1 /********************
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2 * 2004 Jalview Reengineered
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12 package jalview.appletgui;
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14 import jalview.jbappletgui.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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20 import java.awt.event.*;
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24 public class AlignFrame extends GAlignFrame
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26 final AlignmentPanel alignPanel;
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27 final AlignViewport viewport;
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28 public static final int NEW_WINDOW_WIDTH = 700;
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29 public static final int NEW_WINDOW_HEIGHT = 500;
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30 jalview.bin.JalviewLite applet;
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32 public AlignFrame(AlignmentI al)
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35 viewport = new AlignViewport(al, null);
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36 alignPanel = new AlignmentPanel(this, viewport);
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38 alignPanel.validate();
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41 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)
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43 this.applet = applet;
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44 viewport = new AlignViewport(al, applet);
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45 alignPanel = new AlignmentPanel(this, viewport);
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47 alignPanel.validate();
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50 public void inputText_actionPerformed(ActionEvent e)
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52 CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
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53 Frame frame = new Frame();
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55 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500,500);
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59 protected void outputText_actionPerformed(ActionEvent e)
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61 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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62 Frame frame = new Frame();
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64 jalview.bin.JalviewLite.addFrame(frame,"Alignment output - "+e.getActionCommand(),600, 500);
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65 cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
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68 public void closeMenuItem_actionPerformed(ActionEvent e)
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73 Stack historyList = new Stack();
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74 Stack redoList = new Stack();
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76 void updateEditMenuBar()
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78 if(historyList.size()>0)
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80 undoMenuItem.setEnabled(true);
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81 Object [] history = (Object[])historyList.elementAt(0);
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82 undoMenuItem.setLabel("Undo "+history[0]);
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86 undoMenuItem.setEnabled(false);
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87 undoMenuItem.setLabel("Undo");
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90 if(redoList.size()>0)
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92 redoMenuItem.setEnabled(true);
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93 Object [] history = (Object[])redoList.elementAt(0);
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94 redoMenuItem.setLabel("Redo "+history[0]);
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98 redoMenuItem.setEnabled(false);
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99 redoMenuItem.setLabel("Redo");
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103 public void addHistoryItem(String type)
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105 // must make sure we add new sequence objects her, not refs to the existing sequences
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106 redoList.removeAllElements();
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107 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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108 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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110 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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111 viewport.getAlignment().getSequenceAt(i).getSequence());
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114 historyList.addElement(new Object[]{type, seq} );
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115 updateEditMenuBar();
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118 protected void undoMenuItem_actionPerformed(ActionEvent e)
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120 Object [] history = (Object[])historyList.elementAt(0);
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121 historyList.removeElementAt(0);
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122 // add the redo state before continuing!!
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123 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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124 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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126 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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127 viewport.getAlignment().getSequenceAt(i).
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132 redoList.addElement(new Object[] {history[0], seq});
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134 seq = (SequenceI[]) history[1];
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136 AlignmentAnnotation[] old = viewport.alignment.getAlignmentAnnotation();
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137 viewport.setAlignment(new Alignment(seq));
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138 updateEditMenuBar();
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139 for (int i = 0; i < old.length; i++)
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140 viewport.alignment.addAnnotation(old[i]);
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142 viewport.updateConservation();
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143 viewport.updateConsensus();
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144 alignPanel.repaint();
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147 public void moveSelectedSequences(boolean up)
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149 SequenceGroup sg = viewport.getSelectionGroup();
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155 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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157 SequenceI seq = viewport.alignment.getSequenceAt(i);
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158 if (!sg.sequences.contains(seq))
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161 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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162 if (sg.sequences.contains(temp))
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165 viewport.alignment.getSequences().setElementAt(temp, i);
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166 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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171 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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173 SequenceI seq = viewport.alignment.getSequenceAt(i);
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174 if (!sg.sequences.contains(seq))
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177 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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178 if (sg.sequences.contains(temp))
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181 viewport.alignment.getSequences().setElementAt(temp, i);
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182 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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186 alignPanel.repaint();
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190 StringBuffer copiedSequences;
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191 protected void copy_actionPerformed(ActionEvent e)
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193 if(viewport.getSelectionGroup()==null)
