src/jalview/gui/AnnotationPanel.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2006 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 javax.swing.*;\r
  28 \r
  29 \r
  30 /**\r
  31  * DOCUMENT ME!\r
  32  *\r
  33  * @author $author$\r
  34  * @version $Revision$\r
  35  */\r
  36 public class AnnotationPanel extends JPanel implements MouseListener,\r
  37     MouseMotionListener, ActionListener, AdjustmentListener\r
  38 {\r
  39     final String HELIX = "Helix";\r
  40     final String SHEET = "Sheet";\r
  41     final String LABEL = "Label";\r
  42     final String REMOVE = "Remove Annotation";\r
  43     final String COLOUR = "Colour";\r
  44     final Color HELIX_COLOUR = Color.red.darker();\r
  45     final Color SHEET_COLOUR = Color.green.darker().darker();\r
  46 \r
  47     /** DOCUMENT ME!! */\r
  48     AlignViewport av;\r
  49     AlignmentPanel ap;\r
  50     int activeRow = -1;\r
  51     BufferedImage image;\r
  52     BufferedImage fadedImage;\r
  53     Graphics2D gg;\r
  54     FontMetrics fm;\r
  55     int imgWidth = 0;\r
  56     boolean fastPaint = false;\r
  57 \r
  58     //Used For mouse Dragging and resizing graphs\r
  59     int graphStretch = -1;\r
  60     int graphStretchY = -1;\r
  61     int min; //used by mouseDragged to see if user\r
  62     int max; //used by mouseDragged to see if user\r
  63     boolean mouseDragging = false;\r
  64 \r
  65     boolean MAC = false;\r
  66 \r
  67     /**\r
  68      * Creates a new AnnotationPanel object.\r
  69      *\r
  70      * @param ap DOCUMENT ME!\r
  71      */\r
  72     public AnnotationPanel(AlignmentPanel ap)\r
  73     {\r
  74 \r
  75     if(System.getProperty("os.name").startsWith("Mac"))\r
  76       MAC = true;\r
  77 \r
  78         ToolTipManager.sharedInstance().registerComponent(this);\r
  79         ToolTipManager.sharedInstance().setInitialDelay(0);\r
  80         ToolTipManager.sharedInstance().setDismissDelay(10000);\r
  81         this.ap = ap;\r
  82         av = ap.av;\r
  83         this.setLayout(null);\r
  84         addMouseListener(this);\r
  85         addMouseMotionListener(this);\r
  86         ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);\r
  87     }\r
  88 \r
  89     public AnnotationPanel(AlignViewport av)\r
  90     {\r
  91       this.av = av;\r
  92     }\r
  93 \r
  94 \r
  95     /**\r
  96      * DOCUMENT ME!\r
  97      *\r
  98      * @param evt DOCUMENT ME!\r
  99      */\r
 100     public void adjustmentValueChanged(AdjustmentEvent evt)\r
 101     {\r
 102         ap.alabels.setScrollOffset(-evt.getValue());\r
 103     }\r
 104 \r
 105     /**\r
 106      * DOCUMENT ME!\r
 107      */\r
 108     public int adjustPanelHeight()\r
 109     {\r
 110         // setHeight of panels\r
 111         image = null;\r
 112         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 113         int height = 0;\r
 114 \r
 115         if (aa != null)\r
 116         {\r
 117             for (int i = 0; i < aa.length; i++)\r
 118             {\r
 119                 if (!aa[i].visible)\r
 120                 {\r
 121                     continue;\r
 122                 }\r
 123 \r
 124                 aa[i].height = 0;\r
 125 \r
 126                 if (aa[i].hasText)\r
 127                 {\r
 128                     aa[i].height += av.charHeight;\r
 129                 }\r
 130 \r
 131                 if (aa[i].hasIcons)\r
 132                 {\r
 133                     aa[i].height += 16;\r
 134                 }\r
 135 \r
 136                 if (aa[i].graph>0)\r
 137                 {\r
 138                     aa[i].height += aa[i].graphHeight;\r
 139                 }\r
 140 \r
 141                 if (aa[i].height == 0)\r
 142                 {\r
 143                     aa[i].height = 20;\r
 144                 }\r
 145 \r
 146                 height += aa[i].height;\r
 147             }\r
 148         }\r
 149         else\r
