2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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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21 import jalview.datamodel.*;
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24 import java.awt.image.*;
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26 import javax.swing.*;
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33 * @version $Revision$
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35 public class IdCanvas extends JPanel
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37 protected AlignViewport av;
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38 protected boolean showScores = true;
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39 protected int maxIdLength = -1;
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40 protected String maxIdStr = null;
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41 BufferedImage image;
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44 boolean fastPaint = false;
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45 java.util.Vector searchResults;
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47 AnnotationLabels labels = null;
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52 * Creates a new IdCanvas object.
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54 * @param av DOCUMENT ME!
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56 public IdCanvas(AlignViewport av)
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58 setLayout(new BorderLayout());
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60 PaintRefresher.Register(this, av.getSequenceSetId());
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66 * @param gg DOCUMENT ME!
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67 * @param s DOCUMENT ME!
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68 * @param i DOCUMENT ME!
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69 * @param starty DOCUMENT ME!
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70 * @param ypos DOCUMENT ME!
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72 public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty, int ypos)
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75 int panelWidth = getWidth();
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76 int charHeight = av.charHeight;
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78 if ((searchResults != null) && searchResults.contains(s))
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80 gg.setColor(Color.black);
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81 gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
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83 gg.setColor(Color.white);
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85 else if ((av.getSelectionGroup() != null) &&
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86 av.getSelectionGroup().getSequences(null).contains(s))
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88 gg.setColor(Color.lightGray);
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89 gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
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91 gg.setColor(Color.white);
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95 gg.setColor(av.getSequenceColour(s));
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96 gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
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98 gg.setColor(Color.black);
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101 if (av.rightAlignIds)
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103 xPos = panelWidth - fm.stringWidth(
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104 s.getDisplayId(av.getShowJVSuffix())
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108 gg.drawString( s.getDisplayId(av.getShowJVSuffix()),
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109 xPos, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
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111 if (av.hasHiddenRows && av.showHiddenMarkers)
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112 drawMarker(i, starty, ypos);
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120 * @param vertical DOCUMENT ME!
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122 public void fastPaint(int vertical)
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131 gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);
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133 int ss = av.startSeq;
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134 int es = av.endSeq;
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137 if (vertical > 0) // scroll down
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139 ss = es - vertical;
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141 if (ss < av.startSeq)
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142 { // ie scrolling too fast, more than a page at a time
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147 transY = imgHeight - (vertical * av.charHeight);
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150 else if (vertical < 0)
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152 es = ss - vertical;
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154 if (es > av.endSeq)
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160 gg.translate(0, transY);
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164 gg.translate(0, -transY);
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173 * @param g DOCUMENT ME!
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175 public void paintComponent(Graphics g)
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177 g.setColor(Color.white);
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178 g.fillRect(0, 0, getWidth(), getHeight());
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183 g.drawImage(image, 0, 0, this);
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188 int oldHeight = imgHeight;
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190 imgHeight = getHeight();
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191 imgHeight -= (imgHeight % av.charHeight);
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198 if(oldHeight!=imgHeight || image.getWidth(this)!=getWidth())
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200 image = new BufferedImage(getWidth(), imgHeight,
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201 BufferedImage.TYPE_INT_RGB);
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204 gg = (Graphics2D) image.getGraphics();
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206 //Fill in the background
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207 gg.setColor(Color.white);
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208 gg.fillRect(0, 0, getWidth(), imgHeight);
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210 drawIds(av.getStartSeq(), av.endSeq);
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212 g.drawImage(image, 0, 0, this);
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218 * @param starty DOCUMENT ME!
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219 * @param endy DOCUMENT ME!
