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 showScores = false;
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45 boolean displaySearch = false;
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46 int[] searchResults = null;
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49 boolean fastPaint = false;
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54 * Creates a new SeqCanvas object.
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56 * @param av DOCUMENT ME!
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58 public SeqCanvas(AlignViewport av)
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61 fr = new FeatureRenderer(av);
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62 sr = new SequenceRenderer(av);
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63 setLayout(new BorderLayout());
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64 PaintRefresher.Register(this, av.alignment);
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65 setBackground(Color.white);
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71 * @param g DOCUMENT ME!
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72 * @param startx DOCUMENT ME!
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73 * @param endx DOCUMENT ME!
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74 * @param ypos DOCUMENT ME!
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76 void drawNorthScale(Graphics g, int startx, int endx, int ypos)
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78 int scalestartx = startx - (startx % 10) + 10;
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80 g.setColor(Color.black);
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83 for (int i = scalestartx; i < endx; i += 10)
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85 String string = String.valueOf(i);
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86 g.drawString(string, (i - startx - 1) * av.charWidth,
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87 ypos - (av.charHeight / 2));
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89 g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
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90 (ypos + 2) - (av.charHeight / 2),
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91 ((i - startx - 1) * av.charWidth) + (av.charWidth / 2), ypos -
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99 * @param g DOCUMENT ME!
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100 * @param startx DOCUMENT ME!
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101 * @param endx DOCUMENT ME!
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102 * @param ypos DOCUMENT ME!
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104 void drawWestScale(Graphics g, int startx, int endx, int ypos)
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106 FontMetrics fm = getFontMetrics(av.getFont());
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107 ypos += av.charHeight;
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110 for (int i = 0; i < av.alignment.getHeight(); i++)
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112 SequenceI seq = av.alignment.getSequenceAt(i);
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113 int index = startx;
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116 while (index < endx)
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118 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
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125 value = av.alignment.getSequenceAt(i).findPosition(index);
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132 int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2;
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133 g.drawString(value + "", x,
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134 (ypos + (i * av.charHeight)) - (av.charHeight / 5));
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142 * @param g DOCUMENT ME!
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143 * @param startx DOCUMENT ME!
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144 * @param endx DOCUMENT ME!
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145 * @param ypos DOCUMENT ME!
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147 void drawEastScale(Graphics g, int startx, int endx, int ypos)
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149 ypos += av.charHeight;
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152 for (int i = 0; i < av.alignment.getHeight(); i++)
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154 SequenceI seq = av.alignment.getSequenceAt(i);
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158 while (index > startx)
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160 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
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167 value = av.alignment.getSequenceAt(i).findPosition(index);
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174 g.drawString(String.valueOf(value), av.charWidth/2,
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175 (ypos + (i * av.charHeight)) - (av.charHeight / 5));
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183 * @param horizontal DOCUMENT ME!
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184 * @param vertical DOCUMENT ME!
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186 public void fastPaint(int horizontal, int vertical)
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188 if (((horizontal == 0) && (vertical == 0)) || (gg == null))
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193 gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
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194 -vertical * av.charHeight);
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196 int sr = av.startRes;
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197 int er = av.endRes;
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198 int ss = av.startSeq;
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199 int es = av.endSeq;
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203 if (horizontal > 0) // scrollbar pulled right, image to the left
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205 transX = (er - sr - horizontal) * av.charWidth;
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206 sr = er - horizontal;
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208 else if (horizontal < 0)
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210 er = sr - horizontal;
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212 else if (vertical > 0) // scroll down
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214 ss = es - vertical;
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216 if (ss < av.startSeq)
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217 { // ie scrolling too fast, more than a page at a time
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222 transY = imgHeight - (vertical * av.charHeight);
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225 else if (vertical < 0)
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227 es = ss - vertical;
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229 if (es > av.endSeq)
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235 gg.translate(transX, transY);
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237 gg.setColor(Color.white);
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238 gg.fillRect(0, 0, (er - sr + 1) * av.charWidth,
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239 (es - ss) * av.charHeight);
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240 drawPanel(gg, sr, er, ss, es, sr, ss, 0);
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241 gg.translate(-transX, -transY);
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248 * Definitions of startx and endx (hopefully):
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249 * SMJS This is what I'm working towards!
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250 * startx is the first residue (starting at 0) to display.
