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 java.awt.event.*;
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21 import javax.swing.*;
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23 public class AlignFrame extends GAlignFrame
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25 AlignmentPanel alignPanel;
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26 AlignViewport viewport;
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27 public AlignFrame(AlignmentI al)
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30 viewport = new AlignViewport(al,true,true,true,false);
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31 alignPanel = new AlignmentPanel(this, viewport);
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32 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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33 fontNameMenuItem.setText(viewport.getFont().getName());
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34 fontSizeMenuItem.setText(viewport.getFont().getSize()+"");
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37 protected void saveAs_actionPerformed(ActionEvent e)
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39 JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);
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40 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
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41 chooser.setToolTipText("Save");
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42 int value = chooser.showSaveDialog(this);
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43 if(value == JFileChooser.APPROVE_OPTION)
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45 String choice = chooser.getSelectedFile().getPath();
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46 jalview.bin.Cache.LAST_DIRECTORY = choice;
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47 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
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49 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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50 out.println(output);
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53 catch(Exception ex){}
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58 protected void outputText_actionPerformed(ActionEvent e)
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60 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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61 JInternalFrame frame = new JInternalFrame();
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62 cap.formatForOutput();
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63 frame.setContentPane(cap);
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64 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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65 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
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68 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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70 HTMLOutput htmlOutput = new HTMLOutput(viewport.getAlignment(), alignPanel.seqPanel.getColourScheme());
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74 public void saveAsPostscriptMenuItem_actionPerformed(ActionEvent e)
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79 public void closeMenuItem_actionPerformed(ActionEvent e)
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82 this.setClosed(true);
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83 }catch(Exception ex){}
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86 public void groupsMenuItem_actionPerformed(ActionEvent e)
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91 public void groupEditingMenuItem_actionPerformed(ActionEvent e)
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96 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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98 Selection sel = viewport.getSelection();
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99 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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100 sel.addElement( viewport.getAlignment().getSequenceAt(i));
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101 PaintRefresher.Refresh(null);
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104 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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106 viewport.getSelection().clear();
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107 PaintRefresher.Refresh(null);
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110 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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112 Selection sel = viewport.getSelection();
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113 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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115 if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
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116 sel.removeElement(viewport.getAlignment().getSequenceAt(i));
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118 sel.addElement(viewport.getAlignment().getSequenceAt(i));
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120 PaintRefresher.Refresh(null);
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123 public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)
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125 for (int i=0;i < viewport.getSelection().size(); i++)
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126 viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));
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128 viewport.getSelection().clear();
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129 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
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130 alignPanel.RefreshPanels();
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133 public void moveSelectedMenuItem_actionPerformed(ActionEvent e)
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135 copySelectedMenuItem_actionPerformed(null);
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136 deleteSelectedMenuItem_actionPerformed(null);
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137 alignPanel.repaint();
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140 public void copySelectedMenuItem_actionPerformed(ActionEvent e)
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142 if(viewport.getSelection().size()==0)
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145 SequenceI[] s = new Sequence[viewport.getSelection().size()];
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146 for (int i=0; i < viewport.getSelection().size(); i++) {
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147 s[i] = new Sequence(viewport.getSelection().sequenceAt(i));
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149 AlignFrame af = new AlignFrame(new Alignment(s));
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151 int newHeight = s.length * af.viewport.getCharHeight() + 200;
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154 Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
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157 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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159 viewport.getColumnSelection().clear();
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163 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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165 ColumnSelection colSel = viewport.getColumnSelection();
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166 if (colSel.size() > 0)
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168 int min = colSel.getMin();
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169 viewport.getAlignment().trimLeft(min);
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170 colSel.compensateForEdit(0,min);
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171 alignPanel.RefreshPanels();
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175 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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177 ColumnSelection colSel = viewport.getColumnSelection();
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178 if (colSel.size() > 0)
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180 int max = colSel.getMax();
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182 viewport.getAlignment().trimRight(max);
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184 alignPanel.RefreshPanels();
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189 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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191 viewport.getAlignment().removeGaps();
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192 alignPanel.RefreshPanels();
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195 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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199 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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201 current = viewport.getAlignment().getSequenceAt(i);
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202 jSize = current.getLength();
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203 for (int j=0; j < jSize; j++)
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204 if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')
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206 current.deleteCharAt(j);
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212 alignPanel.RefreshPanels();
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215 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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217 String thisChar = "-";
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218 String nextChar = ".";
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219 if(viewport.getGapCharacter().equals("-"))
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224 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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225 viewport.setGapCharacter(thisChar);
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229 public void fontNameMenuItem_actionPerformed(ActionEvent e)
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231 String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
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234 String selection = JOptionPane.showInputDialog(this,
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237 JOptionPane.QUESTION_MESSAGE,
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239 ,fontNameMenuItem.getText()).toString();
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240 if(selection!=null)
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242 fontNameMenuItem.setText(selection);
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248 public void fontSizeMenuItem_actionPerformed(ActionEvent e)
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250 String selection = JOptionPane.showInputDialog(this,
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251 "Select font size",
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253 JOptionPane.QUESTION_MESSAGE,
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254 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
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255 ,fontSizeMenuItem.getText()).toString();
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256 if(selection!=null)
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258 fontSizeMenuItem.setText(selection);
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263 public void fontStyleMenuItem_actionPerformed(ActionEvent e)
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265 String selection = JOptionPane.showInputDialog(this,
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266 "Select font style",
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268 JOptionPane.QUESTION_MESSAGE,
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269 null, new String[]{"plain", "bold", "italic"}
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270 ,fontStyleMenuItem.getText()).toString();
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271 if(selection!=null)
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273 fontStyleMenuItem.setText(selection);
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279 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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281 viewport.setColourText( colourTextMenuItem.isSelected() );
