src/jalview/gui/AnnotationPanel.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.gui;\r
  20 \r
  21 import jalview.datamodel.*;\r
  22 \r
  23 import java.awt.*;\r
  24 import java.awt.event.*;\r
  25 import java.awt.image.*;\r
  26 \r
  27 import java.util.*;\r
  28 \r
  29 import javax.swing.*;\r
  30 \r
  31 \r
  32 /**\r
  33  * DOCUMENT ME!\r
  34  *\r
  35  * @author $author$\r
  36  * @version $Revision$\r
  37  */\r
  38 public class AnnotationPanel extends JPanel implements MouseListener,\r
  39     MouseMotionListener, ActionListener, AdjustmentListener\r
  40 {\r
  41     final String HELIX = "Helix";\r
  42     final String SHEET = "Sheet";\r
  43     final String LABEL = "Label";\r
  44     final String REMOVE = "Remove Annotation";\r
  45     final String COLOUR = "Colour";\r
  46     final Color HELIX_COLOUR = Color.red.darker();\r
  47     final Color SHEET_COLOUR = Color.green.darker().darker();\r
  48 \r
  49     /** DOCUMENT ME!! */\r
  50     AlignViewport av;\r
  51     AlignmentPanel ap;\r
  52     int activeRow = -1;\r
  53     Vector activeRes;\r
  54     BufferedImage image;\r
  55     Graphics2D gg;\r
  56     FontMetrics fm;\r
  57     int imgWidth = 0;\r
  58     boolean fastPaint = false;\r
  59 \r
  60     //Used For mouse Dragging and resizing graphs\r
  61     int graphStretch = -1;\r
  62     int graphStretchY = -1;\r
  63 \r
  64     /**\r
  65      * Creates a new AnnotationPanel object.\r
  66      *\r
  67      * @param ap DOCUMENT ME!\r
  68      */\r
  69     public AnnotationPanel(AlignmentPanel ap)\r
  70     {\r
  71         ToolTipManager.sharedInstance().registerComponent(this);\r
  72         ToolTipManager.sharedInstance().setInitialDelay(0);\r
  73         ToolTipManager.sharedInstance().setDismissDelay(10000);\r
  74         this.ap = ap;\r
  75         av = ap.av;\r
  76         this.setLayout(null);\r
  77         addMouseListener(this);\r
  78         addMouseMotionListener(this);\r
  79         ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);\r
  80     }\r
  81 \r
  82     public AnnotationPanel(AlignViewport av)\r
  83     {\r
  84       this.av = av;\r
  85     }\r
  86 \r
  87 \r
  88     /**\r
  89      * DOCUMENT ME!\r
  90      *\r
  91      * @param evt DOCUMENT ME!\r
  92      */\r
  93     public void adjustmentValueChanged(AdjustmentEvent evt)\r
  94     {\r
  95         ap.alabels.setScrollOffset(-evt.getValue());\r
  96     }\r
  97 \r
  98     /**\r
  99      * DOCUMENT ME!\r
 100      */\r
 101     public int adjustPanelHeight()\r
 102     {\r
 103         // setHeight of panels\r
 104         image = null;\r
 105         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 106         int height = 0;\r
 107 \r
 108         if (aa != null)\r
 109         {\r
 110             for (int i = 0; i < aa.length; i++)\r
 111             {\r
 112                 if (!aa[i].visible)\r
 113                 {\r
 114                     continue;\r
 115                 }\r
 116 \r
 117                 aa[i].height = 0;\r
 118 \r
 119                 if (aa[i].hasText)\r
 120                 {\r
 121                     aa[i].height += av.charHeight;\r
 122                 }\r
 123 \r
 124                 if (aa[i].hasIcons)\r
 125                 {\r
 126                     aa[i].height += 16;\r
 127                 }\r
 128 \r
 129                 if (aa[i].graph>0)\r
 130                 {\r
 131                     aa[i].height += aa[i].graphHeight;\r
 132                 }\r
 133 \r
 134                 if (aa[i].height == 0)\r
 135                 {\r
 136                     aa[i].height = 20;\r
 137                 }\r
 138 \r
 139                 height += aa[i].height;\r
 140             }\r
 141         }\r
 142         else\r
 143         {\r
 144             height = 20;\r
 145         }\r
 146 \r
 147         this.setPreferredSize(new Dimension(1, height));\r
 148 \r
 149         return height;\r
 150     }\r
 151 \r
 152     /**\r
 153      * DOCUMENT ME!\r
 154      *\r
 155      * @param col DOCUMENT ME!\r
 156      */\r
 157     public void removeEditableColumn(int col)\r
 158     {\r
 159         if (activeRow == -1)\r
 160         {\r
 161             AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 162             if(aa==null)\r
 163               return;\r
 164 \r
 165             for (int j = 0; j < aa.length; j++)\r
 166             {\r
 167                 if (aa[j].editable)\r
 168                 {\r
 169                     activeRow = j;\r
