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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25 import java.awt.event.*;
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27 import jalview.datamodel.*;
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29 public class AnnotationPanel
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30 extends Panel implements AdjustmentListener
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37 static String HELIX = "Helix";
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38 static String SHEET = "Sheet";
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39 static String LABEL = "Label";
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40 static String REMOVE = "Remove Annotation";
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41 static String COLOUR = "Colour";
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42 static Color HELIX_COLOUR = Color.red.darker();
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43 static Color SHEET_COLOUR = Color.green.darker().darker();
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50 boolean fastPaint = false;
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52 public static int GRAPH_HEIGHT = 40;
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54 public AnnotationPanel(AlignmentPanel ap)
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58 this.setLayout(null);
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59 adjustPanelHeight();
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61 addMouseMotionListener(new MouseMotionAdapter()
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63 public void mouseMoved(MouseEvent evt)
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69 // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
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73 public AnnotationPanel(AlignViewport av)
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79 public void adjustmentValueChanged(AdjustmentEvent evt)
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81 ap.alabels.setScrollOffset( -evt.getValue());
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84 public int adjustPanelHeight()
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86 // setHeight of panels
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87 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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93 for (int i = 0; i < aa.length; i++)
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104 aa[i].height += av.charHeight;
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106 if (aa[i].hasIcons)
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108 aa[i].height += 16;
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113 aa[i].height += GRAPH_HEIGHT;
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116 if (aa[i].height == 0)
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120 height += aa[i].height;
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128 this.setSize(getSize().width, height);
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130 ap.annotationScroller.setSize(getSize().width, height);
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139 public void addEditableColumn(int i)
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141 if (activeRow == -1)
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143 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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147 for (int j = 0; j < aa.length; j++)
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149 if (aa[j].editable)
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157 if (activeRes == null)
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159 activeRes = new Vector();
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160 activeRes.addElement(String.valueOf(i));
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164 activeRes.addElement(String.valueOf(i));
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167 public void doMouseMoved(MouseEvent evt)
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169 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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177 for (int i = 0; i < aa.length; i++)
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182 height += aa[i].height;
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185 if (evt.getY() < height)
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192 int res = evt.getX() / av.getCharWidth() + av.getStartRes();
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193 if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null)
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195 StringBuffer text = new StringBuffer("Sequence position " + (res + 1) +
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197 aa[row].annotations[res].description);
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198 ap.alignFrame.statusBar.setText(text.toString());
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202 public void update(Graphics g)
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207 public void paint(Graphics g)
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209 imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
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211 if (image == null || imgWidth != image.getWidth(this))
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213 image = createImage(imgWidth, ap.annotationPanel.getSize().height);
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214 gg = image.getGraphics();
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215 gg.setFont(av.getFont());
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216 fm = gg.getFontMetrics();
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222 g.drawImage(image, 0, 0, this);
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227 drawComponent(gg, av.startRes, av.endRes + 1);
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228 g.drawImage(image, 0, 0, this);
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231 public void fastPaint(int horizontal)
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233 if (horizontal == 0
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234 || av.alignment.getAlignmentAnnotation() == null
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235 || av.alignment.getAlignmentAnnotation().length < 1
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242 gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal * av.charWidth, 0);
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243 int sr = av.startRes, er = av.endRes + 1, transX = 0;
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245 if (horizontal > 0) // scrollbar pulled right, image to the left
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247 transX = (er - sr - horizontal) * av.charWidth;
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248 sr = er - horizontal;
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250 else if (horizontal < 0)
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252 er = sr - horizontal;
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255 gg.translate(transX, 0);
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257 drawComponent(gg, sr, er);
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259 gg.translate( -transX, 0);
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268 * @param g DOCUMENT ME!
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269 * @param startRes DOCUMENT ME!
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270 * @param endRes DOCUMENT ME!
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272 public void drawComponent(Graphics g, int startRes, int endRes)
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274 g.setFont(av.getFont());
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277 fm = g.getFontMetrics();
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280 g.setColor(Color.white);
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281 g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);
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283 if ((av.alignment.getAlignmentAnnotation() == null) ||
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284 (av.alignment.getAlignmentAnnotation().length < 1))
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286 g.setColor(Color.white);
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287 g.fillRect(0, 0, getSize().width, getSize().height);
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288 g.setColor(Color.black);
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289 g.drawString("Alignment has no annotations", 20, 15);
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294 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
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299 char[] lastSS = new char[aa.length];
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300 int[] lastSSX = new int[aa.length];
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301 int iconOffset = av.charHeight / 2;
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302 boolean validRes = false;
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304 boolean [] graphGroupDrawn = new boolean[aa.length];
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308 for (int i = 0; i < aa.length; i++)
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310 AlignmentAnnotation row = aa[i];
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321 if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )
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324 // this is so that we draw the characters below the graph
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329 y -= av.charHeight;
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335 iconOffset = av.charHeight / 2;
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342 for (j = startRes; j < endRes; j++)
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344 if ((row.annotations.length <= j) ||
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345 (row.annotations[j] == null))
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354 x = (j - startRes) * av.charWidth;
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356 if (activeRow == i)
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358 g.setColor(Color.red);
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360 if (activeRes != null)
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362 for (int n = 0; n < activeRes.size(); n++)
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364 int v = Integer.parseInt(activeRes.elementAt(n).toString());
