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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36 viewport = new AlignViewport(al,true,true,true,false);
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37 alignPanel = new AlignmentPanel(this, viewport);
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38 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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39 fontNameMenuItem.setText(viewport.getFont().getName());
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40 fontSizeMenuItem.setText(viewport.getFont().getSize()+"");
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43 protected void saveAs_actionPerformed(ActionEvent e)
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45 JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);
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46 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
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47 chooser.setToolTipText("Save");
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48 int value = chooser.showSaveDialog(this);
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49 if(value == JFileChooser.APPROVE_OPTION)
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51 String choice = chooser.getSelectedFile().getPath();
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52 jalview.bin.Cache.LAST_DIRECTORY = choice;
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53 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
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55 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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56 out.println(output);
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59 catch(Exception ex){}
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64 protected void outputText_actionPerformed(ActionEvent e)
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66 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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67 JInternalFrame frame = new JInternalFrame();
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68 cap.formatForOutput();
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69 frame.setContentPane(cap);
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70 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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71 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
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74 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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76 HTMLOutput htmlOutput = new HTMLOutput(viewport);
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80 public void printMenuItem_actionPerformed(ActionEvent e)
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82 //Putting in a thread avoids Swing painting problems
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83 PrintThread thread = new PrintThread();
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87 class PrintThread extends Thread
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91 PrinterJob printJob = PrinterJob.getPrinterJob();
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92 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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93 printJob.setPrintable(alignPanel, pf);
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94 if (printJob.printDialog())
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100 catch (Exception PrintException)
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102 PrintException.printStackTrace();
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112 public void closeMenuItem_actionPerformed(ActionEvent e)
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115 this.setClosed(true);
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116 }catch(Exception ex){}
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119 ArrayList historyList = new ArrayList();
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120 ArrayList redoList = new ArrayList();
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122 void updateEditMenuBar()
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124 if(historyList.size()>0)
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126 undoMenuItem.setEnabled(true);
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127 Object [] history = (Object[])historyList.get(0);
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128 undoMenuItem.setText("Undo "+history[0]);
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132 undoMenuItem.setEnabled(false);
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133 undoMenuItem.setText("Undo");
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136 if(redoList.size()>0)
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138 redoMenuItem.setEnabled(true);
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139 Object [] history = (Object[])redoList.get(0);
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140 redoMenuItem.setText("Redo "+history[0]);
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144 redoMenuItem.setEnabled(false);
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145 redoMenuItem.setText("Redo");
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149 public void addHistoryItem(String type)
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151 // must make sure we add new sequence objects her, not refs to the existing sequences
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153 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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154 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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156 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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157 viewport.getAlignment().getSequenceAt(i).getSequence());
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160 historyList.add(0, new Object[]{type, seq} );
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161 updateEditMenuBar();
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164 protected void undoMenuItem_actionPerformed(ActionEvent e)
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166 Object [] history = (Object[])historyList.remove(0);
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167 // add the redo state before continuing!!
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168 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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169 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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171 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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172 viewport.getAlignment().getSequenceAt(i).
