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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19 package jalview.gui;
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21 import jalview.datamodel.*;
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24 import java.awt.image.*;
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26 import javax.swing.*;
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33 * @version $Revision$
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35 public class SeqCanvas extends JComponent
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38 SequenceRenderer sr;
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44 boolean displaySearch = false;
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45 int[] searchResults = null;
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48 boolean fastPaint = false;
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53 * Creates a new SeqCanvas object.
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55 * @param av DOCUMENT ME!
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57 public SeqCanvas(AlignViewport av)
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60 fr = new FeatureRenderer(av);
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61 sr = new SequenceRenderer(av);
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62 setLayout(new BorderLayout());
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63 PaintRefresher.Register(this, av.alignment);
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64 setBackground(Color.white);
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70 * @param g DOCUMENT ME!
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71 * @param startx DOCUMENT ME!
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72 * @param endx DOCUMENT ME!
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73 * @param ypos DOCUMENT ME!
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75 void drawNorthScale(Graphics g, int startx, int endx, int ypos)
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77 int scalestartx = startx - (startx % 10) + 10;
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79 g.setColor(Color.black);
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82 for (int i = scalestartx; i < endx; i += 10)
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84 String string = String.valueOf(i);
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85 g.drawString(string, (i - startx - 1) * av.charWidth,
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86 ypos - (av.charHeight / 2));
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88 g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
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89 (ypos + 2) - (av.charHeight / 2),
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90 ((i - startx - 1) * av.charWidth) + (av.charWidth / 2), ypos -
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98 * @param g DOCUMENT ME!
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99 * @param startx DOCUMENT ME!
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100 * @param endx DOCUMENT ME!
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101 * @param ypos DOCUMENT ME!
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103 void drawWestScale(Graphics g, int startx, int endx, int ypos)
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105 FontMetrics fm = getFontMetrics(av.getFont());
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106 ypos += av.charHeight;
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109 for (int i = 0; i < av.alignment.getHeight(); i++)
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111 SequenceI seq = av.alignment.getSequenceAt(i);
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112 int index = startx;
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115 while (index < endx)
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117 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
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124 value = av.alignment.getSequenceAt(i).findPosition(index);
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131 int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2;
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132 g.drawString(value + "", x,
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133 (ypos + (i * av.charHeight)) - (av.charHeight / 5));
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141 * @param g DOCUMENT ME!
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142 * @param startx DOCUMENT ME!
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143 * @param endx DOCUMENT ME!
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144 * @param ypos DOCUMENT ME!
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146 void drawEastScale(Graphics g, int startx, int endx, int ypos)
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148 ypos += av.charHeight;
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151 for (int i = 0; i < av.alignment.getHeight(); i++)
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153 SequenceI seq = av.alignment.getSequenceAt(i);
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157 while (index > startx)
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159 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
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166 value = av.alignment.getSequenceAt(i).findPosition(index);
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173 g.drawString(String.valueOf(value), av.charWidth/2,
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174 (ypos + (i * av.charHeight)) - (av.charHeight / 5));
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182 * @param horizontal DOCUMENT ME!
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183 * @param vertical DOCUMENT ME!
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185 public void fastPaint(int horizontal, int vertical)
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187 if (((horizontal == 0) && (vertical == 0)) || (gg == null))
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192 gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
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193 -vertical * av.charHeight);
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195 int sr = av.startRes;
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196 int er = av.endRes;
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197 int ss = av.startSeq;
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198 int es = av.endSeq;
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202 if (horizontal > 0) // scrollbar pulled right, image to the left
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204 transX = (er - sr - horizontal) * av.charWidth;
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205 sr = er - horizontal;
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207 else if (horizontal < 0)
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209 er = sr - horizontal;
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211 else if (vertical > 0) // scroll down
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213 ss = es - vertical;
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215 if (ss < av.startSeq)
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216 { // ie scrolling too fast, more than a page at a time
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221 transY = imgHeight - (vertical * av.charHeight);
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224 else if (vertical < 0)
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226 es = ss - vertical;
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228 if (es > av.endSeq)
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234 gg.translate(transX, transY);
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236 gg.setColor(Color.white);
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237 gg.fillRect(0, 0, (er - sr + 1) * av.charWidth,
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238 (es - ss) * av.charHeight);
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239 drawPanel(gg, sr, er, ss, es, sr, ss, 0);
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240 gg.translate(-transX, -transY);
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247 * Definitions of startx and endx (hopefully):
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248 * SMJS This is what I'm working towards!
