1 /********************
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2 * 2004 Jalview Reengineered
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12 package jalview.gui;
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14 import jalview.jbgui.GAlignFrame;
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15 import jalview.schemes.*;
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16 import jalview.datamodel.*;
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17 import jalview.analysis.*;
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18 import jalview.io.*;
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19 import jalview.ws.*;
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22 import java.awt.event.*;
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23 import java.awt.print.*;
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24 import javax.swing.*;
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25 import javax.swing.event.*;
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27 import jalview.datamodel.SequenceI;
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29 public class AlignFrame extends GAlignFrame
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31 final AlignmentPanel alignPanel;
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32 final AlignViewport viewport;
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33 public AlignFrame(AlignmentI al)
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37 viewport = new AlignViewport(al,true,true,true,false);
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38 alignPanel = new AlignmentPanel(this, viewport);
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39 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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40 fontNameMenuItem.setText(viewport.getFont().getName());
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41 fontSizeMenuItem.setText(viewport.getFont().getSize()+"");
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43 clustalColour.setSelected(true);
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44 clustalColour_actionPerformed(null);
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47 protected void saveAs_actionPerformed(ActionEvent e)
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49 JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);
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50 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
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51 chooser.setToolTipText("Save");
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52 int value = chooser.showSaveDialog(this);
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53 if(value == JFileChooser.APPROVE_OPTION)
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55 String choice = chooser.getSelectedFile().getPath();
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56 jalview.bin.Cache.LAST_DIRECTORY = choice;
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57 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
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59 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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60 out.println(output);
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63 catch(Exception ex){}
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68 protected void outputText_actionPerformed(ActionEvent e)
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70 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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71 JInternalFrame frame = new JInternalFrame();
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72 cap.formatForOutput();
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73 frame.setContentPane(cap);
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74 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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75 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
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78 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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80 HTMLOutput htmlOutput = new HTMLOutput(viewport);
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84 public void printMenuItem_actionPerformed(ActionEvent e)
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86 //Putting in a thread avoids Swing painting problems
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87 PrintThread thread = new PrintThread();
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91 class PrintThread extends Thread
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95 PrinterJob printJob = PrinterJob.getPrinterJob();
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96 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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97 printJob.setPrintable(alignPanel, pf);
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98 if (printJob.printDialog())
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104 catch (Exception PrintException)
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106 PrintException.printStackTrace();
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116 public void closeMenuItem_actionPerformed(ActionEvent e)
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119 this.setClosed(true);
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120 }catch(Exception ex){}
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123 ArrayList historyList = new ArrayList();
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124 ArrayList redoList = new ArrayList();
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126 void updateEditMenuBar()
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128 if(historyList.size()>0)
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130 undoMenuItem.setEnabled(true);
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131 Object [] history = (Object[])historyList.get(0);
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132 undoMenuItem.setText("Undo "+history[0]);
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136 undoMenuItem.setEnabled(false);
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137 undoMenuItem.setText("Undo");
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140 if(redoList.size()>0)
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142 redoMenuItem.setEnabled(true);
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143 Object [] history = (Object[])redoList.get(0);
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144 redoMenuItem.setText("Redo "+history[0]);
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148 redoMenuItem.setEnabled(false);
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149 redoMenuItem.setText("Redo");
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153 public void addHistoryItem(String type)
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155 // must make sure we add new sequence objects her, not refs to the existing sequences
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157 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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158 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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160 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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161 viewport.getAlignment().getSequenceAt(i).getSequence());
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164 historyList.add(0, new Object[]{type, seq} );
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165 updateEditMenuBar();
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168 protected void undoMenuItem_actionPerformed(ActionEvent e)
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170 Object [] history = (Object[])historyList.remove(0);
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171 // add the redo state before continuing!!
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172 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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173 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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175 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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176 viewport.getAlignment().getSequenceAt(i).
