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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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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26 public class AlignFrame extends GAlignFrame
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28 final AlignmentPanel alignPanel;
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29 final AlignViewport viewport;
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30 public AlignFrame(AlignmentI al)
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33 viewport = new AlignViewport(al,true,true,true,false);
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34 alignPanel = new AlignmentPanel(this, viewport);
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35 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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36 fontNameMenuItem.setText(viewport.getFont().getName());
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37 fontSizeMenuItem.setText(viewport.getFont().getSize()+"");
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40 protected void saveAs_actionPerformed(ActionEvent e)
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42 JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);
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43 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
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44 chooser.setToolTipText("Save");
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45 int value = chooser.showSaveDialog(this);
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46 if(value == JFileChooser.APPROVE_OPTION)
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48 String choice = chooser.getSelectedFile().getPath();
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49 jalview.bin.Cache.LAST_DIRECTORY = choice;
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50 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
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52 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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53 out.println(output);
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56 catch(Exception ex){}
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61 protected void outputText_actionPerformed(ActionEvent e)
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63 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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64 JInternalFrame frame = new JInternalFrame();
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65 cap.formatForOutput();
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66 frame.setContentPane(cap);
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67 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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68 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
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71 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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73 HTMLOutput htmlOutput = new HTMLOutput(viewport.getAlignment(), alignPanel.seqPanel.getColourScheme());
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77 public void printMenuItem_actionPerformed(ActionEvent e)
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79 //Putting in a thread avoids Swing painting problems
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80 PrintThread thread = new PrintThread();
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84 class PrintThread extends Thread
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88 PrinterJob printJob = PrinterJob.getPrinterJob();
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90 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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91 printJob.setPrintable(alignPanel, pf);
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92 if (printJob.printDialog())
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98 catch (Exception PrintException)
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100 PrintException.printStackTrace();
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110 public void closeMenuItem_actionPerformed(ActionEvent e)
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113 this.setClosed(true);
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114 }catch(Exception ex){}
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117 ArrayList historyList = new ArrayList();
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118 ArrayList redoList = new ArrayList();
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120 void updateEditMenuBar()
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122 if(historyList.size()>0)
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124 undoMenuItem.setEnabled(true);
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125 Object [] history = (Object[])historyList.get(0);
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126 undoMenuItem.setText("Undo "+history[0]);
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130 undoMenuItem.setEnabled(false);
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131 undoMenuItem.setText("Undo");
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134 if(redoList.size()>0)
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136 redoMenuItem.setEnabled(true);
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137 Object [] history = (Object[])redoList.get(0);
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138 redoMenuItem.setText("Redo "+history[0]);
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142 redoMenuItem.setEnabled(false);
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143 redoMenuItem.setText("Redo");
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147 public void addHistoryItem(String type)
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149 // must make sure we add new sequence objects her, not refs to the existing sequences
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151 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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152 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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154 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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155 viewport.getAlignment().getSequenceAt(i).getSequence());
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158 historyList.add(0, new Object[]{type, seq} );
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159 updateEditMenuBar();
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162 protected void undoMenuItem_actionPerformed(ActionEvent e)
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164 Object [] history = (Object[])historyList.remove(0);
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165 // add the redo state before continuing!!
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166 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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167 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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169 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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170 viewport.getAlignment().getSequenceAt(i).