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249 * startx is the first residue (starting at 0) to display.
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250 * endx is the last residue to display (starting at 0).
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251 * starty is the first sequence to display (starting at 0).
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252 * endy is the last sequence to display (starting at 0).
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253 * NOTE 1: The av limits are set in setFont in this class and
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254 * in the adjustment listener in SeqPanel when the scrollbars move.
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257 // Set this to false to force a full panel paint
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258 public void paintComponent(Graphics g)
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260 if ((img != null) &&
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261 (fastPaint || (getWidth() != g.getClipBounds().width) ||
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262 (getHeight() != g.getClipBounds().height)))
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264 g.drawImage(img, 0, 0, this);
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270 // this draws the whole of the alignment
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271 imgWidth = getWidth();
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272 imgHeight = getHeight();
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274 imgWidth -= (imgWidth % av.charWidth);
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275 imgHeight -= (imgHeight % av.charHeight);
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277 if ((imgWidth < 1) || (imgHeight < 1))
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282 img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);
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283 gg = (Graphics2D) img.getGraphics();
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284 gg.setFont(av.getFont());
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285 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
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286 RenderingHints.VALUE_ANTIALIAS_ON);
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288 gg.setColor(Color.white);
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289 gg.fillRect(0, 0, imgWidth, imgHeight);
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291 chunkWidth = getWrappedCanvasWidth(getWidth());
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292 chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
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294 av.setChunkHeight(chunkHeight);
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295 av.setChunkWidth(chunkWidth);
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297 if (av.getWrapAlignment())
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299 drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
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303 drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq,
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304 av.startRes, av.startSeq, 0);
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307 g.drawImage(img, 0, 0, this);
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313 * @param cwidth DOCUMENT ME!
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315 * @return DOCUMENT ME!
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317 public int getWrappedCanvasWidth(int cwidth)
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319 FontMetrics fm = getFontMetrics(av.getFont());
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324 if (av.scaleRightWrapped)
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326 LABEL_EAST = fm.stringWidth(getMask()+"0");
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329 if (av.scaleLeftWrapped)
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331 LABEL_WEST = fm.stringWidth(getMask());
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334 return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
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339 * Generates a string of zeroes.
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345 for (int i = av.alignment.getWidth(); i > 0; i /= 10)
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355 * @param g DOCUMENT ME!
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356 * @param canvasWidth DOCUMENT ME!
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357 * @param canvasHeight DOCUMENT ME!
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358 * @param startRes DOCUMENT ME!
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360 public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
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364 AlignmentI al = av.getAlignment();
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366 FontMetrics fm = getFontMetrics(av.getFont());
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368 int LABEL_EAST = 0;
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370 if (av.scaleRightWrapped)
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372 LABEL_EAST = fm.stringWidth(getMask()+"0");
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375 int LABEL_WEST = 0;
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377 if (av.scaleLeftWrapped)
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379 LABEL_WEST = fm.stringWidth(getMask());
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382 int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
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383 int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
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385 av.endRes = av.startRes + cWidth;
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387 int endx = (startRes + cWidth) - 1;
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388 int ypos = 2 * av.charHeight;
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390 while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
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392 g.setColor(Color.black);
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394 if (av.scaleLeftWrapped)
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396 drawWestScale(g, startRes, endx, ypos);
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399 if (av.scaleRightWrapped)
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401 g.translate(canvasWidth - LABEL_EAST, 0);
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402 drawEastScale(g, startRes, endx, ypos);
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403 g.translate(-(canvasWidth - LABEL_EAST), 0);
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406 g.translate(LABEL_WEST, 0);
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408 if (av.scaleAboveWrapped)
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410 drawNorthScale(g, startRes, endx, ypos);
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413 // When printing we have an extra clipped region,
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414 // the Printable page which we need to account for here
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415 Shape clip = g.getClip();
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419 g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
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423 g.setClip(0, (int) clip.getBounds().getY(),
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424 cWidth * av.charWidth, (int) clip.getBounds().getHeight());
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427 if(av.alignment.getWidth() >= av.vconsensus.size())
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429 endx = av.vconsensus.size()-2;
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432 drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
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434 g.translate(-LABEL_WEST, 0);
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437 startRes += cWidth;
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438 endx = (startRes + cWidth) - 1;
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440 if (endx > al.getWidth())
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442 endx = al.getWidth();
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450 * @param g1 DOCUMENT ME!
