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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23 import jalview.datamodel.*;
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24 import jalview.schemes.*;
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30 * @version $Revision$
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32 public class SequenceRenderer
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36 boolean renderGaps = true;
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37 SequenceGroup currentSequenceGroup = null;
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38 SequenceGroup[] allGroups = null;
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41 boolean monospacedFont;
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42 boolean forOverview = false;
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45 * Creates a new SequenceRenderer object.
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47 * @param av DOCUMENT ME!
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49 public SequenceRenderer(AlignViewport av)
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57 * @param b DOCUMENT ME!
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59 public void prepare(Graphics g, boolean renderGaps)
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62 fm = g.getFontMetrics();
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64 // If EPS graphics, stringWidth will be a double, not an int
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65 double dwidth = fm.getStringBounds("M", g).getWidth();
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68 (dwidth == fm.getStringBounds("|", g).getWidth()
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69 && (float) av.charWidth == dwidth);
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71 this.renderGaps = renderGaps;
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74 public Color getResidueBoxColour(SequenceI seq, int i)
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76 allGroups = av.alignment.findAllGroups(seq);
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78 if (inCurrentSequenceGroup(i))
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80 if (currentSequenceGroup.getDisplayBoxes())
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82 getBoxColour(currentSequenceGroup.cs, seq, i);
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85 else if (av.getShowBoxes())
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87 getBoxColour(av.globalColourScheme, seq, i);
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90 return resBoxColour;
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96 * @param cs DOCUMENT ME!
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97 * @param seq DOCUMENT ME!
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98 * @param i DOCUMENT ME!
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100 void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
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104 resBoxColour = cs.findColour(seq.getCharAt(i), i);
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106 else if (forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
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108 resBoxColour = Color.lightGray;
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112 resBoxColour = Color.white;
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119 * @param g DOCUMENT ME!
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120 * @param seq DOCUMENT ME!
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121 * @param sg DOCUMENT ME!
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122 * @param start DOCUMENT ME!
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123 * @param end DOCUMENT ME!
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124 * @param x1 DOCUMENT ME!
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125 * @param y1 DOCUMENT ME!
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126 * @param width DOCUMENT ME!
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127 * @param height DOCUMENT ME!
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129 public void drawSequence(SequenceI seq, SequenceGroup[] sg,
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130 int start, int end, int y1)
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134 drawBoxes(seq, start, end, y1);
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136 if (av.validCharWidth)
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138 drawText(seq, start, end, y1);
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145 * @param seq DOCUMENT ME!
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146 * @param start DOCUMENT ME!
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147 * @param end DOCUMENT ME!
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148 * @param x1 DOCUMENT ME!
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149 * @param y1 DOCUMENT ME!
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150 * @param width DOCUMENT ME!
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151 * @param height DOCUMENT ME!
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153 public synchronized void drawBoxes(SequenceI seq, int start, int end, int y1)
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156 int length = seq.getLength();
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159 int curWidth = av.charWidth;
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161 Color tempColour = null;
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165 resBoxColour = Color.white;
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169 if (inCurrentSequenceGroup(i))
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171 if (currentSequenceGroup.getDisplayBoxes())
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173 getBoxColour(currentSequenceGroup.cs, seq, i);
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176 else if (av.getShowBoxes())
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178 getBoxColour(av.globalColourScheme, seq, i);
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183 if (resBoxColour != tempColour)
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185 if (tempColour != null)
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187 graphics.fillRect(av.charWidth * (curStart - start), y1,
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188 curWidth, av.charHeight);
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191 graphics.setColor(resBoxColour);
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194 curWidth = av.charWidth;
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195 tempColour = resBoxColour;
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199 curWidth += av.charWidth;
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205 graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
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213 * @param seq DOCUMENT ME!
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214 * @param start DOCUMENT ME!
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215 * @param end DOCUMENT ME!
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216 * @param x1 DOCUMENT ME!
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217 * @param y1 DOCUMENT ME!
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218 * @param width DOCUMENT ME!
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219 * @param height DOCUMENT ME!