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196 SequenceGroup sg = viewport.getSelectionGroup();
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197 copiedSequences = new StringBuffer();
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199 for(int i=0; i<sg.getSize(); i++)
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201 SequenceI seq = sg.getSequenceAt(i);
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202 copiedSequences.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
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203 +seq.findPosition( sg.getEndRes() )+ "\t"
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204 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
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210 protected void pasteNew_actionPerformed(ActionEvent e)
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215 protected void pasteThis_actionPerformed(ActionEvent e)
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217 addHistoryItem("Paste");
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221 void paste(boolean newAlignment)
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224 if (copiedSequences == null)
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227 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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228 Vector seqs = new Vector();
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229 while (st.hasMoreElements())
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231 String name = st.nextToken();
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232 int start = Integer.parseInt(st.nextToken());
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233 int end = Integer.parseInt(st.nextToken());
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234 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
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237 viewport.alignment.addSequence(sequence);
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239 seqs.addElement(sequence);
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244 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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245 for(int i=0; i<seqs.size(); i++)
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246 newSeqs[i] = (SequenceI)seqs.elementAt(i);
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248 AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);
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249 jalview.bin.JalviewLite.addFrame(af, "Copied sequences", NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
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253 viewport.setEndSeq(viewport.alignment.getHeight());
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254 viewport.alignment.getWidth();
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255 viewport.updateConservation();
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256 viewport.updateConsensus();
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257 alignPanel.repaint();
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260 }catch(Exception ex){}// could be anything being pasted in here
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265 protected void cut_actionPerformed(ActionEvent e)
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267 copy_actionPerformed(null);
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268 delete_actionPerformed(null);
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271 protected void delete_actionPerformed(ActionEvent e)
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273 addHistoryItem("Delete");
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274 if (viewport.getSelectionGroup() == null)
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277 SequenceGroup sg = viewport.getSelectionGroup();
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278 for (int i=0;i < sg.sequences.size(); i++)
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280 SequenceI seq = sg.getSequenceAt(i);
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281 int index = viewport.getAlignment().findIndex(seq);
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282 seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
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284 if(seq.getSequence().length()<1)
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285 viewport.getAlignment().deleteSequence(seq);
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287 viewport.getAlignment().getSequences().setElementAt(seq, index);
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290 viewport.setSelectionGroup(null);
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291 viewport.alignment.deleteGroup(sg);
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292 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getSize().height);
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293 if(viewport.getAlignment().getHeight()<1)
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296 this.setVisible(false);
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297 }catch(Exception ex){}
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298 viewport.updateConservation();
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299 viewport.updateConsensus();
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300 alignPanel.repaint();
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306 protected void redoMenuItem_actionPerformed(ActionEvent e)
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308 Object [] history = (Object[])redoList.pop();
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309 SequenceI[] seq = (SequenceI[]) history[1];
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311 AlignmentAnnotation[] old = viewport.alignment.getAlignmentAnnotation();
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312 viewport.setAlignment(new Alignment(seq));
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313 for (int i = 0; i < old.length; i++)
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314 viewport.alignment.addAnnotation(old[i]);
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316 viewport.updateConservation();
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317 viewport.updateConsensus();
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318 updateEditMenuBar();
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319 alignPanel.repaint();
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323 protected void deleteGroups_actionPerformed(ActionEvent e)
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325 viewport.alignment.deleteAllGroups();
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326 viewport.setSelectionGroup(null);
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328 alignPanel.repaint();
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333 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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335 SequenceGroup sg = new SequenceGroup();
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336 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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337 sg.addSequence( viewport.getAlignment().getSequenceAt(i));
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338 sg.setEndRes(viewport.alignment.getWidth());
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339 viewport.setSelectionGroup(sg);
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340 alignPanel.repaint();
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341 PaintRefresher.Refresh(null);
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344 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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346 viewport.setSelectionGroup(null);
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347 viewport.getColumnSelection().clear();
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348 viewport.setSelectionGroup(null);
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349 PaintRefresher.Refresh(null);
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352 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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354 SequenceGroup sg = viewport.getSelectionGroup();
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355 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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356 sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
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358 PaintRefresher.Refresh(null);
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361 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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363 addHistoryItem("delete columns");
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364 ColumnSelection colSel = viewport.getColumnSelection();
