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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206 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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208 Selection sel = viewport.getSelection();
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209 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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210 sel.addElement( viewport.getAlignment().getSequenceAt(i));
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211 PaintRefresher.Refresh(null);
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214 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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216 viewport.getSelection().clear();
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217 PaintRefresher.Refresh(null);
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220 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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222 Selection sel = viewport.getSelection();
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223 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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225 if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
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226 sel.removeElement(viewport.getAlignment().getSequenceAt(i));
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228 sel.addElement(viewport.getAlignment().getSequenceAt(i));
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230 PaintRefresher.Refresh(null);
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234 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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236 viewport.getColumnSelection().clear();
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240 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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242 addHistoryItem("delete columns");
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243 ColumnSelection colSel = viewport.getColumnSelection();
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244 if (colSel.size() > 0)
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246 int min = colSel.getMin();
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247 viewport.getAlignment().trimLeft(min);
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248 colSel.compensateForEdit(0,min);
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249 alignPanel.RefreshPanels();
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253 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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255 addHistoryItem("delete columns");
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256 ColumnSelection colSel = viewport.getColumnSelection();
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257 if (colSel.size() > 0)
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259 int max = colSel.getMax();
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261 viewport.getAlignment().trimRight(max);
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263 alignPanel.RefreshPanels();
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268 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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270 addHistoryItem("delete gapped columns");
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271 viewport.getAlignment().removeGaps();
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272 alignPanel.RefreshPanels();
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275 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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277 addHistoryItem("delete all gaps");
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280 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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282 current = viewport.getAlignment().getSequenceAt(i);
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283 jSize = current.getLength();
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284 for (int j=0; j < jSize; j++)
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285 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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287 current.deleteCharAt(j);
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293 alignPanel.RefreshPanels();
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296 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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298 char thisChar = '-';
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299 char nextChar = '.';
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300 if(viewport.getGapCharacter()=='-')
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305 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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306 viewport.setGapCharacter(thisChar);
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307 alignPanel.RefreshPanels();
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310 public void findMenuItem_actionPerformed(ActionEvent e)
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312 JOptionPane op = new JOptionPane();
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313 JInternalFrame frame = op.createInternalFrame(this, "Find");
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314 Finder finder = new Finder(viewport, alignPanel, frame);
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315 frame.setContentPane(finder);
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316 frame.setSize(300,110);
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317 frame.setVisible(true);
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322 public void fontNameMenuItem_actionPerformed(ActionEvent e)
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324 String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
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327 String selection = JOptionPane.showInternalInputDialog(this,
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330 JOptionPane.QUESTION_MESSAGE,
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332 ,fontNameMenuItem.getText()).toString();
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333 if(selection!=null)
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335 fontNameMenuItem.setText(selection);
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341 public void fontSizeMenuItem_actionPerformed(ActionEvent e)
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343 String selection = JOptionPane.showInternalInputDialog(this,
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344 "Select font size",
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346 JOptionPane.QUESTION_MESSAGE,
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347 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
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348 ,fontSizeMenuItem.getText()).toString();
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349 if(selection!=null)
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351 fontSizeMenuItem.setText(selection);
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356 public void fontStyleMenuItem_actionPerformed(ActionEvent e)
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358 String selection = JOptionPane.showInternalInputDialog(this,
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359 "Select font style",
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361 JOptionPane.QUESTION_MESSAGE,
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362 null, new String[]{"plain", "bold", "italic"}
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363 ,fontStyleMenuItem.getText()).toString();
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364 if(selection!=null)
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366 fontStyleMenuItem.setText(selection);
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372 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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374 viewport.setColourText( colourTextMenuItem.isSelected() );
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375 alignPanel.RefreshPanels();
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380 int style = java.awt.Font.PLAIN;
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381 if(fontStyleMenuItem.getText().equals("bold"))
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382 style = java.awt.Font.BOLD;
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383 else if(fontStyleMenuItem.getText().equals("italic"))
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384 style = java.awt.Font.ITALIC;
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386 viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
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388 Integer.parseInt(fontSizeMenuItem.getText())));
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389 alignPanel.RefreshPanels();
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393 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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395 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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396 alignPanel.RefreshPanels();
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400 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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402 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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403 alignPanel.RefreshPanels();
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406 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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408 viewport.setShowText( viewTextMenuItem.isSelected() );
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409 alignPanel.RefreshPanels();
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413 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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415 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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416 alignPanel.RefreshPanels();
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420 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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422 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
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425 public void overviewMenuItem_actionPerformed(ActionEvent e)
