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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26 public class SeqCanvas
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30 SequenceRenderer sr;
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38 boolean displaySearch = false;
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39 int[] searchResults = null;
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44 boolean fastPaint = false;
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47 public SeqCanvas(AlignViewport av)
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50 fr = new FeatureRenderer(av);
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51 sr = new SequenceRenderer(av);
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52 PaintRefresher.Register(this, av.alignment);
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55 public AlignViewport getViewport()
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60 public FeatureRenderer getFeatureRenderer()
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65 MCview.AppletPDBCanvas pdbCanvas;
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66 public SequenceRenderer getSequenceRenderer()
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71 public void setPDBCanvas(MCview.AppletPDBCanvas pc)
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77 void drawNorthScale(Graphics g, int startx, int endx, int ypos)
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79 int scalestartx = startx - startx % 10 + 10;
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81 g.setColor(Color.black);
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84 for (int i = scalestartx; i < endx; i += 10)
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86 String string = String.valueOf(i);
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87 g.drawString(string, (i - startx - 1) * av.charWidth,
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88 ypos - av.charHeight / 2);
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90 g.drawLine( (i - startx - 1) * av.charWidth + av.charWidth / 2,
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91 ypos + 2 - av.charHeight / 2,
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92 (i - startx - 1) * av.charWidth + av.charWidth / 2, ypos - 2);
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97 void drawWestScale(Graphics g, int startx, int endx, int ypos)
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99 FontMetrics fm = getFontMetrics(av.getFont());
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100 ypos += av.charHeight;
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102 for (int i = 0; i < av.alignment.getHeight(); i++)
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104 SequenceI seq = av.alignment.getSequenceAt(i);
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105 int index = startx;
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107 while (index < endx)
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109 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
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115 value = av.alignment.getSequenceAt(i).findPosition(index);
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120 int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2;
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121 g.drawString(value + "", x,
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122 ypos + i * av.charHeight - av.charHeight / 5);
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127 void drawEastScale(Graphics g, int startx, int endx, int ypos)
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129 ypos += av.charHeight;
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131 for (int i = 0; i < av.alignment.getHeight(); i++)
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133 SequenceI seq = av.alignment.getSequenceAt(i);
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136 while (index > startx)
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138 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
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144 value = av.alignment.getSequenceAt(i).findPosition(index);
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149 g.drawString(value + "", av.charWidth/2,
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150 ypos + i * av.charHeight - av.charHeight / 5);
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156 public void fastPaint(int horizontal, int vertical)
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163 gg.copyArea(horizontal * av.charWidth,
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164 vertical * av.charHeight,
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167 -horizontal * av.charWidth,
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168 -vertical * av.charHeight);
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170 int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,
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171 transX = 0, transY = 0;
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172 if (horizontal > 0) // scrollbar pulled right, image to the left
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174 transX = (er - sr - horizontal) * av.charWidth;
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175 sr = er - horizontal;
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177 else if (horizontal < 0)
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179 er = sr - horizontal;
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182 else if (vertical > 0) // scroll down
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184 ss = es - vertical;
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185 if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
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191 transY = imgHeight - vertical * av.charHeight;
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194 else if (vertical < 0)
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196 es = ss - vertical;
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197 if (es > av.endSeq)
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203 gg.translate(transX, transY);
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205 gg.setColor(Color.white);
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206 gg.fillRect(0, 0, (er - sr + 1) * av.charWidth, (es - ss) * av.charHeight);
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207 drawPanel(gg, sr, er, ss, es, sr, ss, 0);
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208 gg.translate( -transX, -transY);
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216 * Definitions of startx and endx (hopefully):
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217 * SMJS This is what I'm working towards!
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218 * startx is the first residue (starting at 0) to display.
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219 * endx is the last residue to display (starting at 0).
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220 * starty is the first sequence to display (starting at 0).
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221 * endy is the last sequence to display (starting at 0).
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222 * NOTE 1: The av limits are set in setFont in this class and
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223 * in the adjustment listener in SeqPanel when the scrollbars move.
