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 java.awt.image.*;
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12 import org.jibble.epsgraphics.*;
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13 import javax.imageio.*;
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17 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
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21 OverviewPanel overviewPanel;
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24 IdwidthAdjuster idwidthAdjuster;
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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 = new IdwidthAdjuster(this);
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45 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
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47 Dimension d = calculateIdWidth();
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48 d.setSize( d.width+4, d.height);
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49 idPanel.idCanvas.setPreferredSize( d );
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50 hscrollFillerPanel.setPreferredSize( d );
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52 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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53 scorePanelHolder.add(scorePanel, BorderLayout.CENTER);
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54 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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55 setScrollValues(0,0);
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57 hscroll.addAdjustmentListener(this);
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58 vscroll.addAdjustmentListener(this);
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60 addComponentListener(new ComponentAdapter()
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62 public void componentResized(ComponentEvent evt)
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64 if(seqPanel.getWidth()>0 && seqPanel.getHeight()>0)
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70 // hscroll.setFocusable(false);
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71 // vscroll.setFocusable(false);
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74 addKeyListener(new KeyAdapter()
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76 public void keyPressed(KeyEvent evt)
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78 switch(evt.getKeyCode())
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80 case 27: // escape key
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81 av.setSelectionGroup(null);
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85 alignFrame.cut_actionPerformed(null);
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88 alignFrame.copy_actionPerformed(null);
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91 alignFrame.paste(true);
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94 alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
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96 case KeyEvent.VK_DOWN:
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97 alignFrame.moveSelectedSequences(false);
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99 case KeyEvent.VK_UP:
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100 alignFrame.moveSelectedSequences(true);
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102 case KeyEvent.VK_F:
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103 alignFrame.findMenuItem_actionPerformed(null);
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110 Dimension calculateIdWidth()
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112 Graphics g = this.getGraphics();
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115 javax.swing.JFrame f = new javax.swing.JFrame();
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117 g = f.getGraphics();
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120 FontMetrics fm = g.getFontMetrics(av.font);
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121 AlignmentI al = av.getAlignment();
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126 while (i < al.getHeight() && al.getSequenceAt(i) != null)
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128 SequenceI s = al.getSequenceAt(i);
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129 if(av.getShowFullId())
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130 id = s.getDisplayId();
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134 if (fm.stringWidth(id) > idWidth)
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135 idWidth = fm.stringWidth(id);
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139 return new Dimension(idWidth, 12);
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143 public void highlightSearchResults(int [] results)
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145 seqPanel.seqCanvas.highlightSearchResults( results );
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147 // do we need to scroll the panel?
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148 if(results!=null && (av.getStartSeq()>results[0]
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149 || av.getEndSeq()<results[0]
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150 || av.getStartRes()>results[1]
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151 || av.getEndRes()<results[2]))
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152 setScrollValues(results[1], results[0]);
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158 public OverviewPanel getOverviewPanel()
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160 return overviewPanel;
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163 public void setOverviewPanel(OverviewPanel op)
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165 overviewPanel = op;
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169 public void setGraphPanelVisible(boolean b)
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171 idSpaceFillerPanel.setVisible(b);
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172 scorePanelHolder.setVisible(b);
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175 // bit annoying to call this twice, can you do better?
