viewport.setSelectionGroup(sg);
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440 PaintRefresher.Refresh(null);
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443 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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445 viewport.setSelectionGroup(null);
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446 PaintRefresher.Refresh(null);
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449 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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451 SequenceGroup sg = viewport.getSelectionGroup();
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452 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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453 sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
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455 PaintRefresher.Refresh(null);
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459 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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461 viewport.getColumnSelection().clear();
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465 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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467 addHistoryItem("delete columns");
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468 ColumnSelection colSel = viewport.getColumnSelection();
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469 if (colSel.size() > 0)
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471 int min = colSel.getMin();
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472 viewport.getAlignment().trimLeft(min);
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473 colSel.compensateForEdit(0,min);
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475 if(viewport.getSelectionGroup()!=null)
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476 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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478 Vector groups = viewport.alignment.getGroups();
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479 for(int i=0; i<groups.size(); i++)
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481 SequenceGroup sg = (SequenceGroup) groups.get(i);
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482 if(!sg.adjustForRemoveLeft(min))
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483 viewport.alignment.deleteGroup(sg);
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486 alignPanel.RefreshPanels();
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490 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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492 addHistoryItem("delete columns");
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493 ColumnSelection colSel = viewport.getColumnSelection();
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494 if (colSel.size() > 0)
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496 int max = colSel.getMax();
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497 viewport.getAlignment().trimRight(max);
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498 if(viewport.getSelectionGroup()!=null)
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499 viewport.getSelectionGroup().adjustForRemoveRight(max);
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501 Vector groups = viewport.alignment.getGroups();
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502 for(int i=0; i<groups.size(); i++)
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504 SequenceGroup sg = (SequenceGroup) groups.get(i);
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505 if(!sg.adjustForRemoveRight(max))
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506 viewport.alignment.deleteGroup(sg);
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511 alignPanel.RefreshPanels();
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516 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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518 addHistoryItem("delete gapped columns");
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519 viewport.getAlignment().removeGaps();
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520 viewport.updateConservation();
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521 viewport.updateConsensus();
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522 alignPanel.RefreshPanels();
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525 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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527 addHistoryItem("delete all gaps");
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530 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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532 current = viewport.getAlignment().getSequenceAt(i);
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533 jSize = current.getLength();
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534 for (int j=0; j < jSize; j++)
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535 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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537 current.deleteCharAt(j);
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542 viewport.updateConservation();
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543 viewport.updateConsensus();
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544 alignPanel.RefreshPanels();
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547 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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549 char thisChar = '-';
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550 char nextChar = '.';
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551 if(viewport.getGapCharacter()=='-')
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556 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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557 viewport.setGapCharacter(thisChar);
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558 alignPanel.RefreshPanels();
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561 public void findMenuItem_actionPerformed(ActionEvent e)
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563 JInternalFrame frame = new JInternalFrame();
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564 Finder finder = new Finder(viewport, alignPanel, frame);
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565 frame.setContentPane(finder);
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566 Desktop.addInternalFrame(frame, "Find", 340,110);
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571 public void font_actionPerformed(ActionEvent e)
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573 JInternalFrame frame = new JInternalFrame();
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574 FontChooser fc = new FontChooser( alignPanel, frame );
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575 frame.setContentPane(fc);
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576 Desktop.addInternalFrame(frame, "Change Font", 480,100);
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579 protected void fullSeqId_actionPerformed(ActionEvent e)
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581 viewport.setShowFullId( fullSeqId.isSelected() );
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583 alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
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584 alignPanel.RefreshPanels();
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587 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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589 viewport.setColourText( colourTextMenuItem.isSelected() );
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590 alignPanel.RefreshPanels();