 170 \r
 171                     break;\r
 172                 }\r
 173             }\r
 174         }\r
 175 \r
 176         if ((activeRes != null) && activeRes.contains(String.valueOf(col)))\r
 177         {\r
 178             activeRes.removeElement(String.valueOf(col));\r
 179         }\r
 180 \r
 181         repaint();\r
 182     }\r
 183 \r
 184     /**\r
 185      * DOCUMENT ME!\r
 186      *\r
 187      * @param col DOCUMENT ME!\r
 188      */\r
 189     public void addEditableColumn(int col)\r
 190     {\r
 191         if (activeRow == -1)\r
 192         {\r
 193             AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 194             if(aa==null)\r
 195               return;\r
 196 \r
 197             for (int j = 0; j < aa.length; j++)\r
 198             {\r
 199                 if (aa[j].editable)\r
 200                 {\r
 201                     activeRow = j;\r
 202 \r
 203                     break;\r
 204                 }\r
 205             }\r
 206         }\r
 207 \r
 208         if (activeRes == null)\r
 209         {\r
 210             activeRes = new Vector();\r
 211         }\r
 212 \r
 213         if (!activeRes.contains(String.valueOf(col)))\r
 214         {\r
 215             activeRes.addElement(String.valueOf(col));\r
 216         }\r
 217 \r
 218         repaint();\r
 219     }\r
 220 \r
 221     /**\r
 222      * DOCUMENT ME!\r
 223      *\r
 224      * @param evt DOCUMENT ME!\r
 225      */\r
 226     public void actionPerformed(ActionEvent evt)\r
 227     {\r
 228         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 229         Annotation[] anot = aa[activeRow].annotations;\r
 230 \r
 231         if (evt.getActionCommand().equals(REMOVE))\r
 232         {\r
 233             for (int i = 0; i < activeRes.size(); i++)\r
 234             {\r
 235                 anot[Integer.parseInt(activeRes.get(i).toString())] = null;\r
 236                 anot[Integer.parseInt(activeRes.get(i).toString())] = null;\r
 237             }\r
 238         }\r
 239         else if (evt.getActionCommand().equals(LABEL))\r
 240         {\r
 241             String label = JOptionPane.showInputDialog(this, "Enter Label ",\r
 242                     "Enter label", JOptionPane.QUESTION_MESSAGE);\r
 243 \r
 244             if (label == null)\r
 245             {\r
 246                 return;\r
 247             }\r
 248 \r
 249             if ((label.length() > 0) && !aa[activeRow].hasText)\r
 250             {\r
 251                 aa[activeRow].hasText = true;\r
 252             }\r
 253 \r
 254             for (int i = 0; i < activeRes.size(); i++)\r
 255             {\r
 256                 int index = Integer.parseInt(activeRes.get(i).toString());\r
 257 \r
 258                 if (anot[index] == null)\r
 259                 {\r
 260                     anot[index] = new Annotation(label, "", ' ', 0);\r
 261                 }\r
 262 \r
 263                 anot[index].displayCharacter = label;\r
 264             }\r
 265         }\r
 266         else if (evt.getActionCommand().equals(COLOUR))\r
 267         {\r
 268             Color col = JColorChooser.showDialog(this,\r
 269                     "Choose foreground colour", Color.black);\r
 270 \r
 271             for (int i = 0; i < activeRes.size(); i++)\r
 272             {\r
 273                 int index = Integer.parseInt(activeRes.get(i).toString());\r
 274 \r
 275                 if (anot[index] == null)\r
 276                 {\r
 277                     anot[index] = new Annotation("", "", ' ', 0);\r
 278                 }\r
 279 \r
 280                 anot[index].colour = col;\r
 281             }\r
 282         }\r
 283         else // HELIX OR SHEET\r
 284         {\r
 285             char type = 0;\r
 286             String symbol = "\u03B1";\r
 287 \r
 288             if (evt.getActionCommand().equals(HELIX))\r
 289             {\r
 290                 type = 'H';\r
 291             }\r
 292             else if (evt.getActionCommand().equals(SHEET))\r
 293             {\r
 294                 type = 'E';\r
 295                 symbol = "\u03B2";\r
 296             }\r
 297 \r
 298             if (!aa[activeRow].hasIcons)\r
 299             {\r
 300                 aa[activeRow].hasIcons = true;\r
 301             }\r
 302 \r
 303             String label = JOptionPane.showInputDialog("Enter a label for the structure?",\r
 304                     symbol);\r
 305 \r
 306             if (label == null)\r