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251 * endx is the last residue to display (starting at 0).
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252 * starty is the first sequence to display (starting at 0).
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253 * endy is the last sequence to display (starting at 0).
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254 * NOTE 1: The av limits are set in setFont in this class and
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255 * in the adjustment listener in SeqPanel when the scrollbars move.
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258 // Set this to false to force a full panel paint
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259 public void paintComponent(Graphics g)
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261 if ((img != null) &&
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262 (fastPaint || (getWidth() != g.getClipBounds().width) ||
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263 (getHeight() != g.getClipBounds().height)))
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265 g.drawImage(img, 0, 0, this);
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271 // this draws the whole of the alignment
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272 imgWidth = getWidth();
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273 imgHeight = getHeight();
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275 imgWidth -= (imgWidth % av.charWidth);
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276 imgHeight -= (imgHeight % av.charHeight);
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278 if ((imgWidth < 1) || (imgHeight < 1))
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283 img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);
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284 gg = (Graphics2D) img.getGraphics();
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285 gg.setFont(av.getFont());
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286 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
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287 RenderingHints.VALUE_ANTIALIAS_ON);
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289 gg.setColor(Color.white);
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290 gg.fillRect(0, 0, imgWidth, imgHeight);
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292 chunkWidth = getWrappedCanvasWidth(getWidth());
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293 chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
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295 av.setChunkHeight(chunkHeight);
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296 av.setChunkWidth(chunkWidth);
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298 if (av.getWrapAlignment())
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300 drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
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304 drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq,
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305 av.startRes, av.startSeq, 0);
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308 g.drawImage(img, 0, 0, this);
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314 * @param cwidth DOCUMENT ME!
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316 * @return DOCUMENT ME!
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318 public int getWrappedCanvasWidth(int cwidth)
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320 FontMetrics fm = getFontMetrics(av.getFont());
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325 if (av.scaleRightWrapped)
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327 LABEL_EAST = fm.stringWidth(getMask()+"0");
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330 if (av.scaleLeftWrapped)
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332 LABEL_WEST = fm.stringWidth(getMask());
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335 return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
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340 * Generates a string of zeroes.
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346 for (int i = av.alignment.getWidth(); i > 0; i /= 10)
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356 * @param g DOCUMENT ME!
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357 * @param canvasWidth DOCUMENT ME!
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358 * @param canvasHeight DOCUMENT ME!
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359 * @param startRes DOCUMENT ME!
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361 public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
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365 AlignmentI al = av.getAlignment();
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367 FontMetrics fm = getFontMetrics(av.getFont());
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369 int LABEL_EAST = 0;
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371 if (av.scaleRightWrapped)
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373 LABEL_EAST = fm.stringWidth(getMask()+"0");
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376 int LABEL_WEST = 0;
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378 if (av.scaleLeftWrapped)
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380 LABEL_WEST = fm.stringWidth(getMask());
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383 int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
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384 int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
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386 av.endRes = av.startRes + cWidth;
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388 int endx = (startRes + cWidth) - 1;
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389 int ypos = 2 * av.charHeight;
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391 while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
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393 g.setColor(Color.black);
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395 if (av.scaleLeftWrapped)
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397 drawWestScale(g, startRes, endx, ypos);
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400 if (av.scaleRightWrapped)
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402 g.translate(canvasWidth - LABEL_EAST, 0);
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403 drawEastScale(g, startRes, endx, ypos);
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404 g.translate(-(canvasWidth - LABEL_EAST), 0);
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407 g.translate(LABEL_WEST, 0);
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409 if (av.scaleAboveWrapped)
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411 drawNorthScale(g, startRes, endx, ypos);
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414 // When printing we have an extra clipped region,
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415 // the Printable page which we need to account for here
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416 Shape clip = g.getClip();
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420 g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
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424 g.setClip(0, (int) clip.getBounds().getY(),
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425 cWidth * av.charWidth, (int) clip.getBounds().getHeight());
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428 drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
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430 g.translate(-LABEL_WEST, 0);
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433 startRes += cWidth;
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434 endx = (startRes + cWidth) - 1;
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436 if (endx > al.getWidth())
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438 endx = al.getWidth();
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446 * @param g1 DOCUMENT ME!
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447 * @param x1 DOCUMENT ME!
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448 * @param x2 DOCUMENT ME!