 150         {\r
 151             height = 20;\r
 152         }\r
 153 \r
 154         this.setPreferredSize(new Dimension(1, height));\r
 155 \r
 156         return height;\r
 157     }\r
 158 \r
 159 \r
 160 \r
 161     /**\r
 162      * DOCUMENT ME!\r
 163      *\r
 164      * @param evt DOCUMENT ME!\r
 165      */\r
 166     public void actionPerformed(ActionEvent evt)\r
 167     {\r
 168         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 169         Annotation[] anot = aa[activeRow].annotations;\r
 170 \r
 171         if (evt.getActionCommand().equals(REMOVE))\r
 172         {\r
 173             for (int i = 0; i < av.getColumnSelection().size(); i++)\r
 174             {\r
 175                 anot[av.getColumnSelection().columnAt(i)] = null;\r
 176             }\r
 177         }\r
 178         else if (evt.getActionCommand().equals(LABEL))\r
 179         {\r
 180             String label = JOptionPane.showInputDialog(this, "Enter Label ",\r
 181                     "Enter label", JOptionPane.QUESTION_MESSAGE);\r
 182 \r
 183             if (label == null)\r
 184             {\r
 185                 return;\r
 186             }\r
 187 \r
 188             if ((label.length() > 0) && !aa[activeRow].hasText)\r
 189             {\r
 190                 aa[activeRow].hasText = true;\r
 191             }\r
 192 \r
 193             for (int i = 0; i < av.getColumnSelection().size(); i++)\r
 194             {\r
 195                 int index = av.getColumnSelection().columnAt(i);\r
 196 \r
 197                 if (anot[index] == null)\r
 198                 {\r
 199                     anot[index] = new Annotation(label, "", ' ', 0);\r
 200                 }\r
 201 \r
 202                 anot[index].displayCharacter = label;\r
 203             }\r
 204         }\r
 205         else if (evt.getActionCommand().equals(COLOUR))\r
 206         {\r
 207             Color col = JColorChooser.showDialog(this,\r
 208                     "Choose foreground colour", Color.black);\r
 209 \r
 210             for (int i = 0; i < av.getColumnSelection().size(); i++)\r
 211             {\r
 212                 int index = av.getColumnSelection().columnAt(i);\r
 213 \r
 214                 if (anot[index] == null)\r
 215                 {\r
 216                     anot[index] = new Annotation("", "", ' ', 0);\r
 217                 }\r
 218 \r
 219                 anot[index].colour = col;\r
 220             }\r
 221         }\r
 222         else // HELIX OR SHEET\r
 223         {\r
 224             char type = 0;\r
 225             String symbol = "\u03B1";\r
 226 \r
 227             if (evt.getActionCommand().equals(HELIX))\r
 228             {\r
 229                 type = 'H';\r
 230             }\r
 231             else if (evt.getActionCommand().equals(SHEET))\r
 232             {\r
 233                 type = 'E';\r
 234                 symbol = "\u03B2";\r
 235             }\r
 236 \r
 237             if (!aa[activeRow].hasIcons)\r
 238             {\r
 239                 aa[activeRow].hasIcons = true;\r
 240             }\r
 241 \r
 242             String label = JOptionPane.showInputDialog("Enter a label for the structure?",\r
 243                     symbol);\r
 244 \r
 245             if (label == null)\r
 246             {\r
 247                 return;\r
 248             }\r
 249 \r
 250             if ((label.length() > 0) && !aa[activeRow].hasText)\r
 251             {\r
 252                 aa[activeRow].hasText = true;\r
 253             }\r
 254 \r
 255             for (int i = 0; i < av.getColumnSelection().size(); i++)\r
 256             {\r
 257                 int index = av.getColumnSelection().columnAt(i);\r
 258 \r
 259                 if (anot[index] == null)\r
 260                 {\r
 261                     anot[index] = new Annotation(label, "", type, 0);\r
 262                 }\r
 263 \r
 264                 anot[index].secondaryStructure = type;\r
