1 package jalview.appletgui;
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4 import jalview.datamodel.*;
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5 import jalview.analysis.*;
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8 public class SeqCanvas extends Panel
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11 SequenceRenderer sr;
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19 boolean showScores = false;
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20 boolean displaySearch = false;
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21 int [] searchResults = null;
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26 boolean fastPaint = false;
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29 public SeqCanvas(AlignViewport av)
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32 fr = new FeatureRenderer(av);
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33 sr = new SequenceRenderer(av);
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34 PaintRefresher.Register(this);
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38 void drawNorthScale(Graphics g, int startx, int endx,int ypos) {
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39 int scalestartx = startx - startx % 10 + 10;
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41 g.setColor(Color.black);
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44 for (int i = scalestartx; i < endx; i += 10)
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46 String string = String.valueOf(i);
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47 g.drawString(string, (i - startx - 1) * av.charWidth,
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48 ypos - av.charHeight / 2);
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50 g.drawLine( (i - startx - 1) * av.charWidth + av.charWidth / 2,
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51 ypos + 2 - av.charHeight / 2,
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52 (i - startx - 1) * av.charWidth + av.charWidth / 2, ypos - 2);
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57 void drawWestScale(Graphics g, int startx, int endx, int ypos)
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59 FontMetrics fm = getFontMetrics(av.getFont());
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60 ypos+= av.charHeight;
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62 for (int i = 0; i < av.alignment.getHeight(); i++)
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64 SequenceI seq = av.alignment.getSequenceAt(i);
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67 while (index < endx)
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69 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
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75 value = av.alignment.getSequenceAt(i).findPosition(index);
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80 int x = LABEL_WEST - fm.stringWidth(value+"");
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81 g.drawString(value + "", x, ypos + i*av.charHeight - av.charHeight/5);
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86 void drawEastScale(Graphics g, int startx, int endx, int ypos)
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88 ypos+= av.charHeight;
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90 for (int i = 0; i < av.alignment.getHeight(); i++)
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92 SequenceI seq = av.alignment.getSequenceAt(i);
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95 while (index > startx)
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97 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
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103 value = av.alignment.getSequenceAt(i).findPosition(index);
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107 g.drawString(value + "", 0, ypos + i*av.charHeight - av.charHeight/5);
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114 public void fastPaint(int horizontal, int vertical)
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116 if (horizontal == 0 && vertical == 0 || gg==null)
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119 gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
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120 -vertical * av.charHeight);
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122 int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,
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123 transX = 0, transY = 0;
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124 if (horizontal > 0) // scrollbar pulled right, image to the left
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126 transX = (er - sr - horizontal) * av.charWidth;
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127 sr = er - horizontal;
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129 else if (horizontal < 0)
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130 er = sr - horizontal;
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132 else if (vertical > 0) // scroll down
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134 ss = es - vertical;
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135 if(ss<av.startSeq) // ie scrolling too fast, more than a page at a time
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138 transY = imgHeight - vertical * av.charHeight;
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140 else if (vertical < 0)
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142 es = ss - vertical;
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148 gg.translate(transX, transY);
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150 gg.setColor(Color.white);
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151 gg.fillRect(0,0, (er-sr+1)*av.charWidth, (es-ss)*av.charHeight);
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152 drawPanel(gg, sr, er, ss, es, sr, ss, 0);
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153 gg.translate( -transX, -transY);
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161 * Definitions of startx and endx (hopefully):
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162 * SMJS This is what I'm working towards!
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163 * startx is the first residue (starting at 0) to display.
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164 * endx is the last residue to display (starting at 0).
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165 * starty is the first sequence to display (starting at 0).
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166 * endy is the last sequence to display (starting at 0).
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167 * NOTE 1: The av limits are set in setFont in this class and
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168 * in the adjustment listener in SeqPanel when the scrollbars move.