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181 redoList.add(0, new Object[] {history[0], seq});
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183 seq = (SequenceI[]) history[1];
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184 viewport.setAlignment( new Alignment(seq) );
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185 updateEditMenuBar();
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186 alignPanel.RefreshPanels();
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190 protected void redoMenuItem_actionPerformed(ActionEvent e)
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192 Object [] history = (Object[])redoList.remove(0);
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193 SequenceI[] seq = (SequenceI[]) history[1];
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194 viewport.setAlignment( new Alignment(seq) );
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195 updateEditMenuBar();
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196 alignPanel.RefreshPanels();
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200 public void groupsMenuItem_actionPerformed(ActionEvent e)
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202 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
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203 JInternalFrame frame = new JInternalFrame();
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204 frame.setContentPane(geditor);
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205 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
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206 frame.setResizable(false);
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209 protected void deleteGroups_actionPerformed(ActionEvent e)
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211 viewport.alignment.deleteAllGroups();
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212 viewport.getSelection().clear();
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214 alignPanel.RefreshPanels();
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219 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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221 Selection sel = viewport.getSelection();
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222 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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223 sel.addElement( viewport.getAlignment().getSequenceAt(i));
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224 PaintRefresher.Refresh(null);
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227 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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229 viewport.setRubberbandGroup(null);
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230 viewport.getSelection().clear();
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231 PaintRefresher.Refresh(null);
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234 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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236 Selection sel = viewport.getSelection();
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237 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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239 if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
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240 sel.removeElement(viewport.getAlignment().getSequenceAt(i));
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242 sel.addElement(viewport.getAlignment().getSequenceAt(i));
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244 PaintRefresher.Refresh(null);
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248 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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250 viewport.getColumnSelection().clear();
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254 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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256 addHistoryItem("delete columns");
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257 ColumnSelection colSel = viewport.getColumnSelection();
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258 if (colSel.size() > 0)
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260 int min = colSel.getMin();
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261 viewport.getAlignment().trimLeft(min);
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262 colSel.compensateForEdit(0,min);
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263 alignPanel.RefreshPanels();
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267 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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269 addHistoryItem("delete columns");
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270 ColumnSelection colSel = viewport.getColumnSelection();
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271 if (colSel.size() > 0)
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273 int max = colSel.getMax();
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275 viewport.getAlignment().trimRight(max);
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277 alignPanel.RefreshPanels();
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282 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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284 addHistoryItem("delete gapped columns");
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285 viewport.getAlignment().removeGaps();
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286 alignPanel.RefreshPanels();
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289 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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291 addHistoryItem("delete all gaps");
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294 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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296 current = viewport.getAlignment().getSequenceAt(i);
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297 jSize = current.getLength();
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298 for (int j=0; j < jSize; j++)
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299 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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301 current.deleteCharAt(j);
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307 alignPanel.RefreshPanels();
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310 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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312 char thisChar = '-';
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313 char nextChar = '.';
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314 if(viewport.getGapCharacter()=='-')
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319 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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320 viewport.setGapCharacter(thisChar);
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321 alignPanel.RefreshPanels();
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324 public void findMenuItem_actionPerformed(ActionEvent e)
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326 JOptionPane op = new JOptionPane();
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327 JInternalFrame frame = op.createInternalFrame(this, "Find");
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328 Finder finder = new Finder(viewport, alignPanel, frame);
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329 frame.setClosable(true);
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330 frame.setContentPane(finder);
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331 frame.setSize(340,110);
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332 frame.setVisible(true);
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337 public void fontNameMenuItem_actionPerformed(ActionEvent e)
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339 String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
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342 String selection = JOptionPane.showInternalInputDialog(this,
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345 JOptionPane.QUESTION_MESSAGE,
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347 ,fontNameMenuItem.getText()).toString();
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348 if(selection!=null)
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350 fontNameMenuItem.setText(selection);
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356 public void fontSizeMenuItem_actionPerformed(ActionEvent e)
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358 String selection = JOptionPane.showInternalInputDialog(this,
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359 "Select font size",
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361 JOptionPane.QUESTION_MESSAGE,
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362 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
