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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26 import java.awt.image.BufferedImage;
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33 * @version $Revision$
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35 public class SequenceRenderer
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39 boolean renderGaps = true;
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40 SequenceGroup currentSequenceGroup = null;
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41 SequenceGroup[] allGroups = null;
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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 renderGaps(boolean b)
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68 * @param cs DOCUMENT ME!
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69 * @param seq DOCUMENT ME!
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70 * @param i DOCUMENT ME!
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72 * @return DOCUMENT ME!
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74 public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)
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76 getBoxColour(cs, seq, i);
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78 return resBoxColour;
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82 public Color findSequenceColour(Color initialCol, SequenceI seq, int i)
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85 bi = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);
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87 graphics = bi.getGraphics();
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89 if(initialCol!=null)
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90 bi.setRGB(0,0, initialCol.getRGB());
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92 allGroups = av.alignment.findAllGroups(seq);
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94 i = seq.findIndex(i);
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96 drawBoxes(seq, i,i, 0, 0, 1,1);
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98 return new Color(bi.getRGB(0, 0));
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105 * @param cs DOCUMENT ME!
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106 * @param seq DOCUMENT ME!
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107 * @param i DOCUMENT ME!
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109 void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
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113 resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
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117 resBoxColour = Color.white;
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124 * @param g DOCUMENT ME!
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125 * @param seq DOCUMENT ME!
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126 * @param sg DOCUMENT ME!
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127 * @param start DOCUMENT ME!
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128 * @param end DOCUMENT ME!
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129 * @param x1 DOCUMENT ME!
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130 * @param y1 DOCUMENT ME!
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131 * @param width DOCUMENT ME!
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132 * @param height DOCUMENT ME!
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134 public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
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135 int start, int end, int x1, int y1, int width, int height)
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141 drawBoxes(seq, start, end, x1, y1, (int) width, height);
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143 fm = g.getFontMetrics();
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144 drawText(seq, start, end, x1, y1, (int) width, height);
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150 * @param seq DOCUMENT ME!
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151 * @param start DOCUMENT ME!
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152 * @param end DOCUMENT ME!
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153 * @param x1 DOCUMENT ME!
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154 * @param y1 DOCUMENT ME!
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155 * @param width DOCUMENT ME!
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156 * @param height DOCUMENT ME!
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158 public synchronized void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,
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159 int width, int height)
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162 int length = seq.getLength();
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165 int curWidth = width;
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167 Color tempColour = null;
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171 resBoxColour = Color.white;
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175 if (inCurrentSequenceGroup(i))
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177 if (currentSequenceGroup.getDisplayBoxes())
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179 getBoxColour(currentSequenceGroup.cs, seq, i);
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182 else if (av.getShowBoxes())
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184 getBoxColour(av.getGlobalColourScheme(), seq, i);
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189 if (resBoxColour != tempColour)
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191 if (tempColour != null)
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193 graphics.fillRect(x1 + (width * (curStart - start)), y1,
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197 graphics.setColor(resBoxColour);
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201 tempColour = resBoxColour;
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211 graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,
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219 * @param seq DOCUMENT ME!
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220 * @param start DOCUMENT ME!
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221 * @param end DOCUMENT ME!
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222 * @param x1 DOCUMENT ME!
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223 * @param y1 DOCUMENT ME!
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224 * @param width DOCUMENT ME!
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225 * @param height DOCUMENT ME!
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227 public void drawText(SequenceI seq, int start, int end, int x1, int y1,
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228 int width, int height)
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230 int pady = height / 5;
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231 int charOffset = 0;
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235 // Need to find the sequence position here.
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236 String sequence = seq.getSequence();
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238 if(end+1>=seq.getLength())
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239 end = seq.getLength()-1;
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241 for (int i = start; i <= end; i++)
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243 graphics.setColor(Color.black);
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245 s = sequence.charAt(i);
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247 if (!renderGaps && jalview.util.Comparison.isGap(s))
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252 if (inCurrentSequenceGroup(i))
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254 if (!currentSequenceGroup.getDisplayText())
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259 if (currentSequenceGroup.getColourText())
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261 getBoxColour(currentSequenceGroup.cs, seq, i);
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262 graphics.setColor(resBoxColour.darker());
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267 if (!av.getShowText())
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272 if (av.getColourText())
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274 getBoxColour(av.getGlobalColourScheme(), seq, i);
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276 if (av.getShowBoxes())
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278 graphics.setColor(resBoxColour.darker());
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282 graphics.setColor(resBoxColour);
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287 charOffset = (width - fm.charWidth(s)) / 2;
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288 graphics.drawString(String.valueOf(s),
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289 charOffset + x1 + (int)(width * (i - start)), (y1 + height) - pady);
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297 * @param res DOCUMENT ME!
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299 * @return DOCUMENT ME!
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301 boolean inCurrentSequenceGroup(int res)
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303 if (allGroups == null)
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308 for (int i = 0; i < allGroups.length; i++)
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310 if ((allGroups[i].getStartRes() <= res) &&
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311 (allGroups[i].getEndRes() >= res))
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313 currentSequenceGroup = allGroups[i];
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325 * @param seq DOCUMENT ME!
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326 * @param start DOCUMENT ME!
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327 * @param end DOCUMENT ME!
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328 * @param x1 DOCUMENT ME!
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329 * @param y1 DOCUMENT ME!
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330 * @param width DOCUMENT ME!
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331 * @param height DOCUMENT ME!
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333 public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
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334 int y1, int width, int height)
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336 int pady = height / 5;
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337 int charOffset = 0;
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338 graphics.setColor(Color.BLACK);
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339 graphics.fillRect(x1, y1, width * (end - start + 1), height);
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340 graphics.setColor(Color.white);
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344 // Need to find the sequence position here.
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345 for (int i = start; i <= end; i++)
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347 if (i < seq.getLength())
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349 s = seq.getSequence().charAt(i);
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352 charOffset = (width - fm.charWidth(s)) / 2;
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353 graphics.drawString(String.valueOf(s),
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354 charOffset + x1 + (width * (i - start)), (y1 + height) - pady);
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