2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 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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25 import javax.swing.*;
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32 * @version $Revision$
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34 public class OverviewPanel extends JPanel implements Runnable
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36 BufferedImage miniMe;
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42 int sequencesHeight;
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43 int graphHeight = 20;
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48 boolean resizing = false;
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50 // Can set different properties in this seqCanvas than
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51 // main visible SeqCanvas
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52 SequenceRenderer sr;
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56 * Creates a new OverviewPanel object.
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58 * @param ap DOCUMENT ME!
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60 public OverviewPanel(AlignmentPanel ap)
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66 sr = new SequenceRenderer(av);
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67 sr.renderGaps( false );
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68 sr.forOverview = true;
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69 fr = new FeatureRenderer(av);
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73 // scale the initial size of overviewpanel to shape of alignment
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74 float initialScale = (float) av.alignment.getWidth() / (float) av.alignment.getHeight();
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76 if(av.conservation==null)
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80 if (av.alignment.getWidth() > av.alignment.getHeight())
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84 sequencesHeight = (int) (400f / initialScale);
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85 if(sequencesHeight<40)
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86 sequencesHeight = 40;
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91 width = (int) (400f * initialScale);
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92 sequencesHeight = 300;
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100 addComponentListener(new ComponentAdapter()
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102 public void componentResized(ComponentEvent evt)
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104 if ((getWidth() != width) ||
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105 (getHeight() != (sequencesHeight + graphHeight)))
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107 updateOverviewImage();
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112 addMouseMotionListener(new MouseMotionAdapter()
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114 public void mouseDragged(MouseEvent evt)
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116 if(!av.wrapAlignment)
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117 doMouseDragged(evt);
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121 addMouseListener(new MouseAdapter()
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123 public void mousePressed(MouseEvent evt)
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125 if(!av.wrapAlignment)
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126 doMousePressed(evt);
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129 public void mouseReleased(MouseEvent evt)
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131 if(!av.wrapAlignment)
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132 doMouseReleased(evt);
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136 updateOverviewImage();
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142 * @param evt DOCUMENT ME!
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144 public void doMousePressed(MouseEvent evt)
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156 * @param evt DOCUMENT ME!
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158 public void doMouseReleased(MouseEvent evt)
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164 if(av.hasHiddenColumns)
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166 int col = (int) ( boxX / scalew / av.getCharWidth());
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168 if(av.getColumnSelection().isVisible(col))
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170 ap.setScrollValues(
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171 av.getColumnSelection().findColumnPosition(col),
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172 (int) (boxY / scaleh / av.getCharHeight()));
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175 System.out.println(col +" not visible");
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178 ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
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179 (int) (boxY / scaleh / av.getCharHeight()));
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185 * @param evt DOCUMENT ME!
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187 public void doMouseDragged(MouseEvent evt)
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193 if(av.hasHiddenColumns)
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195 int col = (int) ( boxX / scalew / av.getCharWidth());
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197 if(!av.getColumnSelection().isVisible(col))
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202 ap.setScrollValues(
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203 av.getColumnSelection().findColumnPosition( col ),
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204 (int) (boxY / scaleh / av.getCharHeight()));
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207 ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
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208 (int) (boxY / scaleh / av.getCharHeight()));
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222 if (boxY > (sequencesHeight - boxHeight))
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224 boxY = sequencesHeight - boxHeight + 1;
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232 if (boxX > (width - boxWidth))
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234 if(av.hasHiddenColumns)
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236 //Try smallest possible box
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237 boxWidth = (int) ( (av.endRes - av.startRes + 1) *
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238 av.getCharWidth() * scalew);
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241 boxX = width - boxWidth;
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248 public void updateOverviewImage()
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252 resizeAgain = true;
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258 if ( (getWidth() > 0) && (getHeight() > 0))
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260 width = getWidth();
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261 sequencesHeight = getHeight() - graphHeight;
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264 setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
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265 // setBoxPosition();
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267 Thread thread = new Thread(this);
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272 // This is set true if the user resizes whilst
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273 // the overview is being calculated
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274 boolean resizeAgain = false;
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283 if (av.showSequenceFeatures)
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285 fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
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286 fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
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287 fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;
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288 fr.sequenceFeatures = ap.seqPanel.seqCanvas.getFeatureRenderer().sequenceFeatures;
