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 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
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15 OverviewPanel overviewPanel;
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18 SecondaryStructurePanel ssPanel;
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19 public AlignFrame alignFrame;
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20 ScalePanel scalePanel;
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21 ScorePanel scorePanel;
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23 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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27 seqPanel = new SeqPanel (av, this);
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28 idPanel = new IdPanel (av, this);
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29 scalePanel = new ScalePanel(av, this);
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30 scorePanel = new ScorePanel(av);
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31 ssPanel = new SecondaryStructurePanel(av);
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33 secondaryPanelHolder.add(ssPanel, BorderLayout.CENTER);
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34 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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35 idPanel.addNotify();
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36 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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37 scorePanelHolder.add(scorePanel, BorderLayout.CENTER);
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38 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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39 setScrollValues(0,0);
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41 hscroll.addAdjustmentListener(this);
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42 vscroll.addAdjustmentListener(this);
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44 addComponentListener(new ComponentAdapter()
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46 public void componentResized(ComponentEvent evt)
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52 hscroll.setFocusable(false);
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53 vscroll.setFocusable(false);
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56 addKeyListener(new KeyAdapter()
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58 public void keyPressed(KeyEvent evt)
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60 if(evt.getKeyCode()==27)
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62 av.setRubberbandGroup(null);
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71 public void highlightSearchResults(int [] results)
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73 seqPanel.seqCanvas.highlightSearchResults( results );
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75 // do we need to scroll the panel?
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76 if(results!=null && (av.getStartSeq()>results[0]
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77 || av.getEndSeq()<results[0]
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78 || av.getStartRes()>results[1]
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79 || av.getEndRes()<results[2]))
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80 setScrollValues(results[1], results[0]);
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86 public OverviewPanel getOverviewPanel()
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88 return overviewPanel;
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91 public void setOverviewPanel(OverviewPanel op)
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97 public void setGraphPanelVisible(boolean b)
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99 idSpaceFillerPanel.setVisible(b);
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100 scorePanelHolder.setVisible(b);
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103 // bit annoying to call this twice, can you do better?
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107 public void setSecondaryStructureVisible(boolean b)
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109 secondaryPanelHolder.setVisible(b);
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113 public void setWrapAlignment(boolean wrap)
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115 scorePanelHolder.setVisible(!wrap);
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116 scalePanelHolder.setVisible(!wrap);
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117 secondaryPanelHolder.setVisible(!wrap);
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119 hscroll.setVisible(!wrap);
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121 idSpaceFillerPanel.setVisible(!wrap);
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122 idSpaceFillerPanel1.setVisible(!wrap);
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129 public void setColourScheme()
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131 ColourSchemeI cs = av.getGlobalColourScheme();
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133 if(av.getConservationSelected())
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136 Alignment al = (Alignment)av.getAlignment();
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137 Conservation c = new Conservation("All",
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138 ResidueProperties.propHash, 3, al.getSequences(), 0,
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142 c.verdict(false, 100);
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143 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
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145 av.setGlobalColourScheme( ccs );
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152 public void RefreshPanels()
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156 seqPanel.seqCanvas.paintFlag = true;
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157 idPanel.idCanvas.paintFlag = true;
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158 idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
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160 if(av.getWrapAlignment())
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162 int max = av.alignment.getWidth()/ (seqPanel.seqCanvas.getWidth()/av.charWidth)+1;
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164 int h = (av.alignment.getHeight() + 2)*av.charHeight;
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165 vextent = seqPanel.seqCanvas.getHeight()/h;
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166 vscroll.setValues(0,vextent,0,max);
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170 setScrollValues(av.getStartRes(), av.getStartSeq());
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171 av.getConsensus(true);
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172 if(overviewPanel!=null)
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173 overviewPanel.updateOverviewImage();
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183 public void setScrollValues(int x, int y)
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185 hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();
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186 vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();
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188 if(hextent+x > av.getAlignment().getWidth())
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189 x = av.getAlignment().getWidth()- hextent;
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191 if(vextent+y > av.getAlignment().getHeight())
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192 y = av.getAlignment().getHeight() - vextent;
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200 hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
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201 vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
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209 public void adjustmentValueChanged(AdjustmentEvent evt)
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212 if (evt.getSource() == hscroll)
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214 int x = hscroll.getValue();
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216 av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
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219 if (evt.getSource() == vscroll)
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221 int offy = vscroll.getValue();
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222 if (av.getWrapAlignment())
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224 av.setStartRes( vscroll.getValue() * av.getChunkWidth());
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225 // System.out.println(vscroll.getValue()+" "+ av.getChunkWidth());
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226 // int resSpan = av.alignment.getWidth()/ (seqPanel.seqCanvas.getWidth()/av.charWidth)+1;
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227 // int h = (av.alignment.getHeight() + 2)*av.charHeight;
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228 // vextent = seqPanel.seqCanvas.getHeight()/h;
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229 // vscroll.setValues(0,vextent,0,max);
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232 // av.setStartSeq( );
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236 av.setStartSeq(offy);
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237 av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());
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242 if(overviewPanel!=null)
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243 overviewPanel.setBoxPosition();
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245 seqPanel.seqCanvas.paintFlag=true;
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251 public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
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253 if(av.getWrapAlignment())
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255 return PrintWrappedAlignment(pg, pf, pi);
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258 pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
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260 int pwidth = (int)pf.getImageableWidth();
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261 int pheight = (int)pf.getImageableHeight();
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262 int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
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265 pg.setColor(Color.white);
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266 pg.fillRect(0,0,pwidth, pheight);
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267 pg.setFont( av.getFont() );
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269 ////////////////////////////////////
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270 /// How many sequences and residues can we fit on a printable page?