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365 if (colSel.size() > 0)
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367 int min = colSel.getMin();
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368 viewport.getAlignment().trimLeft(min);
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369 colSel.compensateForEdit(0,min);
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371 if(viewport.getSelectionGroup()!=null)
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372 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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374 Vector groups = viewport.alignment.getGroups();
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375 for(int i=0; i<groups.size(); i++)
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377 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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378 if(!sg.adjustForRemoveLeft(min))
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379 viewport.alignment.deleteGroup(sg);
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382 alignPanel.repaint();
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386 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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388 addHistoryItem("delete columns");
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389 ColumnSelection colSel = viewport.getColumnSelection();
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390 if (colSel.size() > 0)
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392 int max = colSel.getMax();
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393 viewport.getAlignment().trimRight(max);
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394 if(viewport.getSelectionGroup()!=null)
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395 viewport.getSelectionGroup().adjustForRemoveRight(max);
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397 Vector groups = viewport.alignment.getGroups();
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398 for(int i=0; i<groups.size(); i++)
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400 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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401 if(!sg.adjustForRemoveRight(max))
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402 viewport.alignment.deleteGroup(sg);
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407 alignPanel.repaint();
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412 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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414 addHistoryItem("delete gapped columns");
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415 viewport.getAlignment().removeGaps();
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416 viewport.updateConservation();
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417 viewport.updateConsensus();
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418 alignPanel.repaint();
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421 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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423 addHistoryItem("delete all gaps");
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426 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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428 current = viewport.getAlignment().getSequenceAt(i);
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429 jSize = current.getLength();
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430 for (int j=0; j < jSize; j++)
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431 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
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433 current.deleteCharAt(j);
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438 viewport.updateConservation();
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439 viewport.updateConsensus();
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440 alignPanel.repaint();
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444 public void findMenuItem_actionPerformed(ActionEvent e)
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446 Finder finder = new Finder(alignPanel);
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450 public void font_actionPerformed(ActionEvent e)
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452 Frame frame = new Frame();
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453 FontChooser fc = new FontChooser( alignPanel, frame);
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455 jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440,100);
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459 protected void fullSeqId_actionPerformed(ActionEvent e)
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461 viewport.setShowFullId( fullSeqId.getState() );
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462 alignPanel.idPanel.idCanvas.setSize( alignPanel.calculateIdWidth() );
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463 alignPanel.repaint();
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466 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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468 viewport.setColourText( colourTextMenuItem.getState() );
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469 alignPanel.repaint();
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472 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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474 viewport.setWrapAlignment( wrapMenuItem.getState() );
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475 alignPanel.setWrapAlignment( wrapMenuItem.getState() );
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476 scaleAbove.setEnabled( wrapMenuItem.getState() );
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477 scaleLeft.setEnabled( wrapMenuItem.getState());
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478 scaleRight.setEnabled( wrapMenuItem.getState());
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479 alignPanel.repaint();
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482 protected void scaleAbove_actionPerformed(ActionEvent e)
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484 viewport.setScaleAboveWrapped(scaleAbove.getState());
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485 alignPanel.repaint();
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488 protected void scaleLeft_actionPerformed(ActionEvent e)
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490 viewport.setScaleLeftWrapped(scaleLeft.getState());
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491 alignPanel.repaint();
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494 protected void scaleRight_actionPerformed(ActionEvent e)
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496 viewport.setScaleRightWrapped(scaleRight.getState());
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497 alignPanel.repaint();
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502 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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504 viewport.setShowBoxes( viewBoxesMenuItem.getState() );
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505 alignPanel.repaint();
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508 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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510 viewport.setShowText( viewTextMenuItem.getState() );
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511 alignPanel.repaint();
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515 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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517 viewport.setRenderGaps(renderGapsMenuItem.getState());
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518 alignPanel.repaint();
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522 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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524 if(annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
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526 annotationPanelMenuItem.setState(false);
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529 viewport.setShowAnnotation( annotationPanelMenuItem.getState() );
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530 alignPanel.setAnnotationVisible( annotationPanelMenuItem.getState() );
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533 public void overviewMenuItem_actionPerformed(ActionEvent e)
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535 if (alignPanel.overviewPanel != null)
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538 Frame frame = new Frame();
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539 OverviewPanel overview = new OverviewPanel(alignPanel);
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540 frame.add(overview);
