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                   if(SwingUtilities.isRightMouseButton(evt)\r
 367                       && aa[i].threshold!=null)\r
 368                   {\r
 369                     SliderPanel sp = new SliderPanel(aa[i], ap);\r
 370                     return;\r
 371                   }\r
 372                   else\r
 373                   {\r
 374                     //Stretch Graph\r
 375                     graphStretch = i;\r
 376                     graphStretchY = evt.getY();\r
 377                     activeRes = null;\r
 378                   }\r
 379                 }\r
 380                 else\r
 381                 {\r
 382                     activeRes = null;\r
 383                 }\r
 384 \r
 385                 break;\r
 386             }\r
 387         }\r
 388 \r
 389         if (SwingUtilities.isRightMouseButton(evt))\r
 390         {\r
 391             if (activeRes == null)\r
 392             {\r
 393                 return;\r
 394             }\r
 395 \r
 396             JPopupMenu pop = new JPopupMenu("Structure type");\r
 397             JMenuItem item = new JMenuItem(HELIX);\r
 398             item.addActionListener(this);\r
 399             pop.add(item);\r
 400             item = new JMenuItem(SHEET);\r
 401             item.addActionListener(this);\r
 402             pop.add(item);\r
 403             item = new JMenuItem(LABEL);\r
 404             item.addActionListener(this);\r
 405             pop.add(item);\r
 406             item = new JMenuItem(COLOUR);\r
 407             item.addActionListener(this);\r
 408             pop.add(item);\r
 409             item = new JMenuItem(REMOVE);\r
 410             item.addActionListener(this);\r
 411             pop.add(item);\r
 412             pop.show(this, evt.getX(), evt.getY());\r
 413 \r
 414             return;\r
 415         }\r
 416 \r
 417         if (aa == null)\r
 418         {\r
 419             return;\r
 420         }\r
 421 \r
 422         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 423 \r
 424         if (evt.isControlDown() || evt.isAltDown())\r
 425         {\r
 426             addEditableColumn(res);\r
 427         }\r
 428         else if (evt.isShiftDown())\r
 429         {\r
 430             if (activeRes == null)\r
 431             {\r
 432                 activeRes = new Vector();\r
 433             }\r
 434             else\r
 435             {\r
 436                 int start = Integer.parseInt(activeRes.get(activeRes.size() -\r
 437                             1).toString());\r
 438                 int end = res;\r
 439 \r
 440                 if (end < start)\r
 441                 {\r
 442                     int temp = end;\r
 443                     end = start;\r
 444                     start = temp;\r
 445                 }\r
 446 \r
 447                 for (int n = start; n <= end; n++)\r
 448                 {\r
 449                     addEditableColumn(n);\r
 450                 }\r
 451             }\r
 452         }\r
 453         else\r
 454         {\r
 455             activeRes = new Vector();\r
 456             activeRes.addElement(String.valueOf(res));\r
 457         }\r
 458     }\r
 459 \r
 460     /**\r
 461      * DOCUMENT ME!\r
 462      *\r
 463      * @param evt DOCUMENT ME!\r
 464      */\r
 465     public void mouseReleased(MouseEvent evt)\r
 466     {\r
 467       graphStretch = -1;\r
 468       graphStretchY = -1;\r
 469     }\r
 470 \r
 471     /**\r
 472      * DOCUMENT ME!\r
 473      *\r
 474      * @param evt DOCUMENT ME!\r
 475      */\r
 476     public void mouseEntered(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 mouseExited(MouseEvent evt)\r
 486     {\r
 487     }\r
 488 \r
 489     /**\r
 490      * DOCUMENT ME!\r
 491      *\r
 492      * @param evt DOCUMENT ME!\r
 493      */\r
 494     public void mouseDragged(MouseEvent evt)\r
 495     {\r
 496       if(graphStretch>-1)\r
 497       {\r
 498         av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY();\r
 499         if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <10)\r
 500           av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 10;\r
 501         graphStretchY = evt.getY();\r
 502         adjustPanelHeight();\r