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363 ,fontSizeMenuItem.getText()).toString();
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364 if(selection!=null)
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366 fontSizeMenuItem.setText(selection);
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371 public void fontStyleMenuItem_actionPerformed(ActionEvent e)
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373 String selection = JOptionPane.showInternalInputDialog(this,
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374 "Select font style",
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376 JOptionPane.QUESTION_MESSAGE,
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377 null, new String[]{"plain", "bold", "italic"}
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378 ,fontStyleMenuItem.getText()).toString();
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379 if(selection!=null)
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381 fontStyleMenuItem.setText(selection);
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387 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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389 viewport.setColourText( colourTextMenuItem.isSelected() );
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390 alignPanel.RefreshPanels();
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395 int style = java.awt.Font.PLAIN;
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396 if(fontStyleMenuItem.getText().equals("bold"))
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397 style = java.awt.Font.BOLD;
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398 else if(fontStyleMenuItem.getText().equals("italic"))
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399 style = java.awt.Font.ITALIC;
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401 viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
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403 Integer.parseInt(fontSizeMenuItem.getText())));
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404 alignPanel.RefreshPanels();
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408 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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410 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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411 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
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415 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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417 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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418 alignPanel.RefreshPanels();
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421 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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423 viewport.setShowText( viewTextMenuItem.isSelected() );
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424 alignPanel.RefreshPanels();
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428 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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430 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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431 alignPanel.RefreshPanels();
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434 public void secondaryStructure_actionPerformed(ActionEvent evt)
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436 alignPanel.setSecondaryStructureVisible(secondaryStructure.isSelected());
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439 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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441 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
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444 public void overviewMenuItem_actionPerformed(ActionEvent e)
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446 if (alignPanel.overviewPanel != null)
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449 JInternalFrame frame = new JInternalFrame();
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450 OverviewPanel overview = alignPanel.getOverviewPanel();
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452 overview = new OverviewPanel(alignPanel, viewport);
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453 frame.setContentPane(overview);
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454 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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455 frame.getWidth(), frame.getHeight());
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457 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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458 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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460 alignPanel.setOverviewPanel(null);
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463 alignPanel.setOverviewPanel( overview );
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465 }catch(java.lang.OutOfMemoryError ex)
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467 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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468 +"\nTry reducing the font size.",
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469 "Out of memory", JOptionPane.WARNING_MESSAGE);
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475 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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477 viewport.setGlobalColourScheme( null );
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482 public void clustalColour_actionPerformed(ActionEvent e)
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484 viewport.setGlobalColourScheme(
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485 new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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486 abovePIDThreshold.setSelected(false);
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490 public void zappoColour_actionPerformed(ActionEvent e)
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492 viewport.setGlobalColourScheme(new ZappoColourScheme() );
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496 public void taylorColour_actionPerformed(ActionEvent e)
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498 viewport.setGlobalColourScheme(new TaylorColourScheme() );
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503 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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505 viewport.setGlobalColourScheme( new HydrophobicColourScheme() );
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509 public void helixColour_actionPerformed(ActionEvent e)
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511 viewport.setGlobalColourScheme( new HelixColourScheme() );
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516 public void strandColour_actionPerformed(ActionEvent e)
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518 viewport.setGlobalColourScheme(new StrandColourScheme() );
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523 public void turnColour_actionPerformed(ActionEvent e)
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525 viewport.setGlobalColourScheme(new TurnColourScheme() );
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530 public void buriedColour_actionPerformed(ActionEvent e)
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532 viewport.setGlobalColourScheme( new BuriedColourScheme() );
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536 public void nucleotideColour_actionPerformed(ActionEvent e)
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538 viewport.setGlobalColourScheme( new NucleotideColourScheme() );
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543 void changeColour()
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545 if(abovePIDThreshold.isSelected())
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546 abovePIDThreshold_actionPerformed(null);
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547 else if(conservationMenuItem.isSelected())
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548 conservationMenuItem_actionPerformed(null);
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550 alignPanel.RefreshPanels();
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554 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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556 if(abovePIDThreshold.isSelected())
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558 abovePIDThreshold.setSelected(false);
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559 Desktop.hidePIDSlider();
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562 viewport.setConservationSelected(conservationMenuItem.isSelected());
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564 ColourSchemeI oldCs = viewport.getGlobalColourScheme();
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566 ConservationColourScheme ccs = null;