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368 g.fillRect((j - startRes) * av.charWidth, y,
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369 av.charWidth, row.height);
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376 (row.annotations[j].displayCharacter.length() > 0))
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379 int charOffset = (av.charWidth -
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380 fm.charWidth(row.annotations[j].displayCharacter.charAt(
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382 g.setColor(row.annotations[j].colour);
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384 if (j == 0 || row.graph>0)
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386 g.drawString(row.annotations[j].displayCharacter, x+charOffset,
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387 y + iconOffset + 3);
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389 else if (((row.annotations[j - 1] == null) ||
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390 (!row.annotations[j].displayCharacter.equals(
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391 row.annotations[j - 1].displayCharacter))))
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393 g.drawString(row.annotations[j].displayCharacter, x+charOffset,
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394 y + iconOffset + 3);
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401 (row.annotations[j].secondaryStructure != lastSS[i]))
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406 g.setColor(HELIX_COLOUR);
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407 g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
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408 x - lastSSX[i], 7, 8, 8);
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413 g.setColor(SHEET_COLOUR);
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414 g.fillRect(lastSSX[i], y + 4 + iconOffset,
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415 x - lastSSX[i] - 4, 7);
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416 g.fillPolygon(new int[] { x - 4, x - 4, x },
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419 y + iconOffset, y + 14 + iconOffset,
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427 g.setColor(Color.gray);
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428 g.fillRect(lastSSX[i], y + 6 + iconOffset,
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429 x - lastSSX[i], 2);
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436 lastSS[i] = row.annotations[j].secondaryStructure;
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455 g.setColor(HELIX_COLOUR);
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456 g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
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457 x - lastSSX[i], 7, 8, 8);
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462 g.setColor(SHEET_COLOUR);
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464 if (row.annotations.length > endRes
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465 && row.annotations[endRes].secondaryStructure != 'E')
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467 g.fillRect(lastSSX[i], y + 4 + iconOffset,
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468 x - lastSSX[i] - 4, 7);
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469 g.fillPolygon(new int[]
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473 y + iconOffset, y + 14 + iconOffset,
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478 g.fillRect(lastSSX[i], y + 4 + iconOffset,
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479 x - lastSSX[i], 7);
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487 g.setColor(Color.gray);
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488 g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
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496 if(row.graph == AlignmentAnnotation.LINE_GRAPH )
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498 if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])
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500 float groupmax=-999999, groupmin=9999999;
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501 for(int gg=0; gg<aa.length; gg++)
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503 if(aa[gg].graphGroup!=row.graphGroup)
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507 aa[gg].visible = false;
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509 if(aa[gg].graphMax>groupmax)
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510 groupmax = aa[gg].graphMax;
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511 if(aa[gg].graphMin<groupmin)
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512 groupmin = aa[gg].graphMin;
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515 for (int gg = 0; gg < aa.length; gg++)
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517 if (aa[gg].graphGroup == row.graphGroup)
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519 drawLineGraph(g, aa[gg], startRes, endRes, y,
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520 groupmin, groupmax,
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525 graphGroupDrawn[ row.graphGroup ] = true;
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528 drawLineGraph(g, row, startRes, endRes,
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529 y, row.graphMin, row.graphMax, row.graphHeight );
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531 else if(row.graph == AlignmentAnnotation.BAR_GRAPH )
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532 drawBarGraph(g, row, startRes, endRes,
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533 row.graphMin, row.graphMax, y);
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536 if (row.graph>0 && row.hasText)
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538 y += av.charHeight;
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548 public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
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549 int sRes, int eRes,
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551 float min, float max,
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554 if(sRes>aa.annotations.length)
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558 eRes = Math.min(eRes, aa.annotations.length);
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562 //Adjustment for fastpaint to left
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573 float range = max - min;
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577 y2 = (int)(y - (0-min / range)*graphHeight);
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579 g.setColor(Color.gray);
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580 g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);
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583 for (int j = sRes; j < eRes; j++)
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585 if(aa.annotations[j]==null || aa.annotations[j-1]==null)
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590 g.setColor(aa.annotations[j].colour);
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591 y1 = y - (int) (((aa.annotations[j-1].value-min) / range) * graphHeight);
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592 y2 = y - (int) (((aa.annotations[j].value-min) / range) * graphHeight);
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593 g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);
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598 if(aa.threshold!=null)
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600 g.setColor(aa.threshold.colour);
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601 y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
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602 g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
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607 public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
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608 int sRes, int eRes,
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609 float min, float max,
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612 if(sRes>aa.annotations.length)
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616 eRes = Math.min(eRes, aa.annotations.length);
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620 float range = max - min;
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625 y2 = (int)(y - (0-min / (range))*aa.graphHeight);
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627 g.setColor(Color.gray);
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629 g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);
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631 for (int j = sRes; j < eRes; j++)
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634 if (aa.annotations[j] == null)
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640 g.setColor(aa.annotations[j].colour);
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641 y1 = y - (int) (((aa.annotations[j].value-min) / (range)) * aa.graphHeight);
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644 g.fillRect(x, y2, av.charWidth, y1-y2 );
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646 g.fillRect(x, y1, av.charWidth, y2-y1 );
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652 if(aa.threshold!=null)
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654 g.setColor(aa.threshold.colour);
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655 y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
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656 g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
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662 // used by overview window
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663 public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)
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665 g.setColor(Color.white);
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666 g.fillRect(0, 0, width, y);
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667 g.setColor(new Color(0, 0, 180));
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671 for (int j = sRes; j < eRes; j++)
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673 g.setColor(aa.annotations[j].colour);
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675 height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
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678 g.fillRect(x, y - height, av.charWidth, height);
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