 307             {\r
 308                 return;\r
 309             }\r
 310 \r
 311             if ((label.length() > 0) && !aa[activeRow].hasText)\r
 312             {\r
 313                 aa[activeRow].hasText = true;\r
 314             }\r
 315 \r
 316             for (int i = 0; i < activeRes.size(); i++)\r
 317             {\r
 318                 int index = Integer.parseInt(activeRes.get(i).toString());\r
 319 \r
 320                 if (anot[index] == null)\r
 321                 {\r
 322                     anot[index] = new Annotation(label, "", type, 0);\r
 323                 }\r
 324 \r
 325                 anot[index].secondaryStructure = type;\r
 326                 anot[index].displayCharacter = label;\r
 327             }\r
 328         }\r
 329 \r
 330         adjustPanelHeight();\r
 331         activeRes = null;\r
 332         repaint();\r
 333 \r
 334         return;\r
 335     }\r
 336 \r
 337     /**\r
 338      * DOCUMENT ME!\r
 339      *\r
 340      * @param evt DOCUMENT ME!\r
 341      */\r
 342     public void mousePressed(MouseEvent evt)\r
 343     {\r
 344         int height = 0;\r
 345         activeRow = -1;\r
 346 \r
 347         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 348         if(aa==null)\r
 349           return;\r
 350 \r
 351         for (int i = 0; i < aa.length; i++)\r
 352         {\r
 353             if (aa[i].visible)\r
 354             {\r
 355               height += aa[i].height;\r
 356             }\r
 357 \r
 358             if (evt.getY() < height)\r
 359             {\r
 360                 if (aa[i].editable)\r
 361                 {\r
 362                     activeRow = i;\r
 363                 }\r
 364                 else if(aa[i].graph>0)\r
 365                 {\r
 366                     //Stretch Graph\r
 367                     graphStretch = i;\r
 368                     graphStretchY = evt.getY();\r
 369                     activeRes = null;\r
 370                 }\r
 371                 else\r
 372                 {\r
 373                     activeRes = null;\r
 374                 }\r
 375 \r
 376                 break;\r
 377             }\r
 378         }\r
 379 \r
 380         if (SwingUtilities.isRightMouseButton(evt))\r
 381         {\r
 382             if (activeRes == null)\r
 383             {\r
 384                 return;\r
 385             }\r
 386 \r
 387             JPopupMenu pop = new JPopupMenu("Structure type");\r
 388             JMenuItem item = new JMenuItem(HELIX);\r
 389             item.addActionListener(this);\r
 390             pop.add(item);\r
 391             item = new JMenuItem(SHEET);\r
 392             item.addActionListener(this);\r
 393             pop.add(item);\r
 394             item = new JMenuItem(LABEL);\r
 395             item.addActionListener(this);\r
 396             pop.add(item);\r
 397             item = new JMenuItem(COLOUR);\r
 398             item.addActionListener(this);\r
 399             pop.add(item);\r
 400             item = new JMenuItem(REMOVE);\r
 401             item.addActionListener(this);\r
 402             pop.add(item);\r
 403             pop.show(this, evt.getX(), evt.getY());\r
 404 \r
 405             return;\r
 406         }\r
 407 \r
 408         if (aa == null)\r
 409         {\r
 410             return;\r
 411         }\r
 412 \r
 413         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 414 \r
 415         if (evt.isControlDown() || evt.isAltDown())\r
 416         {\r
 417             addEditableColumn(res);\r
 418         }\r
 419         else if (evt.isShiftDown())\r
 420         {\r
 421             if (activeRes == null)\r
 422             {\r
 423                 activeRes = new Vector();\r
 424             }\r
 425             else\r
 426             {\r
 427                 int start = Integer.parseInt(activeRes.get(activeRes.size() -\r
 428                             1).toString());\r
 429                 int end = res;\r
 430 \r
 431                 if (end < start)\r
 432                 {\r
 433                     int temp = end;\r
 434                     end = start;\r
 435                     start = temp;\r
 436                 }\r
 437 \r
 438                 for (int n = start; n <= end; n++)\r
 439                 {\r
 440                     addEditableColumn(n);\r
 441                 }\r
 442             }\r
 443         }\r
 444         else\r
 445         {\r
 446             activeRes = new Vector();\r
 447             activeRes.addElement(String.valueOf(res));\r
