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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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 renderGaps(boolean b)
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65 public Color getResidueBoxColour(SequenceI seq, int i)
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67 allGroups = av.alignment.findAllGroups(seq);
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69 if (inCurrentSequenceGroup(i))
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71 if (currentSequenceGroup.getDisplayBoxes())
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73 getBoxColour(currentSequenceGroup.cs, seq, i);
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76 else if (av.getShowBoxes())
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78 getBoxColour(av.globalColourScheme, seq, i);
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81 return resBoxColour;
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88 * @param cs DOCUMENT ME!
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89 * @param seq DOCUMENT ME!
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90 * @param i DOCUMENT ME!
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92 void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
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96 resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
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100 resBoxColour = Color.white;
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107 * @param g DOCUMENT ME!
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108 * @param seq DOCUMENT ME!
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109 * @param sg DOCUMENT ME!
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110 * @param start DOCUMENT ME!
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111 * @param end DOCUMENT ME!
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112 * @param x1 DOCUMENT ME!
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113 * @param y1 DOCUMENT ME!
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114 * @param width DOCUMENT ME!
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115 * @param height DOCUMENT ME!
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117 public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
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118 int start, int end, int x1, int y1, int width, int height)
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124 drawBoxes(seq, start, end, x1, y1, (int) width, height);
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126 fm = g.getFontMetrics();
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128 monospacedFont = fm.getStringBounds("M",g).getWidth()==fm.getStringBounds("|",g).getWidth();
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130 drawText(seq, start, end, x1, y1, (int) width, height);
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136 * @param seq DOCUMENT ME!
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137 * @param start DOCUMENT ME!
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138 * @param end DOCUMENT ME!
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139 * @param x1 DOCUMENT ME!
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140 * @param y1 DOCUMENT ME!
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141 * @param width DOCUMENT ME!
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142 * @param height DOCUMENT ME!
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144 public synchronized void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,
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145 int width, int height)
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148 int length = seq.getLength();
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151 int curWidth = width;
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153 Color tempColour = null;
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157 resBoxColour = Color.white;
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161 if (inCurrentSequenceGroup(i))
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163 if (currentSequenceGroup.getDisplayBoxes())
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165 getBoxColour(currentSequenceGroup.cs, seq, i);
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168 else if (av.getShowBoxes())
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170 getBoxColour(av.globalColourScheme, seq, i);
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175 if (resBoxColour != tempColour)
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177 if (tempColour != null)
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179 graphics.fillRect(x1 + (width * (curStart - start)), y1,
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183 graphics.setColor(resBoxColour);
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187 tempColour = resBoxColour;
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197 graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,
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205 * @param seq DOCUMENT ME!
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206 * @param start DOCUMENT ME!
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207 * @param end DOCUMENT ME!
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208 * @param x1 DOCUMENT ME!
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209 * @param y1 DOCUMENT ME!
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210 * @param width DOCUMENT ME!
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211 * @param height DOCUMENT ME!
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213 public void drawText(SequenceI seq, int start, int end, int x1, int y1,
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214 int width, int height)
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216 y1 += height - height / 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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227 graphics.drawString(seq.getSequence(start, end + 1), x1, y1);
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231 for (int i = start; i <= end; i++)
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233 graphics.setColor(Color.black);
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234 s = seq.getCharAt(i);
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235 if (!renderGaps && jalview.util.Comparison.isGap(s))
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240 if (inCurrentSequenceGroup(i))
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242 if (!currentSequenceGroup.getDisplayText())
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247 if (currentSequenceGroup.getColourText())
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249 getBoxColour(currentSequenceGroup.cs, seq, i);
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250 graphics.setColor(resBoxColour.darker());
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255 if (!av.getShowText())
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260 if (av.getColourText())
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262 getBoxColour(av.globalColourScheme, seq, i);
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264 if (av.getShowBoxes())
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266 graphics.setColor(resBoxColour.darker());
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270 graphics.setColor(resBoxColour);
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275 charOffset = (width - fm.charWidth(s)) / 2;
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276 graphics.drawString(String.valueOf(s),
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277 charOffset + x1 + width * (i - start),
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287 * @param res DOCUMENT ME!
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289 * @return DOCUMENT ME!
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291 boolean inCurrentSequenceGroup(int res)
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293 if (allGroups == null)
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298 for (int i = 0; i < allGroups.length; i++)
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300 if ((allGroups[i].getStartRes() <= res) &&
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301 (allGroups[i].getEndRes() >= res))
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303 currentSequenceGroup = allGroups[i];
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315 * @param seq DOCUMENT ME!
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316 * @param start DOCUMENT ME!
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317 * @param end DOCUMENT ME!
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318 * @param x1 DOCUMENT ME!
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319 * @param y1 DOCUMENT ME!
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320 * @param width DOCUMENT ME!
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321 * @param height DOCUMENT ME!
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323 public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
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324 int y1, int width, int height)
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326 int pady = height / 5;
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327 int charOffset = 0;
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328 graphics.setColor(Color.BLACK);
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329 graphics.fillRect(x1, y1, width * (end - start + 1), height);
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330 graphics.setColor(Color.white);
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334 // Need to find the sequence position here.
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335 for (int i = start; i <= end; i++)
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337 if (i < seq.getLength())
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339 s = seq.getSequence().charAt(i);
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342 charOffset = (width - fm.charWidth(s)) / 2;
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343 graphics.drawString(String.valueOf(s),
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344 charOffset + x1 + (width * (i - start)), (y1 + height) - pady);
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