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, 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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53 public void highlightSearchResults(int [] results)
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55 seqPanel.seqCanvas.highlightSearchResults( results );
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57 // do we need to scroll the panel?
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58 if(results!=null && (av.getStartSeq()>results[0]
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59 || av.getEndSeq()<results[0]
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60 || av.getStartRes()>results[1]
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61 || av.getEndRes()<results[2]))
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62 setScrollValues(results[1], results[0]);
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68 public OverviewPanel getOverviewPanel()
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70 return overviewPanel;
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73 public void setOverviewPanel(OverviewPanel op)
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79 public void setGraphPanelVisible(boolean b)
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81 idSpaceFillerPanel.setVisible(b);
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82 scorePanelHolder.setVisible(b);
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85 // bit annoying to call this twice, can you do better?
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89 public void setSecondaryStructureVisible(boolean b)
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91 secondaryPanelHolder.setVisible(b);
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95 public void setWrapAlignment(boolean wrap)
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97 scalePanelHolder.setVisible(!wrap);
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98 scorePanelHolder.setVisible(!wrap);
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100 hscroll.setVisible(!wrap);
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101 idSpaceFillerPanel.setVisible(!wrap);
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102 idSpaceFillerPanel1.setVisible(!wrap);
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106 public void setColourScheme()
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108 ColourSchemeI cs = av.getGlobalColourScheme();
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110 if(av.getConservationSelected())
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113 Alignment al = (Alignment)av.getAlignment();
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114 Conservation c = new Conservation("All",
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115 ResidueProperties.propHash, 3, al.getSequences(), 0,
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119 c.verdict(false, 100);
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120 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
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122 av.setGlobalColourScheme( ccs );
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129 public void RefreshPanels()
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133 seqPanel.seqCanvas.paintFlag = true;
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134 idPanel.idCanvas.paintFlag = true;
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135 idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
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136 setScrollValues(av.getStartRes(), av.getStartSeq());
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137 av.getConsensus(true);
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138 if(overviewPanel!=null)
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139 overviewPanel.updateOverviewImage();
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148 public void setScrollValues(int x, int y)
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150 hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();
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151 vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();
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153 if(hextent+x > av.getAlignment().getWidth())
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154 x = av.getAlignment().getWidth()- hextent;
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156 if(vextent+y > av.getAlignment().getHeight())
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157 y = av.getAlignment().getHeight() - vextent;
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165 hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
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166 vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
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174 public void adjustmentValueChanged(AdjustmentEvent evt)
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177 if (evt.getSource() == hscroll)
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179 int x = hscroll.getValue();
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181 av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
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184 if (evt.getSource() == vscroll)
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186 int offy = vscroll.getValue();
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187 av.setStartSeq(offy);
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188 av.setEndSeq(offy + seqPanel.seqCanvas.getHeight()/av.getCharHeight());
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192 if(overviewPanel!=null)
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193 overviewPanel.setBoxPosition();
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195 seqPanel.seqCanvas.paintFlag=true;
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200 public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
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203 pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
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205 int pwidth = (int)pf.getImageableWidth();
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206 int pheight = (int)pf.getImageableHeight();
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207 int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
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209 pg.setColor(Color.white);
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210 pg.fillRect(0,0,pwidth, pheight);
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211 pg.setFont( av.getFont() );
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213 ////////////////////////////////////
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214 /// How many sequences and residues can we fit on a printable page?
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215 int totalRes = (pwidth - idWidth)/av.getCharWidth();
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216 int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
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217 int pagesWide = av.getAlignment().getWidth() / totalRes +1;
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218 int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
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220 if (pi >= pagesWide*pagesHigh)
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221 return Printable.NO_SUCH_PAGE;
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223 /////////////////////////////
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224 /// Only print these sequences and residues on this page
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225 int startRes, endRes, startSeq, endSeq;
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226 startRes = (pi % pagesWide) * totalRes;
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227 endRes = startRes + totalRes-1;
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228 if(endRes>av.getAlignment().getWidth())
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229 endRes = av.getAlignment().getWidth();
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231 startSeq = (pi / pagesWide) * totalSeq;
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232 endSeq = startSeq + totalSeq;
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233 if(endSeq > av.getAlignment().getHeight())
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234 endSeq = av.getAlignment().getHeight();
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239 pg.translate(idWidth,0);
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240 scalePanel.scaleCanvas.drawScale(pg, startRes, endRes, pwidth-idWidth);
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242 pg.translate(-idWidth, 30);
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245 Color currentColor=null;
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246 Color currentTextColor=null;
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247 for(int i=startSeq; i<endSeq; i++)
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249 if (av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
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251 currentColor = Color.gray;
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252 currentTextColor = Color.black;
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256 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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257 currentTextColor = Color.black;
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260 pg.setColor(currentColor);
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261 pg.fillRect(0, jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
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263 av.getCharHeight());
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265 pg.setColor(currentTextColor);
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267 String string = av.getAlignment().getSequenceAt(i).getDisplayId();
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268 pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight
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269 (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
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272 // draw main sequence panel
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273 pg.translate(idWidth,0);
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274 pg.setClip(0,0,pwidth-idWidth, pheight);
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275 seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
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277 return Printable.PAGE_EXISTS;
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