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593 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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595 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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596 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
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597 scaleAbove.setVisible( wrapMenuItem.isSelected() );
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598 scaleLeft.setVisible( wrapMenuItem.isSelected() );
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599 scaleRight.setVisible( wrapMenuItem.isSelected() );
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600 alignPanel.RefreshPanels();
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603 protected void scaleAbove_actionPerformed(ActionEvent e)
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605 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
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606 alignPanel.repaint();
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609 protected void scaleLeft_actionPerformed(ActionEvent e)
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611 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
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612 alignPanel.repaint();
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615 protected void scaleRight_actionPerformed(ActionEvent e)
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617 viewport.setScaleRightWrapped(scaleRight.isSelected());
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618 alignPanel.repaint();
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623 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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625 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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626 alignPanel.RefreshPanels();
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629 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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631 viewport.setShowText( viewTextMenuItem.isSelected() );
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632 alignPanel.RefreshPanels();
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636 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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638 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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639 alignPanel.RefreshPanels();
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642 public void sequenceFeatures_actionPerformed(ActionEvent evt)
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644 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
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645 if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
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647 AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
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648 ((Alignment)viewport.alignment).featuresAdded = true;
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650 alignPanel.RefreshPanels();
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653 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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655 if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
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657 annotationPanelMenuItem.setSelected(false);
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660 viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
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661 alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
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664 public void overviewMenuItem_actionPerformed(ActionEvent e)
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666 if (alignPanel.overviewPanel != null)
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669 JInternalFrame frame = new JInternalFrame();
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670 OverviewPanel overview = alignPanel.getOverviewPanel();
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672 overview = new OverviewPanel(alignPanel, viewport);
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673 frame.setContentPane(overview);
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674 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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675 frame.getWidth(), frame.getHeight());
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677 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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678 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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680 alignPanel.setOverviewPanel(null);
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683 alignPanel.setOverviewPanel( overview );
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685 }catch(java.lang.OutOfMemoryError ex)
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687 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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688 +"\nTry reducing the font size.",
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689 "Out of memory", JOptionPane.WARNING_MESSAGE);
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695 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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697 changeColour( null );
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701 public void clustalColour_actionPerformed(ActionEvent e)
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703 abovePIDThreshold.setSelected(false);
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704 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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707 public void zappoColour_actionPerformed(ActionEvent e)
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709 changeColour(new ZappoColourScheme());
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712 public void taylorColour_actionPerformed(ActionEvent e)
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714 changeColour(new TaylorColourScheme());
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718 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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720 changeColour( new HydrophobicColourScheme() );
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723 public void helixColour_actionPerformed(ActionEvent e)
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725 changeColour(new HelixColourScheme() );
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729 public void strandColour_actionPerformed(ActionEvent e)
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731 changeColour(new StrandColourScheme());
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735 public void turnColour_actionPerformed(ActionEvent e)
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737 changeColour(new TurnColourScheme());
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741 public void buriedColour_actionPerformed(ActionEvent e)
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743 changeColour(new BuriedColourScheme() );
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746 public void nucleotideColour_actionPerformed(ActionEvent e)
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748 changeColour(new NucleotideColourScheme());
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752 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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754 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
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759 void changeColour(ColourSchemeI cs)
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762 if(viewport.getColourAppliesToAllGroups())
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764 Vector groups = viewport.alignment.getGroups();
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765 for(int i=0; i<groups.size(); i++)