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541 // +50 must allow for applet frame window
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542 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
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543 overview.preferredSize().width, overview.preferredSize().height+50);
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546 frame.addWindowListener(new WindowAdapter()
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547 { public void windowClosing(WindowEvent e)
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549 alignPanel.setOverviewPanel(null);
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553 alignPanel.setOverviewPanel( overview );
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558 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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560 changeColour( null );
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564 public void clustalColour_actionPerformed(ActionEvent e)
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566 abovePIDThreshold.setState(false);
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567 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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570 public void zappoColour_actionPerformed(ActionEvent e)
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572 changeColour(new ZappoColourScheme());
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575 public void taylorColour_actionPerformed(ActionEvent e)
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577 changeColour(new TaylorColourScheme());
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581 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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583 changeColour( new HydrophobicColourScheme() );
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586 public void helixColour_actionPerformed(ActionEvent e)
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588 changeColour(new HelixColourScheme() );
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592 public void strandColour_actionPerformed(ActionEvent e)
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594 changeColour(new StrandColourScheme());
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598 public void turnColour_actionPerformed(ActionEvent e)
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600 changeColour(new TurnColourScheme());
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604 public void buriedColour_actionPerformed(ActionEvent e)
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606 changeColour(new BuriedColourScheme() );
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609 public void nucleotideColour_actionPerformed(ActionEvent e)
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611 changeColour(new NucleotideColourScheme());
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615 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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617 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
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622 void changeColour(ColourSchemeI cs)
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626 if ( viewport.getAbovePIDThreshold() )
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628 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
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630 if (cs instanceof ResidueColourScheme)
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631 ( (ResidueColourScheme) cs).setThreshold(threshold);
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632 else if (cs instanceof ScoreColourScheme)
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633 ( (ScoreColourScheme) cs).setThreshold(threshold);
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635 viewport.setGlobalColourScheme(cs);
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637 else if (cs instanceof ResidueColourScheme)
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638 ( (ResidueColourScheme) cs).setThreshold(0);
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639 else if (cs instanceof ScoreColourScheme)
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640 ( (ScoreColourScheme) cs).setThreshold(0);
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644 if (viewport.getConservationSelected())
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646 ConservationColourScheme ccs = null;
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648 Alignment al = (Alignment) viewport.alignment;
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649 Conservation c = new Conservation("All",
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650 ResidueProperties.propHash, 3,
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651 al.getSequences(), 0,
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652 al.getWidth() - 1);
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655 c.verdict(false, viewport.ConsPercGaps);
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657 ccs = new ConservationColourScheme(c, cs);
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659 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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660 ccs.setConsensus( viewport.vconsensus );
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661 viewport.setGlobalColourScheme(ccs);
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663 SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
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668 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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670 cs.setConsensus(viewport.vconsensus);
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671 viewport.setGlobalColourScheme(cs);
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675 if(viewport.getColourAppliesToAllGroups())
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677 Vector groups = viewport.alignment.getGroups();
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678 for(int i=0; i<groups.size(); i++)
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680 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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682 if (cs instanceof ClustalxColourScheme)
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684 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
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689 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
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691 catch (Exception ex)
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693 ex.printStackTrace();
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697 if(viewport.getAbovePIDThreshold())
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699 if (sg.cs instanceof ResidueColourScheme)
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700 ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
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701 else if (sg.cs instanceof ScoreColourScheme)
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702 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
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704 sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
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707 if( viewport.getConservationSelected() )
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709 Conservation c = new Conservation("Group",
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710 ResidueProperties.propHash, 3,
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711 sg.sequences, 0, viewport.alignment.getWidth()-1);
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713 c.verdict(false, viewport.ConsPercGaps);
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714 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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716 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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717 ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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722 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
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723 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
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729 if(alignPanel.getOverviewPanel()!=null)
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730 alignPanel.getOverviewPanel().updateOverviewImage();
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732 alignPanel.repaint();
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735 protected void modifyPID_actionPerformed(ActionEvent e)
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737 if(viewport.getAbovePIDThreshold())
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739 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