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177 redoList.add(0, new Object[] {history[0], seq});
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179 seq = (SequenceI[]) history[1];
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180 viewport.setAlignment( new Alignment(seq) );
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181 updateEditMenuBar();
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182 alignPanel.RefreshPanels();
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186 protected void redoMenuItem_actionPerformed(ActionEvent e)
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188 Object [] history = (Object[])redoList.remove(0);
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189 SequenceI[] seq = (SequenceI[]) history[1];
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190 viewport.setAlignment( new Alignment(seq) );
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191 updateEditMenuBar();
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192 alignPanel.RefreshPanels();
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196 public void groupsMenuItem_actionPerformed(ActionEvent e)
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198 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
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199 JInternalFrame frame = new JInternalFrame();
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200 frame.setContentPane(geditor);
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201 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
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202 frame.setResizable(false);
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205 protected void deleteGroups_actionPerformed(ActionEvent e)
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207 viewport.alignment.deleteAllGroups();
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208 alignPanel.RefreshPanels();
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213 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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215 Selection sel = viewport.getSelection();
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216 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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217 sel.addElement( viewport.getAlignment().getSequenceAt(i));
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218 PaintRefresher.Refresh(null);
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221 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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223 viewport.getSelection().clear();
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224 PaintRefresher.Refresh(null);
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227 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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229 Selection sel = viewport.getSelection();
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230 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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232 if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
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233 sel.removeElement(viewport.getAlignment().getSequenceAt(i));
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235 sel.addElement(viewport.getAlignment().getSequenceAt(i));
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237 PaintRefresher.Refresh(null);
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241 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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243 viewport.getColumnSelection().clear();
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247 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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249 addHistoryItem("delete columns");
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250 ColumnSelection colSel = viewport.getColumnSelection();
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251 if (colSel.size() > 0)
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253 int min = colSel.getMin();
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254 viewport.getAlignment().trimLeft(min);
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255 colSel.compensateForEdit(0,min);
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256 alignPanel.RefreshPanels();
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260 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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262 addHistoryItem("delete columns");
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263 ColumnSelection colSel = viewport.getColumnSelection();
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264 if (colSel.size() > 0)
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266 int max = colSel.getMax();
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268 viewport.getAlignment().trimRight(max);
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270 alignPanel.RefreshPanels();
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275 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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277 addHistoryItem("delete gapped columns");
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278 viewport.getAlignment().removeGaps();
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279 alignPanel.RefreshPanels();
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282 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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284 addHistoryItem("delete all gaps");
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287 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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289 current = viewport.getAlignment().getSequenceAt(i);
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290 jSize = current.getLength();
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291 for (int j=0; j < jSize; j++)
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292 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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294 current.deleteCharAt(j);
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300 alignPanel.RefreshPanels();
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303 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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305 char thisChar = '-';
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306 char nextChar = '.';
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307 if(viewport.getGapCharacter()=='-')
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312 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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313 viewport.setGapCharacter(thisChar);
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314 alignPanel.RefreshPanels();
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317 public void findMenuItem_actionPerformed(ActionEvent e)
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319 JOptionPane op = new JOptionPane();
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320 JInternalFrame frame = op.createInternalFrame(this, "Find");
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321 Finder finder = new Finder(viewport, alignPanel, frame);
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322 frame.setClosable(true);
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323 frame.setContentPane(finder);
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324 frame.setSize(340,110);
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325 frame.setVisible(true);
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330 public void fontNameMenuItem_actionPerformed(ActionEvent e)
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332 String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
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335 String selection = JOptionPane.showInternalInputDialog(this,
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338 JOptionPane.QUESTION_MESSAGE,
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340 ,fontNameMenuItem.getText()).toString();
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341 if(selection!=null)
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343 fontNameMenuItem.setText(selection);
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349 public void fontSizeMenuItem_actionPerformed(ActionEvent e)
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351 String selection = JOptionPane.showInternalInputDialog(this,
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352 "Select font size",
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354 JOptionPane.QUESTION_MESSAGE,
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355 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
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356 ,fontSizeMenuItem.getText()).toString();
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357 if(selection!=null)
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359 fontSizeMenuItem.setText(selection);
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364 public void fontStyleMenuItem_actionPerformed(ActionEvent e)