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225 public void update(Graphics g)
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230 public void paint(Graphics g)
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232 sr.renderGaps(av.renderGaps);
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236 g.drawImage(img, 0, 0, this);
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241 // this draws the whole of the alignment
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242 imgWidth = this.getSize().width;
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243 imgHeight = this.getSize().height;
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245 imgWidth -= imgWidth % av.charWidth;
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246 imgHeight -= imgHeight % av.charHeight;
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248 if (imgWidth < 1 || imgHeight < 1)
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253 if (img == null || imgWidth != img.getWidth(this) ||
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254 imgHeight != img.getHeight(this))
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256 img = createImage(imgWidth, imgHeight);
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257 gg = img.getGraphics();
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258 gg.setFont(av.getFont());
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261 gg.setColor(Color.white);
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262 gg.fillRect(0, 0, imgWidth, imgHeight);
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265 if (av.getWrapAlignment())
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267 drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
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271 drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes,
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275 g.drawImage(img, 0, 0, this);
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277 if (pdbCanvas != null)
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279 pdbCanvas.updateSeqColours();
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283 int LABEL_WEST, LABEL_EAST;
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284 public int getWrappedCanvasWidth(int cwidth)
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286 FontMetrics fm = getFontMetrics(av.getFont());
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291 if (av.scaleRightWrapped)
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293 LABEL_EAST = fm.stringWidth(getMask()+"0");
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296 if (av.scaleLeftWrapped)
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298 LABEL_WEST = fm.stringWidth(getMask());
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301 return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
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306 * Generates a string of zeroes.
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312 for (int i = av.alignment.getWidth(); i > 0; i /= 10)
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319 public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
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322 AlignmentI al = av.getAlignment();
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324 FontMetrics fm = getFontMetrics(av.getFont());
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326 int LABEL_EAST = 0;
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328 if (av.scaleRightWrapped)
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330 LABEL_EAST = fm.stringWidth(getMask()+"0");
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333 int LABEL_WEST = 0;
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335 if (av.scaleLeftWrapped)
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337 LABEL_WEST = fm.stringWidth(getMask());
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340 int hgap = av.charHeight;
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341 if(av.scaleAboveWrapped)
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342 hgap += av.charHeight;
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344 int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
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345 int cHeight = av.getAlignment().getHeight() * av.charHeight;
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347 av.setWrappedWidth(cWidth);
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349 av.endRes = av.startRes + cWidth;
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352 int endx = (startRes + cWidth) - 1;
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356 while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
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358 g.setColor(Color.black);
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360 if (av.scaleLeftWrapped)
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362 drawWestScale(g, startRes, endx, ypos);
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365 if (av.scaleRightWrapped)
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367 g.translate(canvasWidth - LABEL_EAST, 0);
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368 drawEastScale(g, startRes, endx, ypos);
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369 g.translate(-(canvasWidth - LABEL_EAST), 0);
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372 g.translate(LABEL_WEST, 0);
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374 if (av.scaleAboveWrapped)
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376 drawNorthScale(g, startRes, endx, ypos);
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380 if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size())
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382 endx = av.vconsensus.size() - 2;
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386 if(g.getClip()==null)
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387 g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
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389 drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
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393 if(av.showAnnotation)
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395 g.translate(0, cHeight + ypos+4);
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396 if(annotations==null)
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397 annotations = new AnnotationPanel(av);
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399 annotations.drawComponent( g, startRes, endx + 1);
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400 g.translate(0, -cHeight - ypos-4);
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402 g.translate(-LABEL_WEST, 0);
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404 ypos += cHeight+getAnnotationHeight()+hgap;
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407 startRes += cWidth;
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408 endx = (startRes + cWidth) - 1;
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410 if (endx > al.getWidth())
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412 endx = al.getWidth();
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418 AnnotationPanel annotations;
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419 int getAnnotationHeight()
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421 if(!av.showAnnotation)
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424 if(annotations==null)
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425 annotations = new AnnotationPanel(av);
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427 return annotations.adjustPanelHeight();
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430 synchronized public void drawPanel(Graphics g, int x1, int x2, int y1, int y2,
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431 int startx, int starty, int offset)
