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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20 package jalview.appletgui;
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24 import jalview.datamodel.*;
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25 import jalview.schemes.*;
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27 public class SequenceRenderer
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31 boolean renderGaps = true;
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32 SequenceGroup currentSequenceGroup = null;
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33 SequenceGroup[] allGroups = null;
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36 boolean forOverview = false;
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38 public SequenceRenderer(AlignViewport av)
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46 * @param b DOCUMENT ME!
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48 public void prepare(Graphics g, boolean renderGaps)
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51 fm = g.getFontMetrics();
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53 this.renderGaps = renderGaps;
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56 public Color getResidueBoxColour(SequenceI seq, int i)
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58 allGroups = av.alignment.findAllGroups(seq);
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60 if (inCurrentSequenceGroup(i))
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62 if (currentSequenceGroup.getDisplayBoxes())
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64 getBoxColour(currentSequenceGroup.cs, seq, i);
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67 else if (av.getShowBoxes())
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69 getBoxColour(av.globalColourScheme, seq, i);
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72 return resBoxColour;
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75 void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
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79 resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
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81 else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
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83 resBoxColour = Color.lightGray;
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87 resBoxColour = Color.white;
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92 public Color findSequenceColour(SequenceI seq, int i)
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94 allGroups = av.alignment.findAllGroups(seq);
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95 drawBoxes(seq, i,i, 0);
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96 return resBoxColour;
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99 public void drawSequence(SequenceI seq, SequenceGroup[] sg,
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100 int start, int end, int y1)
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104 drawBoxes(seq, start, end, y1);
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106 if(av.validCharWidth)
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108 drawText(seq, start, end, y1);
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112 public void drawBoxes(SequenceI seq, int start, int end, int y1)
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115 int length = seq.getLength();
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118 int curWidth = av.charWidth;
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120 Color tempColour = null;
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123 resBoxColour = Color.white;
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126 if (inCurrentSequenceGroup(i))
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128 if (currentSequenceGroup.getDisplayBoxes())
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130 getBoxColour(currentSequenceGroup.cs, seq, i);
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133 else if (av.getShowBoxes())
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135 getBoxColour(av.getGlobalColourScheme(), seq, i);
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140 if (resBoxColour != tempColour)
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142 if (tempColour != null)
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144 graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
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147 graphics.setColor(resBoxColour);
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150 curWidth = av.charWidth;
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151 tempColour = resBoxColour;
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156 curWidth += av.charWidth;
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162 graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth, av.charHeight);
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165 public void drawText(SequenceI seq, int start, int end, int y1)
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167 Font boldFont = null;
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168 boolean bold = false;
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169 if(av.upperCasebold)
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171 boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);
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173 graphics.setFont(av.getFont());
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176 y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
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178 int charOffset = 0;
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180 // Need to find the sequence position here.
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181 if(end+1>=seq.getLength())
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182 end = seq.getLength()-1;
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186 for (int i = start; i <= end; i++)
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188 graphics.setColor(Color.black);
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190 s = seq.getCharAt(i);
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191 if (!renderGaps && jalview.util.Comparison.isGap(s))
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196 if (inCurrentSequenceGroup(i))
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198 if (!currentSequenceGroup.getDisplayText())
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203 if (currentSequenceGroup.getColourText())
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205 getBoxColour(currentSequenceGroup.cs, seq, i);
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206 graphics.setColor(resBoxColour.darker());
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211 if (!av.getShowText())
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216 if (av.getColourText())
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218 getBoxColour(av.getGlobalColourScheme(), seq, i);
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219 if (av.getShowBoxes())
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221 graphics.setColor(resBoxColour.darker());
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225 graphics.setColor(resBoxColour);
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230 if (av.upperCasebold)
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232 fm = graphics.getFontMetrics();
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233 if ('A' <= s && s <= 'Z')
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238 graphics.setFont(boldFont);
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244 graphics.setFont(av.font);
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250 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
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251 graphics.drawString(String.valueOf(s),
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252 charOffset + av.charWidth * (i - start),
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258 boolean inCurrentSequenceGroup(int res)
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260 if (allGroups == null)
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265 for (int i = 0; i < allGroups.length; i++)
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267 if (allGroups[i].getStartRes() <= res && allGroups[i].getEndRes() >= res)
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269 currentSequenceGroup = allGroups[i];
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277 public void drawHighlightedText(SequenceI seq, int start, int end, int x1, int y1)
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279 int pady = av.charHeight / 5;
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280 int charOffset = 0;
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281 graphics.setColor(Color.black);
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282 graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
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283 graphics.setColor(Color.white);
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286 // Need to find the sequence position here.
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287 if(av.validCharWidth)
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289 for (int i = start; i <= end; i++)
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291 if (i < seq.getLength())
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293 s = seq.getSequence().charAt(i);
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296 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
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297 graphics.drawString(String.valueOf(s),
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298 charOffset + x1 + av.charWidth * (i - start),
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299 y1 + av.charHeight - pady);
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304 public void drawCursor(SequenceI seq, int res, int x1, int y1)
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306 int pady = av.charHeight / 5;
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307 int charOffset = 0;
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308 graphics.setColor(Color.black);
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309 graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
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310 graphics.setColor(Color.white);
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312 graphics.setColor(Color.white);
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314 char s = seq.getCharAt(res);
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315 if (av.validCharWidth)
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318 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
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319 graphics.drawString(String.valueOf(s),
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321 (y1 + av.charHeight) - pady);
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