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291 int alwidth = av.alignment.getWidth();
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292 int alheight = av.alignment.getHeight()
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293 +av.alignment.getHiddenSequences().getSize();
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295 setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
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297 int fullsizeWidth = alwidth * av.getCharWidth();
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298 int fullsizeHeight = alheight * av.getCharHeight();
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300 scalew = (float) width / (float) fullsizeWidth;
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301 scaleh = (float) sequencesHeight / (float) fullsizeHeight;
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303 miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
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304 BufferedImage.TYPE_INT_RGB);
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307 Graphics mg = miniMe.getGraphics();
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308 mg.setColor(Color.orange);
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309 mg.fillRect(0,0,width, miniMe.getHeight());
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311 float sampleCol = (float) alwidth / (float) width;
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312 float sampleRow = (float) alheight / (float) sequencesHeight;
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314 int lastcol=-1, lastrow=-1;
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315 int color = Color.white.getRGB();
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317 jalview.datamodel.SequenceI seq;
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318 boolean hiddenRow = false;
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319 for (row = 0; row < sequencesHeight; row++)
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321 if((int)(row*sampleRow)==lastrow)
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323 //No need to recalculate the colours,
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324 //Just copy from the row above
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325 for (col = 0; col < width; col++)
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327 miniMe.setRGB(col, row, miniMe.getRGB(col, row-1));
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332 lastrow = (int)(row*sampleRow);
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335 if (av.hasHiddenRows)
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337 seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
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342 av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(lastrow);
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345 seq = av.alignment.getSequenceAt(index);
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353 seq = av.alignment.getSequenceAt(lastrow);
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357 System.out.println(lastrow+" null");
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361 for (col = 0; col < width; col++)
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363 if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)
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365 miniMe.setRGB(col,row,color);
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370 lastcol = (int)(col*sampleCol);
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372 if (seq.getLength() > lastcol)
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374 color = sr.getResidueBoxColour(
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375 seq, lastcol).getRGB();
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377 if (av.showSequenceFeatures)
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378 color = fr.findFeatureColour(color, lastrow, lastcol);
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382 color = -1; //White
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386 (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
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388 color = new Color(color).darker().darker().getRGB();
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392 miniMe.setRGB(col,row,color);
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398 if (av.conservation != null)
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400 for (col = 0; col < width; col++)
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402 lastcol = (int) (col * sampleCol);
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404 mg.translate(col, sequencesHeight);
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405 ap.annotationPanel.drawGraph(mg, av.conservation,
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406 (int) (sampleCol) + 1,
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408 (int) (col * sampleCol),
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409 (int) (col * sampleCol) + 1);
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410 mg.translate( -col, -sequencesHeight);
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422 resizeAgain = false;
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423 updateOverviewImage();
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430 public void setBoxPosition()
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432 int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
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433 int fullsizeHeight = (av.alignment.getHeight()
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434 +av.alignment.getHiddenSequences().getSize()) * av.getCharHeight();
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436 int startRes = av.getStartRes();
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437 int endRes = av.getEndRes();
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439 if(av.hasHiddenColumns)
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441 startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
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442 endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
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446 scalew = (float) width / (float) fullsizeWidth;
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447 scaleh = (float) sequencesHeight / (float) fullsizeHeight;
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449 boxX = (int) (startRes * av.getCharWidth() * scalew);
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450 boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);
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452 if(av.hasHiddenColumns)
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453 boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
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455 boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
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457 boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) -
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465 * @param g DOCUMENT ME!
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467 public void paintComponent(Graphics g)
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469 if (miniMe != null && !resizing)
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471 g.drawImage(miniMe, 0, 0, this);
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475 g.setColor(Color.white);
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476 g.fillRect(0, 0, getWidth(), getHeight());
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477 g.setColor(Color.black);
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478 g.setFont(new Font("Verdana", Font.BOLD, 15));
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479 g.drawString("Recalculating", 5, sequencesHeight / 2);
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480 g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);
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484 g.setColor(Color.red);
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485 g.drawRect(boxX, boxY, boxWidth, boxHeight);
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486 g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
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