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179 public void setSecondaryStructureVisible(boolean b)
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181 secondaryPanelHolder.setVisible(b);
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185 public void setWrapAlignment(boolean wrap)
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187 scorePanelHolder.setVisible(!wrap);
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188 scalePanelHolder.setVisible(!wrap);
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189 secondaryPanelHolder.setVisible(!wrap);
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191 hscroll.setVisible(!wrap);
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193 idwidthAdjuster.setVisible(!wrap);
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194 idSpaceFillerPanel.setVisible(!wrap);
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195 idSpaceFillerPanel1.setVisible(!wrap);
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202 public void setColourScheme()
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204 ColourSchemeI cs = av.getGlobalColourScheme();
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206 if(av.getConservationSelected())
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209 Alignment al = (Alignment)av.getAlignment();
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210 Conservation c = new Conservation("All",
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211 ResidueProperties.propHash, 3, al.getSequences(), 0,
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215 c.verdict(false, 100);
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216 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
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218 av.setGlobalColourScheme( ccs );
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225 public void RefreshPanels()
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229 idPanelHolder.setPreferredSize(idPanel.idCanvas.getPreferredSize());
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230 if(idPanel.idCanvas.getPreferredSize()!=null)
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231 hscrollFillerPanel.setPreferredSize(new Dimension(idPanel.idCanvas.getPreferredSize().width, 12));
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232 idSpaceFillerPanel1.setPreferredSize(new Dimension(500,
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233 av.charHeight / 2 + 12));
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234 scalePanelHolder.setPreferredSize(new Dimension(500,
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235 av.charHeight / 2 + 12));
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236 if (av.getWrapAlignment())
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238 int max = av.alignment.getWidth() /
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239 (seqPanel.seqCanvas.getWidth() / av.charWidth) + 1;
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241 int h = (av.alignment.getHeight() + 2) * av.charHeight;
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242 vextent = seqPanel.seqCanvas.getHeight() / h;
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243 vscroll.setValues(0, vextent, 0, max);
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247 setScrollValues(av.getStartRes(), av.getStartSeq());
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248 av.getConsensus(true);
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249 if (overviewPanel != null)
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250 overviewPanel.updateOverviewImage();
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259 // return value is true if the scroll is valid
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260 public boolean scrollUp(boolean up)
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264 if(vscroll.getValue()<1)
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266 vscroll.setValue(vscroll.getValue() - 1);
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270 if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
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272 vscroll.setValue(vscroll.getValue() + 1);
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278 public boolean scrollRight(boolean right)
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282 if(hscroll.getValue()<1)
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284 hscroll.setValue(hscroll.getValue() - 1);
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288 if(hextent+hscroll.getValue() >= av.getAlignment().getWidth())
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290 hscroll.setValue(hscroll.getValue() + 1);
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297 public void setScrollValues(int x, int y)
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299 hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();
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300 vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();
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302 if(hextent+x > av.getAlignment().getWidth())
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303 x = av.getAlignment().getWidth()- hextent;
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305 if(vextent+y > av.getAlignment().getHeight())
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306 y = av.getAlignment().getHeight() - vextent;
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314 hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
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315 vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
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323 public void adjustmentValueChanged(AdjustmentEvent evt)
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326 if (evt.getSource() == hscroll)
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328 int x = hscroll.getValue();
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330 av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
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333 if (evt.getSource() == vscroll)
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335 int offy = vscroll.getValue();
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336 if (av.getWrapAlignment())
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338 av.setStartRes( vscroll.getValue() * av.getChunkWidth());
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342 av.setStartSeq(offy);
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343 av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());
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348 if(overviewPanel!=null)
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349 overviewPanel.setBoxPosition();
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354 public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
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356 pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
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358 int pwidth = (int) pf.getImageableWidth();
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359 int pheight = (int) pf.getImageableHeight();
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361 if (av.getWrapAlignment())
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362 return printWrappedAlignment(pg, pwidth,pheight, pi);
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364 return printUnwrapped(pg,pwidth, pheight,pi);
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367 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
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370 int idWidth = calculateIdWidth().width;
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373 pg.setColor(Color.white);
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374 pg.fillRect(0,0,pwidth, pheight);
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375 pg.setFont( av.getFont() );
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377 ////////////////////////////////////
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378 /// How many sequences and residues can we fit on a printable page?
