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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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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37 public SequenceRenderer(AlignViewport av)
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42 public void renderGaps(boolean b)
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47 public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)
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49 getBoxColour(cs, seq, i);
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50 return resBoxColour;
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53 void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
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57 resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
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61 resBoxColour = Color.white;
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65 public Color findSequenceColour(SequenceI seq, int i)
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67 allGroups = av.alignment.findAllGroups(seq);
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68 drawBoxes(seq, i,i, 0, 0, 1,1);
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69 return resBoxColour;
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72 public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
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73 int start, int end, int x1, int y1, int width,
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80 drawBoxes(seq, start, end, x1, y1, (int) width, height);
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82 fm = g.getFontMetrics();
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83 drawText(seq, start, end, x1, y1, (int) width, height);
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87 public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,
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88 int width, int height)
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91 int length = seq.getLength();
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94 int curWidth = width;
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96 Color tempColour = null;
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99 resBoxColour = Color.white;
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102 if (inCurrentSequenceGroup(i))
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104 if (currentSequenceGroup.getDisplayBoxes())
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106 getBoxColour(currentSequenceGroup.cs, seq, i);
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109 else if (av.getShowBoxes())
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111 getBoxColour(av.getGlobalColourScheme(), seq, i);
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116 if (resBoxColour != tempColour)
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118 if (tempColour != null)
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120 graphics.fillRect(x1 + width * (curStart - start), y1, curWidth,
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123 graphics.setColor(resBoxColour);
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127 tempColour = resBoxColour;
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138 graphics.fillRect(x1 + width * (curStart - start), y1, curWidth, height);
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141 public void drawText(SequenceI seq, int start, int end, int x1, int y1,
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142 int width, int height)
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144 int pady = height / 5;
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145 int charOffset = 0;
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147 // Need to find the sequence position here.
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149 String sequence = seq.getSequence();
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151 if(end+1>=seq.getLength())
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152 end = seq.getLength()-1;
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154 for (int i = start; i <= end; i++)
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156 graphics.setColor(Color.black);
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158 s = sequence.charAt(i);
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160 if (!renderGaps && jalview.util.Comparison.isGap(s))
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165 if (inCurrentSequenceGroup(i))
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167 if (!currentSequenceGroup.getDisplayText())
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172 if (currentSequenceGroup.getColourText())
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174 getBoxColour(currentSequenceGroup.cs, seq, i);
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175 graphics.setColor(resBoxColour.darker());
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180 if (!av.getShowText())
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185 if (av.getColourText())
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187 getBoxColour(av.getGlobalColourScheme(), seq, i);
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188 if (av.getShowBoxes())
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190 graphics.setColor(resBoxColour.darker());
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194 graphics.setColor(resBoxColour);
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199 charOffset = (width - fm.charWidth(s)) / 2;
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200 graphics.drawString(String.valueOf(s),
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201 charOffset + x1 + width * (i - start),
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202 y1 + height - pady);
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207 boolean inCurrentSequenceGroup(int res)
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209 if (allGroups == null)
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214 for (int i = 0; i < allGroups.length; i++)
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216 if (allGroups[i].getStartRes() <= res && allGroups[i].getEndRes() >= res)
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218 currentSequenceGroup = allGroups[i];
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226 public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
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227 int y1, int width, int height)
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229 int pady = height / 5;
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230 int charOffset = 0;
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231 graphics.setColor(Color.black);
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232 graphics.fillRect(x1, y1, width * (end - start + 1), height);
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233 graphics.setColor(Color.white);
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236 // Need to find the sequence position here.
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237 for (int i = start; i <= end; i++)
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239 if (i < seq.getLength())
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241 s = seq.getSequence().charAt(i);
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244 charOffset = (width - fm.charWidth(s)) / 2;
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245 graphics.drawString(String.valueOf(s),
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246 charOffset + x1 + width * (i - start),
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247 y1 + height - pady);
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