2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
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3 * Copyright (C) 2014 The Jalview Authors
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3
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10 * of the License, or (at your option) any later version.
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12 * Jalview is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty
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14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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15 * PURPOSE. See the GNU General Public License for more details.
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17 * You should have received a copy of the GNU General Public License
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18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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19 * The Jalview Authors are detailed in the 'AUTHORS' file.
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21 package jalview.appletgui;
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23 import jalview.datamodel.AlignmentI;
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24 import jalview.datamodel.SearchResults;
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25 import jalview.datamodel.SequenceGroup;
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26 import jalview.datamodel.SequenceI;
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28 import java.awt.Color;
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29 import java.awt.FontMetrics;
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30 import java.awt.Graphics;
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31 import java.awt.Image;
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32 import java.awt.Panel;
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34 public class SeqCanvas extends Panel
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38 SequenceRenderer sr;
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50 SearchResults searchResults = null;
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52 boolean fastPaint = false;
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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 PaintRefresher.Register(this, av.getSequenceSetId());
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66 public AlignViewport getViewport()
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71 public FeatureRenderer getFeatureRenderer()
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76 public SequenceRenderer getSequenceRenderer()
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81 void drawNorthScale(Graphics g, int startx, int endx, int ypos)
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83 int scalestartx = startx - startx % 10 + 10;
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85 g.setColor(Color.black);
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88 for (int i = scalestartx; i < endx; i += 10)
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91 if (av.hasHiddenColumns())
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93 value = av.getColumnSelection().adjustForHiddenColumns(value);
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96 g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,
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97 ypos - (av.charHeight / 2));
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99 g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
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100 (ypos + 2) - (av.charHeight / 2),
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101 ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
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106 void drawWestScale(Graphics g, int startx, int endx, int ypos)
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108 FontMetrics fm = getFontMetrics(av.getFont());
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109 ypos += av.charHeight;
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110 if (av.hasHiddenColumns())
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112 startx = av.getColumnSelection().adjustForHiddenColumns(startx);
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113 endx = av.getColumnSelection().adjustForHiddenColumns(endx);
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116 int maxwidth = av.getAlignment().getWidth();
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117 if (av.hasHiddenColumns())
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119 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
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123 for (int i = 0; i < av.getAlignment().getHeight(); i++)
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125 SequenceI seq = av.getAlignment().getSequenceAt(i);
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126 int index = startx;
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129 while (index < endx)
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131 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
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138 value = av.getAlignment().getSequenceAt(i).findPosition(index);
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145 int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
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146 - av.charWidth / 2;
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147 g.drawString(value + "", x, (ypos + (i * av.charHeight))
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148 - (av.charHeight / 5));
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153 void drawEastScale(Graphics g, int startx, int endx, int ypos)
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155 ypos += av.charHeight;
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157 if (av.hasHiddenColumns())
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159 endx = av.getColumnSelection().adjustForHiddenColumns(endx);
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164 for (int i = 0; i < av.getAlignment().getHeight(); i++)
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166 seq = av.getAlignment().getSequenceAt(i);
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170 while (index > startx)
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172 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
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179 value = seq.findPosition(index);
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186 g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))
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187 - (av.charHeight / 5));
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194 void fastPaint(int horizontal, int vertical)
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196 if (fastPaint || gg == null)
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201 // Its possible on certain browsers that the call to fastpaint
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202 // is faster than it can paint, so this check here catches
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203 // this possibility
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204 if (lastsr + horizontal != av.startRes)
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206 horizontal = av.startRes - lastsr;
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209 lastsr = av.startRes;
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212 gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,
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213 imgWidth - horizontal * av.charWidth, imgHeight - vertical
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214 * av.charHeight, -horizontal * av.charWidth, -vertical
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217 int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;
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219 if (horizontal > 0) // scrollbar pulled right, image to the left
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221 transX = (er - sr - horizontal) * av.charWidth;
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222 sr = er - horizontal;
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224 else if (horizontal < 0)
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226 er = sr - horizontal;
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229 else if (vertical > 0) // scroll down
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231 ss = es - vertical;
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232 if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
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238 transY = imgHeight - vertical * av.charHeight;
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241 else if (vertical < 0)
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243 es = ss - vertical;
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244 if (es > av.endSeq)
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250 gg.translate(transX, transY);
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252 drawPanel(gg, sr, er, ss, es, 0);
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253 gg.translate(-transX, -transY);
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260 * Definitions of startx and endx (hopefully): SMJS This is what I'm working
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261 * towards! startx is the first residue (starting at 0) to display. endx is
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262 * the last residue to display (starting at 0). starty is the first sequence
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263 * to display (starting at 0). endy is the last sequence to display (starting
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264 * at 0). NOTE 1: The av limits are set in setFont in this class and in the
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265 * adjustment listener in SeqPanel when the scrollbars move.
