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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44 protected void saveAs_actionPerformed(ActionEvent e)
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46 JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);
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47 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
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48 chooser.setToolTipText("Save");
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49 int value = chooser.showSaveDialog(this);
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50 if(value == JFileChooser.APPROVE_OPTION)
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52 String choice = chooser.getSelectedFile().getPath();
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53 jalview.bin.Cache.LAST_DIRECTORY = choice;
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54 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
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56 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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57 out.println(output);
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60 catch(Exception ex){}
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65 protected void outputText_actionPerformed(ActionEvent e)
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67 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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68 JInternalFrame frame = new JInternalFrame();
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69 cap.formatForOutput();
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70 frame.setContentPane(cap);
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71 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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72 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
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75 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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77 HTMLOutput htmlOutput = new HTMLOutput(viewport);
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81 public void printMenuItem_actionPerformed(ActionEvent e)
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83 //Putting in a thread avoids Swing painting problems
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84 PrintThread thread = new PrintThread();
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88 class PrintThread extends Thread
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92 PrinterJob printJob = PrinterJob.getPrinterJob();
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93 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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94 printJob.setPrintable(alignPanel, pf);
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95 if (printJob.printDialog())
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101 catch (Exception PrintException)
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103 PrintException.printStackTrace();
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113 public void closeMenuItem_actionPerformed(ActionEvent e)
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116 this.setClosed(true);
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117 }catch(Exception ex){}
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120 ArrayList historyList = new ArrayList();
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121 ArrayList redoList = new ArrayList();
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123 void updateEditMenuBar()
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125 if(historyList.size()>0)
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127 undoMenuItem.setEnabled(true);
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128 Object [] history = (Object[])historyList.get(0);
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129 undoMenuItem.setText("Undo "+history[0]);
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133 undoMenuItem.setEnabled(false);
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134 undoMenuItem.setText("Undo");
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137 if(redoList.size()>0)
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139 redoMenuItem.setEnabled(true);
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140 Object [] history = (Object[])redoList.get(0);
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141 redoMenuItem.setText("Redo "+history[0]);
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145 redoMenuItem.setEnabled(false);
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146 redoMenuItem.setText("Redo");
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150 public void addHistoryItem(String type)
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152 // must make sure we add new sequence objects her, not refs to the existing sequences
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154 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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155 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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157 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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158 viewport.getAlignment().getSequenceAt(i).getSequence());
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161 historyList.add(0, new Object[]{type, seq} );
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162 updateEditMenuBar();
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165 protected void undoMenuItem_actionPerformed(ActionEvent e)
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167 Object [] history = (Object[])historyList.remove(0);
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168 // add the redo state before continuing!!
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169 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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170 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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172 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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173 viewport.getAlignment().getSequenceAt(i).
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178 redoList.add(0, new Object[] {history[0], seq});
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180 seq = (SequenceI[]) history[1];
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181 viewport.setAlignment( new Alignment(seq) );
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182 updateEditMenuBar();
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183 alignPanel.RefreshPanels();
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187 protected void redoMenuItem_actionPerformed(ActionEvent e)
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189 Object [] history = (Object[])redoList.remove(0);
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190 SequenceI[] seq = (SequenceI[]) history[1];
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191 viewport.setAlignment( new Alignment(seq) );
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192 updateEditMenuBar();
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193 alignPanel.RefreshPanels();
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197 public void groupsMenuItem_actionPerformed(ActionEvent e)
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199 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
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200 JInternalFrame frame = new JInternalFrame();
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201 frame.setContentPane(geditor);
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202 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
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203 frame.setResizable(false);
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206 protected void deleteGroups_actionPerformed(ActionEvent e)
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208 viewport.alignment.deleteAllGroups();
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209 viewport.getSelection().clear();