 503         ap.repaint();\r
 504       }\r
 505     }\r
 506 \r
 507     /**\r
 508      * DOCUMENT ME!\r
 509      *\r
 510      * @param evt DOCUMENT ME!\r
 511      */\r
 512     public void mouseMoved(MouseEvent evt)\r
 513     {\r
 514         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 515 \r
 516         if (aa == null)\r
 517         {\r
 518             return;\r
 519         }\r
 520 \r
 521         int row = -1;\r
 522         int height = 0;\r
 523 \r
 524         for (int i = 0; i < aa.length; i++)\r
 525         {\r
 526             if (aa[i].visible)\r
 527             {\r
 528                 height += aa[i].height;\r
 529             }\r
 530 \r
 531             if (evt.getY() < height)\r
 532             {\r
 533                 row = i;\r
 534 \r
 535                 break;\r
 536             }\r
 537         }\r
 538 \r
 539         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 540 \r
 541         if (row > -1 && res<aa[row].annotations.length)\r
 542         {\r
 543             if(aa[row].graphGroup>-1)\r
 544             {\r
 545               StringBuffer tip = new StringBuffer("<html>");\r
 546               for (int gg = 0; gg < aa.length; gg++)\r
 547               {\r
 548                 if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res]!=null)\r
 549                   tip.append(aa[gg].label+" "+aa[gg].annotations[res].description+"<br>" );\r
 550               }\r
 551               if(tip.length()!=6)\r
 552               {\r
 553                 tip.setLength(tip.length() - 4);\r
 554                 this.setToolTipText(tip.toString() + "</html>");\r
 555               }\r
 556             }\r
 557             else if(aa[row].annotations[res] != null)\r
 558               this.setToolTipText(aa[row].annotations[res].description);\r
 559 \r
 560             if(aa[row].annotations[res]!=null)\r
 561             {\r
 562               StringBuffer text = new StringBuffer("Sequence position " +\r
 563                                                    (res + 1) + "  " +\r
 564                                                    aa[row].annotations[res].description);\r
 565 \r
 566               ap.alignFrame.statusBar.setText(text.toString());\r
 567             }\r
 568         }\r
 569     }\r
 570 \r
 571     /**\r
 572      * DOCUMENT ME!\r
 573      *\r
 574      * @param evt DOCUMENT ME!\r
 575      */\r
 576     public void mouseClicked(MouseEvent evt)\r
 577     {\r
 578     }\r
 579 \r
 580     /**\r
 581      * DOCUMENT ME!\r
 582      *\r
 583      * @param g DOCUMENT ME!\r
 584      */\r
 585     public void paintComponent(Graphics g)\r
 586     {\r
 587       g.setColor(Color.white);\r
 588       g.fillRect(0, 0, getWidth(), getHeight());\r
 589 \r
 590       if(image!=null)\r
 591       {if (fastPaint\r
 592             || (getVisibleRect().width != g.getClipBounds().width)\r
 593             || (getVisibleRect().height != g.getClipBounds().height))\r
 594         {\r
 595           g.drawImage(image, 0, 0, this);\r
 596           fastPaint = false;\r
 597           return;\r
 598         }\r
 599       }\r
 600       imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\r
 601 \r
 602       if (image == null || imgWidth != image.getWidth()\r
 603           || image.getHeight(this) != getHeight())\r
 604       {\r
 605         image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),\r
 606                                   BufferedImage.TYPE_INT_RGB);\r
 607         gg = (Graphics2D) image.getGraphics();\r
 608 \r
 609         if(av.antiAlias)\r
 610         gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
 611                             RenderingHints.VALUE_ANTIALIAS_ON);\r
 612 \r
 613         gg.setFont(av.getFont());\r
 614         fm = gg.getFontMetrics();\r
 615       }\r
 616 \r
 617 \r
 618       drawComponent(gg, av.startRes, av.endRes + 1);\r
 619       g.drawImage(image, 0, 0, this);\r
 620     }\r
 621 \r
 622     /**\r
 623      * DOCUMENT ME!\r
 624      *\r
 625      * @param horizontal DOCUMENT ME!\r
 626      */\r
 627     public void fastPaint(int horizontal)\r
 628     {\r
 629         if ((horizontal == 0) || gg==null ||\r
 630                 (av.alignment.getAlignmentAnnotation() == null) ||\r