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366 String selection = JOptionPane.showInternalInputDialog(this,
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367 "Select font style",
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369 JOptionPane.QUESTION_MESSAGE,
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370 null, new String[]{"plain", "bold", "italic"}
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371 ,fontStyleMenuItem.getText()).toString();
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372 if(selection!=null)
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374 fontStyleMenuItem.setText(selection);
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380 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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382 viewport.setColourText( colourTextMenuItem.isSelected() );
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383 alignPanel.RefreshPanels();
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388 int style = java.awt.Font.PLAIN;
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389 if(fontStyleMenuItem.getText().equals("bold"))
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390 style = java.awt.Font.BOLD;
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391 else if(fontStyleMenuItem.getText().equals("italic"))
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392 style = java.awt.Font.ITALIC;
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394 viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
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396 Integer.parseInt(fontSizeMenuItem.getText())));
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397 alignPanel.RefreshPanels();
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401 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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403 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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404 alignPanel.RefreshPanels();
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408 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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410 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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411 alignPanel.RefreshPanels();
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414 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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416 viewport.setShowText( viewTextMenuItem.isSelected() );
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417 alignPanel.RefreshPanels();
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421 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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423 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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424 alignPanel.RefreshPanels();
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427 public void secondaryStructure_actionPerformed(ActionEvent evt)
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429 alignPanel.setSecondaryStructureVisible(secondaryStructure.isSelected());
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432 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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434 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
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437 public void overviewMenuItem_actionPerformed(ActionEvent e)
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439 if (alignPanel.overviewPanel != null)
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442 JInternalFrame frame = new JInternalFrame();
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443 OverviewPanel overview = alignPanel.getOverviewPanel();
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445 overview = new OverviewPanel(alignPanel, viewport);
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446 frame.setContentPane(overview);
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447 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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448 frame.getWidth(), frame.getHeight());
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450 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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451 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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453 alignPanel.setOverviewPanel(null);
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456 alignPanel.setOverviewPanel( overview );
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458 }catch(java.lang.OutOfMemoryError ex)
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460 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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461 +"\nTry reducing the font size.",
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462 "Out of memory", JOptionPane.WARNING_MESSAGE);
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468 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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470 viewport.setGlobalColourScheme( null );
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475 public void Colour_actionPerformed(ActionEvent e)
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477 viewport.setGlobalColourScheme(new ClustalxColourScheme( ));
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478 conservationMenuItem.setSelected(false);
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479 abovePIDThreshold.setSelected(false);
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483 public void zappoColour_actionPerformed(ActionEvent e)
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485 viewport.setGlobalColourScheme(new ZappoColourScheme() );
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489 public void taylorColour_actionPerformed(ActionEvent e)
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491 viewport.setGlobalColourScheme(new TaylorColourScheme() );
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496 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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498 viewport.setGlobalColourScheme( new HydrophobicColourScheme() );
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502 public void helixColour_actionPerformed(ActionEvent e)
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504 viewport.setGlobalColourScheme( new HelixColourScheme() );
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509 public void strandColour_actionPerformed(ActionEvent e)
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511 viewport.setGlobalColourScheme(new StrandColourScheme() );
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516 public void turnColour_actionPerformed(ActionEvent e)
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518 viewport.setGlobalColourScheme(new TurnColourScheme() );
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523 public void buriedColour_actionPerformed(ActionEvent e)
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525 viewport.setGlobalColourScheme( new BuriedColourScheme() );
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529 public void nucleotideColour_actionPerformed(ActionEvent e)
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531 viewport.setGlobalColourScheme( new NucleotideColourScheme() );
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536 void changeColour()
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538 if(abovePIDThreshold.isSelected())
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539 abovePIDThreshold_actionPerformed(null);
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540 else if(conservationMenuItem.isSelected())
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541 conservationMenuItem_actionPerformed(null);
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544 alignPanel.RefreshPanels();
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547 void addConservationOrPIDColour()
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549 int x=0, y=0, threshold = 70;
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551 if(sliderFrame!=null)
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554 x = sliderFrame.getX();
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555 y = sliderFrame.getY();
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556 SliderPanel sp = (SliderPanel) sliderFrame.getContentPane();
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557 threshold = sp.getValue();
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558 sliderFrame.setClosed(true);
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560 catch (Exception ex)
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561 { ex.printStackTrace(); }
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563 ColourSchemeI oldCs = viewport.getGlobalColourScheme();
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565 ConservationColourScheme ccs = null;
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566 if (oldCs instanceof ConservationColourScheme)
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567 ccs = (ConservationColourScheme) oldCs;
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569 if(conservationMenuItem.isSelected())