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267 public void update(Graphics g)
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272 public void paint(Graphics g)
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276 && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g
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277 .getClipBounds().height)))
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279 g.drawImage(img, 0, 0, this);
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286 g.drawImage(img, 0, 0, this);
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291 // this draws the whole of the alignment
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292 imgWidth = this.getSize().width;
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293 imgHeight = this.getSize().height;
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295 imgWidth -= imgWidth % av.charWidth;
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296 imgHeight -= imgHeight % av.charHeight;
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298 if (imgWidth < 1 || imgHeight < 1)
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303 if (img == null || imgWidth != img.getWidth(this)
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304 || imgHeight != img.getHeight(this))
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306 img = createImage(imgWidth, imgHeight);
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307 gg = img.getGraphics();
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308 gg.setFont(av.getFont());
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311 gg.setColor(Color.white);
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312 gg.fillRect(0, 0, imgWidth, imgHeight);
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314 if (av.getWrapAlignment())
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316 drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
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320 drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
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323 g.drawImage(img, 0, 0, this);
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327 int LABEL_WEST, LABEL_EAST;
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329 public int getWrappedCanvasWidth(int cwidth)
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331 cwidth -= cwidth % av.charWidth;
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333 FontMetrics fm = getFontMetrics(av.getFont());
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338 if (av.scaleRightWrapped)
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340 LABEL_EAST = fm.stringWidth(getMask());
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343 if (av.scaleLeftWrapped)
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345 LABEL_WEST = fm.stringWidth(getMask());
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348 return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
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352 * Generates a string of zeroes.
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361 AlignmentI alignment = av.getAlignment();
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362 for (int i = 0; i < alignment.getHeight(); i++)
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364 tmp = alignment.getSequenceAt(i).getEnd();
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365 if (tmp > maxWidth)
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371 for (int i = maxWidth; i > 0; i /= 10)
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378 public void drawWrappedPanel(Graphics g, int canvasWidth,
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379 int canvasHeight, int startRes)
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381 AlignmentI al = av.getAlignment();
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383 FontMetrics fm = getFontMetrics(av.getFont());
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385 if (av.scaleRightWrapped)
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387 LABEL_EAST = fm.stringWidth(getMask());
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390 if (av.scaleLeftWrapped)
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392 LABEL_WEST = fm.stringWidth(getMask());
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395 int hgap = av.charHeight;
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396 if (av.scaleAboveWrapped)
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398 hgap += av.charHeight;
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401 int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
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402 int cHeight = av.getAlignment().getHeight() * av.charHeight;
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404 av.setWrappedWidth(cWidth);
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406 av.endRes = av.startRes + cWidth;
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411 int maxwidth = av.getAlignment().getWidth() - 1;
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413 if (av.hasHiddenColumns())
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415 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
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418 while ((ypos <= canvasHeight) && (startRes < maxwidth))
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420 endx = startRes + cWidth - 1;
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422 if (endx > maxwidth)
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427 g.setColor(Color.black);
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429 if (av.scaleLeftWrapped)
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431 drawWestScale(g, startRes, endx, ypos);
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434 if (av.scaleRightWrapped)
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436 g.translate(canvasWidth - LABEL_EAST, 0);
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437 drawEastScale(g, startRes, endx, ypos);
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438 g.translate(-(canvasWidth - LABEL_EAST), 0);
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441 g.translate(LABEL_WEST, 0);
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443 if (av.scaleAboveWrapped)
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445 drawNorthScale(g, startRes, endx, ypos);
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447 if (av.hasHiddenColumns() && av.showHiddenMarkers)
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449 g.setColor(Color.blue);
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451 for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