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428 JInternalFrame frame = new JInternalFrame();
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429 OverviewPanel overview = alignPanel.getOverviewPanel();
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431 overview = new OverviewPanel(alignPanel, viewport);
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432 frame.setContentPane(overview);
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433 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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434 frame.getWidth(), frame.getHeight());
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436 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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437 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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439 alignPanel.setOverviewPanel(null);
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442 alignPanel.setOverviewPanel( overview );
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444 }catch(java.lang.OutOfMemoryError ex)
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446 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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447 +"\nTry reducing the font size.",
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448 "Out of memory", JOptionPane.WARNING_MESSAGE);
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454 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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456 viewport.setGlobalColourScheme( null );
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461 public void Colour_actionPerformed(ActionEvent e)
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463 viewport.setGlobalColourScheme(new ClustalxColourScheme( ));
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464 conservationMenuItem.setSelected(false);
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465 abovePIDThreshold.setSelected(false);
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469 public void zappoColour_actionPerformed(ActionEvent e)
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471 viewport.setGlobalColourScheme(new ZappoColourScheme() );
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475 public void taylorColour_actionPerformed(ActionEvent e)
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477 viewport.setGlobalColourScheme(new TaylorColourScheme() );
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482 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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484 viewport.setGlobalColourScheme( new HydrophobicColourScheme() );
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488 public void helixColour_actionPerformed(ActionEvent e)
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490 viewport.setGlobalColourScheme( new HelixColourScheme() );
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495 public void strandColour_actionPerformed(ActionEvent e)
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497 viewport.setGlobalColourScheme(new StrandColourScheme() );
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502 public void turnColour_actionPerformed(ActionEvent e)
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504 viewport.setGlobalColourScheme(new TurnColourScheme() );
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509 public void buriedColour_actionPerformed(ActionEvent e)
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511 viewport.setGlobalColourScheme( new BuriedColourScheme() );
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515 void changeColour()
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517 if(abovePIDThreshold.isSelected())
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518 abovePIDThreshold_actionPerformed(null);
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519 else if(conservationMenuItem.isSelected())
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520 conservationMenuItem_actionPerformed(null);
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522 alignPanel.seqPanel.seqCanvas.paintFlag = true;
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523 alignPanel.repaint();
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526 void addConservationOrPIDColour()
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528 int x=0, y=0, threshold = 70;
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530 if(sliderFrame!=null)
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533 x = sliderFrame.getX();
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534 y = sliderFrame.getY();
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535 SliderPanel sp = (SliderPanel) sliderFrame.getContentPane();
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536 threshold = sp.getValue();
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537 sliderFrame.setClosed(true);
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539 catch (Exception ex)
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540 { ex.printStackTrace(); }
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542 ColourSchemeI oldCs = viewport.getGlobalColourScheme();
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544 ConservationColourScheme ccs = null;
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545 if (oldCs instanceof ConservationColourScheme)
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546 ccs = (ConservationColourScheme) oldCs;
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548 if(conservationMenuItem.isSelected())
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550 Alignment al = (Alignment)viewport.alignment;
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551 Conservation c = new Conservation("All",
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552 ResidueProperties.propHash, 3, al.getSequences(), 0,
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556 c.verdict(false, 100);
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559 ccs = new ConservationColourScheme(c, ccs.cs);
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561 ccs = new ConservationColourScheme(c, oldCs);
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563 viewport.setGlobalColourScheme( ccs );
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566 else if(oldCs instanceof ConservationColourScheme)
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569 viewport.setGlobalColourScheme( oldCs );
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573 if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() )
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575 sliderFrame = new JInternalFrame();
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576 sliderFrame.setMaximizable(false);
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577 sliderFrame.setResizable(false);
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579 SliderPanel sp = null;
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580 if (conservationMenuItem.isSelected())
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584 sp = new SliderPanel(alignPanel, threshold, true,ccs);
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585 Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment (Global colour)", 400, 90);
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588 else if (abovePIDThreshold.isSelected())
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590 sp = new SliderPanel(alignPanel, threshold, false, oldCs);
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592 Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);
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595 sliderFrame.setContentPane(sp);
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597 sliderFrame.setLocation(x,y);
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604 if (oldCs instanceof ResidueColourScheme)
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606 ResidueColourScheme rcs = (ResidueColourScheme) oldCs;
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607 rcs.setThreshold(threshold);
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609 else if (oldCs instanceof ScoreColourScheme)
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611 ScoreColourScheme scs = (ScoreColourScheme) oldCs;
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612 scs.setThreshold(threshold);
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615 alignPanel.seqPanel.seqCanvas.paintFlag = true;
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616 alignPanel.repaint();
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620 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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622 if(abovePIDThreshold.isSelected())
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623 abovePIDThreshold.setSelected(false);
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625 viewport.setConservationSelected(conservationMenuItem.isSelected());
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627 addConservationOrPIDColour();
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630 JInternalFrame sliderFrame;
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631 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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633 if(conservationMenuItem.isSelected())
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634 conservationMenuItem.setSelected(false);
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636 addConservationOrPIDColour();
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641 public void userDefinedColour_actionPerformed(ActionEvent e)
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643 JInternalFrame frame = new JInternalFrame();
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644 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
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645 frame.setContentPane(chooser);
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646 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
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647 frame.setResizable(false);
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648 frame.setIconifiable(false);
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649 frame.setMaximizable(false);
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652 public void PIDColour_actionPerformed(ActionEvent e)
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654 viewport.setGlobalColourScheme( new PIDColourScheme() );