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211 alignPanel.RefreshPanels();
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216 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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218 Selection sel = viewport.getSelection();
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219 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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220 sel.addElement( viewport.getAlignment().getSequenceAt(i));
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221 PaintRefresher.Refresh(null);
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224 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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226 viewport.setRubberbandGroup(null);
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227 viewport.getSelection().clear();
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228 PaintRefresher.Refresh(null);
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231 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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233 Selection sel = viewport.getSelection();
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234 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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236 if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
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237 sel.removeElement(viewport.getAlignment().getSequenceAt(i));
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239 sel.addElement(viewport.getAlignment().getSequenceAt(i));
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241 PaintRefresher.Refresh(null);
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245 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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247 viewport.getColumnSelection().clear();
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251 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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253 addHistoryItem("delete columns");
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254 ColumnSelection colSel = viewport.getColumnSelection();
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255 if (colSel.size() > 0)
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257 int min = colSel.getMin();
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258 viewport.getAlignment().trimLeft(min);
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259 colSel.compensateForEdit(0,min);
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260 alignPanel.RefreshPanels();
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264 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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266 addHistoryItem("delete columns");
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267 ColumnSelection colSel = viewport.getColumnSelection();
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268 if (colSel.size() > 0)
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270 int max = colSel.getMax();
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272 viewport.getAlignment().trimRight(max);
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274 alignPanel.RefreshPanels();
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279 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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281 addHistoryItem("delete gapped columns");
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282 viewport.getAlignment().removeGaps();
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283 alignPanel.RefreshPanels();
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286 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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288 addHistoryItem("delete all gaps");
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291 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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293 current = viewport.getAlignment().getSequenceAt(i);
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294 jSize = current.getLength();
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295 for (int j=0; j < jSize; j++)
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296 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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298 current.deleteCharAt(j);
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304 alignPanel.RefreshPanels();
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307 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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309 char thisChar = '-';
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310 char nextChar = '.';
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311 if(viewport.getGapCharacter()=='-')
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316 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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317 viewport.setGapCharacter(thisChar);
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318 alignPanel.RefreshPanels();
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321 public void findMenuItem_actionPerformed(ActionEvent e)
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323 JOptionPane op = new JOptionPane();
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324 JInternalFrame frame = op.createInternalFrame(this, "Find");
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325 Finder finder = new Finder(viewport, alignPanel, frame);
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326 frame.setClosable(true);
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327 frame.setContentPane(finder);
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328 frame.setSize(340,110);
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329 frame.setVisible(true);
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334 public void fontNameMenuItem_actionPerformed(ActionEvent e)
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336 String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
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339 String selection = JOptionPane.showInternalInputDialog(this,
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342 JOptionPane.QUESTION_MESSAGE,
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344 ,fontNameMenuItem.getText()).toString();
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345 if(selection!=null)
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347 fontNameMenuItem.setText(selection);
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353 public void fontSizeMenuItem_actionPerformed(ActionEvent e)
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355 String selection = JOptionPane.showInternalInputDialog(this,
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356 "Select font size",
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358 JOptionPane.QUESTION_MESSAGE,
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359 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
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360 ,fontSizeMenuItem.getText()).toString();
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361 if(selection!=null)
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363 fontSizeMenuItem.setText(selection);
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368 public void fontStyleMenuItem_actionPerformed(ActionEvent e)
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370 String selection = JOptionPane.showInternalInputDialog(this,
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371 "Select font style",
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373 JOptionPane.QUESTION_MESSAGE,
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374 null, new String[]{"plain", "bold", "italic"}
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375 ,fontStyleMenuItem.getText()).toString();
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376 if(selection!=null)
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378 fontStyleMenuItem.setText(selection);
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384 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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386 viewport.setColourText( colourTextMenuItem.isSelected() );
