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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89 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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90 printJob.setPrintable(alignPanel, pf);
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91 if (printJob.printDialog())
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97 catch (Exception PrintException)
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99 PrintException.printStackTrace();
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109 public void closeMenuItem_actionPerformed(ActionEvent e)
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112 this.setClosed(true);
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113 }catch(Exception ex){}
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116 ArrayList historyList = new ArrayList();
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117 ArrayList redoList = new ArrayList();
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119 void updateEditMenuBar()
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121 if(historyList.size()>0)
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123 undoMenuItem.setEnabled(true);
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124 Object [] history = (Object[])historyList.get(0);
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125 undoMenuItem.setText("Undo "+history[0]);
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129 undoMenuItem.setEnabled(false);
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130 undoMenuItem.setText("Undo");
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133 if(redoList.size()>0)
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135 redoMenuItem.setEnabled(true);
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136 Object [] history = (Object[])redoList.get(0);
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137 redoMenuItem.setText("Redo "+history[0]);
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141 redoMenuItem.setEnabled(false);
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142 redoMenuItem.setText("Redo");
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146 public void addHistoryItem(String type)
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148 // must make sure we add new sequence objects her, not refs to the existing sequences
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150 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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151 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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153 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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154 viewport.getAlignment().getSequenceAt(i).getSequence());
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157 historyList.add(0, new Object[]{type, seq} );
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158 updateEditMenuBar();
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161 protected void undoMenuItem_actionPerformed(ActionEvent e)
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163 Object [] history = (Object[])historyList.remove(0);
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164 // add the redo state before continuing!!
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165 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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166 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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168 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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169 viewport.getAlignment().getSequenceAt(i).
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174 redoList.add(0, new Object[] {history[0], seq});
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176 seq = (SequenceI[]) history[1];
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177 viewport.setAlignment( new Alignment(seq) );
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178 updateEditMenuBar();
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179 alignPanel.RefreshPanels();
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183 protected void redoMenuItem_actionPerformed(ActionEvent e)
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185 Object [] history = (Object[])redoList.remove(0);
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186 SequenceI[] seq = (SequenceI[]) history[1];
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187 viewport.setAlignment( new Alignment(seq) );
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188 updateEditMenuBar();
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189 alignPanel.RefreshPanels();
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194 public void groupsMenuItem_actionPerformed(ActionEvent e)
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196 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
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197 JInternalFrame frame = new JInternalFrame();
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198 frame.setContentPane(geditor);
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199 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
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200 frame.setResizable(false);
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203 public void groupEditingMenuItem_actionPerformed(ActionEvent e)
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205 viewport.setGroupEdit( groupEditingMenuItem.isSelected() );
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208 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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210 Selection sel = viewport.getSelection();
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211 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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212 sel.addElement( viewport.getAlignment().getSequenceAt(i));
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213 PaintRefresher.Refresh(null);
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216 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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218 viewport.getSelection().clear();
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219 PaintRefresher.Refresh(null);
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222 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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224 Selection sel = viewport.getSelection();
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225 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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227 if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
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228 sel.removeElement(viewport.getAlignment().getSequenceAt(i));
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230 sel.addElement(viewport.getAlignment().getSequenceAt(i));
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232 PaintRefresher.Refresh(null);
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235 public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)
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237 addHistoryItem("delete selection");
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239 for (int i=0;i < viewport.getSelection().size(); i++)
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240 viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));
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242 viewport.getSelection().clear();
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243 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
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244 alignPanel.RefreshPanels();
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247 public void moveSelectedMenuItem_actionPerformed(ActionEvent e)
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249 copySelectedMenuItem_actionPerformed(null);
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250 deleteSelectedMenuItem_actionPerformed(null);
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251 alignPanel.repaint();
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254 public void copySelectedMenuItem_actionPerformed(ActionEvent e)
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256 if(viewport.getSelection().size()==0)
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259 SequenceI[] s = new Sequence[viewport.getSelection().size()];
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260 for (int i=0; i < viewport.getSelection().size(); i++) {