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175 redoList.add(0, new Object[] {history[0], seq});
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177 seq = (SequenceI[]) history[1];
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178 viewport.setAlignment( new Alignment(seq) );
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179 updateEditMenuBar();
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180 alignPanel.RefreshPanels();
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184 protected void redoMenuItem_actionPerformed(ActionEvent e)
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186 Object [] history = (Object[])redoList.remove(0);
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187 SequenceI[] seq = (SequenceI[]) history[1];
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188 viewport.setAlignment( new Alignment(seq) );
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189 updateEditMenuBar();
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190 alignPanel.RefreshPanels();
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195 public void groupsMenuItem_actionPerformed(ActionEvent e)
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197 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
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198 JInternalFrame frame = new JInternalFrame();
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199 frame.setContentPane(geditor);
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200 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
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201 frame.setResizable(false);
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204 public void groupEditingMenuItem_actionPerformed(ActionEvent e)
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206 viewport.setGroupEdit( groupEditingMenuItem.isSelected() );
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209 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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211 Selection sel = viewport.getSelection();
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212 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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213 sel.addElement( viewport.getAlignment().getSequenceAt(i));
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214 PaintRefresher.Refresh(null);
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217 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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219 viewport.getSelection().clear();
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220 PaintRefresher.Refresh(null);
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223 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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225 Selection sel = viewport.getSelection();
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226 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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228 if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
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229 sel.removeElement(viewport.getAlignment().getSequenceAt(i));
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231 sel.addElement(viewport.getAlignment().getSequenceAt(i));
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233 PaintRefresher.Refresh(null);
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236 public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)
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238 addHistoryItem("delete selection");
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240 for (int i=0;i < viewport.getSelection().size(); i++)
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241 viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));
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243 viewport.getSelection().clear();
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244 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
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245 alignPanel.RefreshPanels();
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248 public void moveSelectedMenuItem_actionPerformed(ActionEvent e)
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250 copySelectedMenuItem_actionPerformed(null);
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251 deleteSelectedMenuItem_actionPerformed(null);
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252 alignPanel.repaint();
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255 public void copySelectedMenuItem_actionPerformed(ActionEvent e)
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257 if(viewport.getSelection().size()==0)
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260 SequenceI[] s = new Sequence[viewport.getSelection().size()];
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261 for (int i=0; i < viewport.getSelection().size(); i++) {
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262 s[i] = new Sequence(viewport.getSelection().sequenceAt(i));
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264 AlignFrame af = new AlignFrame(new Alignment(s));
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265 int newHeight = s.length * af.viewport.getCharHeight() + 200;
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268 Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
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271 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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273 viewport.getColumnSelection().clear();
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277 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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279 addHistoryItem("delete columns");
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280 ColumnSelection colSel = viewport.getColumnSelection();
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281 if (colSel.size() > 0)
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283 int min = colSel.getMin();
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284 viewport.getAlignment().trimLeft(min);
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285 colSel.compensateForEdit(0,min);
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286 alignPanel.RefreshPanels();
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290 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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292 addHistoryItem("delete columns");
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293 ColumnSelection colSel = viewport.getColumnSelection();
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294 if (colSel.size() > 0)
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296 int max = colSel.getMax();
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298 viewport.getAlignment().trimRight(max);
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300 alignPanel.RefreshPanels();
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305 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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307 addHistoryItem("delete gapped columns");
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308 viewport.getAlignment().removeGaps();
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309 alignPanel.RefreshPanels();
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312 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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314 addHistoryItem("delete all gaps");
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317 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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319 current = viewport.getAlignment().getSequenceAt(i);
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320 jSize = current.getLength();
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321 for (int j=0; j < jSize; j++)
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322 if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')
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324 current.deleteCharAt(j);
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330 alignPanel.RefreshPanels();
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333 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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335 String thisChar = "-";
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336 String nextChar = ".";
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337 if(viewport.getGapCharacter().equals("-"))
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342 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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343 viewport.setGapCharacter(thisChar);
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347 public void fontNameMenuItem_actionPerformed(ActionEvent e)
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349 String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
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352 String selection = JOptionPane.showInputDialog(this,
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355 JOptionPane.QUESTION_MESSAGE,
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357 ,fontNameMenuItem.getText()).toString();
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358 if(selection!=null)
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360 fontNameMenuItem.setText(selection);
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366 public void fontSizeMenuItem_actionPerformed(ActionEvent e)
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368 String selection = JOptionPane.showInputDialog(this,
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369 "Select font size",
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371 JOptionPane.QUESTION_MESSAGE,