 631                 (av.alignment.getAlignmentAnnotation().length < 1))\r
 632         {\r
 633             repaint();\r
 634             return;\r
 635         }\r
 636 \r
 637         gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);\r
 638 \r
 639         int sr = av.startRes;\r
 640         int er = av.endRes + 1;\r
 641         int transX = 0;\r
 642 \r
 643         if (horizontal > 0) // scrollbar pulled right, image to the left\r
 644         {\r
 645             transX = (er - sr - horizontal) * av.charWidth;\r
 646             sr = er - horizontal;\r
 647         }\r
 648         else if (horizontal < 0)\r
 649         {\r
 650             er = sr - horizontal;\r
 651         }\r
 652 \r
 653         gg.translate(transX, 0);\r
 654 \r
 655         drawComponent(gg, sr, er);\r
 656 \r
 657         gg.translate(-transX, 0);\r
 658 \r
 659         fastPaint = true;\r
 660 \r
 661         repaint();\r
 662 \r
 663     }\r
 664 \r
 665     /**\r
 666      * DOCUMENT ME!\r
 667      *\r
 668      * @param g DOCUMENT ME!\r
 669      * @param startRes DOCUMENT ME!\r
 670      * @param endRes DOCUMENT ME!\r
 671      */\r
 672     public void drawComponent(Graphics g, int startRes, int endRes)\r
 673     {\r
 674       g.setFont(av.getFont());\r
 675 \r
 676       if (fm == null)\r
 677         fm = g.getFontMetrics();\r
 678 \r
 679 \r
 680         g.setColor(Color.white);\r
 681         g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());\r
 682 \r
 683         if ((av.alignment.getAlignmentAnnotation() == null) ||\r
 684                 (av.alignment.getAlignmentAnnotation().length < 1))\r
 685         {\r
 686             g.setColor(Color.white);\r
 687             g.fillRect(0, 0, getWidth(), getHeight());\r
 688             g.setColor(Color.black);\r
 689             g.drawString("Alignment has no annotations", 20, 15);\r
 690 \r
 691             return;\r
 692         }\r
 693 \r
 694         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 695 \r
 696         int j;\r
 697         int x = 0;\r
 698         int y = 0;\r
 699         char[] lastSS = new char[aa.length];\r
 700         int[] lastSSX = new int[aa.length];\r
 701         int iconOffset = av.charHeight / 2;\r
 702         boolean validRes = false;\r
 703 \r
 704         boolean [] graphGroupDrawn = new boolean[aa.length];\r
 705 \r
 706 \r
 707         //\u03B2 \u03B1\r
 708         for (int i = 0; i < aa.length; i++)\r
 709         {\r
 710             AlignmentAnnotation row = aa[i];\r
 711 \r
 712             if (!row.visible)\r
 713             {\r
 714                 continue;\r
 715             }\r
 716 \r
 717 \r
 718 \r
 719             if (row.graph>0)\r
 720             {\r
 721                 if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )\r
 722                   continue;\r
 723 \r
 724                 // this is so that we draw the characters below the graph\r
 725                 y += row.height;\r
 726 \r
 727                 if (row.hasText)\r
 728                 {\r
 729                     y -= av.charHeight;\r
 730                 }\r
 731             }\r
 732 \r
 733             if (row.hasText)\r
 734             {\r
 735                 iconOffset = av.charHeight / 2;\r
 736             }\r
 737             else\r
 738             {\r
 739                 iconOffset = 0;\r
 740             }\r
 741 \r
 742             for (j = startRes; j < endRes; j++)\r
 743             {\r
 744                 if ((row.annotations.length <= j) ||\r
 745                         (row.annotations[j] == null))\r
 746                 {\r
 747                     validRes = false;\r
 748                 }\r
 749                 else\r
 750                 {\r
 751                     validRes = true;\r
 752                 }\r
 753 \r
 754                 x = (j - startRes) * av.charWidth;\r
 755 \r
 756                 if (activeRow == i)\r
 757                 {\r
 758                     g.setColor(Color.red);\r
 759 \r
 760                     if (activeRes != null)\r
 761                     {\r
 762                         for (int n = 0; n < activeRes.size(); n++)\r
 763                         {\r
 764                             int v = Integer.parseInt(activeRes.get(n).toString());\r