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449 * @param y1 DOCUMENT ME!
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450 * @param y2 DOCUMENT ME!
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451 * @param startx DOCUMENT ME!
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452 * @param starty DOCUMENT ME!
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453 * @param offset DOCUMENT ME!
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455 synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,
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456 int y2, int startx, int starty, int offset)
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458 Graphics2D g = (Graphics2D) g1;
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459 g.setFont(av.getFont());
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460 sr.renderGaps(av.renderGaps);
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464 /// First draw the sequences
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465 /////////////////////////////
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466 for (int i = y1; i < y2; i++)
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468 nextSeq = av.alignment.getSequenceAt(i);
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470 sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),
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471 x1, x2, (x1 - startx) * av.charWidth,
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472 offset + ((i - starty) * av.charHeight), av.charWidth,
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475 if (av.showSequenceFeatures)
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477 fr.drawSequence(g, nextSeq,
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478 av.alignment.findAllGroups(nextSeq), x1, x2,
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479 (x1 - startx) * av.charWidth,
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480 offset + ((i - starty) * av.charHeight), av.charWidth,
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486 /////////////////////////////////////
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487 // Now outline any areas if necessary
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488 /////////////////////////////////////
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489 SequenceGroup group = av.getSelectionGroup();
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490 java.util.Vector groups = av.alignment.getGroups();
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495 int groupIndex = -1;
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497 if ((group == null) && (groups.size() > 0))
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499 group = (SequenceGroup) groups.elementAt(0);
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510 boolean inGroup = false;
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514 for (i = y1; i < y2; i++)
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516 sx = (group.getStartRes() - startx) * av.charWidth;
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517 sy = offset + ((i - starty) * av.charHeight);
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518 ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -
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522 if ((sx < (x2-x1)*av.charWidth) &&
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523 group.sequences.contains(av.alignment.getSequenceAt(
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526 if ((bottom == -1) &&
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527 !group.sequences.contains(
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528 av.alignment.getSequenceAt(i + 1)))
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530 bottom = sy + av.charHeight;
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535 if (((top == -1) && (i == 0)) ||
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536 !group.sequences.contains(
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537 av.alignment.getSequenceAt(i - 1)))
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545 if (group == av.getSelectionGroup())
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547 g.setStroke(new BasicStroke(1,
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548 BasicStroke.CAP_BUTT,
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549 BasicStroke.JOIN_ROUND, 3f,
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550 new float[] { 5f, 3f }, 0f));
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551 g.setColor(Color.RED);
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555 g.setStroke(new BasicStroke());
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556 g.setColor(group.getOutlineColour());
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564 g.drawLine(sx, oldY, sx, sy);
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565 g.drawLine(sx + ex, oldY, sx + ex, sy);
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569 g.drawLine(sx, top, sx + ex, top);
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575 g.drawLine(sx, bottom, sx + ex, bottom);
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589 g.drawLine(sx, top, sx + ex, top);
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595 g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
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599 sy = offset + ((i - starty) * av.charHeight);
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600 g.drawLine(sx, oldY, sx, sy);
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601 g.drawLine(sx + ex, oldY, sx + ex, sy);
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607 if (groupIndex >= groups.size())
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612 group = (SequenceGroup) groups.elementAt(groupIndex);
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614 while (groupIndex < groups.size());
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617 /// Highlight search Results once all sequences have been drawn
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618 //////////////////////////////////////////////////////////
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621 for (int r = 0; r < searchResults.length; r += 3)
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623 int searchSeq = searchResults[r];
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625 if ((searchSeq >= y1) && (searchSeq < y2))
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627 SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);
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629 int searchStart = seq.findIndex(searchResults[r + 1]) - 1;
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630 int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;
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632 SequenceRenderer ssr = (SequenceRenderer) sr;
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634 if (searchStart < x1)
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639 if (searchEnd > x2)
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644 ssr.drawHighlightedText(seq, searchStart, searchEnd,
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645 (searchStart - startx) * av.charWidth,
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646 offset + ((searchSeq - starty) * av.charHeight),
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647 av.charWidth, av.charHeight);
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656 * @param results DOCUMENT ME!
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658 public void highlightSearchResults(int[] results)
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660 // results are in the order sequence, startRes, endRes
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661 if (results == null)
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663 displaySearch = false;
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667 displaySearch = true;
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670 searchResults = results;
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