 448         }\r
 449     }\r
 450 \r
 451     /**\r
 452      * DOCUMENT ME!\r
 453      *\r
 454      * @param evt DOCUMENT ME!\r
 455      */\r
 456     public void mouseReleased(MouseEvent evt)\r
 457     {\r
 458       graphStretch = -1;\r
 459       graphStretchY = -1;\r
 460     }\r
 461 \r
 462     /**\r
 463      * DOCUMENT ME!\r
 464      *\r
 465      * @param evt DOCUMENT ME!\r
 466      */\r
 467     public void mouseEntered(MouseEvent evt)\r
 468     {\r
 469     }\r
 470 \r
 471     /**\r
 472      * DOCUMENT ME!\r
 473      *\r
 474      * @param evt DOCUMENT ME!\r
 475      */\r
 476     public void mouseExited(MouseEvent evt)\r
 477     {\r
 478     }\r
 479 \r
 480     /**\r
 481      * DOCUMENT ME!\r
 482      *\r
 483      * @param evt DOCUMENT ME!\r
 484      */\r
 485     public void mouseDragged(MouseEvent evt)\r
 486     {\r
 487       if(graphStretch>-1)\r
 488       {\r
 489         av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY();\r
 490         if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <10)\r
 491           av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 10;\r
 492         graphStretchY = evt.getY();\r
 493         adjustPanelHeight();\r
 494         ap.repaint();\r
 495       }\r
 496     }\r
 497 \r
 498     /**\r
 499      * DOCUMENT ME!\r
 500      *\r
 501      * @param evt DOCUMENT ME!\r
 502      */\r
 503     public void mouseMoved(MouseEvent evt)\r
 504     {\r
 505         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 506 \r
 507         if (aa == null)\r
 508         {\r
 509             return;\r
 510         }\r
 511 \r
 512         int row = -1;\r
 513         int height = 0;\r
 514 \r
 515         for (int i = 0; i < aa.length; i++)\r
 516         {\r
 517             if (aa[i].visible)\r
 518             {\r
 519                 height += aa[i].height;\r
 520             }\r
 521 \r
 522             if (evt.getY() < height)\r
 523             {\r
 524                 row = i;\r
 525 \r
 526                 break;\r
 527             }\r
 528         }\r
 529 \r
 530         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 531 \r
 532         if (row > -1 && res<aa[row].annotations.length)\r
 533         {\r
 534             if(aa[row].graphGroup>-1)\r
 535             {\r
 536               StringBuffer tip = new StringBuffer("<html>");\r
 537               for (int gg = 0; gg < aa.length; gg++)\r
 538               {\r
 539                 if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res]!=null)\r
 540                   tip.append(aa[gg].label+" "+aa[gg].annotations[res].description+"<br>" );\r
 541               }\r
 542               if(tip.length()!=6)\r
 543               {\r
 544                 tip.setLength(tip.length() - 4);\r
 545                 this.setToolTipText(tip.toString() + "</html>");\r
 546               }\r
 547             }\r
 548             else if(aa[row].annotations[res] != null)\r
 549               this.setToolTipText(aa[row].annotations[res].description);\r
 550 \r
 551             if(aa[row].annotations[res]!=null)\r
 552             {\r
 553               StringBuffer text = new StringBuffer("Sequence position " +\r
 554                                                    (res + 1) + "  " +\r
 555                                                    aa[row].annotations[res].description);\r
 556 \r
 557               ap.alignFrame.statusBar.setText(text.toString());\r
 558             }\r
 559         }\r
 560     }\r
 561 \r
 562     /**\r
 563      * DOCUMENT ME!\r
 564      *\r
 565      * @param evt DOCUMENT ME!\r
 566      */\r
 567     public void mouseClicked(MouseEvent evt)\r
 568     {\r
 569     }\r
 570 \r
 571     /**\r
 572      * DOCUMENT ME!\r
 573      *\r
 574      * @param g DOCUMENT ME!\r
 575      */\r
 576     public void paintComponent(Graphics g)\r
 577     {\r
 578       g.setColor(Color.white);\r
 579       g.fillRect(0, 0, getWidth(), getHeight());\r
 580 \r
 581       if(image!=null)\r
 582       {if (fastPaint\r
 583             || (getVisibleRect().width != g.getClipBounds().width)\r
 584             || (getVisibleRect().height != g.getClipBounds().height))\r
 585         {\r
 586           g.drawImage(image, 0, 0, this);\r
 587           fastPaint = false;\r
 588           return;\r
 589         }\r
 590       }\r
 591       imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\r
 592 \r
 593       if (image == null || imgWidth != image.getWidth()\r