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221 public void drawText(SequenceI seq, int start, int end, int y1)
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223 y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
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224 int charOffset = 0;
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227 if (end + 1 >= seq.getLength())
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229 end = seq.getLength() - 1;
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231 graphics.setColor(av.textColour);
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235 && allGroups.length == 0
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236 && !av.getColourText()
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237 && av.thresholdTextColour == 0)
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241 graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
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245 char gap = av.getGapCharacter();
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246 graphics.drawString(seq.getSequenceAsString(start, end + 1).replace(gap,
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252 boolean getboxColour = false;
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253 for (int i = start; i <= end; i++)
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255 graphics.setColor(av.textColour);
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256 getboxColour = false;
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257 s = seq.getCharAt(i);
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258 if (!renderGaps && jalview.util.Comparison.isGap(s))
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263 if (inCurrentSequenceGroup(i))
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265 if (!currentSequenceGroup.getDisplayText())
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270 if (currentSequenceGroup.thresholdTextColour > 0
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271 || currentSequenceGroup.getColourText())
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273 getboxColour = true;
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274 getBoxColour(currentSequenceGroup.cs, seq, i);
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276 if (currentSequenceGroup.getColourText())
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278 graphics.setColor(resBoxColour.darker());
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281 if (currentSequenceGroup.thresholdTextColour > 0)
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283 if (resBoxColour.getRed() +
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284 resBoxColour.getBlue() +
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285 resBoxColour.getGreen() <
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286 currentSequenceGroup.thresholdTextColour)
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288 graphics.setColor(currentSequenceGroup.textColour2);
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294 graphics.setColor(currentSequenceGroup.textColour);
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300 if (!av.getShowText())
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305 if (av.getColourText())
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307 getboxColour = true;
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308 getBoxColour(av.globalColourScheme, seq, i);
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310 if (av.getShowBoxes())
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312 graphics.setColor(resBoxColour.darker());
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316 graphics.setColor(resBoxColour);
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320 if (av.thresholdTextColour > 0)
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324 getBoxColour(av.globalColourScheme, seq, i);
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327 if (resBoxColour.getRed() +
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328 resBoxColour.getBlue() +
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329 resBoxColour.getGreen() < av.thresholdTextColour)
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331 graphics.setColor(av.textColour2);
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337 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
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338 graphics.drawString(String.valueOf(s),
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339 charOffset + av.charWidth * (i - start),
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349 * @param res DOCUMENT ME!
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351 * @return DOCUMENT ME!
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353 boolean inCurrentSequenceGroup(int res)
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355 if (allGroups == null)
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360 for (int i = 0; i < allGroups.length; i++)
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362 if ( (allGroups[i].getStartRes() <= res) &&
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363 (allGroups[i].getEndRes() >= res))
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365 currentSequenceGroup = allGroups[i];
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377 * @param seq DOCUMENT ME!
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378 * @param start DOCUMENT ME!
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379 * @param end DOCUMENT ME!
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380 * @param x1 DOCUMENT ME!
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381 * @param y1 DOCUMENT ME!
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382 * @param width DOCUMENT ME!
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383 * @param height DOCUMENT ME!
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385 public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
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388 int pady = av.charHeight / 5;
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389 int charOffset = 0;
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390 graphics.setColor(Color.BLACK);
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391 graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
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392 graphics.setColor(Color.white);
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396 // Need to find the sequence position here.
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397 if (av.validCharWidth)
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399 for (int i = start; i <= end; i++)
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401 if (i < seq.getLength())
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403 s = seq.getCharAt(i);
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406 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
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407 graphics.drawString(String.valueOf(s),
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408 charOffset + x1 + (av.charWidth * (i - start)),
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409 (y1 + av.charHeight) - pady);
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414 public void drawCursor(SequenceI seq, int res, int x1, int y1)
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416 int pady = av.charHeight / 5;
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417 int charOffset = 0;
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418 graphics.setColor(Color.black);
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419 graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
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421 if (av.validCharWidth)
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423 graphics.setColor(Color.white);
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425 char s = seq.getCharAt(res);
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427 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
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428 graphics.drawString(String.valueOf(s),
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430 (y1 + av.charHeight) - pady);
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