 765 \r
 766                             if (v == j)\r
 767                             {\r
 768                                 g.fillRect((j - startRes) * av.charWidth, y,\r
 769                                     av.charWidth, row.height);\r
 770                             }\r
 771                         }\r
 772                     }\r
 773                 }\r
 774 \r
 775                 if (validRes &&\r
 776                         (row.annotations[j].displayCharacter.length() > 0))\r
 777                 {\r
 778 \r
 779                     int charOffset = (av.charWidth -\r
 780                         fm.charWidth(row.annotations[j].displayCharacter.charAt(\r
 781                                 0))) / 2;\r
 782                     g.setColor(row.annotations[j].colour);\r
 783 \r
 784                     if (j == 0 || row.graph>0)\r
 785                     {\r
 786                         g.drawString(row.annotations[j].displayCharacter, x+charOffset,\r
 787                             y + iconOffset + 3);\r
 788                     }\r
 789                     else if (((row.annotations[j - 1] == null) ||\r
 790                             (row.annotations[j].displayCharacter != row.annotations[j -\r
 791                             1].displayCharacter)))\r
 792                     {\r
 793                         g.drawString(row.annotations[j].displayCharacter, x+charOffset,\r
 794                             y + iconOffset + 3);\r
 795                     }\r
 796                 }\r
 797 \r
 798                 if (row.hasIcons)\r
 799                 {\r
 800                     if (!validRes ||\r
 801                             (row.annotations[j].secondaryStructure != lastSS[i]))\r
 802                     {\r
 803                         switch (lastSS[i])\r
 804                         {\r
 805                         case 'H':\r
 806                             g.setColor(HELIX_COLOUR);\r
 807                             g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,\r
 808                                 x - lastSSX[i], 7, 8, 8);\r
 809 \r
 810                             break;\r
 811 \r
 812                         case 'E':\r
 813                             g.setColor(SHEET_COLOUR);\r
 814                             g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
 815                                 x - lastSSX[i] - 4, 7);\r
 816                             g.fillPolygon(new int[] { x - 4, x - 4, x },\r
 817                                 new int[]\r
 818                                 {\r
 819                                     y + iconOffset, y + 14 + iconOffset,\r
 820                                     y + 8 + iconOffset\r
 821                                 }, 3);\r
 822 \r
 823                             break;\r
 824 \r
 825 \r
 826                         default:\r
 827                             g.setColor(Color.gray);\r
 828                             g.fillRect(lastSSX[i], y + 6 + iconOffset,\r
 829                                 x - lastSSX[i], 2);\r
 830 \r
 831                             break;\r
 832                         }\r
 833 \r
 834                         if (validRes)\r
 835                         {\r
 836                             lastSS[i] = row.annotations[j].secondaryStructure;\r
 837                         }\r
 838                         else\r
 839                         {\r
 840                             lastSS[i] = ' ';\r
 841                         }\r
 842 \r
 843                         lastSSX[i] = x;\r
 844                     }\r
 845                 }\r
 846             }\r
 847 \r
 848             x += av.charWidth;\r
 849 \r
 850             if (row.hasIcons)\r
 851             {\r
 852                 switch (lastSS[i])\r
 853                 {\r
 854                 case 'H':\r
 855                     g.setColor(HELIX_COLOUR);\r
 856                     g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,\r
 857                         x - lastSSX[i], 7, 8, 8);\r
 858 \r
 859                     break;\r
 860 \r
 861                 case 'E':\r
 862                     g.setColor(SHEET_COLOUR);\r
 863 \r
 864                     if (row.annotations[endRes] !=null\r