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454 res = av.getColumnSelection().findHiddenRegionPosition(i)
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457 if (res < 0 || res > endx - startRes)
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462 gg.fillPolygon(new int[]
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463 { res * av.charWidth - av.charHeight / 4,
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464 res * av.charWidth + av.charHeight / 4, res * av.charWidth },
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466 { ypos - (av.charHeight / 2), ypos - (av.charHeight / 2),
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467 ypos - (av.charHeight / 2) + 8 }, 3);
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472 if (g.getClip() == null)
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474 g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
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477 drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
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480 if (av.showAnnotation)
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482 g.translate(0, cHeight + ypos + 4);
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483 if (annotations == null)
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485 annotations = new AnnotationPanel(av);
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488 annotations.drawComponent(g, startRes, endx + 1);
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489 g.translate(0, -cHeight - ypos - 4);
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491 g.translate(-LABEL_WEST, 0);
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493 ypos += cHeight + getAnnotationHeight() + hgap;
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495 startRes += cWidth;
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500 AnnotationPanel annotations;
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502 int getAnnotationHeight()
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504 if (!av.showAnnotation)
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509 if (annotations == null)
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511 annotations = new AnnotationPanel(av);
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514 return annotations.adjustPanelHeight();
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517 void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
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518 int endSeq, int offset)
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522 if (!av.hasHiddenColumns())
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524 draw(g1, startRes, endRes, startSeq, endSeq, offset);
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530 int blockStart = startRes;
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531 int blockEnd = endRes;
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533 if (av.hasHiddenColumns())
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535 for (int[] region : av.getColumnSelection().getHiddenColumns())
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537 int hideStart = region[0];
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538 int hideEnd = region[1];
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540 if (hideStart <= blockStart)
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542 blockStart += (hideEnd - hideStart) + 1;
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546 blockEnd = hideStart - 1;
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548 g1.translate(screenY * av.charWidth, 0);
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550 draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
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552 if (av.getShowHiddenMarkers())
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554 g1.setColor(Color.blue);
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555 g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1,
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556 0 + offset, (blockEnd - blockStart + 1) * av.charWidth
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557 - 1, (endSeq - startSeq) * av.charHeight
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561 g1.translate(-screenY * av.charWidth, 0);
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562 screenY += blockEnd - blockStart + 1;
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563 blockStart = hideEnd + 1;
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566 if (screenY <= (endRes - startRes))
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568 blockEnd = blockStart + (endRes - startRes) - screenY;
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569 g1.translate(screenY * av.charWidth, 0);
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570 draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
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572 g1.translate(-screenY * av.charWidth, 0);
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578 // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
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579 // int x1, int x2, int y1, int y2, int startx, int starty,
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580 void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,
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583 g.setFont(av.getFont());
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584 sr.prepare(g, av.renderGaps);
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588 // / First draw the sequences
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589 // ///////////////////////////
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590 for (int i = startSeq; i < endSeq; i++)
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592 nextSeq = av.getAlignment().getSequenceAt(i);
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594 if (nextSeq == null)
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599 sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
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600 startRes, endRes, offset + ((i - startSeq) * av.charHeight));
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602 if (av.isShowSequenceFeatures())
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604 fr.drawSequence(g, nextSeq, startRes, endRes, offset
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605 + ((i - startSeq) * av.charHeight));
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608 // / Highlight search Results once all sequences have been drawn