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282 alignPanel.RefreshPanels();
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287 int style = java.awt.Font.PLAIN;
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288 if(fontStyleMenuItem.getText().equals("bold"))
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289 style = java.awt.Font.BOLD;
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290 else if(fontStyleMenuItem.getText().equals("italic"))
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291 style = java.awt.Font.ITALIC;
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293 viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
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295 Integer.parseInt(fontSizeMenuItem.getText())));
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296 alignPanel.RefreshPanels();
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300 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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302 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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303 alignPanel.RefreshPanels();
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306 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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308 viewport.setShowText( viewTextMenuItem.isSelected() );
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309 alignPanel.RefreshPanels();
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313 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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315 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
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318 public void overviewMenuItem_actionPerformed(ActionEvent e)
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321 JInternalFrame frame = new JInternalFrame();
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322 OverviewPanel overview = alignPanel.getOverviewPanel();
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324 overview = new OverviewPanel(alignPanel, viewport);
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325 frame.setContentPane(overview);
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326 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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327 frame.getWidth(), frame.getHeight());
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329 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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330 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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332 alignPanel.setOverviewPanel(null);
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335 alignPanel.setOverviewPanel( overview );
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337 }catch(java.lang.OutOfMemoryError ex)
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339 JOptionPane.showMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!",
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340 "Out of memory", JOptionPane.WARNING_MESSAGE);
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347 public void clustalColour_actionPerformed(ActionEvent e)
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349 // alignPanel.setColourScheme( new ClustalxColourScheme() );
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352 public void zappoColour_actionPerformed(ActionEvent e)
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354 alignPanel.setColourScheme( new ZappoColourScheme() );
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357 public void taylorColour_actionPerformed(ActionEvent e)
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359 alignPanel.setColourScheme( new TaylorColourScheme() );
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363 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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365 alignPanel.setColourScheme( new HydrophobicColourScheme() );
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368 public void helixColour_actionPerformed(ActionEvent e)
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370 alignPanel.seqPanel.setColourScheme( new HelixColourScheme() );
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373 public void strandColour_actionPerformed(ActionEvent e)
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375 alignPanel.setColourScheme( new StrandColourScheme() );
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378 public void turnColour_actionPerformed(ActionEvent e)
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380 alignPanel.setColourScheme( new TurnColourScheme() );
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383 public void buriedColour_actionPerformed(ActionEvent e)
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385 alignPanel.setColourScheme( new BuriedColourScheme() );
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388 public void conservationColour_actionPerformed(ActionEvent e)
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393 public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
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399 public void abovePIDColour_actionPerformed(ActionEvent e)
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401 alignPanel.setColourScheme( new PIDColourScheme() );
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405 public void userDefinedColour_actionPerformed(ActionEvent e)
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407 JInternalFrame frame = new JInternalFrame();
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408 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel.seqPanel );
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409 frame.setContentPane(chooser);
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410 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
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411 frame.setResizable(false);
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412 frame.setIconifiable(false);
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413 frame.setMaximizable(false);
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416 public void PIDColour_actionPerformed(ActionEvent e)
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418 alignPanel.setColourScheme( new PIDColourScheme() );
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421 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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423 alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) );
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427 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
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429 ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );
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430 Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
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434 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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436 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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437 alignPanel.RefreshPanels();
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440 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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442 AlignmentSorter.sortByID( viewport.getAlignment() );
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443 alignPanel.RefreshPanels();
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446 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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448 AlignmentSorter.sortGroups(viewport.getAlignment());
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449 AlignmentSorter.sortGroups(viewport.getAlignment());
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450 alignPanel.RefreshPanels();
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453 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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455 if(viewport.getCurrentTree()==null)
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458 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
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459 alignPanel.RefreshPanels();
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462 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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467 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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469 if(viewport.getSelection().size()<2)
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470 JOptionPane.showMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
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473 JInternalFrame frame = new JInternalFrame();
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474 frame.setContentPane(new PairwiseAlignPanel(viewport));
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475 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
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479 public void PCAMenuItem_actionPerformed(ActionEvent e)
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481 if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
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482 || viewport.getAlignment().getHeight()<4)
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484 JOptionPane.showMessageDialog(this, "Principal component analysis must take\n"
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485 +"at least 4 input sequences.",
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486 "Sequence selection insufficient",
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487 JOptionPane.WARNING_MESSAGE);
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491 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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492 JInternalFrame frame = new JInternalFrame();
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493 frame.setContentPane(pcaPanel);
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494 Desktop.addInternalFrame(frame, "Principal component analysis", 400,400);
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497 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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499 NewTreePanel("AV", "PID", "Average distance tree using PID");
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502 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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504 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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508 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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510 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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513 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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515 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
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518 void NewTreePanel(String type, String pwType, String title)
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520 JInternalFrame frame = new javax.swing.JInternalFrame();
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522 if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
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524 tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
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525 viewport.getStartRes(), viewport.getEndRes());
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529 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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530 type, pwType, viewport.getStartRes(),
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531 viewport.getEndRes());
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534 frame.setContentPane(tp);
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535 Desktop.addInternalFrame(frame, title, 600, 500);
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540 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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542 JOptionPane.showMessageDialog(this, "Jalview is currently being reengineered"
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543 +"\nwithin the Barton Group, Dundee University."
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544 +"\nThis will be available as a web service 2005",
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545 "Web service", JOptionPane.INFORMATION_MESSAGE);
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