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261 s[i] = new Sequence(viewport.getSelection().sequenceAt(i));
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263 AlignFrame af = new AlignFrame(new Alignment(s));
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264 int newHeight = s.length * af.viewport.getCharHeight() + 200;
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267 Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
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270 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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272 viewport.getColumnSelection().clear();
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276 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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278 addHistoryItem("delete columns");
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279 ColumnSelection colSel = viewport.getColumnSelection();
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280 if (colSel.size() > 0)
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282 int min = colSel.getMin();
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283 viewport.getAlignment().trimLeft(min);
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284 colSel.compensateForEdit(0,min);
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285 alignPanel.RefreshPanels();
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289 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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291 addHistoryItem("delete columns");
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292 ColumnSelection colSel = viewport.getColumnSelection();
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293 if (colSel.size() > 0)
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295 int max = colSel.getMax();
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297 viewport.getAlignment().trimRight(max);
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299 alignPanel.RefreshPanels();
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304 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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306 addHistoryItem("delete gapped columns");
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307 viewport.getAlignment().removeGaps();
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308 alignPanel.RefreshPanels();
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311 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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313 addHistoryItem("delete all gaps");
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316 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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318 current = viewport.getAlignment().getSequenceAt(i);
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319 jSize = current.getLength();
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320 for (int j=0; j < jSize; j++)
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321 if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')
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323 current.deleteCharAt(j);
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329 alignPanel.RefreshPanels();
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332 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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334 char thisChar = '-';
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335 char nextChar = '.';
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336 if(viewport.getGapCharacter()=='-')
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341 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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342 viewport.setGapCharacter(thisChar);
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343 alignPanel.RefreshPanels();
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346 public void findMenuItem_actionPerformed(ActionEvent e)
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348 JOptionPane op = new JOptionPane();
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349 JInternalFrame frame = op.createInternalFrame(this, "Find");
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350 Finder finder = new Finder(viewport, alignPanel, frame);
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351 frame.setContentPane(finder);
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352 frame.setSize(300,110);
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353 frame.setVisible(true);
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358 public void fontNameMenuItem_actionPerformed(ActionEvent e)
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360 String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
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363 String selection = JOptionPane.showInternalInputDialog(this,
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366 JOptionPane.QUESTION_MESSAGE,
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368 ,fontNameMenuItem.getText()).toString();
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369 if(selection!=null)
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371 fontNameMenuItem.setText(selection);
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377 public void fontSizeMenuItem_actionPerformed(ActionEvent e)
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379 String selection = JOptionPane.showInternalInputDialog(this,
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380 "Select font size",
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382 JOptionPane.QUESTION_MESSAGE,
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383 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
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384 ,fontSizeMenuItem.getText()).toString();
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385 if(selection!=null)
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387 fontSizeMenuItem.setText(selection);
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392 public void fontStyleMenuItem_actionPerformed(ActionEvent e)
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394 String selection = JOptionPane.showInternalInputDialog(this,
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395 "Select font style",
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397 JOptionPane.QUESTION_MESSAGE,
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398 null, new String[]{"plain", "bold", "italic"}
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399 ,fontStyleMenuItem.getText()).toString();
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400 if(selection!=null)
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402 fontStyleMenuItem.setText(selection);
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408 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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410 updateResidueView();
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415 int style = java.awt.Font.PLAIN;
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416 if(fontStyleMenuItem.getText().equals("bold"))
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417 style = java.awt.Font.BOLD;
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418 else if(fontStyleMenuItem.getText().equals("italic"))
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419 style = java.awt.Font.ITALIC;
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421 viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
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423 Integer.parseInt(fontSizeMenuItem.getText())));
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424 alignPanel.RefreshPanels();
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428 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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430 updateResidueView();
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434 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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436 updateResidueView();
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439 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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441 updateResidueView();
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445 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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447 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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448 alignPanel.RefreshPanels();
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452 void updateResidueView()
