3 import jalview.jbgui.GAlignmentPanel;
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4 import jalview.schemes.*;
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5 import jalview.analysis.*;
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6 import jalview.datamodel.*;
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8 import java.awt.event.*;
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9 import java.awt.print.*;
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11 import com.sun.image.codec.jpeg.*;
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13 import java.awt.image.*;
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18 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
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22 OverviewPanel overviewPanel;
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25 SecondaryStructurePanel ssPanel;
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26 public AlignFrame alignFrame;
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27 ScalePanel scalePanel;
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28 ScorePanel scorePanel;
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30 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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34 seqPanel = new SeqPanel (av, this);
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35 idPanel = new IdPanel (av, this);
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37 scalePanel = new ScalePanel(av, this);
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38 scorePanel = new ScorePanel(av);
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39 ssPanel = new SecondaryStructurePanel(av);
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41 secondaryPanelHolder.add(ssPanel, BorderLayout.CENTER);
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43 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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44 IdwidthAdjuster iap = new IdwidthAdjuster(this);
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45 idSpaceFillerPanel1.add(iap, BorderLayout.CENTER);
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47 idPanel.idCanvas.setPreferredSize(calculateIdWidth());
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48 hscrollFillerPanel.setPreferredSize(calculateIdWidth());
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50 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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51 scorePanelHolder.add(scorePanel, BorderLayout.CENTER);
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52 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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53 setScrollValues(0,0);
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55 hscroll.addAdjustmentListener(this);
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56 vscroll.addAdjustmentListener(this);
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58 addComponentListener(new ComponentAdapter()
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60 public void componentResized(ComponentEvent evt)
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67 // hscroll.setFocusable(false);
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68 // vscroll.setFocusable(false);
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71 addKeyListener(new KeyAdapter()
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73 public void keyPressed(KeyEvent evt)
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75 switch(evt.getKeyCode())
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77 case 27: // escape key
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78 av.setSelectionGroup(null);
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82 alignFrame.cut_actionPerformed(null);
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85 alignFrame.copy_actionPerformed(null);
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88 alignFrame.paste(true);
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91 alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
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93 case KeyEvent.VK_DOWN:
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94 alignFrame.moveSelectedSequences(false);
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96 case KeyEvent.VK_UP:
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97 alignFrame.moveSelectedSequences(true);
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100 alignFrame.findMenuItem_actionPerformed(null);
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107 Dimension calculateIdWidth()
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109 Graphics g = this.getGraphics();
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112 javax.swing.JFrame f = new javax.swing.JFrame();
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114 g = f.getGraphics();
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117 FontMetrics fm = g.getFontMetrics(av.font);
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118 AlignmentI al = av.getAlignment();
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123 while (i < al.getHeight() && al.getSequenceAt(i) != null)
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125 SequenceI s = al.getSequenceAt(i);
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126 if(av.getShowFullId())
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127 id = s.getDisplayId();
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131 if (fm.stringWidth(id) > idWidth)
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132 idWidth = fm.stringWidth(id);
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136 return new Dimension(idWidth, 12);
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140 public void highlightSearchResults(int [] results)
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142 seqPanel.seqCanvas.highlightSearchResults( results );
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144 // do we need to scroll the panel?
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145 if(results!=null && (av.getStartSeq()>results[0]
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146 || av.getEndSeq()<results[0]
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147 || av.getStartRes()>results[1]
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148 || av.getEndRes()<results[2]))
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149 setScrollValues(results[1], results[0]);
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155 public OverviewPanel getOverviewPanel()
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157 return overviewPanel;
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160 public void setOverviewPanel(OverviewPanel op)
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162 overviewPanel = op;
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166 public void setGraphPanelVisible(boolean b)
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168 idSpaceFillerPanel.setVisible(b);
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169 scorePanelHolder.setVisible(b);
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172 // bit annoying to call this twice, can you do better?
