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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36 boolean forOverview = false;
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38 public SequenceRenderer(AlignViewport av)
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43 public void renderGaps(boolean b)
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48 public Color getResidueBoxColour(SequenceI seq, int i)
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50 allGroups = av.alignment.findAllGroups(seq);
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52 if (inCurrentSequenceGroup(i))
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54 if (currentSequenceGroup.getDisplayBoxes())
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56 getBoxColour(currentSequenceGroup.cs, seq, i);
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59 else if (av.getShowBoxes())
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61 getBoxColour(av.globalColourScheme, seq, i);
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64 return resBoxColour;
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67 void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
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71 resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
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73 else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
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75 resBoxColour = Color.lightGray;
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79 resBoxColour = Color.white;
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84 public Color findSequenceColour(SequenceI seq, int i)
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86 allGroups = av.alignment.findAllGroups(seq);
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87 drawBoxes(seq, i,i, 0, 0, 1,1);
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88 return resBoxColour;
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91 public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
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92 int start, int end, int x1, int y1, int width,
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99 drawBoxes(seq, start, end, x1, y1, (int) width, height);
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101 fm = g.getFontMetrics();
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102 drawText(seq, start, end, x1, y1, (int) width, height);
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106 public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,
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107 int width, int height)
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110 int length = seq.getLength();
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113 int curWidth = width;
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115 Color tempColour = null;
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118 resBoxColour = Color.white;
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121 if (inCurrentSequenceGroup(i))
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123 if (currentSequenceGroup.getDisplayBoxes())
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125 getBoxColour(currentSequenceGroup.cs, seq, i);
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128 else if (av.getShowBoxes())
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130 getBoxColour(av.getGlobalColourScheme(), seq, i);
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135 if (resBoxColour != tempColour)
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137 if (tempColour != null)
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139 graphics.fillRect(x1 + width * (curStart - start), y1, curWidth,
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142 graphics.setColor(resBoxColour);
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146 tempColour = resBoxColour;
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157 graphics.fillRect(x1 + width * (curStart - start), y1, curWidth, height);
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160 public void drawText(SequenceI seq, int start, int end, int x1, int y1,
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161 int width, int height)
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164 y1 += height - height / 5; // height/5 replaces pady
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166 int charOffset = 0;
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168 // Need to find the sequence position here.
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169 if(end+1>=seq.getLength())
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170 end = seq.getLength()-1;
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174 for (int i = start; i <= end; i++)
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176 graphics.setColor(Color.black);
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178 s = seq.getCharAt(i);
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179 if (!renderGaps && jalview.util.Comparison.isGap(s))
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184 if (inCurrentSequenceGroup(i))
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186 if (!currentSequenceGroup.getDisplayText())
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191 if (currentSequenceGroup.getColourText())
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193 getBoxColour(currentSequenceGroup.cs, seq, i);
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194 graphics.setColor(resBoxColour.darker());
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199 if (!av.getShowText())
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204 if (av.getColourText())
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206 getBoxColour(av.getGlobalColourScheme(), seq, i);
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207 if (av.getShowBoxes())
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209 graphics.setColor(resBoxColour.darker());
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213 graphics.setColor(resBoxColour);
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218 charOffset = (width - fm.charWidth(s)) / 2;
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219 graphics.drawString(String.valueOf(s),
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220 charOffset + x1 + width * (i - start),
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226 boolean inCurrentSequenceGroup(int res)
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228 if (allGroups == null)
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233 for (int i = 0; i < allGroups.length; i++)
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235 if (allGroups[i].getStartRes() <= res && allGroups[i].getEndRes() >= res)
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237 currentSequenceGroup = allGroups[i];
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245 public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
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246 int y1, int width, int height)
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248 int pady = height / 5;
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249 int charOffset = 0;
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250 graphics.setColor(Color.black);
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251 graphics.fillRect(x1, y1, width * (end - start + 1), height);
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252 graphics.setColor(Color.white);
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255 // Need to find the sequence position here.
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256 for (int i = start; i <= end; i++)
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258 if (i < seq.getLength())
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260 s = seq.getSequence().charAt(i);
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263 charOffset = (width - fm.charWidth(s)) / 2;
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264 graphics.drawString(String.valueOf(s),
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265 charOffset + x1 + width * (i - start),
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266 y1 + height - pady);
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