2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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22 import java.awt.event.*;
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23 import java.awt.image.*;
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24 import javax.swing.*;
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30 * @version $Revision$
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32 public class OverviewPanel
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33 extends JPanel implements Runnable
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35 BufferedImage miniMe;
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41 int sequencesHeight;
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42 int graphHeight = 20;
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47 boolean resizing = false;
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49 // Can set different properties in this seqCanvas than
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50 // main visible SeqCanvas
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51 SequenceRenderer sr;
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55 * Creates a new OverviewPanel object.
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57 * @param ap DOCUMENT ME!
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59 public OverviewPanel(AlignmentPanel ap)
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65 sr = new SequenceRenderer(av);
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66 sr.renderGaps = false;
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67 sr.forOverview = true;
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68 fr = new FeatureRenderer(ap);
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70 // scale the initial size of overviewpanel to shape of alignment
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71 float initialScale = (float) av.alignment.getWidth() /
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72 (float) av.alignment.getHeight();
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74 if (av.conservation == null)
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79 if (av.alignment.getWidth() > av.alignment.getHeight())
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83 sequencesHeight = (int) (400f / initialScale);
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84 if (sequencesHeight < 40)
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86 sequencesHeight = 40;
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92 width = (int) (400f * initialScale);
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93 sequencesHeight = 300;
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101 addComponentListener(new ComponentAdapter()
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103 public void componentResized(ComponentEvent evt)
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105 if ( (getWidth() != width) ||
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106 (getHeight() != (sequencesHeight + graphHeight)))
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108 updateOverviewImage();
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113 addMouseMotionListener(new MouseMotionAdapter()
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115 public void mouseDragged(MouseEvent evt)
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117 if (!av.wrapAlignment)
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126 addMouseListener(new MouseAdapter()
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128 public void mousePressed(MouseEvent evt)
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130 if (!av.wrapAlignment)
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139 updateOverviewImage();
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152 if (boxY > (sequencesHeight - boxHeight))
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154 boxY = sequencesHeight - boxHeight + 1;
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162 if (boxX > (width - boxWidth))
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164 if (av.hasHiddenColumns)
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166 //Try smallest possible box
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167 boxWidth = (int) ( (av.endRes - av.startRes + 1) *
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168 av.getCharWidth() * scalew);
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170 boxX = width - boxWidth;
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173 int col = (int) (boxX / scalew / av.getCharWidth());
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174 int row = (int) (boxY / scaleh / av.getCharHeight());
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176 if (av.hasHiddenColumns)
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178 if (!av.getColumnSelection().isVisible(col))
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183 col = av.getColumnSelection().findColumnPosition(col);
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186 if (av.hasHiddenRows)
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188 row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);
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191 ap.setScrollValues(col, row);
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198 public void updateOverviewImage()
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202 resizeAgain = true;
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208 if ( (getWidth() > 0) && (getHeight() > 0))
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210 width = getWidth();
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211 sequencesHeight = getHeight() - graphHeight;
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214 setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
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216 Thread thread = new Thread(this);
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221 // This is set true if the user resizes whilst
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222 // the overview is being calculated
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223 boolean resizeAgain = false;
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232 if (av.showSequenceFeatures)
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234 fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
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237 int alwidth = av.alignment.getWidth();
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238 int alheight = av.alignment.getHeight()
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239 + av.alignment.getHiddenSequences().getSize();
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241 setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
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243 int fullsizeWidth = alwidth * av.getCharWidth();
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244 int fullsizeHeight = alheight * av.getCharHeight();
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246 scalew = (float) width / (float) fullsizeWidth;
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247 scaleh = (float) sequencesHeight / (float) fullsizeHeight;
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249 miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
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250 BufferedImage.TYPE_INT_RGB);
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252 Graphics mg = miniMe.getGraphics();
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253 mg.setColor(Color.orange);
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254 mg.fillRect(0, 0, width, miniMe.getHeight());
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256 float sampleCol = (float) alwidth / (float) width;
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257 float sampleRow = (float) alheight / (float) sequencesHeight;
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259 int lastcol = -1, lastrow = -1;
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260 int color = Color.white.getRGB();
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262 jalview.datamodel.SequenceI seq;
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263 boolean hiddenRow = false;
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264 for (row = 0; row < sequencesHeight; row++)
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266 if ( (int) (row * sampleRow) == lastrow)
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268 //No need to recalculate the colours,
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269 //Just copy from the row above
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270 for (col = 0; col < width; col++)
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272 miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));
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277 lastrow = (int) (row * sampleRow);
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280 if (av.hasHiddenRows)
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282 seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
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286 av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
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289 seq = av.alignment.getSequenceAt(index);
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298 seq = av.alignment.getSequenceAt(lastrow);
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303 System.out.println(lastrow + " null");
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307 for (col = 0; col < width; col++)
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309 if ( (int) (col * sampleCol) == lastcol &&
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310 (int) (row * sampleRow) == lastrow)
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312 miniMe.setRGB(col, row, color);
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316 lastcol = (int) (col * sampleCol);
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318 if (seq.getLength() > lastcol)
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320 color = sr.getResidueBoxColour(
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321 seq, lastcol).getRGB();
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323 if (av.showSequenceFeatures)
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325 color = fr.findFeatureColour(color, seq, lastcol);
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330 color = -1; //White
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334 (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
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336 color = new Color(color).darker().darker().getRGB();
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339 miniMe.setRGB(col, row, color);
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344 if (av.conservation != null)
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346 for (col = 0; col < width; col++)
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348 lastcol = (int) (col * sampleCol);
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350 mg.translate(col, sequencesHeight);
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351 ap.annotationPanel.drawGraph(mg, av.conservation,
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352 (int) (sampleCol) + 1,
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354 (int) (col * sampleCol),
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355 (int) (col * sampleCol) + 1);
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356 mg.translate( -col, -sequencesHeight);
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368 resizeAgain = false;
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369 updateOverviewImage();
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376 public void setBoxPosition()
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378 int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
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379 int fullsizeHeight = (av.alignment.getHeight()
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380 + av.alignment.getHiddenSequences().getSize()) *
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381 av.getCharHeight();
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383 int startRes = av.getStartRes();
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384 int endRes = av.getEndRes();
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386 if (av.hasHiddenColumns)
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388 startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
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389 endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
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392 int startSeq = av.startSeq;
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393 int endSeq = av.endSeq;
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395 if (av.hasHiddenRows)
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398 av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);
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401 av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);
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405 scalew = (float) width / (float) fullsizeWidth;
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406 scaleh = (float) sequencesHeight / (float) fullsizeHeight;
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408 boxX = (int) (startRes * av.getCharWidth() * scalew);
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409 boxY = (int) (startSeq * av.getCharHeight() * scaleh);
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411 if (av.hasHiddenColumns)
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413 boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
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417 boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
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420 boxHeight = (int) ( (endSeq - startSeq) * av.getCharHeight() * scaleh);
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428 * @param g DOCUMENT ME!
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430 public void paintComponent(Graphics g)
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434 g.setColor(Color.white);
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435 g.fillRect(0,0,getWidth(),getHeight());
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437 else if (miniMe != null)
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439 g.drawImage(miniMe, 0, 0, this);
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442 g.setColor(Color.red);
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443 g.drawRect(boxX, boxY, boxWidth, boxHeight);
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444 g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
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