 865                         && row.annotations[endRes].secondaryStructure != 'E')\r
 866                     {\r
 867                       g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
 868                                  x - lastSSX[i] - 4, 7);\r
 869                       g.fillPolygon(new int[]\r
 870                                     {x - 4, x - 4, x},\r
 871                                     new int[]\r
 872                                     {\r
 873                                     y + iconOffset, y + 14 + iconOffset,\r
 874                                     y + 7 + iconOffset\r
 875                       }, 3);\r
 876                     }\r
 877                     else\r
 878                       g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
 879                                  x - lastSSX[i], 7);\r
 880 \r
 881                     break;\r
 882 \r
 883                 case 'C':\r
 884                     break;\r
 885 \r
 886                 default:\r
 887                     g.setColor(Color.gray);\r
 888                     g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);\r
 889 \r
 890                     break;\r
 891                 }\r
 892             }\r
 893 \r
 894             if (row.graph>0)\r
 895             {\r
 896                 if(row.graph == AlignmentAnnotation.LINE_GRAPH )\r
 897                 {\r
 898                   if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])\r
 899                    {\r
 900                      float groupmax=-999999, groupmin=9999999;\r
 901                      for(int gg=0; gg<aa.length; gg++)\r
 902                      {\r
 903                        if(aa[gg].graphGroup!=row.graphGroup)\r
 904                          continue;\r
 905 \r
 906                        if(aa[gg]!=row)\r
 907                          aa[gg].visible = false;\r
 908 \r
 909                        if(aa[gg].graphMax>groupmax)\r
 910                          groupmax = aa[gg].graphMax;\r
 911                        if(aa[gg].graphMin<groupmin)\r
 912                          groupmin = aa[gg].graphMin;\r
 913                      }\r
 914 \r
 915                      for (int gg = 0; gg < aa.length; gg++)\r
 916                      {\r
 917                        if (aa[gg].graphGroup == row.graphGroup)\r
 918                        {\r
 919                          drawLineGraph(g, aa[gg], startRes, endRes, y,\r
 920                                        groupmin, groupmax,\r
 921                                        row.graphHeight);\r
 922                        }\r
 923                      }\r
 924 \r
 925                      graphGroupDrawn[ row.graphGroup ] = true;\r
 926                    }\r
 927                    else\r
 928                      drawLineGraph(g, row, startRes, endRes,\r
 929                                    y, row.graphMin, row.graphMax, row.graphHeight  );\r
 930                 }\r
 931                 else if(row.graph == AlignmentAnnotation.BAR_GRAPH )\r
 932                    drawBarGraph(g, row, startRes, endRes,\r
 933                                 row.graphMin, row.graphMax, y);\r
 934             }\r
 935 \r
 936             if (row.graph>0 && row.hasText)\r
 937             {\r
 938                 y += av.charHeight;\r
 939             }\r
 940 \r
 941             if (row.graph==0)\r
 942             {\r
 943                 y += aa[i].height;\r
 944             }\r
 945         }\r
 946     }\r
 947 \r
 948     public void drawLineGraph(Graphics g, AlignmentAnnotation aa,\r
 949                               int sRes, int eRes,\r
 950                               int y,\r
 951                               float min, float max,\r
 952                               int graphHeight)\r
 953     {\r
 954       if(sRes>aa.annotations.length)\r
 955         return;\r
 956 \r
 957       int x = 0;\r
 958 \r
 959       //Adjustment for fastpaint to left\r
 960       if(eRes<av.endRes)\r
 961         eRes++;\r
 962 \r
 963       if(sRes==0)\r
 964       {\r
 965         sRes++;\r
 966         x+=av.charWidth;\r
 967       }\r
 968 \r
 969       int y1=y, y2=y;\r
 970       float range = max - min;\r
 971 \r