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567 if (oldCs instanceof ConservationColourScheme)
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568 ccs = (ConservationColourScheme) oldCs;
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570 if (conservationMenuItem.isSelected())
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572 Alignment al = (Alignment) viewport.alignment;
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573 Conservation c = new Conservation("All",
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574 ResidueProperties.propHash, 3,
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575 al.getSequences(), 0,
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579 c.verdict(false, 100);
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582 ccs = new ConservationColourScheme(c, ccs.cs);
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584 ccs = new ConservationColourScheme(c, oldCs);
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587 int threshold = Desktop.setConservationSliderSource(alignPanel, ccs, "Background");
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589 ccs.inc = threshold;
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591 if (ccs.cs instanceof ResidueColourScheme)
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592 ((ResidueColourScheme) ccs.cs).setThreshold(0);
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593 else if (ccs.cs instanceof ScoreColourScheme)
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594 ((ScoreColourScheme)ccs.cs).setThreshold(0);
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596 viewport.setGlobalColourScheme(ccs);
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600 else if (oldCs instanceof ConservationColourScheme)
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602 /// ie, if we remove ConservationColourScheme from backgroundColour
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604 viewport.setGlobalColourScheme(oldCs);
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605 Desktop.hideConservationSlider();
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609 alignPanel.RefreshPanels();
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613 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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615 if(conservationMenuItem.isSelected())
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616 conservationMenuItem.setSelected(false);
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618 ColourSchemeI oldCs = viewport.getGlobalColourScheme();
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620 if (oldCs instanceof ConservationColourScheme)
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622 ConservationColourScheme ccs = (ConservationColourScheme) oldCs;
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626 if(abovePIDThreshold.isSelected())
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628 threshold = Desktop.setPIDSliderSource(alignPanel, oldCs, "Background");
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629 Desktop.hideConservationSlider();
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632 Desktop.hidePIDSlider();
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634 if (oldCs instanceof ResidueColourScheme)
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635 ((ResidueColourScheme) oldCs).setThreshold(threshold);
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636 else if (oldCs instanceof ScoreColourScheme)
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637 ((ScoreColourScheme)oldCs).setThreshold(threshold);
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639 viewport.setGlobalColourScheme(oldCs);
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641 alignPanel.RefreshPanels();
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646 public void userDefinedColour_actionPerformed(ActionEvent e)
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648 JInternalFrame frame = new JInternalFrame();
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649 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
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650 frame.setContentPane(chooser);
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651 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
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652 frame.setResizable(false);
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653 frame.setIconifiable(false);
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654 frame.setMaximizable(false);
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657 public void PIDColour_actionPerformed(ActionEvent e)
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659 viewport.setGlobalColourScheme( new PIDColourScheme() );
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660 alignPanel.setColourScheme( );
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664 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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666 viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport) );
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672 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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674 addHistoryItem("sort");
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675 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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676 alignPanel.RefreshPanels();
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679 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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681 addHistoryItem("sort");
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682 AlignmentSorter.sortByID( viewport.getAlignment() );
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683 alignPanel.RefreshPanels();
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686 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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688 addHistoryItem("sort");
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689 AlignmentSorter.sortByGroup(viewport.getAlignment());
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690 AlignmentSorter.sortGroups(viewport.getAlignment());
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691 alignPanel.RefreshPanels();
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694 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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696 addHistoryItem("sort");
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697 if(viewport.getCurrentTree()==null)
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700 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
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701 alignPanel.RefreshPanels();
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704 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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706 RedundancyPanel sp = new RedundancyPanel(alignPanel);
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707 JInternalFrame frame = new JInternalFrame();
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708 frame.setContentPane(sp);
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709 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
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710 frame.setMaximizable(false);
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711 frame.setResizable(false);
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715 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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717 if(viewport.getSelection().size()<2)
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718 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
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721 JInternalFrame frame = new JInternalFrame();
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722 frame.setContentPane(new PairwiseAlignPanel(viewport));
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723 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
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727 public void PCAMenuItem_actionPerformed(ActionEvent e)
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729 if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
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730 || viewport.getAlignment().getHeight()<4)
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732 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
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733 +"at least 4 input sequences.",
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734 "Sequence selection insufficient",
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735 JOptionPane.WARNING_MESSAGE);
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740 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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741 JInternalFrame frame = new JInternalFrame();
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742 frame.setContentPane(pcaPanel);
