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 java.awt.event.*;
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21 import javax.swing.*;
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24 public class AlignFrame extends GAlignFrame
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26 final AlignmentPanel alignPanel;
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27 final AlignViewport viewport;
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28 public AlignFrame(AlignmentI al)
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31 viewport = new AlignViewport(al,true,true,true,false);
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32 alignPanel = new AlignmentPanel(this, viewport);
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33 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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34 fontNameMenuItem.setText(viewport.getFont().getName());
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35 fontSizeMenuItem.setText(viewport.getFont().getSize()+"");
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38 protected void saveAs_actionPerformed(ActionEvent e)
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40 JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);
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41 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
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42 chooser.setToolTipText("Save");
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43 int value = chooser.showSaveDialog(this);
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44 if(value == JFileChooser.APPROVE_OPTION)
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46 String choice = chooser.getSelectedFile().getPath();
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47 jalview.bin.Cache.LAST_DIRECTORY = choice;
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48 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
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50 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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51 out.println(output);
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54 catch(Exception ex){}
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59 protected void outputText_actionPerformed(ActionEvent e)
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61 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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62 JInternalFrame frame = new JInternalFrame();
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63 cap.formatForOutput();
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64 frame.setContentPane(cap);
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65 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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66 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
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69 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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71 HTMLOutput htmlOutput = new HTMLOutput(viewport.getAlignment(), alignPanel.seqPanel.getColourScheme());
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75 public void saveAsPostscriptMenuItem_actionPerformed(ActionEvent e)
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80 public void closeMenuItem_actionPerformed(ActionEvent e)
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83 this.setClosed(true);
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84 }catch(Exception ex){}
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87 ArrayList historyList = new ArrayList();
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88 ArrayList redoList = new ArrayList();
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90 void updateEditMenuBar()
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92 if(historyList.size()>0)
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94 undoMenuItem.setEnabled(true);
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95 Object [] history = (Object[])historyList.get(0);
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96 undoMenuItem.setText("Undo "+history[0]);
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100 undoMenuItem.setEnabled(false);
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101 undoMenuItem.setText("Undo");
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104 if(redoList.size()>0)
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106 redoMenuItem.setEnabled(true);
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107 Object [] history = (Object[])redoList.get(0);
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108 redoMenuItem.setText("Redo "+history[0]);
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112 redoMenuItem.setEnabled(false);
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113 redoMenuItem.setText("Redo");
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117 public void addHistoryItem(String type)
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119 // must make sure we add new sequence objects her, not refs to the existing sequences
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121 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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122 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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124 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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125 viewport.getAlignment().getSequenceAt(i).getSequence());
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128 historyList.add(0, new Object[]{type, seq} );
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129 updateEditMenuBar();
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132 protected void undoMenuItem_actionPerformed(ActionEvent e)
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134 Object [] history = (Object[])historyList.remove(0);
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135 // add the redo state before continuing!!
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136 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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137 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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139 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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140 viewport.getAlignment().getSequenceAt(i).
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145 redoList.add(0, new Object[] {history[0], seq});
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147 seq = (SequenceI[]) history[1];
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148 viewport.setAlignment( new Alignment(seq) );
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149 updateEditMenuBar();
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150 alignPanel.RefreshPanels();
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154 protected void redoMenuItem_actionPerformed(ActionEvent e)
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156 Object [] history = (Object[])redoList.remove(0);
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157 SequenceI[] seq = (SequenceI[]) history[1];
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158 viewport.setAlignment( new Alignment(seq) );
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159 updateEditMenuBar();
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160 alignPanel.RefreshPanels();
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165 public void groupsMenuItem_actionPerformed(ActionEvent e)
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167 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
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168 JInternalFrame frame = new JInternalFrame();
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169 frame.setContentPane(geditor);
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170 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
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171 frame.setResizable(false);
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174 public void groupEditingMenuItem_actionPerformed(ActionEvent e)
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176 viewport.setGroupEdit( groupEditingMenuItem.isSelected() );
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179 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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181 Selection sel = viewport.getSelection();
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182 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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183 sel.addElement( viewport.getAlignment().getSequenceAt(i));
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184 PaintRefresher.Refresh(null);
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187 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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189 viewport.getSelection().clear();
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190 PaintRefresher.Refresh(null);
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193 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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195 Selection sel = viewport.getSelection();
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196 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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198 if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
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199 sel.removeElement(viewport.getAlignment().getSequenceAt(i));
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201 sel.addElement(viewport.getAlignment().getSequenceAt(i));
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203 PaintRefresher.Refresh(null);
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206 public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)
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208 addHistoryItem("delete selection");
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210 for (int i=0;i < viewport.getSelection().size(); i++)
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211 viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));
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213 viewport.getSelection().clear();
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214 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
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215 alignPanel.RefreshPanels();
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218 public void moveSelectedMenuItem_actionPerformed(ActionEvent e)
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220 copySelectedMenuItem_actionPerformed(null);
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221 deleteSelectedMenuItem_actionPerformed(null);