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387 alignPanel.RefreshPanels();
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392 int style = java.awt.Font.PLAIN;
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393 if(fontStyleMenuItem.getText().equals("bold"))
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394 style = java.awt.Font.BOLD;
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395 else if(fontStyleMenuItem.getText().equals("italic"))
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396 style = java.awt.Font.ITALIC;
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398 viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
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400 Integer.parseInt(fontSizeMenuItem.getText())));
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401 alignPanel.RefreshPanels();
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405 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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407 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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408 alignPanel.RefreshPanels();
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412 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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414 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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415 alignPanel.RefreshPanels();
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418 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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420 viewport.setShowText( viewTextMenuItem.isSelected() );
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421 alignPanel.RefreshPanels();
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425 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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427 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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428 alignPanel.RefreshPanels();
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431 public void secondaryStructure_actionPerformed(ActionEvent evt)
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433 alignPanel.setSecondaryStructureVisible(secondaryStructure.isSelected());
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436 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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438 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
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441 public void overviewMenuItem_actionPerformed(ActionEvent e)
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443 if (alignPanel.overviewPanel != null)
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446 JInternalFrame frame = new JInternalFrame();
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447 OverviewPanel overview = alignPanel.getOverviewPanel();
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449 overview = new OverviewPanel(alignPanel, viewport);
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450 frame.setContentPane(overview);
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451 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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452 frame.getWidth(), frame.getHeight());
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454 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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455 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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457 alignPanel.setOverviewPanel(null);
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460 alignPanel.setOverviewPanel( overview );
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462 }catch(java.lang.OutOfMemoryError ex)
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464 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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465 +"\nTry reducing the font size.",
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466 "Out of memory", JOptionPane.WARNING_MESSAGE);
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472 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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474 viewport.setGlobalColourScheme( null );
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479 public void clustalColour_actionPerformed(ActionEvent e)
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481 viewport.setGlobalColourScheme(new ClustalxColourScheme( ));
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482 conservationMenuItem.setSelected(false);
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483 abovePIDThreshold.setSelected(false);
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487 public void zappoColour_actionPerformed(ActionEvent e)
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489 viewport.setGlobalColourScheme(new ZappoColourScheme() );
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493 public void taylorColour_actionPerformed(ActionEvent e)
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495 viewport.setGlobalColourScheme(new TaylorColourScheme() );
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500 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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502 viewport.setGlobalColourScheme( new HydrophobicColourScheme() );
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506 public void helixColour_actionPerformed(ActionEvent e)
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508 viewport.setGlobalColourScheme( new HelixColourScheme() );
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513 public void strandColour_actionPerformed(ActionEvent e)
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515 viewport.setGlobalColourScheme(new StrandColourScheme() );
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520 public void turnColour_actionPerformed(ActionEvent e)
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522 viewport.setGlobalColourScheme(new TurnColourScheme() );
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527 public void buriedColour_actionPerformed(ActionEvent e)
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529 viewport.setGlobalColourScheme( new BuriedColourScheme() );
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533 public void nucleotideColour_actionPerformed(ActionEvent e)
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535 viewport.setGlobalColourScheme( new NucleotideColourScheme() );
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540 void changeColour()
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542 if(abovePIDThreshold.isSelected())
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543 abovePIDThreshold_actionPerformed(null);
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544 else if(conservationMenuItem.isSelected())
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545 conservationMenuItem_actionPerformed(null);
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548 alignPanel.RefreshPanels();
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551 void addConservationOrPIDColour()
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553 int x=0, y=0, threshold = 70;
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555 if(sliderFrame!=null)
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558 x = sliderFrame.getX();
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559 y = sliderFrame.getY();
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560 SliderPanel sp = (SliderPanel) sliderFrame.getContentPane();
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561 threshold = sp.getValue();
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562 sliderFrame.setClosed(true);
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564 catch (Exception ex)
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565 { ex.printStackTrace(); }
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567 ColourSchemeI oldCs = viewport.getGlobalColourScheme();
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569 ConservationColourScheme ccs = null;