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454 if (viewport.getSelection().size() == 0)
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456 for (int i = 0; i < viewport.alignment.getGroups().size(); i++)
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458 SequenceGroup sg = (SequenceGroup) viewport.alignment.getGroups().elementAt(i);
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459 sg.setDisplayBoxes( viewBoxesMenuItem.isSelected() );
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460 sg.setDisplayText( viewTextMenuItem.isSelected() );
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461 sg.setColourText( colourTextMenuItem.isSelected() );
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466 SequenceGroup sg = viewport.alignment.findGroup( (Sequence) viewport.sel.sequenceAt(0));
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467 if (alignPanel.seqPanel.isNewSelection(sg))
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469 sg = viewport.getAlignment().addGroup();
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470 for (int i = 0; i < viewport.getSelection().size(); i++)
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472 viewport.alignment.removeFromGroup(viewport.alignment.findGroup( (
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473 Sequence) viewport.sel.sequenceAt(i)),
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474 (Sequence) viewport.sel.sequenceAt(
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476 viewport.alignment.addToGroup(sg,
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477 (Sequence) viewport.sel.sequenceAt(i));
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481 sg.setDisplayBoxes(viewBoxesMenuItem.isSelected());
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482 sg.setDisplayText(viewTextMenuItem.isSelected());
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483 sg.setColourText(colourTextMenuItem.isSelected());
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485 alignPanel.RefreshPanels();
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489 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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491 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
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494 public void overviewMenuItem_actionPerformed(ActionEvent e)
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497 JInternalFrame frame = new JInternalFrame();
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498 OverviewPanel overview = alignPanel.getOverviewPanel();
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500 overview = new OverviewPanel(alignPanel, viewport);
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501 frame.setContentPane(overview);
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502 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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503 frame.getWidth(), frame.getHeight());
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505 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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506 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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508 alignPanel.setOverviewPanel(null);
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511 alignPanel.setOverviewPanel( overview );
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513 }catch(java.lang.OutOfMemoryError ex)
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515 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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516 +"\nTry reducing the font size.",
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517 "Out of memory", JOptionPane.WARNING_MESSAGE);
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523 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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525 alignPanel.setColourScheme(null, false);
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529 public void clustalColour_actionPerformed(ActionEvent e)
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531 // alignPanel.setColourScheme( new ClustalxColourScheme() );
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534 public void zappoColour_actionPerformed(ActionEvent e)
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536 alignPanel.setColourScheme( new ZappoColourScheme(), conservationMenuItem.isSelected() );
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539 public void taylorColour_actionPerformed(ActionEvent e)
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541 alignPanel.setColourScheme( new TaylorColourScheme(),conservationMenuItem.isSelected() );
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545 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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547 alignPanel.setColourScheme( new HydrophobicColourScheme(),conservationMenuItem.isSelected() );
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550 public void helixColour_actionPerformed(ActionEvent e)
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552 alignPanel.setColourScheme( new HelixColourScheme(),conservationMenuItem.isSelected() );
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556 public void strandColour_actionPerformed(ActionEvent e)
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558 alignPanel.setColourScheme( new StrandColourScheme() ,conservationMenuItem.isSelected() );
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562 public void turnColour_actionPerformed(ActionEvent e)
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564 alignPanel.setColourScheme( new TurnColourScheme() ,conservationMenuItem.isSelected() );
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568 public void buriedColour_actionPerformed(ActionEvent e)
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570 alignPanel.setColourScheme( new BuriedColourScheme() ,conservationMenuItem.isSelected() );
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574 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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576 alignPanel.setColourScheme ( alignPanel.seqPanel.getColourScheme(),conservationMenuItem.isSelected() );
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577 conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() );
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582 public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
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584 ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);
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585 JInternalFrame frame = new JInternalFrame();
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586 frame.setContentPane(cip);
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587 Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);
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588 frame.setMaximizable(false);
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592 public void abovePIDColour_actionPerformed(ActionEvent e)
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594 alignPanel.setColourScheme( new PIDColourScheme() ,conservationMenuItem.isSelected() );
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598 public void userDefinedColour_actionPerformed(ActionEvent e)
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600 JInternalFrame frame = new JInternalFrame();
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601 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel.seqPanel );
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602 frame.setContentPane(chooser);
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603 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
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604 frame.setResizable(false);
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605 frame.setIconifiable(false);
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606 frame.setMaximizable(false);
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609 public void PIDColour_actionPerformed(ActionEvent e)
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611 alignPanel.setColourScheme( new PIDColourScheme(),conservationMenuItem.isSelected() );
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615 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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617 alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) ,conservationMenuItem.isSelected() );
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622 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