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372 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
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373 ,fontSizeMenuItem.getText()).toString();
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374 if(selection!=null)
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376 fontSizeMenuItem.setText(selection);
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381 public void fontStyleMenuItem_actionPerformed(ActionEvent e)
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383 String selection = JOptionPane.showInputDialog(this,
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384 "Select font style",
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386 JOptionPane.QUESTION_MESSAGE,
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387 null, new String[]{"plain", "bold", "italic"}
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388 ,fontStyleMenuItem.getText()).toString();
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389 if(selection!=null)
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391 fontStyleMenuItem.setText(selection);
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397 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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399 updateResidueView();
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404 int style = java.awt.Font.PLAIN;
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405 if(fontStyleMenuItem.getText().equals("bold"))
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406 style = java.awt.Font.BOLD;
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407 else if(fontStyleMenuItem.getText().equals("italic"))
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408 style = java.awt.Font.ITALIC;
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410 viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
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412 Integer.parseInt(fontSizeMenuItem.getText())));
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413 alignPanel.RefreshPanels();
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417 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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419 updateResidueView();
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423 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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425 updateResidueView();
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428 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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430 updateResidueView();
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433 void updateResidueView()
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435 if (viewport.getSelection().size() == 0)
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437 for (int i = 0; i < viewport.alignment.getGroups().size(); i++)
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439 SequenceGroup sg = (SequenceGroup) viewport.alignment.getGroups().elementAt(i);
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440 sg.setDisplayBoxes( viewBoxesMenuItem.isSelected() );
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441 sg.setDisplayText( viewTextMenuItem.isSelected() );
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442 sg.setColourText( colourTextMenuItem.isSelected() );
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447 SequenceGroup sg = viewport.alignment.findGroup( (Sequence) viewport.sel.sequenceAt(0));
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448 if (alignPanel.seqPanel.isNewSelection(sg))
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450 sg = viewport.getAlignment().addGroup();
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451 for (int i = 0; i < viewport.getSelection().size(); i++)
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453 viewport.alignment.removeFromGroup(viewport.alignment.findGroup( (
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454 Sequence) viewport.sel.sequenceAt(i)),
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455 (Sequence) viewport.sel.sequenceAt(
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457 viewport.alignment.addToGroup(sg,
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458 (Sequence) viewport.sel.sequenceAt(i));
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462 sg.setDisplayBoxes(viewBoxesMenuItem.isSelected());
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463 sg.setDisplayText(viewTextMenuItem.isSelected());
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464 sg.setColourText(colourTextMenuItem.isSelected());
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466 alignPanel.RefreshPanels();
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470 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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472 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
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475 public void overviewMenuItem_actionPerformed(ActionEvent e)
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478 JInternalFrame frame = new JInternalFrame();
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479 OverviewPanel overview = alignPanel.getOverviewPanel();
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481 overview = new OverviewPanel(alignPanel, viewport);
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482 frame.setContentPane(overview);
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483 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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484 frame.getWidth(), frame.getHeight());
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486 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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487 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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489 alignPanel.setOverviewPanel(null);
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492 alignPanel.setOverviewPanel( overview );
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494 }catch(java.lang.OutOfMemoryError ex)
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496 JOptionPane.showMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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497 +"\nTry reducing the font size.",
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498 "Out of memory", JOptionPane.WARNING_MESSAGE);
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504 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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506 alignPanel.setColourScheme(null, false);
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510 public void clustalColour_actionPerformed(ActionEvent e)
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512 // alignPanel.setColourScheme( new ClustalxColourScheme() );
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515 public void zappoColour_actionPerformed(ActionEvent e)
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517 alignPanel.setColourScheme( new ZappoColourScheme(), conservationMenuItem.isSelected() );
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520 public void taylorColour_actionPerformed(ActionEvent e)
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522 alignPanel.setColourScheme( new TaylorColourScheme(),conservationMenuItem.isSelected() );
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526 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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528 alignPanel.setColourScheme( new HydrophobicColourScheme(),conservationMenuItem.isSelected() );
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531 public void helixColour_actionPerformed(ActionEvent e)
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533 alignPanel.setColourScheme( new HelixColourScheme(),conservationMenuItem.isSelected() );
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537 public void strandColour_actionPerformed(ActionEvent e)
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539 alignPanel.setColourScheme( new StrandColourScheme() ,conservationMenuItem.isSelected() );
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543 public void turnColour_actionPerformed(ActionEvent e)
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545 alignPanel.setColourScheme( new TurnColourScheme() ,conservationMenuItem.isSelected() );
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549 public void buriedColour_actionPerformed(ActionEvent e)
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551 alignPanel.setColourScheme( new BuriedColourScheme() ,conservationMenuItem.isSelected() );
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555 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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557 alignPanel.setColourScheme ( alignPanel.seqPanel.getColourScheme(),conservationMenuItem.isSelected() );
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558 conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() );
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563 public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
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565 ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);
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566 JInternalFrame frame = new JInternalFrame();
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567 frame.setContentPane(cip);
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568 Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);
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569 frame.setMaximizable(false);
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573 public void abovePIDColour_actionPerformed(ActionEvent e)