 594           || image.getHeight(this) != getHeight())\r
 595       {\r
 596         image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),\r
 597                                   BufferedImage.TYPE_INT_RGB);\r
 598         gg = (Graphics2D) image.getGraphics();\r
 599 \r
 600         if(av.antiAlias)\r
 601         gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
 602                             RenderingHints.VALUE_ANTIALIAS_ON);\r
 603 \r
 604         gg.setFont(av.getFont());\r
 605         fm = gg.getFontMetrics();\r
 606       }\r
 607 \r
 608 \r
 609       drawComponent(gg, av.startRes, av.endRes + 1);\r
 610       g.drawImage(image, 0, 0, this);\r
 611     }\r
 612 \r
 613     /**\r
 614      * DOCUMENT ME!\r
 615      *\r
 616      * @param horizontal DOCUMENT ME!\r
 617      */\r
 618     public void fastPaint(int horizontal)\r
 619     {\r
 620         if ((horizontal == 0) || gg==null ||\r
 621                 (av.alignment.getAlignmentAnnotation() == null) ||\r
 622                 (av.alignment.getAlignmentAnnotation().length < 1))\r
 623         {\r
 624             repaint();\r
 625             return;\r
 626         }\r
 627 \r
 628         gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);\r
 629 \r
 630         int sr = av.startRes;\r
 631         int er = av.endRes + 1;\r
 632         int transX = 0;\r
 633 \r
 634         if (horizontal > 0) // scrollbar pulled right, image to the left\r
 635         {\r
 636             transX = (er - sr - horizontal) * av.charWidth;\r
 637             sr = er - horizontal;\r
 638         }\r
 639         else if (horizontal < 0)\r
 640         {\r
 641             er = sr - horizontal;\r
 642         }\r
 643 \r
 644         gg.translate(transX, 0);\r
 645 \r
 646         drawComponent(gg, sr, er);\r
 647 \r
 648         gg.translate(-transX, 0);\r
 649 \r
 650         fastPaint = true;\r
 651 \r
 652         repaint();\r
 653 \r
 654     }\r
 655 \r
 656     /**\r
 657      * DOCUMENT ME!\r
 658      *\r
 659      * @param g DOCUMENT ME!\r
 660      * @param startRes DOCUMENT ME!\r
 661      * @param endRes DOCUMENT ME!\r
 662      */\r
 663     public void drawComponent(Graphics g, int startRes, int endRes)\r
 664     {\r
 665       g.setFont(av.getFont());\r
 666 \r
 667       if (fm == null)\r
 668         fm = g.getFontMetrics();\r
 669 \r
 670 \r
 671         g.setColor(Color.white);\r
 672         g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());\r
 673 \r
 674         if ((av.alignment.getAlignmentAnnotation() == null) ||\r
 675                 (av.alignment.getAlignmentAnnotation().length < 1))\r
 676         {\r
 677             g.setColor(Color.white);\r
 678             g.fillRect(0, 0, getWidth(), getHeight());\r
 679             g.setColor(Color.black);\r
 680             g.drawString("Alignment has no annotations", 20, 15);\r
 681 \r
 682             return;\r
 683         }\r
 684 \r
 685         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 686 \r
 687         int j;\r
 688         int x = 0;\r
 689         int y = 0;\r
 690         char[] lastSS = new char[aa.length];\r
 691         int[] lastSSX = new int[aa.length];\r
 692         int iconOffset = av.charHeight / 2;\r
 693         boolean validRes = false;\r
 694 \r
 695         boolean [] graphGroupDrawn = new boolean[aa.length];\r
 696 \r
 697 \r
 698         //\u03B2 \u03B1\r
 699         for (int i = 0; i < aa.length; i++)\r
 700         {\r
 701             AlignmentAnnotation row = aa[i];\r
 702 \r
 703             if (!row.visible)\r
 704             {\r
 705                 continue;\r
 706             }\r
 707 \r
 708 \r
 709 \r
 710             if (row.graph>0)\r
 711             {\r
 712                 if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )\r
 713                   continue;\r
 714 \r
 715                 // this is so that we draw the characters below the graph\r
 716                 y += row.height;\r
 717 \r
 718                 if (row.hasText)\r
 719                 {\r
 720                     y -= av.charHeight;\r
 721                 }\r
 722             }\r
 723 \r
 724             if (row.hasText)\r
 725             {\r
 726                 iconOffset = av.charHeight / 2;\r
 727             }\r
 728             else\r
 729             {\r
 730                 iconOffset = 0;\r
 731             }\r
 732 \r
 733             for (j = startRes; j < endRes; j++)\r
 734             {\r
 735                 if ((row.annotations.length <= j) ||\r
