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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21 import jalview.datamodel.*;
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23 import jalview.schemes.*;
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31 * @version $Revision$
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33 public class SequenceRenderer
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37 boolean renderGaps = true;
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38 SequenceGroup currentSequenceGroup = null;
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39 SequenceGroup[] allGroups = null;
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42 boolean monospacedFont;
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43 boolean forOverview = false;
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46 * Creates a new SequenceRenderer object.
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48 * @param av DOCUMENT ME!
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50 public SequenceRenderer(AlignViewport av)
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58 * @param b DOCUMENT ME!
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60 public void prepare(Graphics g, boolean renderGaps)
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63 fm = g.getFontMetrics();
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64 monospacedFont = fm.getStringBounds("M",g).getWidth()==fm.getStringBounds("|",g).getWidth();
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65 this.renderGaps = renderGaps;
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69 public Color getResidueBoxColour(SequenceI seq, int i)
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71 allGroups = av.alignment.findAllGroups(seq);
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73 if (inCurrentSequenceGroup(i))
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75 if (currentSequenceGroup.getDisplayBoxes())
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77 getBoxColour(currentSequenceGroup.cs, seq, i);
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80 else if (av.getShowBoxes())
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82 getBoxColour(av.globalColourScheme, seq, i);
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85 return resBoxColour;
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92 * @param cs DOCUMENT ME!
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93 * @param seq DOCUMENT ME!
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94 * @param i DOCUMENT ME!
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96 void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
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100 resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
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102 else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
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104 resBoxColour = Color.lightGray;
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108 resBoxColour = Color.white;
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115 * @param g DOCUMENT ME!
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116 * @param seq DOCUMENT ME!
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117 * @param sg DOCUMENT ME!
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118 * @param start DOCUMENT ME!
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119 * @param end DOCUMENT ME!
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120 * @param x1 DOCUMENT ME!
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121 * @param y1 DOCUMENT ME!
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122 * @param width DOCUMENT ME!
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123 * @param height DOCUMENT ME!
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125 public void drawSequence(SequenceI seq, SequenceGroup[] sg,
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126 int start, int end, int y1)
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130 drawBoxes(seq, start, end, y1);
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132 drawText(seq, start, end, y1);
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138 * @param seq DOCUMENT ME!
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139 * @param start DOCUMENT ME!
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140 * @param end DOCUMENT ME!
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141 * @param x1 DOCUMENT ME!
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142 * @param y1 DOCUMENT ME!
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143 * @param width DOCUMENT ME!
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144 * @param height DOCUMENT ME!
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146 public synchronized void drawBoxes(SequenceI seq, int start, int end, int y1)
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149 int length = seq.getLength();
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152 int curWidth = av.charWidth;
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154 Color tempColour = null;
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158 resBoxColour = Color.white;
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162 if (inCurrentSequenceGroup(i))
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164 if (currentSequenceGroup.getDisplayBoxes())
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166 getBoxColour(currentSequenceGroup.cs, seq, i);
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169 else if (av.getShowBoxes())
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171 getBoxColour(av.globalColourScheme, seq, i);
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176 if (resBoxColour != tempColour)
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178 if (tempColour != null)
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180 graphics.fillRect( av.charWidth * (curStart - start), y1,
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181 curWidth, av.charHeight);
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184 graphics.setColor(resBoxColour);
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187 curWidth = av.charWidth;
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188 tempColour = resBoxColour;
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192 curWidth += av.charWidth;
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198 graphics.fillRect( av.charWidth * (curStart - start), y1, curWidth,
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206 * @param seq DOCUMENT ME!
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207 * @param start DOCUMENT ME!
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208 * @param end DOCUMENT ME!
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209 * @param x1 DOCUMENT ME!
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210 * @param y1 DOCUMENT ME!
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211 * @param width DOCUMENT ME!
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212 * @param height DOCUMENT ME!
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214 public void drawText(SequenceI seq, int start, int end, int y1)
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216 y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
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217 int charOffset = 0;
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220 if(end+1>=seq.getLength())
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221 end = seq.getLength()-1;
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222 graphics.setColor(Color.black);
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225 if(monospacedFont && av.showText && allGroups.length==0 && !av.getColourText())
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228 graphics.drawString(seq.getSequence(start, end + 1), 0, y1);
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231 char gap = av.getGapCharacter();
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232 graphics.drawString( seq.getSequence(start, end+1).replace(gap, ' '), 0, y1);
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237 for (int i = start; i <= end; i++)
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239 graphics.setColor(Color.black);
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240 s = seq.getCharAt(i);
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241 if (!renderGaps && jalview.util.Comparison.isGap(s))
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246 if (inCurrentSequenceGroup(i))
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248 if (!currentSequenceGroup.getDisplayText())
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253 if (currentSequenceGroup.getColourText())
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255 getBoxColour(currentSequenceGroup.cs, seq, i);
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256 graphics.setColor(resBoxColour.darker());
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261 if (!av.getShowText())
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266 if (av.getColourText())
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268 getBoxColour(av.globalColourScheme, seq, i);
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270 if (av.getShowBoxes())
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272 graphics.setColor(resBoxColour.darker());
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276 graphics.setColor(resBoxColour);
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281 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
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283 // System.out.print(s);
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284 graphics.drawString(String.valueOf(s),
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285 charOffset + av.charWidth * (i - start),
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289 // System.out.println("\n");
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296 * @param res DOCUMENT ME!
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298 * @return DOCUMENT ME!
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300 boolean inCurrentSequenceGroup(int res)
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302 if (allGroups == null)
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307 for (int i = 0; i < allGroups.length; i++)
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309 if ((allGroups[i].getStartRes() <= res) &&
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310 (allGroups[i].getEndRes() >= res))
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312 currentSequenceGroup = allGroups[i];
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324 * @param seq DOCUMENT ME!
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325 * @param start DOCUMENT ME!
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326 * @param end DOCUMENT ME!
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327 * @param x1 DOCUMENT ME!
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328 * @param y1 DOCUMENT ME!
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329 * @param width DOCUMENT ME!
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330 * @param height DOCUMENT ME!
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332 public void drawHighlightedText(SequenceI seq, int start, int end, int x1, int y1)
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334 int pady = av.charHeight / 5;
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335 int charOffset = 0;
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336 graphics.setColor(Color.BLACK);
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337 graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
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338 graphics.setColor(Color.white);
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342 // Need to find the sequence position here.
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343 for (int i = start; i <= end; i++)
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345 if (i < seq.getLength())
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347 s = seq.getSequence().charAt(i);
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350 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
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351 graphics.drawString(String.valueOf(s),
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352 charOffset + x1 + (av.charWidth * (i - start)),
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353 (y1 + av.charHeight) - pady);
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357 public void drawCursor(SequenceI seq, int res, int x1, int y1)
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359 int pady = av.charHeight / 5;
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360 int charOffset = 0;
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361 graphics.setColor(Color.black);
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362 graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
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363 graphics.setColor(Color.white);
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365 graphics.setColor(Color.white);
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367 char s = seq.getCharAt(res);
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369 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
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370 graphics.drawString(String.valueOf(s),
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372 (y1 + av.charHeight) - pady);
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