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655 alignPanel.setColourScheme( );
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659 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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661 viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport) );
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662 alignPanel.setColourScheme();
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667 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
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669 ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );
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670 Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
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674 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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676 addHistoryItem("sort");
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677 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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678 alignPanel.RefreshPanels();
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681 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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683 addHistoryItem("sort");
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684 AlignmentSorter.sortByID( viewport.getAlignment() );
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685 alignPanel.RefreshPanels();
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688 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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690 addHistoryItem("sort");
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691 AlignmentSorter.sortByGroup(viewport.getAlignment());
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692 AlignmentSorter.sortGroups(viewport.getAlignment());
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693 alignPanel.RefreshPanels();
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696 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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698 addHistoryItem("sort");
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699 if(viewport.getCurrentTree()==null)
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702 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
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703 alignPanel.RefreshPanels();
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706 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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708 RedundancyPanel sp = new RedundancyPanel(alignPanel);
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709 JInternalFrame frame = new JInternalFrame();
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710 frame.setContentPane(sp);
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711 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
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712 frame.setMaximizable(false);
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713 frame.setResizable(false);
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717 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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719 if(viewport.getSelection().size()<2)
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720 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
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723 JInternalFrame frame = new JInternalFrame();
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724 frame.setContentPane(new PairwiseAlignPanel(viewport));
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725 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
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729 public void PCAMenuItem_actionPerformed(ActionEvent e)
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731 if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
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732 || viewport.getAlignment().getHeight()<4)
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734 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
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735 +"at least 4 input sequences.",
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736 "Sequence selection insufficient",
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737 JOptionPane.WARNING_MESSAGE);
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742 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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743 JInternalFrame frame = new JInternalFrame();
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744 frame.setContentPane(pcaPanel);
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745 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
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746 }catch(java.lang.OutOfMemoryError ex)
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748 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
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749 "Out of memory", JOptionPane.WARNING_MESSAGE);
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755 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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757 NewTreePanel("AV", "PID", "Average distance tree using PID");
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760 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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762 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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766 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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768 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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771 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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773 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
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776 void NewTreePanel(String type, String pwType, String title)
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778 JInternalFrame frame = new javax.swing.JInternalFrame();
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780 if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
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782 tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
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783 viewport.getStartRes(), viewport.getEndRes());
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787 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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788 type, pwType, viewport.getStartRes(),
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789 viewport.getEndRes());
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792 frame.setContentPane(tp);
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793 Desktop.addInternalFrame(frame, title, 600, 500);
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798 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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801 // Should check to see if the server settings are valid
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802 // Need visual-delay indication here.
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803 Jemboss jemboss = new Jemboss();
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805 Vector sv = viewport.getAlignment().getSequences();
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806 SequenceI[] seqs = new SequenceI[sv.size()];
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811 seqs[i] = (SequenceI) sv.elementAt(i);
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812 } while (++i<sv.size());
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814 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
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816 if (alignment != null)
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818 AlignFrame af = new AlignFrame(new Alignment(alignment));
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819 Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
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820 700, 500); // JBPNote - is there a new window geom. property ?
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824 public void pdbTest_actionPerformed(ActionEvent e)
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827 JOptionPane.showInternalInputDialog(this, "Enter pdb code",
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828 "PDB test viewer", JOptionPane.QUESTION_MESSAGE);
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830 String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";
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831 if (reply.length()>1)
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832 url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;
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836 PDBfile pdb = new PDBfile(url,
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838 Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);
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839 seq.setPDBfile(pdb);
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840 ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;
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841 ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;
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842 // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();
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844 rotCanvas rc = new rotCanvas(pdb);
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845 JInternalFrame frame = new JInternalFrame();
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846 frame.setContentPane(rc);
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847 Desktop.addInternalFrame(frame, url, 400,400);
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849 catch (Exception ex)
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851 ex.printStackTrace();
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857 public void doKeyPressed(KeyEvent evt)
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860 System.out.println(evt.getKeyChar());
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861 if(evt.isControlDown() && evt.getKeyChar()=='f')
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862 findMenuItem_actionPerformed(null);
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