 736                         (row.annotations[j] == null))\r
 737                 {\r
 738                     validRes = false;\r
 739                 }\r
 740                 else\r
 741                 {\r
 742                     validRes = true;\r
 743                 }\r
 744 \r
 745                 x = (j - startRes) * av.charWidth;\r
 746 \r
 747                 if (activeRow == i)\r
 748                 {\r
 749                     g.setColor(Color.red);\r
 750 \r
 751                     if (activeRes != null)\r
 752                     {\r
 753                         for (int n = 0; n < activeRes.size(); n++)\r
 754                         {\r
 755                             int v = Integer.parseInt(activeRes.get(n).toString());\r
 756 \r
 757                             if (v == j)\r
 758                             {\r
 759                                 g.fillRect((j - startRes) * av.charWidth, y,\r
 760                                     av.charWidth, row.height);\r
 761                             }\r
 762                         }\r
 763                     }\r
 764                 }\r
 765 \r
 766                 if (validRes &&\r
 767                         (row.annotations[j].displayCharacter.length() > 0))\r
 768                 {\r
 769 \r
 770                     int charOffset = (av.charWidth -\r
 771                         fm.charWidth(row.annotations[j].displayCharacter.charAt(\r
 772                                 0))) / 2;\r
 773                     g.setColor(row.annotations[j].colour);\r
 774 \r
 775                     if (j == 0 || row.graph>0)\r
 776                     {\r
 777                         g.drawString(row.annotations[j].displayCharacter, x+charOffset,\r
 778                             y + iconOffset + 3);\r
 779                     }\r
 780                     else if (((row.annotations[j - 1] == null) ||\r
 781                             (row.annotations[j].displayCharacter != row.annotations[j -\r
 782                             1].displayCharacter)))\r
 783                     {\r
 784                         g.drawString(row.annotations[j].displayCharacter, x+charOffset,\r
 785                             y + iconOffset + 3);\r
 786                     }\r
 787                 }\r
 788 \r
 789                 if (row.hasIcons)\r
 790                 {\r
 791                     if (!validRes ||\r
 792                             (row.annotations[j].secondaryStructure != lastSS[i]))\r
 793                     {\r
 794                         switch (lastSS[i])\r
 795                         {\r
 796                         case 'H':\r
 797                             g.setColor(HELIX_COLOUR);\r
 798                             g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,\r
 799                                 x - lastSSX[i], 7, 8, 8);\r
 800 \r
 801                             break;\r
 802 \r
 803                         case 'E':\r
 804                             g.setColor(SHEET_COLOUR);\r
 805                             g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
 806                                 x - lastSSX[i] - 4, 7);\r
 807                             g.fillPolygon(new int[] { x - 4, x - 4, x },\r
 808                                 new int[]\r
 809                                 {\r
 810                                     y + iconOffset, y + 14 + iconOffset,\r
 811                                     y + 8 + iconOffset\r
 812                                 }, 3);\r
 813 \r
 814                             break;\r
 815 \r
 816 \r
 817                         default:\r
 818                             g.setColor(Color.gray);\r
 819                             g.fillRect(lastSSX[i], y + 6 + iconOffset,\r
 820                                 x - lastSSX[i], 2);\r
 821 \r
 822                             break;\r
 823                         }\r
 824 \r
 825                         if (validRes)\r
 826                         {\r
 827                             lastSS[i] = row.annotations[j].secondaryStructure;\r
 828                         }\r
 829                         else\r
 830                         {\r
 831                             lastSS[i] = ' ';\r
 832                         }\r
 833 \r
 834                         lastSSX[i] = x;\r
 835                     }\r
 836                 }\r
 837             }\r
 838 \r
 839             x += av.charWidth;\r
 840 \r
 841             if (row.hasIcons)\r