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176 public void setSecondaryStructureVisible(boolean b)
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178 secondaryPanelHolder.setVisible(b);
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182 public void setWrapAlignment(boolean wrap)
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184 scorePanelHolder.setVisible(!wrap);
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185 scalePanelHolder.setVisible(!wrap);
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186 secondaryPanelHolder.setVisible(!wrap);
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188 hscroll.setVisible(!wrap);
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190 // idSpaceFillerPanel.setVisible(!wrap);
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191 // idWidthAdjusterPanel.setVisible(!wrap);
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198 public void setColourScheme()
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200 ColourSchemeI cs = av.getGlobalColourScheme();
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202 if(av.getConservationSelected())
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205 Alignment al = (Alignment)av.getAlignment();
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206 Conservation c = new Conservation("All",
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207 ResidueProperties.propHash, 3, al.getSequences(), 0,
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211 c.verdict(false, 100);
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212 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
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214 av.setGlobalColourScheme( ccs );
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221 public void RefreshPanels()
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225 idPanelHolder.setPreferredSize(idPanel.idCanvas.getPreferredSize());
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226 if(idPanel.idCanvas.getPreferredSize()!=null)
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227 hscrollFillerPanel.setPreferredSize(new Dimension(idPanel.idCanvas.getPreferredSize().width, 12));
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228 idSpaceFillerPanel1.setPreferredSize(new Dimension(500,
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229 av.charHeight / 2 + 12));
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230 scalePanelHolder.setPreferredSize(new Dimension(500,
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231 av.charHeight / 2 + 12));
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232 if (av.getWrapAlignment())
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234 int max = av.alignment.getWidth() /
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235 (seqPanel.seqCanvas.getWidth() / av.charWidth) + 1;
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237 int h = (av.alignment.getHeight() + 2) * av.charHeight;
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238 vextent = seqPanel.seqCanvas.getHeight() / h;
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239 vscroll.setValues(0, vextent, 0, max);
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243 setScrollValues(av.getStartRes(), av.getStartSeq());
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244 av.getConsensus(true);
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245 if (overviewPanel != null)
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246 overviewPanel.updateOverviewImage();
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255 // return value is true if the scroll is valid
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256 public boolean scrollUp(boolean up)
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260 if(vscroll.getValue()<1)
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262 vscroll.setValue(vscroll.getValue() - 1);
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266 if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
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268 vscroll.setValue(vscroll.getValue() + 1);
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274 public boolean scrollRight(boolean right)
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278 if(hscroll.getValue()<1)
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280 hscroll.setValue(hscroll.getValue() - 1);
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284 if(hextent+hscroll.getValue() >= av.getAlignment().getWidth())
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286 hscroll.setValue(hscroll.getValue() + 1);
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293 public void setScrollValues(int x, int y)
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295 hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();
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296 vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();
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298 if(hextent+x > av.getAlignment().getWidth())
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299 x = av.getAlignment().getWidth()- hextent;
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301 if(vextent+y > av.getAlignment().getHeight())
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302 y = av.getAlignment().getHeight() - vextent;
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310 hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
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311 vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
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319 public void adjustmentValueChanged(AdjustmentEvent evt)
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322 if (evt.getSource() == hscroll)
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324 int x = hscroll.getValue();
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326 av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
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329 if (evt.getSource() == vscroll)
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331 int offy = vscroll.getValue();
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332 if (av.getWrapAlignment())
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334 av.setStartRes( vscroll.getValue() * av.getChunkWidth());
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338 av.setStartSeq(offy);
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339 av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());
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344 if(overviewPanel!=null)
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345 overviewPanel.setBoxPosition();
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350 public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
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352 pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
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354 int pwidth = (int) pf.getImageableWidth();
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355 int pheight = (int) pf.getImageableHeight();
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357 if (av.getWrapAlignment())
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358 return printWrappedAlignment(pg, pwidth,pheight, pi);
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360 return printUnwrapped(pg,pwidth, pheight,pi);
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363 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
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366 int idWidth = calculateIdWidth().width;
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369 pg.setColor(Color.white);
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370 pg.fillRect(0,0,pwidth, pheight);
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371 pg.setFont( av.getFont() );
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373 ////////////////////////////////////
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374 /// How many sequences and residues can we fit on a printable page?