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170 public void update(Graphics g)
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175 public void paint(Graphics g)
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179 g.drawImage(img, 0, 0, this);
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184 // this draws the whole of the alignment
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185 imgWidth = this.getSize().width;
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186 imgHeight = this.getSize().height;
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188 imgWidth -= imgWidth%av.charWidth;
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189 imgHeight-= imgHeight%av.charHeight;
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191 if(imgWidth<1 || imgHeight<1)
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194 if(img==null || imgWidth!=img.getWidth(this) || imgHeight!=img.getHeight(this))
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196 img = createImage(imgWidth, imgHeight);
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197 gg = img.getGraphics();
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198 gg.setFont(av.getFont());
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201 gg.setColor(Color.white);
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202 gg.fillRect(0,0,imgWidth,imgHeight);
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204 chunkWidth = getWrappedCanvasWidth( getSize().width );
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205 chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;
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207 av.setChunkHeight(chunkHeight);
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208 av.setChunkWidth(chunkWidth);
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211 if (av.getWrapAlignment())
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212 drawWrappedPanel(gg, getSize().width, getSize().height, av.startRes);
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214 drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0);
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216 g.drawImage(img, 0, 0, this);
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220 int LABEL_WEST, LABEL_EAST;
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221 public int getWrappedCanvasWidth(int cwidth)
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223 FontMetrics fm = getFontMetrics(av.getFont());
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228 if(av.scaleRightWrapped)
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229 LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" );
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231 if(av.scaleLeftWrapped)
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232 LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" );
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234 return (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
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237 public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)
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239 AlignmentI al = av.getAlignment();
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241 FontMetrics fm = getFontMetrics(av.getFont());
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243 int LABEL_EAST = 0;
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244 if(av.scaleRightWrapped)
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245 LABEL_EAST = fm.stringWidth( al.getWidth()+"000" );
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246 int LABEL_WEST = 0;
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247 if(av.scaleLeftWrapped)
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248 LABEL_WEST = fm.stringWidth(al.getWidth()+"0");
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251 int cWidth = (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
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252 int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;
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254 av.endRes = av.startRes + cWidth;
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256 int endx = startRes+cWidth-1;
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257 int ypos = 2*av.charHeight;
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259 while (ypos <= canvasHeight && startRes<av.alignment.getWidth() )
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261 g.setColor(Color.black);
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263 if(av.scaleLeftWrapped)
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264 drawWestScale(g, startRes, endx, ypos);
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266 if(av.scaleRightWrapped)
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268 g.translate(canvasWidth - LABEL_EAST +av.charWidth, 0);
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269 drawEastScale(g, startRes, endx, ypos);
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270 g.translate( - (canvasWidth - LABEL_EAST+av.charWidth), 0);
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273 g.translate(LABEL_WEST,0);
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274 if(av.scaleAboveWrapped)
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275 drawNorthScale(g, startRes, endx, ypos);
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278 // When printing we have an extra clipped region,
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279 // the Printable page which we need to account for here
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280 Shape clip = g.getClip();
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282 g.setClip(0, 0, cWidth*av.charWidth, canvasHeight);
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285 (int)clip.getBounds().y,
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286 cWidth*av.charWidth,
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287 (int)clip.getBounds().height
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290 drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
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292 g.translate(-LABEL_WEST,0);
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295 startRes += cWidth;
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296 endx = startRes + cWidth - 1;
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298 if (endx > al.getWidth())
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299 endx = al.getWidth();
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305 synchronized public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
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307 g.setFont(av.getFont());
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308 sr.renderGaps(av.renderGaps);
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312 /// First draw the sequences
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313 /////////////////////////////
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314 for (int i = y1 ; i < y2 ;i++)
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316 nextSeq = av.alignment.getSequenceAt(i);
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318 sr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ),x1,x2,
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319 (x1 - startx) * av.charWidth,
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320 offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
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321 av.charWidth,av.charHeight);
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323 if(av.showSequenceFeatures)
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325 fr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ), x1, x2,
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326 (x1 - startx) * av.charWidth,
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328 AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
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329 av.charWidth, av.charHeight);
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333 /////////////////////////////////////
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335 // Now outline any areas if necessary
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336 /////////////////////////////////////
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337 SequenceGroup group = av.getSelectionGroup();
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338 java.util.Vector groups = av.alignment.getGroups();
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340 int sx = -1, sy = -1, ex = -1;
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341 int groupIndex = -1;
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342 if (group == null && groups.size() > 0)
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344 group = (SequenceGroup) groups.elementAt(0);
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353 boolean inGroup = false;
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354 int top=-1, bottom =-1;
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355 for (i = y1; i < y2; i++)
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357 sx = (group.getStartRes() - startx) * av.charWidth;
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358 sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
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359 ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth -1;
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361 if (sx < getSize().width
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363 && group.sequences.contains(av.alignment.getSequenceAt(i)))
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365 if (bottom == -1 && (i==av.alignment.getHeight()-1 ||
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366 !group.sequences.contains(av.alignment.getSequenceAt(i + 1))))
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367 bottom = sy + av.charHeight ;
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371 if (top == -1 && i==0 ||
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372 !group.sequences.contains(av.alignment.getSequenceAt(i - 1)))
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378 if (group == av.getSelectionGroup())
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380 g.setColor(new Color(255,0,0));
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384 g.setColor(group.getOutlineColour());
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392 g.drawLine(sx, oldY, sx, sy );
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393 g.drawLine(sx+ex, oldY, sx+ex, sy );
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397 g.drawLine(sx, top, sx + ex, top);
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402 g.drawLine(sx, bottom, sx + ex, bottom);
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417 g.drawLine(sx, top, sx + ex, top);
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422 g.drawLine(sx, bottom-1, sx + ex, bottom-1);
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426 sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
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427 g.drawLine(sx, oldY, sx, sy );
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428 g.drawLine(sx+ex, oldY, sx+ex, sy );
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432 if (groupIndex >= groups.size())
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435 group = (SequenceGroup) groups.elementAt(groupIndex);
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438 while (groupIndex < groups.size());
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441 /// Highlight search Results once all sequences have been drawn
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442 //////////////////////////////////////////////////////////
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445 for(int r=0; r<searchResults.length; r+=3)
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447 int searchSeq = searchResults[r];
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449 if (searchSeq >= y1 && searchSeq < y2)
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451 SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);
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453 int searchStart = seq.findIndex( searchResults[r+1] )-1;
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454 int searchEnd = seq.findIndex( searchResults[r+2] )-1;
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456 SequenceRenderer ssr = (SequenceRenderer) sr;
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462 ssr.drawHighlightedText(seq,
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465 (searchStart - startx) * av.charWidth,
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467 AlignmentUtil.getPixelHeight(starty, searchSeq,
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479 public void highlightSearchResults(int [] results)
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481 // results are in the order sequence, startRes, endRes
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483 displaySearch = false;
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485 displaySearch = true;
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487 searchResults = results;
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