 842             {\r
 843                 switch (lastSS[i])\r
 844                 {\r
 845                 case 'H':\r
 846                     g.setColor(HELIX_COLOUR);\r
 847                     g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,\r
 848                         x - lastSSX[i], 7, 8, 8);\r
 849 \r
 850                     break;\r
 851 \r
 852                 case 'E':\r
 853                     g.setColor(SHEET_COLOUR);\r
 854 \r
 855                     if (row.annotations[endRes] !=null\r
 856                         && row.annotations[endRes].secondaryStructure != 'E')\r
 857                     {\r
 858                       g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
 859                                  x - lastSSX[i] - 4, 7);\r
 860                       g.fillPolygon(new int[]\r
 861                                     {x - 4, x - 4, x},\r
 862                                     new int[]\r
 863                                     {\r
 864                                     y + iconOffset, y + 14 + iconOffset,\r
 865                                     y + 7 + iconOffset\r
 866                       }, 3);\r
 867                     }\r
 868                     else\r
 869                       g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
 870                                  x - lastSSX[i], 7);\r
 871 \r
 872                     break;\r
 873 \r
 874                 case 'C':\r
 875                     break;\r
 876 \r
 877                 default:\r
 878                     g.setColor(Color.gray);\r
 879                     g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);\r
 880 \r
 881                     break;\r
 882                 }\r
 883             }\r
 884 \r
 885             if (row.graph>0)\r
 886             {\r
 887                 if(row.graph == AlignmentAnnotation.LINE_GRAPH )\r
 888                 {\r
 889                   if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])\r
 890                    {\r
 891                      float groupmax=-999999, groupmin=9999999;\r
 892                      for(int gg=0; gg<aa.length; gg++)\r
 893                      {\r
 894                        if(aa[gg].graphGroup!=row.graphGroup)\r
 895                          continue;\r
 896 \r
 897                        if(aa[gg]!=row)\r
 898                          aa[gg].visible = false;\r
 899 \r
 900                        if(aa[gg].graphMax>groupmax)\r
 901                          groupmax = aa[gg].graphMax;\r
 902                        if(aa[gg].graphMin<groupmin)\r
 903                          groupmin = aa[gg].graphMin;\r
 904                      }\r
 905 \r
 906                      for (int gg = 0; gg < aa.length; gg++)\r
 907                      {\r
 908                        if (aa[gg].graphGroup == row.graphGroup)\r
 909                        {\r
 910                          drawLineGraph(g, aa[gg], startRes, endRes, y,\r
 911                                        groupmin, groupmax,\r
 912                                        row.graphHeight);\r
 913                        }\r
 914                      }\r
 915 \r
 916                      graphGroupDrawn[ row.graphGroup ] = true;\r
 917                    }\r
 918                    else\r
 919                      drawLineGraph(g, row, startRes, endRes,\r
 920                                    y, row.graphMin, row.graphMax, row.graphHeight  );\r
 921                 }\r
 922                 else if(row.graph == AlignmentAnnotation.BAR_GRAPH )\r
 923                    drawBarGraph(g, row, startRes, endRes,\r
 924                                 row.graphMin, row.graphMax, y);\r
 925             }\r
 926 \r
 927             if (row.graph>0 && row.hasText)\r
 928             {\r
 929                 y += av.charHeight;\r
 930             }\r
 931 \r
 932             if (row.graph==0)\r
 933             {\r
 934                 y += aa[i].height;\r
 935             }\r
 936         }\r
 937     }\r
 938 \r
 939     public void drawLineGraph(Graphics g, AlignmentAnnotation aa,\r
 940                               int sRes, int eRes,\r
 941                               int y,\r
 942                               float min, float max,\r
 943                               int graphHeight)\r
 944     {\r
 945       if(sRes>aa.annotations.length)\r
 946         return;\r
 947 \r
 948       int x = 0;\r
 949 \r
 950       //Adjustment for fastpaint to left\r
 951       if(eRes<av.endRes)\r