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375 int totalRes = (pwidth - idWidth)/av.getCharWidth();
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376 int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
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377 int pagesWide = av.getAlignment().getWidth() / totalRes +1;
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378 int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
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380 if (pi >= pagesWide*pagesHigh)
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381 return Printable.NO_SUCH_PAGE;
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383 /////////////////////////////
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384 /// Only print these sequences and residues on this page
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385 int startRes, endRes, startSeq, endSeq;
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386 startRes = (pi % pagesWide) * totalRes;
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387 endRes = startRes + totalRes-1;
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388 if(endRes>av.getAlignment().getWidth())
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389 endRes = av.getAlignment().getWidth();
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391 startSeq = (pi / pagesWide) * totalSeq;
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392 endSeq = startSeq + totalSeq;
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393 if(endSeq > av.getAlignment().getHeight())
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394 endSeq = av.getAlignment().getHeight();
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399 pg.translate(idWidth,0);
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400 scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);
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402 pg.translate(-idWidth, 30);
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405 Color currentColor=null;
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406 Color currentTextColor=null;
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407 for(int i=startSeq; i<endSeq; i++)
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409 if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))
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411 currentColor = Color.gray;
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412 currentTextColor = Color.black;
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416 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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417 currentTextColor = Color.black;
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420 pg.setColor(currentColor);
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421 pg.fillRect(0, jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
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423 av.getCharHeight());
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425 pg.setColor(currentTextColor);
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427 String string = av.getAlignment().getSequenceAt(i).getDisplayId();
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428 pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight
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429 (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
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432 // draw main sequence panel
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433 pg.translate(idWidth,0);
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434 pg.setClip(0,0,pwidth-idWidth, pheight);
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435 seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
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437 return Printable.PAGE_EXISTS;
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441 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
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444 int idWidth = calculateIdWidth().width;
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446 if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)
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447 pwidth = seqPanel.seqCanvas.getWidth() + idWidth;
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450 pg.setColor(Color.white);
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451 pg.fillRect(0,0,pwidth, pheight);
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452 pg.setFont( av.getFont() );
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454 ////////////////////////////////////
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455 /// How many sequences and residues can we fit on a printable page?
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456 AlignmentI da = av.alignment;
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457 int endy = da.getHeight();
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458 int chunkHeight = (da.getHeight() + 2)*av.charHeight;
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459 int chunkWidth = (pwidth-idWidth)/av.charWidth;
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461 int noChunksOnPage = pheight / chunkHeight;
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462 int totalChunks = da.getWidth() / chunkWidth;
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464 if ( pi*noChunksOnPage > totalChunks )
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465 return Printable.NO_SUCH_PAGE;
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469 pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);
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471 int row = pi*noChunksOnPage;
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472 pg.setColor(Color.black);
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473 for(int ypos=2*av.charHeight;
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474 ypos <= pheight && row*chunkWidth<da.getWidth();
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475 ypos += chunkHeight, row++ )
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477 for (int i = 0; i < endy; i++)
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479 SequenceI s = da.getSequenceAt(i);
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480 pg.drawString(s.getDisplayId(), 0,
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481 AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
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482 av.charHeight - (av.charHeight / 5));
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486 // draw main sequence panel
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487 pg.translate(idWidth,0);
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488 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);
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491 return Printable.PAGE_EXISTS;
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495 public void makeJPG(int width, int height)
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500 BufferedImage bi = new BufferedImage(width, height,
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501 BufferedImage.TYPE_INT_RGB);
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502 Graphics pg = bi.getGraphics();
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506 if (av.getWrapAlignment())
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507 printWrappedAlignment(pg, width, height, 0);
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509 printUnwrapped(pg, width, height, 0);
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511 catch (Exception ex)
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514 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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515 "LAST_DIRECTORY"));
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516 chooser.setFileView(new jalview.io.JalviewFileView());
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517 chooser.setDialogTitle("Create JPG image from alignment");
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518 chooser.setToolTipText("Save");
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520 int value = chooser.showSaveDialog(this);
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521 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
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524 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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525 JPEGImageEncoder jie = JPEGCodec.createJPEGEncoder(out);
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526 JPEGEncodeParam param = JPEGCodec.getDefaultJPEGEncodeParam(bi);
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527 param.setQuality(1.0f, true);
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529 jie.encode(bi, param);
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534 catch (IOException ex)
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536 System.out.println("ex Writing image ");
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