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222 alignPanel.repaint();
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225 public void copySelectedMenuItem_actionPerformed(ActionEvent e)
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227 if(viewport.getSelection().size()==0)
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230 SequenceI[] s = new Sequence[viewport.getSelection().size()];
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231 for (int i=0; i < viewport.getSelection().size(); i++) {
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232 s[i] = new Sequence(viewport.getSelection().sequenceAt(i));
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234 AlignFrame af = new AlignFrame(new Alignment(s));
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235 int newHeight = s.length * af.viewport.getCharHeight() + 200;
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238 Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
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241 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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243 viewport.getColumnSelection().clear();
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247 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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249 addHistoryItem("delete columns");
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250 ColumnSelection colSel = viewport.getColumnSelection();
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251 if (colSel.size() > 0)
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253 int min = colSel.getMin();
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254 viewport.getAlignment().trimLeft(min);
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255 colSel.compensateForEdit(0,min);
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256 alignPanel.RefreshPanels();
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260 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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262 addHistoryItem("delete columns");
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263 ColumnSelection colSel = viewport.getColumnSelection();
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264 if (colSel.size() > 0)
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266 int max = colSel.getMax();
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268 viewport.getAlignment().trimRight(max);
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270 alignPanel.RefreshPanels();
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275 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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277 addHistoryItem("delete gapped columns");
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278 viewport.getAlignment().removeGaps();
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279 alignPanel.RefreshPanels();
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282 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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284 addHistoryItem("delete all gaps");
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287 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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289 current = viewport.getAlignment().getSequenceAt(i);
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290 jSize = current.getLength();
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291 for (int j=0; j < jSize; j++)
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292 if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')
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294 current.deleteCharAt(j);
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300 alignPanel.RefreshPanels();
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303 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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305 String thisChar = "-";
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306 String nextChar = ".";
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307 if(viewport.getGapCharacter().equals("-"))
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312 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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313 viewport.setGapCharacter(thisChar);
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317 public void fontNameMenuItem_actionPerformed(ActionEvent e)
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319 String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
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322 String selection = JOptionPane.showInputDialog(this,
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325 JOptionPane.QUESTION_MESSAGE,
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327 ,fontNameMenuItem.getText()).toString();
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328 if(selection!=null)
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330 fontNameMenuItem.setText(selection);
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336 public void fontSizeMenuItem_actionPerformed(ActionEvent e)
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338 String selection = JOptionPane.showInputDialog(this,
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339 "Select font size",
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341 JOptionPane.QUESTION_MESSAGE,
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342 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
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343 ,fontSizeMenuItem.getText()).toString();
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344 if(selection!=null)
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346 fontSizeMenuItem.setText(selection);
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351 public void fontStyleMenuItem_actionPerformed(ActionEvent e)
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353 String selection = JOptionPane.showInputDialog(this,
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354 "Select font style",
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356 JOptionPane.QUESTION_MESSAGE,
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357 null, new String[]{"plain", "bold", "italic"}
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358 ,fontStyleMenuItem.getText()).toString();
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359 if(selection!=null)
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361 fontStyleMenuItem.setText(selection);
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367 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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369 viewport.setColourText( colourTextMenuItem.isSelected() );
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370 alignPanel.RefreshPanels();
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375 int style = java.awt.Font.PLAIN;
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376 if(fontStyleMenuItem.getText().equals("bold"))
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377 style = java.awt.Font.BOLD;
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378 else if(fontStyleMenuItem.getText().equals("italic"))
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379 style = java.awt.Font.ITALIC;
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381 viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
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383 Integer.parseInt(fontSizeMenuItem.getText())));
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384 alignPanel.RefreshPanels();
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388 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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390 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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391 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
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395 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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397 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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398 alignPanel.RefreshPanels();
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401 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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403 viewport.setShowText( viewTextMenuItem.isSelected() );
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404 alignPanel.RefreshPanels();
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408 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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410 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
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413 public void overviewMenuItem_actionPerformed(ActionEvent e)
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416 JInternalFrame frame = new JInternalFrame();
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417 OverviewPanel overview = alignPanel.getOverviewPanel();
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419 overview = new OverviewPanel(alignPanel, viewport);
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420 frame.setContentPane(overview);
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421 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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422 frame.getWidth(), frame.getHeight());
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424 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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425 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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427 alignPanel.setOverviewPanel(null);
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430 alignPanel.setOverviewPanel( overview );
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432 }catch(java.lang.OutOfMemoryError ex)
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434 JOptionPane.showMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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435 +"\nTry reducing the font size.",
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436 "Out of memory", JOptionPane.WARNING_MESSAGE);
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442 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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444 alignPanel.setColourScheme(null, false);
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448 public void clustalColour_actionPerformed(ActionEvent e)
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450 // alignPanel.setColourScheme( new ClustalxColourScheme() );
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453 public void zappoColour_actionPerformed(ActionEvent e)