 952         eRes++;\r
 953 \r
 954       if(sRes==0)\r
 955       {\r
 956         sRes++;\r
 957         x+=av.charWidth;\r
 958       }\r
 959 \r
 960       int y1=y, y2=y;\r
 961       float range = max - min;\r
 962 \r
 963       ////Draw origin\r
 964       if(min<0)\r
 965         y2 = (int)(y - (0-min / range)*graphHeight);\r
 966 \r
 967       g.setColor(Color.gray);\r
 968       g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
 969 \r
 970 \r
 971       if(aa.threshold!=null)\r
 972       {\r
 973           g.setColor(aa.threshold.colour);\r
 974           Graphics2D g2 = (Graphics2D)g;\r
 975           g2.setStroke(new BasicStroke(1,\r
 976                                         BasicStroke.CAP_SQUARE,\r
 977                                         BasicStroke.JOIN_ROUND, 3f,\r
 978                                         new float[] { 5f, 3f }, 0f));\r
 979 \r
 980           y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);\r
 981           g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
 982           g2.setStroke(new BasicStroke());\r
 983       }\r
 984 \r
 985       eRes = Math.min(eRes, aa.annotations.length);\r
 986       for (int j = sRes; j < eRes; j++)\r
 987       {\r
 988         if(aa.annotations[j]==null || aa.annotations[j-1]==null)\r
 989         {\r
 990           x+=av.charWidth;\r
 991           continue;\r
 992         }\r
 993           g.setColor(aa.annotations[j].colour);\r
 994           y1 = y - (int) (((aa.annotations[j-1].value-min) / range) * graphHeight);\r
 995           y2 = y - (int) (((aa.annotations[j].value-min) / range) * graphHeight);\r
 996           g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);\r
 997           x += av.charWidth;\r
 998        }\r
 999     }\r
1000 \r
1001     public void drawBarGraph(Graphics g, AlignmentAnnotation aa,\r
1002                              int sRes, int eRes,\r
1003                              float min, float max,\r
1004                              int y)\r
1005     {\r
1006       if(sRes>aa.annotations.length)\r
1007         return;\r
1008 \r
1009       int x=0, y1, y2;\r
1010 \r
1011       float range = max - min;\r
1012 \r
1013       if(aa.threshold!=null)\r
1014       {\r
1015           g.setColor(aa.threshold.colour);\r
1016           Graphics2D g2 = (Graphics2D)g;\r
1017           g2.setStroke(new BasicStroke(1,\r
1018                                         BasicStroke.CAP_SQUARE,\r
1019                                         BasicStroke.JOIN_ROUND, 3f,\r
1020                                         new float[] { 5f, 3f }, 0f));\r
1021 \r
1022           y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);\r
1023           g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
1024           g2.setStroke(new BasicStroke());\r
1025       }\r
1026 \r
1027       y1 = y2 = y;\r
1028 \r
1029       if(min<0)\r
1030         y2 = (int)(y - (0-min / (range))*aa.graphHeight);\r
1031 \r
1032       g.setColor(Color.gray);\r
1033 \r
1034       g.drawLine(x,y2,(eRes-sRes+1)*av.charWidth,y2);\r
1035 \r
1036       eRes = Math.min(eRes, aa.annotations.length-1);\r
1037 \r
1038 \r
1039       for (int j = sRes; j < eRes; j++)\r
1040       {\r
1041 \r
1042         if (aa.annotations[j] == null)\r
1043         {\r
1044           x += av.charWidth;\r
1045           continue;\r
1046         }\r
1047 \r
1048           g.setColor(aa.annotations[j].colour);\r
1049           y1 = y - (int) (((aa.annotations[j].value-min) / (range)) * aa.graphHeight);\r
1050 \r
1051           if(y1-y2>0)\r
1052             g.fillRect(x, y2, av.charWidth, y1-y2 );\r
1053           else\r
1054             g.fillRect(x, y1, av.charWidth, y2-y1 );\r
1055 \r
1056           x += av.charWidth;\r
1057       }\r
1058 \r
1059     }\r
1060 \r
1061     // used by overview window\r
1062     public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)\r
1063     {\r
1064       g.setColor(Color.white);\r
1065       g.fillRect(0, 0, width, y);\r
1066       g.setColor(new Color(0, 0, 180));\r
1067 \r
1068       int x = 0, height;\r
1069 \r
1070       for (int j = sRes; j < eRes; j++)\r
1071       {\r
1072           g.setColor(aa.annotations[j].colour);\r
1073 \r
1074           height = (int) ((aa.annotations[j].value / aa.graphMax) * y);\r
1075           if(height>y)\r
1076             height = y;\r
1077 \r
1078           g.fillRect(x, y - height, av.charWidth, height);\r
1079           x += av.charWidth;\r
1080       }\r
1081     }\r
1082 \r
1083 }\r