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570 if (oldCs instanceof ConservationColourScheme)
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571 ccs = (ConservationColourScheme) oldCs;
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573 if(conservationMenuItem.isSelected())
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575 Alignment al = (Alignment)viewport.alignment;
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576 Conservation c = new Conservation("All",
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577 ResidueProperties.propHash, 3, al.getSequences(), 0,
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581 c.verdict(false, 100);
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584 ccs = new ConservationColourScheme(c, ccs.cs);
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586 ccs = new ConservationColourScheme(c, oldCs);
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588 viewport.setGlobalColourScheme( ccs );
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591 else if(oldCs instanceof ConservationColourScheme)
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594 viewport.setGlobalColourScheme( oldCs );
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598 if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() )
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600 sliderFrame = new JInternalFrame();
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601 sliderFrame.setMaximizable(false);
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602 sliderFrame.setResizable(false);
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604 SliderPanel sp = null;
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605 if (conservationMenuItem.isSelected())
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609 sp = new SliderPanel(alignPanel, threshold, true,ccs);
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610 Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment (Global colour)", 400, 90);
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613 else if (abovePIDThreshold.isSelected())
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615 sp = new SliderPanel(alignPanel, threshold, false, oldCs);
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617 Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);
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620 sliderFrame.setContentPane(sp);
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622 sliderFrame.setLocation(x,y);
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629 if (oldCs instanceof ResidueColourScheme)
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631 ResidueColourScheme rcs = (ResidueColourScheme) oldCs;
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632 rcs.setThreshold(threshold);
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634 else if (oldCs instanceof ScoreColourScheme)
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636 ScoreColourScheme scs = (ScoreColourScheme) oldCs;
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637 scs.setThreshold(threshold);
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643 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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645 if(abovePIDThreshold.isSelected())
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646 abovePIDThreshold.setSelected(false);
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648 viewport.setConservationSelected(conservationMenuItem.isSelected());
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650 addConservationOrPIDColour();
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653 JInternalFrame sliderFrame;
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654 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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656 if(conservationMenuItem.isSelected())
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657 conservationMenuItem.setSelected(false);
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659 addConservationOrPIDColour();
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664 public void userDefinedColour_actionPerformed(ActionEvent e)
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666 JInternalFrame frame = new JInternalFrame();
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667 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
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668 frame.setContentPane(chooser);
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669 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
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670 frame.setResizable(false);
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671 frame.setIconifiable(false);
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672 frame.setMaximizable(false);
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675 public void PIDColour_actionPerformed(ActionEvent e)
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677 viewport.setGlobalColourScheme( new PIDColourScheme() );
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678 alignPanel.setColourScheme( );
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682 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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684 viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport) );
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685 alignPanel.setColourScheme();
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690 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
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692 ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );
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693 Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
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697 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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699 addHistoryItem("sort");
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700 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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701 alignPanel.RefreshPanels();
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704 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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706 addHistoryItem("sort");
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707 AlignmentSorter.sortByID( viewport.getAlignment() );
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708 alignPanel.RefreshPanels();
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711 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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713 addHistoryItem("sort");
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714 AlignmentSorter.sortByGroup(viewport.getAlignment());
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715 AlignmentSorter.sortGroups(viewport.getAlignment());
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716 alignPanel.RefreshPanels();
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719 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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721 addHistoryItem("sort");
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722 if(viewport.getCurrentTree()==null)
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725 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
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726 alignPanel.RefreshPanels();
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729 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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731 RedundancyPanel sp = new RedundancyPanel(alignPanel);
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732 JInternalFrame frame = new JInternalFrame();
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733 frame.setContentPane(sp);
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734 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
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735 frame.setMaximizable(false);
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736 frame.setResizable(false);
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740 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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742 if(viewport.getSelection().size()<2)