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571 Alignment al = (Alignment)viewport.alignment;
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572 Conservation c = new Conservation("All",
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573 ResidueProperties.propHash, 3, al.getSequences(), 0,
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577 c.verdict(false, 100);
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580 ccs = new ConservationColourScheme(c, ccs.cs);
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582 ccs = new ConservationColourScheme(c, oldCs);
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584 viewport.setGlobalColourScheme( ccs );
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587 else if(oldCs instanceof ConservationColourScheme)
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590 viewport.setGlobalColourScheme( oldCs );
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594 if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() )
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596 sliderFrame = new JInternalFrame();
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597 sliderFrame.setMaximizable(false);
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598 sliderFrame.setResizable(false);
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600 SliderPanel sp = null;
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601 if (conservationMenuItem.isSelected())
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605 sp = new SliderPanel(alignPanel, threshold, true,ccs);
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606 Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment (Global colour)", 400, 90);
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609 else if (abovePIDThreshold.isSelected())
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611 sp = new SliderPanel(alignPanel, threshold, false, oldCs);
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613 Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);
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616 sliderFrame.setContentPane(sp);
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618 sliderFrame.setLocation(x,y);
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625 if (oldCs instanceof ResidueColourScheme)
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627 ResidueColourScheme rcs = (ResidueColourScheme) oldCs;
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628 rcs.setThreshold(threshold);
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630 else if (oldCs instanceof ScoreColourScheme)
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632 ScoreColourScheme scs = (ScoreColourScheme) oldCs;
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633 scs.setThreshold(threshold);
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639 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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641 if(abovePIDThreshold.isSelected())
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642 abovePIDThreshold.setSelected(false);
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644 viewport.setConservationSelected(conservationMenuItem.isSelected());
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646 addConservationOrPIDColour();
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649 JInternalFrame sliderFrame;
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650 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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652 if(conservationMenuItem.isSelected())
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653 conservationMenuItem.setSelected(false);
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655 addConservationOrPIDColour();
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660 public void userDefinedColour_actionPerformed(ActionEvent e)
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662 JInternalFrame frame = new JInternalFrame();
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663 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
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664 frame.setContentPane(chooser);
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665 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
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666 frame.setResizable(false);
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667 frame.setIconifiable(false);
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668 frame.setMaximizable(false);
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671 public void PIDColour_actionPerformed(ActionEvent e)
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673 viewport.setGlobalColourScheme( new PIDColourScheme() );
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674 alignPanel.setColourScheme( );
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678 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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680 viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport) );
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681 alignPanel.setColourScheme();
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686 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
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688 ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );
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689 Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
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693 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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695 addHistoryItem("sort");
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696 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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697 alignPanel.RefreshPanels();
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700 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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702 addHistoryItem("sort");
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703 AlignmentSorter.sortByID( viewport.getAlignment() );
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704 alignPanel.RefreshPanels();
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707 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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709 addHistoryItem("sort");
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710 AlignmentSorter.sortByGroup(viewport.getAlignment());
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711 AlignmentSorter.sortGroups(viewport.getAlignment());
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712 alignPanel.RefreshPanels();
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715 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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717 addHistoryItem("sort");
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718 if(viewport.getCurrentTree()==null)
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721 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
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722 alignPanel.RefreshPanels();
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725 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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727 RedundancyPanel sp = new RedundancyPanel(alignPanel);
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728 JInternalFrame frame = new JInternalFrame();
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729 frame.setContentPane(sp);
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730 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
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731 frame.setMaximizable(false);
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732 frame.setResizable(false);
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736 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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738 if(viewport.getSelection().size()<2)
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739 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
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742 JInternalFrame frame = new JInternalFrame();
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743 frame.setContentPane(new PairwiseAlignPanel(viewport));
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744 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
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748 public void PCAMenuItem_actionPerformed(ActionEvent e)
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750 if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
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751 || viewport.getAlignment().getHeight()<4)
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753 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
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754 +"at least 4 input sequences.",
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755 "Sequence selection insufficient",
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756 JOptionPane.WARNING_MESSAGE);