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767 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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770 if(abovePIDThreshold.isSelected())
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771 abovePIDThreshold_actionPerformed(null);
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772 else if( viewport.getConservationSelected() )
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774 Conservation c = new Conservation("Group",
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775 ResidueProperties.propHash, 3,
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776 sg.sequences, sg.getStartRes(),
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779 c.verdict(false, 100);
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780 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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789 if ( viewport.getAbovePIDThreshold())
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792 threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
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793 Desktop.hideConservationSlider();
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795 if (cs instanceof ResidueColourScheme)
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796 ( (ResidueColourScheme) cs).setThreshold(threshold);
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797 else if (cs instanceof ScoreColourScheme)
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798 ( (ScoreColourScheme) cs).setThreshold(threshold);
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800 viewport.setGlobalColourScheme(cs);
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804 if (cs instanceof ResidueColourScheme)
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805 ( (ResidueColourScheme) cs).setThreshold(0);
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806 else if (cs instanceof ScoreColourScheme)
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807 ( (ScoreColourScheme) cs).setThreshold(0);
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812 if ( viewport.getConservationSelected() )
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814 ConservationColourScheme ccs = null;
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816 Alignment al = (Alignment) viewport.alignment;
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817 Conservation c = new Conservation("All",
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818 ResidueProperties.propHash, 3,
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819 al.getSequences(), 0,
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823 c.verdict(false, 100);
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825 ccs = new ConservationColourScheme(c, cs);
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827 int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,
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830 ccs.inc = threshold;
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832 viewport.setGlobalColourScheme(ccs);
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836 viewport.setGlobalColourScheme( cs );
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838 alignPanel.RefreshPanels();
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842 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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844 viewport.setConservationSelected(conservationMenuItem.isSelected());
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845 if(coloursChanging)
\r
848 coloursChanging = true;
\r
850 viewport.setAbovePIDThreshold(false);
\r
851 abovePIDThreshold.setSelected(false);
\r
852 Desktop.hidePIDSlider();
\r
853 if(!viewport.getConservationSelected())
\r
854 Desktop.hideConservationSlider();
\r
856 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
857 if(cs instanceof ConservationColourScheme )
\r
858 changeColour( ((ConservationColourScheme)cs).cs );
\r
860 changeColour( cs );
\r
862 coloursChanging = false;
\r
865 boolean coloursChanging = false;
\r
866 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
868 if(coloursChanging)
\r
871 coloursChanging = true;
\r
872 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
874 conservationMenuItem.setSelected(false);
\r
875 viewport.setConservationSelected(false);
\r
876 Desktop.hideConservationSlider();
\r
878 if(!viewport.getAbovePIDThreshold())
\r
879 Desktop.hidePIDSlider();
\r
882 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
883 if(cs instanceof ConservationColourScheme )
\r
884 changeColour( ((ConservationColourScheme)cs).cs );
\r
886 changeColour( cs );
\r
888 coloursChanging = false;
\r
893 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
895 JInternalFrame frame = new JInternalFrame();
\r
896 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
\r
897 frame.setContentPane(chooser);
\r
898 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
\r
899 frame.setResizable(false);
\r
900 frame.setIconifiable(false);
\r
901 frame.setMaximizable(false);
\r
904 public void PIDColour_actionPerformed(ActionEvent e)
\r
906 changeColour( new PIDColourScheme() );
\r
910 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
912 changeColour(new Blosum62ColourScheme(viewport) );
\r
917 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
919 addHistoryItem("sort");
\r
920 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
\r
921 alignPanel.RefreshPanels();
\r
924 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
926 addHistoryItem("sort");
\r
927 AlignmentSorter.sortByID( viewport.getAlignment() );
\r
928 alignPanel.RefreshPanels();
\r
931 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
933 addHistoryItem("sort");
\r
934 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
935 AlignmentSorter.sortGroups(viewport.getAlignment());
\r
936 alignPanel.RefreshPanels();
\r
939 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
\r
941 addHistoryItem("sort");
\r
942 if(viewport.getCurrentTree()==null)
\r
945 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
\r
946 alignPanel.RefreshPanels();
\r
949 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
951 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
952 JInternalFrame frame = new JInternalFrame();
\r
953 frame.setContentPane(sp);
\r
954 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
\r
955 frame.setMaximizable(false);
\r
956 frame.setResizable(false);
\r
960 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
962 if(viewport.getSelectionGroup().getSize()<2)
\r
963 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
\r
966 JInternalFrame frame = new JInternalFrame();
\r
967 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
968 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
972 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
975 if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
\r
976 || viewport.getAlignment().getHeight()<4)
\r
978 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
\r
979 +"at least 4 input sequences.",
\r
980 "Sequence selection insufficient",
\r
981 JOptionPane.WARNING_MESSAGE);
\r
986 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
987 JInternalFrame frame = new JInternalFrame();
\r
988 frame.setContentPane(pcaPanel);
\r
989 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
\r
990 }catch(java.lang.OutOfMemoryError ex)
\r
992 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
\r
993 "Out of memory", JOptionPane.WARNING_MESSAGE);
\r
999 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1001 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1004 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1006 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1010 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1012 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1015 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1017 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1020 void NewTreePanel(String type, String pwType, String title)
\r
1022 //are the sequences aligned?