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743 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
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746 JInternalFrame frame = new JInternalFrame();
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747 frame.setContentPane(new PairwiseAlignPanel(viewport));
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748 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
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752 public void PCAMenuItem_actionPerformed(ActionEvent e)
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754 if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
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755 || viewport.getAlignment().getHeight()<4)
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757 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
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758 +"at least 4 input sequences.",
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759 "Sequence selection insufficient",
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760 JOptionPane.WARNING_MESSAGE);
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765 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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766 JInternalFrame frame = new JInternalFrame();
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767 frame.setContentPane(pcaPanel);
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768 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
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769 }catch(java.lang.OutOfMemoryError ex)
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771 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
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772 "Out of memory", JOptionPane.WARNING_MESSAGE);
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778 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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780 NewTreePanel("AV", "PID", "Average distance tree using PID");
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783 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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785 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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789 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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791 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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794 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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796 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
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799 void NewTreePanel(String type, String pwType, String title)
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801 JInternalFrame frame = new javax.swing.JInternalFrame();
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803 if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
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805 tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
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806 viewport.getStartRes(), viewport.getEndRes());
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810 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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811 type, pwType, viewport.getStartRes(),
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812 viewport.getEndRes());
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815 frame.setContentPane(tp);
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816 Desktop.addInternalFrame(frame, title, 600, 500);
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822 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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824 JInternalFrame frame = new JInternalFrame();
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825 ClustalThread ct = new ClustalThread(frame);
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826 Thread t = new Thread(ct);
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828 frame.setContentPane(ct);
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829 Desktop.addInternalFrame(frame, title, 300, 80);
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833 class ClustalThread extends JPanel implements Runnable
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836 int imageIndex = 0;
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837 boolean webServiceRunning = false;
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838 JInternalFrame frame;
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839 public ClustalThread(JInternalFrame frame)
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841 this.frame = frame;
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842 image = new Image[9];
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843 for(int i=0; i<9; i++)
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845 java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");
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848 image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
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849 MediaTracker mt = new MediaTracker(this);
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850 mt.addImage(image[i], i);
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851 try{mt.waitForID(i);}
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852 catch(Exception ex){}
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855 DNATwirler twirler = new DNATwirler();
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857 webServiceRunning = true;
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860 class DNATwirler extends Thread
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864 while(webServiceRunning)
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872 catch(Exception ex){}
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878 // Should check to see if the server settings are valid
\r
879 // Need visual-delay indication here.
\r
882 jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
\r
883 Vector sv = viewport.getAlignment().getSequences();
\r
884 SequenceI[] seqs = new SequenceI[sv.size()];
\r
889 seqs[i] = (SequenceI) sv.elementAt(i);
\r
891 while (++i < sv.size());
\r
893 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
\r
895 if (alignment != null)
\r
897 AlignFrame af = new AlignFrame(new Alignment(alignment));
\r
898 Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
\r
899 700, 500); // JBPNote - is there a new window geom. property ?
\r
902 JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
\r
903 JOptionPane.WARNING_MESSAGE);
\r
905 webServiceRunning = false;
\r
907 frame.setClosed(true);
\r
908 }catch(Exception ex){}
\r
911 public void paintComponent(Graphics g)
\r
913 g.setColor(Color.white);
\r
914 g.fillRect(0,0,getWidth(), getHeight());
\r
917 g.drawImage(image[imageIndex],10,10,this);
\r
919 g.setFont(new Font("Arial", Font.BOLD, 12));
\r
920 g.setColor(Color.black);
\r
921 g.drawString("Clustal Alignment Web Service running", 30,30);
\r
928 public void pdbTest_actionPerformed(ActionEvent e)
\r
931 JOptionPane.showInternalInputDialog(this, "Enter pdb code",
\r
932 "PDB test viewer", JOptionPane.QUESTION_MESSAGE);
\r
934 String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";
\r
935 if (reply.length()>1)
\r
936 url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;
\r
940 PDBfile pdb = new PDBfile(url,
\r
942 Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);
\r
943 seq.setPDBfile(pdb);
\r
944 ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;
\r
945 ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;
\r
946 // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();
\r
948 rotCanvas rc = new rotCanvas(pdb);
\r
949 JInternalFrame frame = new JInternalFrame();
\r
950 frame.setContentPane(rc);
\r
951 Desktop.addInternalFrame(frame, url, 400,400);
\r
953 catch (Exception ex)
\r
955 ex.printStackTrace();
\r
961 public void doKeyPressed(KeyEvent evt)
\r
964 System.out.println(evt.getKeyChar());
\r
965 if(evt.isControlDown() && evt.getKeyChar()=='f')
\r
966 findMenuItem_actionPerformed(null);
\r