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743 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
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744 }catch(java.lang.OutOfMemoryError ex)
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746 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
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747 "Out of memory", JOptionPane.WARNING_MESSAGE);
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753 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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755 NewTreePanel("AV", "PID", "Average distance tree using PID");
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758 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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760 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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764 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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766 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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769 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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771 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
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774 void NewTreePanel(String type, String pwType, String title)
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776 JInternalFrame frame = new javax.swing.JInternalFrame();
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778 if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
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780 tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
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781 viewport.getStartRes(), viewport.getEndRes());
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785 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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786 type, pwType, viewport.getStartRes(),
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787 viewport.getEndRes());
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790 frame.setContentPane(tp);
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791 Desktop.addInternalFrame(frame, title, 600, 500);
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797 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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799 JInternalFrame frame = new JInternalFrame();
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800 ClustalThread ct = new ClustalThread(frame);
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801 Thread t = new Thread(ct);
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803 frame.setContentPane(ct);
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804 Desktop.addInternalFrame(frame, title, 300, 80);
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808 class ClustalThread extends JPanel implements Runnable
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811 int imageIndex = 0;
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812 boolean webServiceRunning = false;
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813 JInternalFrame frame;
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814 public ClustalThread(JInternalFrame frame)
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816 this.frame = frame;
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817 image = new Image[9];
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818 for(int i=0; i<9; i++)
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820 java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");
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823 image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
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824 MediaTracker mt = new MediaTracker(this);
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825 mt.addImage(image[i], i);
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826 try{mt.waitForID(i);}
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827 catch(Exception ex){}
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830 DNATwirler twirler = new DNATwirler();
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832 webServiceRunning = true;
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835 class DNATwirler extends Thread
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839 while(webServiceRunning)
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847 catch(Exception ex){}
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853 // Should check to see if the server settings are valid
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854 // Need visual-delay indication here.
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857 jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
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858 Vector sv = viewport.getAlignment().getSequences();
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859 SequenceI[] seqs = new SequenceI[sv.size()];
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864 seqs[i] = (SequenceI) sv.elementAt(i);
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866 while (++i < sv.size());
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868 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
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870 if (alignment != null)
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872 AlignFrame af = new AlignFrame(new Alignment(alignment));
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873 Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
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874 700, 500); // JBPNote - is there a new window geom. property ?
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877 JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
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878 JOptionPane.WARNING_MESSAGE);
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880 webServiceRunning = false;
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882 frame.setClosed(true);
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883 }catch(Exception ex){}
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886 public void paintComponent(Graphics g)
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888 g.setColor(Color.white);
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889 g.fillRect(0,0,getWidth(), getHeight());
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892 g.drawImage(image[imageIndex],10,10,this);
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894 g.setFont(new Font("Arial", Font.BOLD, 12));
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895 g.setColor(Color.black);
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896 g.drawString("Clustal Alignment Web Service running", 30,30);
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903 public void pdbTest_actionPerformed(ActionEvent e)
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906 JOptionPane.showInternalInputDialog(this, "Enter pdb code",
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907 "PDB test viewer", JOptionPane.QUESTION_MESSAGE);
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909 String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";
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910 if (reply.length()>1)
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911 url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;
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915 PDBfile pdb = new PDBfile(url,
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917 Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);
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918 seq.setPDBfile(pdb);
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919 ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;
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920 ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;
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921 // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();
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923 rotCanvas rc = new rotCanvas(pdb);
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924 JInternalFrame frame = new JInternalFrame();
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925 frame.setContentPane(rc);
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926 Desktop.addInternalFrame(frame, url, 400,400);
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928 catch (Exception ex)
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930 ex.printStackTrace();
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936 public void doKeyPressed(KeyEvent evt)
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939 System.out.println(evt.getKeyChar());
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940 if(evt.isControlDown() && evt.getKeyChar()=='f')
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941 findMenuItem_actionPerformed(null);
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