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271 int totalRes = (pwidth - idWidth)/av.getCharWidth();
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272 int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
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273 int pagesWide = av.getAlignment().getWidth() / totalRes +1;
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274 int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
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276 if (pi >= pagesWide*pagesHigh)
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277 return Printable.NO_SUCH_PAGE;
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279 /////////////////////////////
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280 /// Only print these sequences and residues on this page
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281 int startRes, endRes, startSeq, endSeq;
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282 startRes = (pi % pagesWide) * totalRes;
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283 endRes = startRes + totalRes-1;
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284 if(endRes>av.getAlignment().getWidth())
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285 endRes = av.getAlignment().getWidth();
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287 startSeq = (pi / pagesWide) * totalSeq;
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288 endSeq = startSeq + totalSeq;
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289 if(endSeq > av.getAlignment().getHeight())
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290 endSeq = av.getAlignment().getHeight();
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295 pg.translate(idWidth,0);
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296 scalePanel.scaleCanvas.drawScale(pg, startRes, endRes, pwidth-idWidth);
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298 pg.translate(-idWidth, 30);
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301 Color currentColor=null;
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302 Color currentTextColor=null;
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303 for(int i=startSeq; i<endSeq; i++)
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305 if (av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
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307 currentColor = Color.gray;
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308 currentTextColor = Color.black;
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312 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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313 currentTextColor = Color.black;
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316 pg.setColor(currentColor);
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317 pg.fillRect(0, jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
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319 av.getCharHeight());
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321 pg.setColor(currentTextColor);
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323 String string = av.getAlignment().getSequenceAt(i).getDisplayId();
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324 pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight
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325 (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
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328 // draw main sequence panel
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329 pg.translate(idWidth,0);
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330 pg.setClip(0,0,pwidth-idWidth, pheight);
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331 seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
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333 return Printable.PAGE_EXISTS;
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336 class VPanel extends javax.swing.JPanel
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339 public VPanel(Image i)
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344 public void paintComponent(Graphics g)
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347 g.drawImage(image,0,0,this);
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352 public int PrintWrappedAlignment(Graphics pg, PageFormat pf, int pi)
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354 pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
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356 int pwidth = (int)pf.getImageableWidth();
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357 int pheight = (int)pf.getImageableHeight();
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358 int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
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360 if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)
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361 pwidth = seqPanel.seqCanvas.getWidth() + idWidth;
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363 pg.setColor(Color.white);
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364 pg.fillRect(0,0,pwidth, pheight);
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365 pg.setFont( av.getFont() );
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367 ////////////////////////////////////
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368 /// How many sequences and residues can we fit on a printable page?
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369 AlignmentI da = av.alignment;
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370 int endy = da.getHeight();
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371 int chunkHeight = (da.getHeight() + 2)*av.charHeight;
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372 int chunkWidth = (pwidth-idWidth)/av.charWidth;
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374 int noChunksOnPage = pheight / chunkHeight;
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375 int totalChunks = endy / chunkHeight;
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377 if ( pi*noChunksOnPage > totalChunks )
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378 return Printable.NO_SUCH_PAGE;
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382 pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);
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384 int row = pi*noChunksOnPage;
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385 pg.setColor(Color.black);
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386 for(int ypos=2*av.charHeight;
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387 ypos <= pheight && row*chunkWidth<da.getWidth();
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388 ypos += chunkHeight, row++ )
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390 for (int i = 0; i < endy; i++)
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392 SequenceI s = da.getSequenceAt(i);
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393 pg.drawString(s.getDisplayId(), 0,
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394 AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
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395 av.charHeight - (av.charHeight / 5));
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399 // draw main sequence panel
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400 pg.translate(idWidth,0);
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401 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);
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404 return Printable.NO_SUCH_PAGE;//.PAGE_EXISTS;
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