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 public AlignFrame alignFrame;
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19 ScalePanel scalePanel;
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20 ScorePanel scorePanel;
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22 public AlignmentPanel(AlignFrame af, AlignViewport av)
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26 seqPanel = new SeqPanel (av, this);
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27 idPanel = new IdPanel (av, this);
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28 scalePanel = new ScalePanel(av);
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29 scorePanel = new ScorePanel(av);
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31 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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32 idPanel.addNotify();
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33 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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34 scorePanelHolder.add(scorePanel, BorderLayout.CENTER);
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35 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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36 setScrollValues(0,0);
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38 hscroll.addAdjustmentListener(this);
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39 vscroll.addAdjustmentListener(this);
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41 addComponentListener(new ComponentAdapter()
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43 public void componentResized(ComponentEvent evt)
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50 public void highlightSearchResults(int [] results)
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52 seqPanel.seqCanvas.highlightSearchResults( results );
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54 // do we need to scroll the panel?
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55 if(results!=null && (av.getStartSeq()>results[0]
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56 || av.getEndSeq()<results[0]
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57 || av.getStartRes()>results[1]
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58 || av.getEndRes()<results[2]))
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59 setScrollValues(results[1], results[0]);
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65 public OverviewPanel getOverviewPanel()
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67 return overviewPanel;
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70 public void setOverviewPanel(OverviewPanel op)
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76 public void setGraphPanelVisible(boolean b)
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78 scorePanelHolder.setVisible(b);
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79 idSpaceFillerPanel.setVisible(b);
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83 public void setWrapAlignment(boolean wrap)
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85 scalePanelHolder.setVisible(!wrap);
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86 scorePanelHolder.setVisible(!wrap);
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88 hscroll.setVisible(!wrap);
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89 idSpaceFillerPanel.setVisible(!wrap);
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90 idSpaceFillerPanel1.setVisible(!wrap);
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94 public void setColourScheme()
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96 ColourSchemeI cs = av.getGlobalColourScheme();
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98 if(av.getConservationSelected())
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101 Alignment al = (Alignment)av.getAlignment();
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102 Conservation c = new Conservation("All", al.cons,
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103 ResidueProperties.propHash, 3, al.getSequences(), 0,
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107 c.verdict(false, 100);
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108 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
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110 av.setGlobalColourScheme( ccs );
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113 seqPanel.seqCanvas.paintFlag = true;
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117 seqCanvas.paintFlag = true;
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118 if (av.getSelection().size() == 0)
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120 seqCanvas.globalColorScheme = cs;
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121 for (int i = 0; i < av.alignment.getGroups().size();i++)
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123 SequenceGroup sg = (SequenceGroup)av.alignment.getGroups().elementAt(i);
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125 if(!showConservation
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126 && !(sg.cs instanceof Blosum62ColourScheme)
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127 && sg.cs instanceof ConservationColourScheme)
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129 // remove ConservationColouring from existing Conservation group
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130 ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
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133 else if(showConservation && !(sg.cs instanceof ConservationColourScheme))
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135 // add ConservationColouring to new group
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136 Conservation c = sg.getConservation();
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137 Alignment al = (Alignment) av.getAlignment();
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138 c = new Conservation("All", al.cons,
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139 ResidueProperties.propHash, 3, sg.sequences, 0,
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142 c.verdict(false, 100);
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143 sg.setConservation(c);
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144 sg.cs = new ConservationColourScheme(sg);
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150 SequenceGroup sg = av.alignment.findGroup((Sequence)av.sel.sequenceAt(0));
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152 if( isNewSelection(sg) )
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154 sg = av.getAlignment().addGroup();
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155 for (int i=0; i < av.getSelection().size(); i++)
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157 av.alignment.removeFromGroup(av.alignment.findGroup( (Sequence) av.