 972       ////Draw origin\r
 973       if(min<0)\r
 974         y2 = (int)(y - (0-min / range)*graphHeight);\r
 975 \r
 976       g.setColor(Color.gray);\r
 977       g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
 978 \r
 979 \r
 980       if(aa.threshold!=null)\r
 981       {\r
 982           g.setColor(aa.threshold.colour);\r
 983           Graphics2D g2 = (Graphics2D)g;\r
 984           g2.setStroke(new BasicStroke(1,\r
 985                                         BasicStroke.CAP_SQUARE,\r
 986                                         BasicStroke.JOIN_ROUND, 3f,\r
 987                                         new float[] { 5f, 3f }, 0f));\r
 988 \r
 989           y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);\r
 990           g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
 991           g2.setStroke(new BasicStroke());\r
 992       }\r
 993 \r
 994       eRes = Math.min(eRes, aa.annotations.length);\r
 995       for (int j = sRes; j < eRes; j++)\r
 996       {\r
 997         if(aa.annotations[j]==null || aa.annotations[j-1]==null)\r
 998         {\r
 999           x+=av.charWidth;\r
1000           continue;\r
1001         }\r
1002           g.setColor(aa.annotations[j].colour);\r
1003           y1 = y - (int) (((aa.annotations[j-1].value-min) / range) * graphHeight);\r
1004           y2 = y - (int) (((aa.annotations[j].value-min) / range) * graphHeight);\r
1005           g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);\r
1006           x += av.charWidth;\r
1007        }\r
1008     }\r
1009 \r
1010     public void drawBarGraph(Graphics g, AlignmentAnnotation aa,\r
1011                              int sRes, int eRes,\r
1012                              float min, float max,\r
1013                              int y)\r
1014     {\r
1015       if(sRes>aa.annotations.length)\r
1016         return;\r
1017 \r
1018       int x=0, y1, y2;\r
1019 \r
1020       float range = max - min;\r
1021 \r
1022       if(aa.threshold!=null)\r
1023       {\r
1024           g.setColor(aa.threshold.colour);\r
1025           Graphics2D g2 = (Graphics2D)g;\r
1026           g2.setStroke(new BasicStroke(1,\r
1027                                         BasicStroke.CAP_SQUARE,\r
1028                                         BasicStroke.JOIN_ROUND, 3f,\r
1029                                         new float[] { 5f, 3f }, 0f));\r
1030 \r
1031           y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);\r
1032           g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
1033           g2.setStroke(new BasicStroke());\r
1034       }\r
1035 \r
1036       y1 = y2 = y;\r
1037 \r
1038       if(min<0)\r
1039         y2 = (int)(y - (0-min / (range))*aa.graphHeight);\r
1040 \r
1041       g.setColor(Color.gray);\r
1042 \r
1043       g.drawLine(x,y2,(eRes-sRes+1)*av.charWidth,y2);\r
1044 \r
1045       eRes = Math.min(eRes, aa.annotations.length-1);\r
1046 \r
1047 \r
1048       for (int j = sRes; j < eRes; j++)\r
1049       {\r
1050 \r
1051         if (aa.annotations[j] == null)\r
1052         {\r
1053           x += av.charWidth;\r
1054           continue;\r
1055         }\r
1056 \r
1057           g.setColor(aa.annotations[j].colour);\r
1058           y1 = y - (int) (((aa.annotations[j].value-min) / (range)) * aa.graphHeight);\r
1059 \r
1060           if(y1-y2>0)\r
1061             g.fillRect(x, y2, av.charWidth, y1-y2 );\r
1062           else\r
1063             g.fillRect(x, y1, av.charWidth, y2-y1 );\r
1064 \r
1065           x += av.charWidth;\r
1066       }\r
1067 \r
1068     }\r
1069 \r
1070     // used by overview window\r
1071     public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)\r
1072     {\r
1073       g.setColor(Color.white);\r
1074       g.fillRect(0, 0, width, y);\r
1075       g.setColor(new Color(0, 0, 180));\r
1076 \r
1077       int x = 0, height;\r
1078 \r
1079       for (int j = sRes; j < eRes; j++)\r
1080       {\r
1081           g.setColor(aa.annotations[j].colour);\r
1082 \r
1083           height = (int) ((aa.annotations[j].value / aa.graphMax) * y);\r
1084           if(height>y)\r
1085             height = y;\r
1086 \r
1087           g.fillRect(x, y - height, av.charWidth, height);\r
1088           x += av.charWidth;\r
1089       }\r
1090     }\r
1091 \r
1092 }\r