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221 void drawIds(int starty, int endy)
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223 if(av.seqNameItalics)
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224 idfont = new Font(av.getFont().getName(), Font.ITALIC,
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225 av.getFont().getSize());
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227 idfont = av.getFont();
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229 gg.setFont(idfont);
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230 fm = gg.getFontMetrics();
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233 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
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234 RenderingHints.VALUE_ANTIALIAS_ON);
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236 Color currentColor = Color.white;
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237 Color currentTextColor = Color.black;
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239 if (av.getWrapAlignment())
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241 int maxwidth = av.alignment.getWidth();
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242 int alheight = av.alignment.getHeight();
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244 if (av.hasHiddenColumns)
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245 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
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247 int annotationHeight = 0;
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250 if(av.showAnnotation)
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253 ap = new AnnotationPanel(av);
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255 annotationHeight = ap.adjustPanelHeight();
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256 if (labels == null)
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257 labels = new AnnotationLabels(av);
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260 int hgap = av.charHeight;
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261 if (av.scaleAboveWrapped)
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262 hgap += av.charHeight;
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264 int cHeight = alheight * av.charHeight
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266 + annotationHeight;
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268 int rowSize = av.getEndRes() - av.getStartRes();
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271 // Draw the rest of the panels
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272 for (int ypos = hgap, row = av.startRes;
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273 (ypos <= getHeight()) && (row < maxwidth);
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274 ypos += cHeight, row += rowSize)
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276 for (int i = starty; i < alheight; i++)
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278 SequenceI s = av.alignment.getSequenceAt(i);
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279 if (av.hasHiddenRows)
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284 gg.setFont(idfont);
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286 drawIdString(gg, s, i, 0, ypos);
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289 if(labels!=null && av.showAnnotation)
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291 gg.translate(0, ypos+(alheight * av.charHeight));
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292 labels.drawComponent(gg, getWidth());
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293 gg.translate(0, -ypos-(alheight * av.charHeight));
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299 //No need to hang on to labels if we're not wrapped
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302 //Now draw the id strings
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303 int panelWidth = getWidth();
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306 SequenceI sequence;
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307 //Now draw the id strings
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308 for (int i = starty; i < endy; i++)
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310 sequence = av.alignment.getSequenceAt(i);
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315 if (av.hasHiddenRows)
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317 setHiddenFont(sequence);
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320 // Selected sequence colours
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321 if ( (searchResults != null) &&
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322 searchResults.contains(sequence))
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324 currentColor = Color.black;
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325 currentTextColor = Color.white;
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327 else if ( (av.getSelectionGroup() != null) &&
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328 av.getSelectionGroup().getSequences(null).contains(
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331 currentColor = Color.lightGray;
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332 currentTextColor = Color.black;
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336 currentColor = av.getSequenceColour(sequence);
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337 currentTextColor = Color.black;
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340 gg.setColor(currentColor);
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342 gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),
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345 gg.setColor(currentTextColor);
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347 String string = sequence.getDisplayId( av.getShowJVSuffix());
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350 if(av.rightAlignIds)
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352 xPos = panelWidth - fm.stringWidth(string) - 4;
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355 gg.drawString(string, xPos,
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356 (((i - starty) * av.charHeight) + av.charHeight) -
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357 (av.charHeight / 5));
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359 if(av.hasHiddenRows && av.showHiddenMarkers)
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360 drawMarker(i, starty, 0);
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367 void drawMarker(int i, int starty, int yoffset)
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370 SequenceI [] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
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371 //Use this method here instead of calling hiddenSeq adjust
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373 int hSize = hseqs.length;
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375 int hiddenIndex = i;
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376 int lastIndex = i - 1;
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377 int nextIndex = i + 1;
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379 for(int j=0; j<hSize; j++)
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381 if (hseqs[j] != null)
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383 if(j-1<hiddenIndex)
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392 boolean below = (hiddenIndex > lastIndex + 1);
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393 boolean above = (nextIndex > hiddenIndex+1);
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396 gg.setColor(Color.blue);
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399 gg.fillPolygon(new int[]
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400 {getWidth()- av.charHeight,
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401 getWidth()- av.charHeight,
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405 (i - starty) * av.charHeight +yoffset,
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406 (i - starty) * av.charHeight +yoffset+ av.charHeight / 4,
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407 (i - starty) * av.charHeight+yoffset
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412 gg.fillPolygon(new int[]
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413 {getWidth()- av.charHeight,
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414 getWidth()- av.charHeight,
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418 (i - starty+1) * av.charHeight +yoffset,
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419 (i - starty+1) * av.charHeight +yoffset- av.charHeight / 4,
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420 (i - starty+1) * av.charHeight +yoffset
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426 void setHiddenFont(SequenceI seq)
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428 Font bold = new Font(av.getFont().getName(), Font.BOLD,
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429 av.getFont().getSize());
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432 if (av.hiddenRepSequences!=null &&
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433 av.hiddenRepSequences.containsKey(seq))
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436 gg.setFont(idfont);
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442 * @param found DOCUMENT ME!
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444 public void setHighlighted(java.util.Vector found)
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446 searchResults = found;
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