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158 sel.sequenceAt(i)),
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159 (Sequence) av.sel.sequenceAt(i));
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160 av.alignment.addToGroup(sg, (Sequence) av.sel.sequenceAt(i));
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167 // Selection is made, we only want to change the conservationColour for selected group
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168 if( showConservation
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169 && !(sg.cs instanceof ConservationColourScheme)
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170 && !(sg.cs instanceof Blosum62ColourScheme))
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172 Conservation c = sg.getConservation();
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173 Alignment al = (Alignment) av.getAlignment();
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175 c = new Conservation("All", al.cons,
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176 ResidueProperties.propHash, 3, sg.sequences, 0,
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179 c.verdict(false, 100);
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180 sg.setConservation(c);
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181 sg.cs = new ConservationColourScheme(sg);
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183 else if( !showConservation && sg.cs instanceof ConservationColourScheme)
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185 ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
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192 boolean isNewSelection(SequenceGroup sg)
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197 if(sg.getSize()!=av.getSelection().size())
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200 for(int i=0; i<sg.getSize(); i++)
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201 if( !av.getSelection().contains( sg.getSequenceAt(i) ))
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208 public ColourSchemeI getColourScheme()
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210 if(av.getSelection().size()>0)
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211 return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs;
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213 return seqCanvas.globalColorScheme;
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217 /* public void setColourScheme(jalview.schemes.ColourSchemeI cs, boolean conservation)
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219 seqPanel.setColourScheme(cs, conservation);
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221 av.setGlobalColourScheme(cs);
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223 if(overviewPanel!=null)
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224 overviewPanel.updateOverviewImage();
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227 void updateResidueView()
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229 if (viewport.getSelection().size() == 0)
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231 for (int i = 0; i < viewport.alignment.getGroups().size(); i++)
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233 SequenceGroup sg = (SequenceGroup) viewport.alignment.getGroups().elementAt(i);
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234 sg.setDisplayBoxes( viewBoxesMenuItem.isSelected() );
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235 sg.setDisplayText( viewTextMenuItem.isSelected() );
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236 sg.setColourText( colourTextMenuItem.isSelected() );
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241 SequenceGroup sg = viewport.alignment.findGroup( (Sequence) viewport.sel.sequenceAt(0));
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242 if (alignPanel.seqPanel.isNewSelection(sg))
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244 sg = viewport.getAlignment().addGroup();
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245 for (int i = 0; i < viewport.getSelection().size(); i++)
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247 viewport.alignment.removeFromGroup(viewport.alignment.findGroup( (
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248 Sequence) viewport.sel.sequenceAt(i)),
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249 (Sequence) viewport.sel.sequenceAt(
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251 viewport.alignment.addToGroup(sg,
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252 (Sequence) viewport.sel.sequenceAt(i));
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256 sg.setDisplayBoxes(viewBoxesMenuItem.isSelected());
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257 sg.setDisplayText(viewTextMenuItem.isSelected());
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258 sg.setColourText(colourTextMenuItem.isSelected());
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260 alignPanel.RefreshPanels();
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265 public void RefreshPanels()
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268 seqPanel.seqCanvas.paintFlag = true;
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269 idPanel.idCanvas.paintFlag = true;
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270 idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
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271 setScrollValues(av.getStartRes(), av.getStartSeq());
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272 av.getConsensus(true);
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275 if(overviewPanel!=null)
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276 overviewPanel.updateOverviewImage();
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283 public void setScrollValues(int x, int y)
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285 hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();
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286 vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();
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288 if(hextent+x > av.getAlignment().getWidth())
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289 x = av.getAlignment().getWidth()- hextent;
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291 if(vextent+y > av.getAlignment().getHeight())
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292 y = av.getAlignment().getHeight() - vextent;
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300 hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
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301 vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
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307 public void adjustmentValueChanged(AdjustmentEvent evt)
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310 if (evt.getSource() == hscroll)
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312 int x = hscroll.getValue();
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314 av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
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317 if (evt.getSource() == vscroll)
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319 int offy = vscroll.getValue();
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320 av.setStartSeq(offy);
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321 av.setEndSeq(offy + seqPanel.seqCanvas.getHeight()/av.getCharHeight());
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325 if(overviewPanel!=null)
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326 overviewPanel.setBoxPosition();
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328 seqPanel.seqCanvas.paintFlag=true;
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333 public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
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336 pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
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338 int pwidth = (int)pf.getImageableWidth();
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339 int pheight = (int)pf.getImageableHeight();
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340 int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
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342 pg.setColor(Color.white);
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343 pg.fillRect(0,0,pwidth, pheight);
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344 pg.setFont( av.getFont() );
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346 ////////////////////////////////////
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347 /// How many sequences and residues can we fit on a printable page?
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348 int totalRes = (pwidth - idWidth)/av.getCharWidth();
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349 int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
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350 int pagesWide = av.getAlignment().getWidth() / totalRes +1;
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351 int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
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353 if (pi >= pagesWide*pagesHigh)
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354 return Printable.NO_SUCH_PAGE;
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356 /////////////////////////////
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357 /// Only print these sequences and residues on this page
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358 int startRes, endRes, startSeq, endSeq;
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359 startRes = (pi % pagesWide) * totalRes;
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360 endRes = startRes + totalRes-1;
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361 if(endRes>av.getAlignment().getWidth())
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362 endRes = av.getAlignment().getWidth();
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364 startSeq = (pi / pagesWide) * totalSeq;
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365 endSeq = startSeq + totalSeq;
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366 if(endSeq > av.getAlignment().getHeight())
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367 endSeq = av.getAlignment().getHeight();
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372 pg.translate(idWidth,0);
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373 scalePanel.scaleCanvas.drawScale(pg, startRes, endRes, pwidth-idWidth);
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375 pg.translate(-idWidth, 30);
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378 Color currentColor=null;
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379 Color currentTextColor=null;
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380 for(int i=startSeq; i<endSeq; i++)
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382 if (av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
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384 currentColor = Color.gray;
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385 currentTextColor = Color.black;
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389 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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390 currentTextColor = Color.black;
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393 pg.setColor(currentColor);
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394 pg.fillRect(0, jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
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396 av.getCharHeight());
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398 pg.setColor(currentTextColor);
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400 String string = av.getAlignment().getSequenceAt(i).getDisplayId();
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401 pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight
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402 (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
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405 // draw main sequence panel
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406 pg.translate(idWidth,0);
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407 pg.setClip(0,0,pwidth-idWidth, pheight);
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408 seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
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410 return Printable.PAGE_EXISTS;
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