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761 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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762 JInternalFrame frame = new JInternalFrame();
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763 frame.setContentPane(pcaPanel);
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764 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
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765 }catch(java.lang.OutOfMemoryError ex)
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767 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
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768 "Out of memory", JOptionPane.WARNING_MESSAGE);
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774 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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776 NewTreePanel("AV", "PID", "Average distance tree using PID");
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779 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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781 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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785 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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787 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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790 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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792 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
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795 void NewTreePanel(String type, String pwType, String title)
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797 JInternalFrame frame = new javax.swing.JInternalFrame();
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799 if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
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801 tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
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802 viewport.getStartRes(), viewport.getEndRes());
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806 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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807 type, pwType, viewport.getStartRes(),
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808 viewport.getEndRes());
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811 frame.setContentPane(tp);
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812 Desktop.addInternalFrame(frame, title, 600, 500);
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818 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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820 JInternalFrame frame = new JInternalFrame();
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821 ClustalThread ct = new ClustalThread(frame);
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822 Thread t = new Thread(ct);
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824 frame.setContentPane(ct);
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825 Desktop.addInternalFrame(frame, title, 300, 80);
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829 class ClustalThread extends JPanel implements Runnable
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832 int imageIndex = 0;
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833 boolean webServiceRunning = false;
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834 JInternalFrame frame;
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835 public ClustalThread(JInternalFrame frame)
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837 this.frame = frame;
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838 image = new Image[9];
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839 for(int i=0; i<9; i++)
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841 java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");
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844 image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
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845 MediaTracker mt = new MediaTracker(this);
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846 mt.addImage(image[i], i);
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847 try{mt.waitForID(i);}
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848 catch(Exception ex){}
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851 DNATwirler twirler = new DNATwirler();
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853 webServiceRunning = true;
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856 class DNATwirler extends Thread
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860 while(webServiceRunning)
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868 catch(Exception ex){}
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874 // Should check to see if the server settings are valid
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875 // Need visual-delay indication here.
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878 jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
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879 Vector sv = viewport.getAlignment().getSequences();
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880 SequenceI[] seqs = new SequenceI[sv.size()];
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885 seqs[i] = (SequenceI) sv.elementAt(i);
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887 while (++i < sv.size());
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889 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
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891 if (alignment != null)
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893 AlignFrame af = new AlignFrame(new Alignment(alignment));
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894 Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
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895 700, 500); // JBPNote - is there a new window geom. property ?
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898 JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
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899 JOptionPane.WARNING_MESSAGE);
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901 webServiceRunning = false;
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903 frame.setClosed(true);
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904 }catch(Exception ex){}
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907 public void paintComponent(Graphics g)
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909 g.setColor(Color.white);
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910 g.fillRect(0,0,getWidth(), getHeight());
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913 g.drawImage(image[imageIndex],10,10,this);
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915 g.setFont(new Font("Arial", Font.BOLD, 12));
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916 g.setColor(Color.black);
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917 g.drawString("Clustal Alignment Web Service running", 30,30);
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924 public void pdbTest_actionPerformed(ActionEvent e)
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927 JOptionPane.showInternalInputDialog(this, "Enter pdb code",
\r
928 "PDB test viewer", JOptionPane.QUESTION_MESSAGE);
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930 String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";
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931 if (reply.length()>1)
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932 url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;
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936 PDBfile pdb = new PDBfile(url,
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938 Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);
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939 seq.setPDBfile(pdb);
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940 ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;
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941 ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;
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942 // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();
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944 rotCanvas rc = new rotCanvas(pdb);
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945 JInternalFrame frame = new JInternalFrame();
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946 frame.setContentPane(rc);
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947 Desktop.addInternalFrame(frame, url, 400,400);
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949 catch (Exception ex)
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951 ex.printStackTrace();
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957 public void doKeyPressed(KeyEvent evt)
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960 System.out.println(evt.getKeyChar());
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961 if(evt.isControlDown() && evt.getKeyChar()=='f')
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962 findMenuItem_actionPerformed(null);
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