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624 ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );
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625 Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
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629 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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631 addHistoryItem("sort");
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632 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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633 alignPanel.RefreshPanels();
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636 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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638 addHistoryItem("sort");
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639 AlignmentSorter.sortByID( viewport.getAlignment() );
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640 alignPanel.RefreshPanels();
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643 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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645 addHistoryItem("sort");
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646 AlignmentSorter.sortByGroup(viewport.getAlignment());
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647 AlignmentSorter.sortGroups(viewport.getAlignment());
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648 alignPanel.RefreshPanels();
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651 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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653 addHistoryItem("sort");
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654 if(viewport.getCurrentTree()==null)
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657 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
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658 alignPanel.RefreshPanels();
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661 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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666 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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668 if(viewport.getSelection().size()<2)
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669 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
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672 JInternalFrame frame = new JInternalFrame();
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673 frame.setContentPane(new PairwiseAlignPanel(viewport));
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674 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
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678 public void PCAMenuItem_actionPerformed(ActionEvent e)
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680 if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
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681 || viewport.getAlignment().getHeight()<4)
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683 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
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684 +"at least 4 input sequences.",
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685 "Sequence selection insufficient",
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686 JOptionPane.WARNING_MESSAGE);
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691 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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692 JInternalFrame frame = new JInternalFrame();
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693 frame.setContentPane(pcaPanel);
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694 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
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695 }catch(java.lang.OutOfMemoryError ex)
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697 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
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698 "Out of memory", JOptionPane.WARNING_MESSAGE);
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704 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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706 NewTreePanel("AV", "PID", "Average distance tree using PID");
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709 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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711 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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715 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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717 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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720 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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722 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
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725 void NewTreePanel(String type, String pwType, String title)
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727 JInternalFrame frame = new javax.swing.JInternalFrame();
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729 if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
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731 tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
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732 viewport.getStartRes(), viewport.getEndRes());
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736 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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737 type, pwType, viewport.getStartRes(),
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738 viewport.getEndRes());
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741 frame.setContentPane(tp);
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742 Desktop.addInternalFrame(frame, title, 600, 500);
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747 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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749 JOptionPane.showInternalMessageDialog(this, "Jalview is currently being reengineered"
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750 +"\nwithin the Barton Group, Dundee University."
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751 +"\nThis will be available as a web service 2005",
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752 "Web service", JOptionPane.INFORMATION_MESSAGE);
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755 public void pdbTest_actionPerformed(ActionEvent e)
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757 String reply = JOptionPane.showInternalInputDialog(this, "Enter pdb code", "PDB test viewer", JOptionPane.QUESTION_MESSAGE);
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759 String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";
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760 if (reply.length()>1)
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761 url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;
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765 PDBfile pdb = new PDBfile(url,
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767 Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);
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768 seq.setPDBfile(pdb);
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769 ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;
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770 ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;
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771 // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();
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773 rotCanvas rc = new rotCanvas(pdb);
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774 JInternalFrame frame = new JInternalFrame();
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775 frame.setContentPane(rc);
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776 Desktop.addInternalFrame(frame, url, 400,400);
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778 catch (Exception ex)
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780 ex.printStackTrace();
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786 public void doKeyPressed(KeyEvent evt)
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789 System.out.println(evt.getKeyChar());
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790 if(evt.isControlDown() && evt.getKeyChar()=='f')
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791 findMenuItem_actionPerformed(null);
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