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575 alignPanel.setColourScheme( new PIDColourScheme() ,conservationMenuItem.isSelected() );
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579 public void userDefinedColour_actionPerformed(ActionEvent e)
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581 JInternalFrame frame = new JInternalFrame();
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582 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel.seqPanel );
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583 frame.setContentPane(chooser);
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584 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
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585 frame.setResizable(false);
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586 frame.setIconifiable(false);
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587 frame.setMaximizable(false);
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590 public void PIDColour_actionPerformed(ActionEvent e)
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592 alignPanel.setColourScheme( new PIDColourScheme(),conservationMenuItem.isSelected() );
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596 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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598 alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) ,conservationMenuItem.isSelected() );
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603 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
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605 ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );
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606 Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
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610 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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612 addHistoryItem("sort");
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613 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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614 alignPanel.RefreshPanels();
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617 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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619 addHistoryItem("sort");
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620 AlignmentSorter.sortByID( viewport.getAlignment() );
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621 alignPanel.RefreshPanels();
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624 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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626 addHistoryItem("sort");
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627 AlignmentSorter.sortGroups(viewport.getAlignment());
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628 AlignmentSorter.sortGroups(viewport.getAlignment());
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629 alignPanel.RefreshPanels();
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632 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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634 addHistoryItem("sort");
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635 if(viewport.getCurrentTree()==null)
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638 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
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639 alignPanel.RefreshPanels();
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642 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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647 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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649 if(viewport.getSelection().size()<2)
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650 JOptionPane.showMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
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653 JInternalFrame frame = new JInternalFrame();
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654 frame.setContentPane(new PairwiseAlignPanel(viewport));
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655 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
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659 public void PCAMenuItem_actionPerformed(ActionEvent e)
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661 if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
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662 || viewport.getAlignment().getHeight()<4)
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664 JOptionPane.showMessageDialog(this, "Principal component analysis must take\n"
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665 +"at least 4 input sequences.",
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666 "Sequence selection insufficient",
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667 JOptionPane.WARNING_MESSAGE);
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672 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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673 JInternalFrame frame = new JInternalFrame();
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674 frame.setContentPane(pcaPanel);
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675 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
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676 }catch(java.lang.OutOfMemoryError ex)
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678 JOptionPane.showMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
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679 "Out of memory", JOptionPane.WARNING_MESSAGE);
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685 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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687 NewTreePanel("AV", "PID", "Average distance tree using PID");
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690 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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692 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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696 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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698 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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701 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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703 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
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706 void NewTreePanel(String type, String pwType, String title)
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708 JInternalFrame frame = new javax.swing.JInternalFrame();
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710 if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
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712 tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
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713 viewport.getStartRes(), viewport.getEndRes());
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717 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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718 type, pwType, viewport.getStartRes(),
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719 viewport.getEndRes());
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722 frame.setContentPane(tp);
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723 Desktop.addInternalFrame(frame, title, 600, 500);
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728 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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730 JOptionPane.showMessageDialog(this, "Jalview is currently being reengineered"
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731 +"\nwithin the Barton Group, Dundee University."
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732 +"\nThis will be available as a web service 2005",
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733 "Web service", JOptionPane.INFORMATION_MESSAGE);
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736 public void pdbTest_actionPerformed(ActionEvent e)
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738 String reply = JOptionPane.showInputDialog(this, "Enter pdb code", "PDB test viewer", JOptionPane.QUESTION_MESSAGE);
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740 String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";
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741 if (reply.length()>1)
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742 url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;
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746 PDBfile pdb = new PDBfile(url,
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748 Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);
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749 seq.setPDBfile(pdb);
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750 ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;
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751 ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;
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752 // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();
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754 rotCanvas rc = new rotCanvas(pdb);
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755 JInternalFrame frame = new JInternalFrame();
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756 frame.setContentPane(rc);
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757 Desktop.addInternalFrame(frame, url, 400,400);
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759 catch (Exception ex)
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761 ex.printStackTrace();
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