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455 alignPanel.setColourScheme( new ZappoColourScheme(), conservationMenuItem.isSelected() );
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458 public void taylorColour_actionPerformed(ActionEvent e)
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460 alignPanel.setColourScheme( new TaylorColourScheme(),conservationMenuItem.isSelected() );
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464 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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466 alignPanel.setColourScheme( new HydrophobicColourScheme(),conservationMenuItem.isSelected() );
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469 public void helixColour_actionPerformed(ActionEvent e)
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471 alignPanel.setColourScheme( new HelixColourScheme(),conservationMenuItem.isSelected() );
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475 public void strandColour_actionPerformed(ActionEvent e)
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477 alignPanel.setColourScheme( new StrandColourScheme() ,conservationMenuItem.isSelected() );
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481 public void turnColour_actionPerformed(ActionEvent e)
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483 alignPanel.setColourScheme( new TurnColourScheme() ,conservationMenuItem.isSelected() );
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487 public void buriedColour_actionPerformed(ActionEvent e)
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489 alignPanel.setColourScheme( new BuriedColourScheme() ,conservationMenuItem.isSelected() );
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493 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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495 alignPanel.setColourScheme ( alignPanel.seqPanel.getColourScheme(),conservationMenuItem.isSelected() );
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496 conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() );
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501 public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
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503 ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);
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504 JInternalFrame frame = new JInternalFrame();
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505 frame.setContentPane(cip);
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506 Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);
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507 frame.setMaximizable(false);
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511 public void abovePIDColour_actionPerformed(ActionEvent e)
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513 alignPanel.setColourScheme( new PIDColourScheme() ,conservationMenuItem.isSelected() );
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517 public void userDefinedColour_actionPerformed(ActionEvent e)
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519 JInternalFrame frame = new JInternalFrame();
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520 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel.seqPanel );
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521 frame.setContentPane(chooser);
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522 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
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523 frame.setResizable(false);
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524 frame.setIconifiable(false);
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525 frame.setMaximizable(false);
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528 public void PIDColour_actionPerformed(ActionEvent e)
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530 alignPanel.setColourScheme( new PIDColourScheme(),conservationMenuItem.isSelected() );
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534 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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536 alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) ,conservationMenuItem.isSelected() );
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541 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
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543 ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );
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544 Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
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548 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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550 addHistoryItem("sort");
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551 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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552 alignPanel.RefreshPanels();
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555 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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557 addHistoryItem("sort");
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558 AlignmentSorter.sortByID( viewport.getAlignment() );
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559 alignPanel.RefreshPanels();
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562 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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564 addHistoryItem("sort");
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565 AlignmentSorter.sortGroups(viewport.getAlignment());
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566 AlignmentSorter.sortGroups(viewport.getAlignment());
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567 alignPanel.RefreshPanels();
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570 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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572 addHistoryItem("sort");
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573 if(viewport.getCurrentTree()==null)
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576 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
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577 alignPanel.RefreshPanels();
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580 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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585 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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587 if(viewport.getSelection().size()<2)
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588 JOptionPane.showMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
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591 JInternalFrame frame = new JInternalFrame();
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592 frame.setContentPane(new PairwiseAlignPanel(viewport));
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593 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
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597 public void PCAMenuItem_actionPerformed(ActionEvent e)
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599 if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
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600 || viewport.getAlignment().getHeight()<4)
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602 JOptionPane.showMessageDialog(this, "Principal component analysis must take\n"
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603 +"at least 4 input sequences.",
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604 "Sequence selection insufficient",
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605 JOptionPane.WARNING_MESSAGE);
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610 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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611 JInternalFrame frame = new JInternalFrame();
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612 frame.setContentPane(pcaPanel);
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613 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
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614 }catch(java.lang.OutOfMemoryError ex)
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616 JOptionPane.showMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
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617 "Out of memory", JOptionPane.WARNING_MESSAGE);
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623 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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625 NewTreePanel("AV", "PID", "Average distance tree using PID");
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628 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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630 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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634 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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636 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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639 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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641 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
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644 void NewTreePanel(String type, String pwType, String title)
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646 JInternalFrame frame = new javax.swing.JInternalFrame();
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648 if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
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650 tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
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651 viewport.getStartRes(), viewport.getEndRes());
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655 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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656 type, pwType, viewport.getStartRes(),
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657 viewport.getEndRes());
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660 frame.setContentPane(tp);
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661 Desktop.addInternalFrame(frame, title, 600, 500);
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666 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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668 JOptionPane.showMessageDialog(this, "Jalview is currently being reengineered"
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669 +"\nwithin the Barton Group, Dundee University."
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670 +"\nThis will be available as a web service 2005",
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671 "Web service", JOptionPane.INFORMATION_MESSAGE);
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