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434 g.setFont(av.getFont());
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435 sr.renderGaps(av.renderGaps);
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438 /// First draw the sequences
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439 /////////////////////////////
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440 for (int i = y1; i < y2; i++)
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442 nextSeq = av.alignment.getSequenceAt(i);
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444 sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,
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445 (x1 - startx) * av.charWidth,
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447 (i - starty) * av.charHeight,
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448 av.charWidth, av.charHeight);
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450 if (av.showSequenceFeatures)
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452 fr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,
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453 (x1 - startx) * av.charWidth,
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455 (i - starty) * av.charHeight,
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456 av.charWidth, av.charHeight);
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460 /////////////////////////////////////
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462 // Now outline any areas if necessary
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463 /////////////////////////////////////
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464 SequenceGroup group = av.getSelectionGroup();
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465 java.util.Vector groups = av.alignment.getGroups();
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467 int sx = -1, sy = -1, ex = -1;
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468 int groupIndex = -1;
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469 if (group == null && groups.size() > 0)
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471 group = (SequenceGroup) groups.elementAt(0);
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480 boolean inGroup = false;
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484 for (i = y1; i < y2; i++)
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486 sx = (group.getStartRes() - startx) * av.charWidth;
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487 sy = offset + ((i - starty) * av.charHeight);
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488 ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -
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491 if(sx+ex<0 || sx>imgWidth)
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496 if ( (sx <= (x2-x1)*av.charWidth) &&
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497 group.sequences.contains(av.alignment.getSequenceAt(
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503 if(i == y2-1 || // Dont check for i+1 if on the bottom row
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504 !group.sequences.contains(av.alignment.getSequenceAt(i+1 )))
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506 bottom = sy + av.charHeight;
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511 if (((top == -1) && (i == 0)) ||
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512 !group.sequences.contains(
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513 av.alignment.getSequenceAt(i - 1)))
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521 if (group == av.getSelectionGroup())
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524 g.setColor(Color.red);
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528 g.setColor(group.getOutlineColour());
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536 if (sx >= 0 && sx < imgWidth)
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537 g.drawLine(sx, oldY, sx, sy);
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539 if (sx + ex < imgWidth)
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540 g.drawLine(sx + ex, oldY, sx + ex, sy);
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548 if (sx + ex > imgWidth)
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551 else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)
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552 ex = (x2 - x1 + 1) * av.charWidth;
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556 g.drawLine(sx, top, sx + ex, top);
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562 g.drawLine(sx, bottom, sx + ex, bottom);
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573 sy = offset + ( (i - starty) * av.charHeight);
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574 if (sx >= 0 && sx < imgWidth)
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575 g.drawLine(sx, oldY, sx, sy);
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577 if (sx + ex < imgWidth)
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578 g.drawLine(sx + ex, oldY, sx + ex, sy);
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586 if (sx + ex > imgWidth)
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588 else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)
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589 ex = (x2 - x1 + 1) * av.charWidth;
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593 g.drawLine(sx, top, sx + ex, top);
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599 g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
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608 if (groupIndex >= groups.size())
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613 group = (SequenceGroup) groups.elementAt(groupIndex);
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615 while (groupIndex < groups.size());
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618 /// Highlight search Results once all sequences have been drawn
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619 //////////////////////////////////////////////////////////
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622 for (int r = 0; r < searchResults.length; r += 3)
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624 int searchSeq = searchResults[r];
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626 if (searchSeq >= y1 && searchSeq < y2)
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628 SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);
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630 int searchStart = seq.findIndex(searchResults[r + 1]) - 1;
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631 int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;
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633 SequenceRenderer ssr = (SequenceRenderer) sr;
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634 if (searchStart < x1)
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638 if (searchEnd > x2)
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643 ssr.drawHighlightedText(seq,
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646 (searchStart - startx) * av.charWidth,
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648 (searchSeq-starty)*av.charHeight,
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657 public void highlightSearchResults(int[] results)
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659 // results are in the order sequence, startRes, endRes
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660 if (results == null)
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662 displaySearch = false;
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666 displaySearch = true;
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669 searchResults = results;
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