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609 // ////////////////////////////////////////////////////////
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610 if (searchResults != null)
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612 int[] visibleResults = searchResults.getResults(nextSeq, startRes,
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614 if (visibleResults != null)
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616 for (int r = 0; r < visibleResults.length; r += 2)
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618 sr.drawHighlightedText(nextSeq, visibleResults[r],
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619 visibleResults[r + 1], (visibleResults[r] - startRes)
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620 * av.charWidth, offset
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621 + ((i - startSeq) * av.charHeight));
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626 if (av.cursorMode && cursorY == i && cursorX >= startRes
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627 && cursorX <= endRes)
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629 sr.drawCursor(nextSeq, cursorX,
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630 (cursorX - startRes) * av.charWidth, offset
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631 + ((i - startSeq) * av.charHeight));
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635 if (av.getSelectionGroup() != null
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636 || av.getAlignment().getGroups().size() > 0)
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638 drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
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643 void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
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644 int startSeq, int endSeq, int offset)
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647 // ///////////////////////////////////
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648 // Now outline any areas if necessary
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649 // ///////////////////////////////////
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650 SequenceGroup group = av.getSelectionGroup();
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655 int groupIndex = -1;
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657 if ((group == null) && (av.getAlignment().getGroups().size() > 0))
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659 group = av.getAlignment().getGroups().get(0);
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669 boolean inGroup = false;
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672 int alHeight = av.getAlignment().getHeight() - 1;
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674 for (i = startSeq; i < endSeq; i++)
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676 sx = (group.getStartRes() - startRes) * av.charWidth;
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677 sy = offset + ((i - startSeq) * av.charHeight);
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678 ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1;
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680 if (sx + ex < 0 || sx > imgWidth)
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685 if ((sx <= (endRes - startRes) * av.charWidth)
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686 && group.getSequences(null).contains(
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687 av.getAlignment().getSequenceAt(i)))
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690 && (i >= alHeight || !group.getSequences(null)
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692 av.getAlignment().getSequenceAt(i + 1))))
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694 bottom = sy + av.charHeight;
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699 if (((top == -1) && (i == 0))
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700 || !group.getSequences(null).contains(
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701 av.getAlignment().getSequenceAt(i - 1)))
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709 if (group == av.getSelectionGroup())
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711 g.setColor(Color.red);
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715 g.setColor(group.getOutlineColour());
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723 if (sx >= 0 && sx < imgWidth)
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725 g.drawLine(sx, oldY, sx, sy);
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728 if (sx + ex < imgWidth)
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730 g.drawLine(sx + ex, oldY, sx + ex, sy);
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739 if (sx + ex > imgWidth)
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744 else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
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746 ex = (endRes - startRes + 1) * av.charWidth;
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751 g.drawLine(sx, top, sx + ex, top);
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757 g.drawLine(sx, bottom, sx + ex, bottom);
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768 sy = offset + ((i - startSeq) * av.charHeight);
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769 if (sx >= 0 && sx < imgWidth)
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771 g.drawLine(sx, oldY, sx, sy);
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774 if (sx + ex < imgWidth)
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776 g.drawLine(sx + ex, oldY, sx + ex, sy);
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785 if (sx + ex > imgWidth)
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789 else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
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791 ex = (endRes - startRes + 1) * av.charWidth;
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796 g.drawLine(sx, top, sx + ex, top);
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802 g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
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811 if (groupIndex >= av.getAlignment().getGroups().size())
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816 group = av.getAlignment().getGroups()
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818 } while (groupIndex < av.getAlignment().getGroups().size());
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823 public void highlightSearchResults(SearchResults results)
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825 searchResults = results;
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