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451 * @param x1 DOCUMENT ME!
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452 * @param x2 DOCUMENT ME!
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453 * @param y1 DOCUMENT ME!
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454 * @param y2 DOCUMENT ME!
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455 * @param startx DOCUMENT ME!
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456 * @param starty DOCUMENT ME!
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457 * @param offset DOCUMENT ME!
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459 synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,
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460 int y2, int startx, int starty, int offset)
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462 Graphics2D g = (Graphics2D) g1;
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463 g.setFont(av.getFont());
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464 sr.renderGaps(av.renderGaps);
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468 /// First draw the sequences
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469 /////////////////////////////
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470 for (int i = y1; i < y2; i++)
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472 nextSeq = av.alignment.getSequenceAt(i);
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474 sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),
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475 x1, x2, (x1 - startx) * av.charWidth,
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476 offset + ((i - starty) * av.charHeight), av.charWidth,
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479 if (av.showSequenceFeatures)
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481 fr.drawSequence(g, nextSeq,
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482 av.alignment.findAllGroups(nextSeq), x1, x2,
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483 (x1 - startx) * av.charWidth,
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484 offset + ((i - starty) * av.charHeight), av.charWidth,
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490 /////////////////////////////////////
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491 // Now outline any areas if necessary
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492 /////////////////////////////////////
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493 SequenceGroup group = av.getSelectionGroup();
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494 java.util.Vector groups = av.alignment.getGroups();
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499 int groupIndex = -1;
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501 if ((group == null) && (groups.size() > 0))
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503 group = (SequenceGroup) groups.elementAt(0);
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514 boolean inGroup = false;
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518 for (i = y1; i < y2; i++)
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520 sx = (group.getStartRes() - startx) * av.charWidth;
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521 sy = offset + ((i - starty) * av.charHeight);
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522 ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -
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526 if ((sx < (x2-x1)*av.charWidth) &&
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527 group.sequences.contains(av.alignment.getSequenceAt(
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530 if ((bottom == -1) &&
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531 !group.sequences.contains(
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532 av.alignment.getSequenceAt(i + 1)))
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534 bottom = sy + av.charHeight;
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539 if (((top == -1) && (i == 0)) ||
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540 !group.sequences.contains(
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541 av.alignment.getSequenceAt(i - 1)))
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549 if (group == av.getSelectionGroup())
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551 g.setStroke(new BasicStroke(1,
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552 BasicStroke.CAP_BUTT,
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553 BasicStroke.JOIN_ROUND, 3f,
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554 new float[] { 5f, 3f }, 0f));
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555 g.setColor(Color.RED);
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559 g.setStroke(new BasicStroke());
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560 g.setColor(group.getOutlineColour());
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568 g.drawLine(sx, oldY, sx, sy);
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569 g.drawLine(sx + ex, oldY, sx + ex, sy);
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573 g.drawLine(sx, top, sx + ex, top);
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579 g.drawLine(sx, bottom, sx + ex, bottom);
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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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603 sy = offset + ((i - starty) * av.charHeight);
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604 g.drawLine(sx, oldY, sx, sy);
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605 g.drawLine(sx + ex, oldY, sx + ex, sy);
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611 if (groupIndex >= groups.size())
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616 group = (SequenceGroup) groups.elementAt(groupIndex);
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618 while (groupIndex < groups.size());
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621 /// Highlight search Results once all sequences have been drawn
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622 //////////////////////////////////////////////////////////
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625 for (int r = 0; r < searchResults.length; r += 3)
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627 int searchSeq = searchResults[r];
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629 if ((searchSeq >= y1) && (searchSeq < y2))
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631 SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);
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633 int searchStart = seq.findIndex(searchResults[r + 1]) - 1;
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634 int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;
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636 SequenceRenderer ssr = (SequenceRenderer) sr;
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638 if (searchStart < x1)
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643 if (searchEnd > x2)
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648 ssr.drawHighlightedText(seq, searchStart, searchEnd,
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649 (searchStart - startx) * av.charWidth,
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650 offset + ((searchSeq - starty) * av.charHeight),
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651 av.charWidth, av.charHeight);
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660 * @param results DOCUMENT ME!
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662 public void highlightSearchResults(int[] results)
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664 // results are in the order sequence, startRes, endRes
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665 if (results == null)
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667 displaySearch = false;
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671 displaySearch = true;
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674 searchResults = results;
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