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379 int totalRes = (pwidth - idWidth)/av.getCharWidth();
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380 int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
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381 int pagesWide = av.getAlignment().getWidth() / totalRes +1;
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382 int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
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384 if (pi >= pagesWide*pagesHigh)
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385 return Printable.NO_SUCH_PAGE;
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387 /////////////////////////////
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388 /// Only print these sequences and residues on this page
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389 int startRes, endRes, startSeq, endSeq;
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390 startRes = (pi % pagesWide) * totalRes;
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391 endRes = startRes + totalRes-1;
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392 if(endRes>av.getAlignment().getWidth())
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393 endRes = av.getAlignment().getWidth();
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395 startSeq = (pi / pagesWide) * totalSeq;
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396 endSeq = startSeq + totalSeq;
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397 if(endSeq > av.getAlignment().getHeight())
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398 endSeq = av.getAlignment().getHeight();
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403 pg.translate(30,0);
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404 scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);
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406 pg.translate(-30, 30);
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409 Color currentColor=null;
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410 Color currentTextColor=null;
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411 for(int i=startSeq; i<endSeq; i++)
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413 if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))
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415 currentColor = Color.gray;
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416 currentTextColor = Color.black;
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420 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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421 currentTextColor = Color.black;
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424 pg.setColor(currentColor);
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425 pg.fillRect(0, jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
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427 av.getCharHeight());
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429 pg.setColor(currentTextColor);
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431 String string = av.getAlignment().getSequenceAt(i).getName();
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432 if(av.getShowFullId())
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433 string = av.getAlignment().getSequenceAt(i).getDisplayId();
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435 pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight
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436 (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
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439 // draw main sequence panel
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440 pg.translate(idWidth+4,0);
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441 pg.setClip(0,0,pwidth-idWidth, pheight);
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442 seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
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444 return Printable.PAGE_EXISTS;
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448 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
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451 int idWidth = calculateIdWidth().width;
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453 if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)
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454 pwidth = seqPanel.seqCanvas.getWidth() + idWidth;
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457 pg.setColor(Color.white);
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458 pg.fillRect(0,0,pwidth, pheight);
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459 pg.setFont( av.getFont() );
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461 ////////////////////////////////////
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462 /// How many sequences and residues can we fit on a printable page?
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463 AlignmentI da = av.alignment;
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464 int endy = da.getHeight();
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465 int chunkHeight = (da.getHeight() + 2)*av.charHeight;
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466 int chunkWidth = (pwidth-idWidth)/av.charWidth;
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468 int noChunksOnPage = pheight / chunkHeight;
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469 int totalChunks = da.getWidth() / chunkWidth;
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471 if ( pi*noChunksOnPage > totalChunks )
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472 return Printable.NO_SUCH_PAGE;
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476 pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);
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478 int row = pi*noChunksOnPage;
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479 pg.setColor(Color.black);
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480 for(int ypos=2*av.charHeight;
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481 ypos <= pheight && row*chunkWidth<da.getWidth();
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482 ypos += chunkHeight, row++ )
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484 for (int i = 0; i < endy; i++)
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486 SequenceI s = da.getSequenceAt(i);
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487 String string = s.getName();
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488 if (av.getShowFullId())
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489 string = s.getDisplayId();
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491 pg.drawString(string, 0,
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492 AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
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493 av.charHeight - (av.charHeight / 5));
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497 // draw main sequence panel
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498 pg.translate(idWidth+4,0);
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499 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);
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502 return Printable.PAGE_EXISTS;
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507 public void makeEPS()
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509 int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
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510 int width = seqPanel.getWidth() + idPanel.getWidth();
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512 if (!av.getWrapAlignment())
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514 height = (av.alignment.getHeight()+1) * av.charHeight + 30;
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515 width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
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520 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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521 "LAST_DIRECTORY"), new String[]{"eps"}, "Encapsulated Postscript");
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522 chooser.setFileView(new jalview.io.JalviewFileView());
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523 chooser.setDialogTitle("Create EPS file from alignment");
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524 chooser.setToolTipText("Save");
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526 int value = chooser.showSaveDialog(this);
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527 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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530 jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
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531 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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532 EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height);
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534 if (av.getWrapAlignment())
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535 printWrappedAlignment(pg, width, height, 0);
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537 printUnwrapped(pg, width, height, 0);
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543 catch (Exception ex)
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545 ex.printStackTrace();
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549 public void makePNG()
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551 int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
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552 int width = seqPanel.getWidth() + idPanel.getWidth();
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554 if (!av.getWrapAlignment())
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556 height = (av.alignment.getHeight()+1) * av.charHeight + 30;
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557 width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
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564 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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565 "LAST_DIRECTORY"), new String[]{"png"}, "Portable network graphics");
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566 chooser.setFileView(new jalview.io.JalviewFileView());
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567 chooser.setDialogTitle("Create EPS file from alignment");
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568 chooser.setToolTipText("Save");
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570 int value = chooser.showSaveDialog(this);
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571 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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574 jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
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575 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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577 BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
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578 Graphics png = bi.getGraphics();
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581 if (av.getWrapAlignment())
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582 printWrappedAlignment(png, width, height, 0);
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584 printUnwrapped(png, width, height, 0);
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586 ImageIO.write(bi, "png", out);
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589 catch (Exception ex)
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591 ex.printStackTrace();
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