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741 SliderPanel.showPIDSlider();
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745 protected void modifyConservation_actionPerformed(ActionEvent e)
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747 if(viewport.getConservationSelected())
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749 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
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751 SliderPanel.showConservationSlider();
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756 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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758 viewport.setConservationSelected(conservationMenuItem.getState());
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760 viewport.setAbovePIDThreshold(false);
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761 abovePIDThreshold.setState(false);
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763 ColourSchemeI cs = viewport.getGlobalColourScheme();
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764 if(cs instanceof ConservationColourScheme )
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765 changeColour( ((ConservationColourScheme)cs).cs );
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767 changeColour( cs );
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769 modifyConservation_actionPerformed(null);
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772 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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774 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
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776 conservationMenuItem.setState(false);
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777 viewport.setConservationSelected(false);
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779 ColourSchemeI cs = viewport.getGlobalColourScheme();
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781 if(cs instanceof ConservationColourScheme )
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782 changeColour( ((ConservationColourScheme)cs).cs );
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784 changeColour( cs );
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786 modifyPID_actionPerformed(null);
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791 public void userDefinedColour_actionPerformed(ActionEvent e)
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793 UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
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796 public void PIDColour_actionPerformed(ActionEvent e)
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798 changeColour( new PIDColourScheme() );
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802 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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804 changeColour(new Blosum62ColourScheme() );
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809 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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811 addHistoryItem("sort");
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812 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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813 alignPanel.repaint();
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816 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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818 addHistoryItem("sort");
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819 AlignmentSorter.sortByID( viewport.getAlignment() );
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820 alignPanel.repaint();
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823 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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825 addHistoryItem("sort");
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826 AlignmentSorter.sortByGroup(viewport.getAlignment());
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827 AlignmentSorter.sortGroups(viewport.getAlignment());
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828 alignPanel.repaint();
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831 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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833 RedundancyPanel sp = new RedundancyPanel(alignPanel);
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834 Frame frame = new Frame();
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836 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", 400, 120);
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840 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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842 if(viewport.getSelectionGroup().getSize()>1)
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844 Frame frame = new Frame();
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845 frame.add(new PairwiseAlignPanel(viewport));
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846 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
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850 public void PCAMenuItem_actionPerformed(ActionEvent e)
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853 if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
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854 || viewport.getAlignment().getHeight()<4)
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860 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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861 Frame frame = new Frame();
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862 frame.add(pcaPanel);
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863 jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis", 400, 400);
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864 }catch(java.lang.OutOfMemoryError ex)
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871 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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873 NewTreePanel("AV", "PID", "Average distance tree using PID");
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876 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
878 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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882 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
884 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
887 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
889 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
892 void NewTreePanel(String type, String pwType, String title)
\r
894 //are the sequences aligned?
\r
895 if(!viewport.alignment.isAligned())
\r
900 final TreePanel tp;
\r
901 if (viewport.getSelectionGroup() != null &&
\r
902 viewport.getSelectionGroup().getSize() > 3)
\r
904 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
906 0, viewport.alignment.getWidth());
\r
910 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
911 type, pwType, 0, viewport.alignment.getWidth());
\r
914 addTreeMenuItem(tp, title);
\r
916 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
919 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
921 final MenuItem item = new MenuItem(title);
\r
922 sortByTreeMenu.add(item);
\r
923 item.addActionListener(new java.awt.event.ActionListener()
\r
925 public void actionPerformed(ActionEvent e)
\r
927 addHistoryItem("sort");
\r
928 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
929 alignPanel.repaint();
\r
933 treePanel.addWindowListener(new WindowAdapter()
\r
935 public void windowClosing(WindowEvent e)
\r
937 sortByTreeMenu.remove(item);
\r
942 protected void documentation_actionPerformed(ActionEvent e) {
\r
944 jalview.bin.JalviewLite.showURL("http://www.jalview.org");
\r
948 protected void about_actionPerformed(ActionEvent e)
\r
950 class AboutPanel extends Canvas
\r
952 public void paint(Graphics g)
\r
954 g.setColor(Color.white);
\r
955 g.fillRect(0,0,getSize().width, getSize().height);
\r
956 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
957 FontMetrics fm = g.getFontMetrics();
\r
958 int fh = fm.getHeight();
\r
960 g.setColor(Color.black);
\r
961 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
962 g.drawString("JalView 2005", 200,y+=fh);
\r
963 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
964 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",x,y+=fh*2);
\r
965 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",x,y+=fh);
\r
966 g.drawString("If you use JalView, please cite:",x,y+=fh+8);
\r
967 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",x,y+=fh);
\r
968 g.drawString("Bioinformatics, 2004 12;426-7.",x,y+=fh);
\r
971 Frame frame = new Frame();
\r
972 frame.add(new AboutPanel());
\r
973 jalview.bin.JalviewLite.addFrame(frame, "Jalview 2005", 580,200);
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