\r
1023 if(!viewport.alignment.isAligned())
\r
1025 JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
\r
1026 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
\r
1030 TreePanel tp=null;
\r
1031 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)
\r
1033 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,
\r
1034 0, viewport.alignment.getWidth());
\r
1038 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1039 type, pwType, 0, viewport.alignment.getWidth());
\r
1042 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1048 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
1050 JInternalFrame frame = new JInternalFrame();
\r
1051 ClustalThread ct = new ClustalThread(frame);
\r
1052 Thread t = new Thread(ct);
\r
1054 frame.setContentPane(ct);
\r
1055 Desktop.addInternalFrame(frame, title, 300, 80);
\r
1059 class ClustalThread extends JPanel implements Runnable
\r
1063 boolean webServiceRunning = false;
\r
1064 JInternalFrame frame;
\r
1065 public ClustalThread(JInternalFrame frame)
\r
1067 this.frame = frame;
\r
1069 java.net.URL url = getClass().getResource("/images/logo.gif");
\r
1072 image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
\r
1073 MediaTracker mt = new MediaTracker(this);
\r
1074 mt.addImage(image, 0);
\r
1079 catch (Exception ex)
\r
1083 ImageSpinner spinner = new ImageSpinner();
\r
1085 webServiceRunning = true;
\r
1088 class ImageSpinner extends Thread
\r
1092 while(webServiceRunning)
\r
1100 catch(Exception ex){}
\r
1106 // Should check to see if the server settings are valid
\r
1107 // Need visual-delay indication here.
\r
1110 jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
\r
1111 Vector sv = viewport.getAlignment().getSequences();
\r
1112 SequenceI[] seqs = new SequenceI[sv.size()];
\r
1117 seqs[i] = (SequenceI) sv.elementAt(i);
\r
1119 while (++i < sv.size());
\r
1121 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
\r
1123 if (alignment != null)
\r
1125 AlignFrame af = new AlignFrame(new Alignment(alignment));
\r
1126 af.clustalColour.setSelected(true);
\r
1127 af.clustalColour_actionPerformed(null);
\r
1128 Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
\r
1129 700, 500); // JBPNote - is there a new window geom. property ?
\r
1132 JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
\r
1133 JOptionPane.WARNING_MESSAGE);
\r
1135 webServiceRunning = false;
\r
1137 frame.setClosed(true);
\r
1138 }catch(Exception ex){}
\r
1141 public void paintComponent(Graphics g1)
\r
1143 Graphics2D g = (Graphics2D)g1;
\r
1144 g.setColor(Color.white);
\r
1145 g.fillRect(0,0,getWidth(), getHeight());
\r
1149 g.rotate (Math.toRadians(angle), 28, 28);
\r
1151 g.drawImage(image,10,10,this);
\r
1152 g.rotate (-Math.toRadians(angle), 28, 28 );
\r
1154 g.setFont(new Font("Arial", Font.BOLD, 12));
\r
1155 g.setColor(Color.black);
\r
1156 g.drawString("Clustal Alignment Web Service running", 60,30);
\r
1159 protected void jpred_actionPerformed(ActionEvent e)
\r
1162 JInternalFrame frame = new JInternalFrame();
\r
1163 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
\r
1165 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1166 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1167 if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
\r
1169 JPredClient ct = new JPredClient( (SequenceI)
\r
1170 seqs.getSequenceAt(0));
\r
1175 SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
\r
1176 for (int i = 0; i < sz; i++)
\r
1178 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1181 JPredClient ct = new JPredClient(msa);
\r
1187 Vector seqs = viewport.getAlignment().getSequences();
\r
1189 if (seqs.size() == 1 || !viewport.alignment.isAligned())
\r
1191 JPredClient ct = new JPredClient( (SequenceI)
\r
1192 seqs.elementAt(0));
\r
1196 SequenceI[] msa = new SequenceI[seqs.size()];
\r
1197 for (int i = 0; i < seqs.size(); i++)
\r
1199 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1202 JPredClient ct = new JPredClient(msa);
\r
1208 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
\r
1209 // Pick the tree file
\r
1210 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
1211 getProperty("LAST_DIRECTORY"));
\r
1212 chooser.setFileView(new JalviewFileView());
\r
1213 chooser.setDialogTitle("Select a newick-like tree file");
\r
1214 chooser.setToolTipText("Load a tree file");
\r
1215 int value = chooser.showOpenDialog(null);
\r
1216 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
1218 String choice = chooser.getSelectedFile().getPath();
\r
1219 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1220 TreePanel treepanel = null;
\r
1223 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
\r
1226 if (fin.getTree() != null)
\r
1228 TreePanel tp = null;
\r
1229 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1230 fin, "FromFile", choice);
\r
1231 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1234 catch (Exception ex)
\r
1236 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1237 "Problem reading tree file",
\r
1239 JOptionPane.WARNING_MESSAGE);
\r
1240 ex.printStackTrace();
\r