 265                 anot[index].displayCharacter = label;\r
 266             }\r
 267         }\r
 268 \r
 269         adjustPanelHeight();\r
 270         repaint();\r
 271 \r
 272         return;\r
 273     }\r
 274 \r
 275     /**\r
 276      * DOCUMENT ME!\r
 277      *\r
 278      * @param evt DOCUMENT ME!\r
 279      */\r
 280     public void mousePressed(MouseEvent evt)\r
 281     {\r
 282 \r
 283 \r
 284         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 285         if(aa==null)\r
 286           return;\r
 287 \r
 288 \r
 289         int height = 0;\r
 290         activeRow = -1;\r
 291 \r
 292 \r
 293         for (int i = 0; i < aa.length; i++)\r
 294         {\r
 295             if (aa[i].visible)\r
 296             {\r
 297               height += aa[i].height;\r
 298             }\r
 299 \r
 300             if (evt.getY() < height)\r
 301             {\r
 302                 if (aa[i].editable)\r
 303                 {\r
 304                     activeRow = i;\r
 305                 }\r
 306                 else if(aa[i].graph>0)\r
 307                 {\r
 308                     //Stretch Graph\r
 309                     graphStretch = i;\r
 310                     graphStretchY = evt.getY();\r
 311                 }\r
 312 \r
 313                 break;\r
 314             }\r
 315         }\r
 316 \r
 317 \r
 318         if (SwingUtilities.isRightMouseButton(evt) && activeRow!=-1)\r
 319         {\r
 320             if (av.getColumnSelection() == null)\r
 321             {\r
 322                 return;\r
 323             }\r
 324 \r
 325             JPopupMenu pop = new JPopupMenu("Structure type");\r
 326             JMenuItem item = new JMenuItem(HELIX);\r
 327             item.addActionListener(this);\r
 328             pop.add(item);\r
 329             item = new JMenuItem(SHEET);\r
 330             item.addActionListener(this);\r
 331             pop.add(item);\r
 332             item = new JMenuItem(LABEL);\r
 333             item.addActionListener(this);\r
 334             pop.add(item);\r
 335             item = new JMenuItem(COLOUR);\r
 336             item.addActionListener(this);\r
 337             pop.add(item);\r
 338             item = new JMenuItem(REMOVE);\r
 339             item.addActionListener(this);\r
 340             pop.add(item);\r
 341             pop.show(this, evt.getX(), evt.getY());\r
 342 \r
 343             return;\r
 344         }\r
 345 \r
 346         if (aa == null)\r
 347         {\r
 348             return;\r
 349         }\r
 350 \r
 351         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 352 \r
 353         min = res;\r
 354         max = res;\r
 355 \r
 356         if (av.getColumnSelection().contains(res))\r
 357           av.getColumnSelection().removeElement(res);\r
 358         else\r
 359         {\r
 360             av.getColumnSelection().addElement(res);\r
 361             SequenceGroup sg = new SequenceGroup();\r
 362 \r
 363             for (int i = 0; i < av.alignment.getSequences().size(); i++)\r
 364             {\r
 365                 sg.addSequence(av.alignment.getSequenceAt(i), false);\r
 366             }\r
 367 \r
 368             sg.setStartRes(res);\r
 369             sg.setEndRes(res);\r
 370             av.setSelectionGroup(sg);\r
 371         }\r
 372 \r
 373         ap.repaint();\r
 374 \r
 375     }\r
 376 \r
 377     /**\r
 378      * DOCUMENT ME!\r
 379      *\r
 380      * @param evt DOCUMENT ME!\r
 381      */\r
 382     public void mouseReleased(MouseEvent evt)\r
 383     {\r
 384       graphStretch = -1;\r
 385       graphStretchY = -1;\r
 386       mouseDragging = false;\r
 387     }\r
 388 \r
 389     /**\r
 390      * DOCUMENT ME!\r
 391      *\r
 392      * @param evt DOCUMENT ME!\r
 393      */\r
 394     public void mouseEntered(MouseEvent evt)\r
 395     {\r
 396       if(mouseDragging)\r
 397         ap.seqPanel.scrollCanvas(null);\r
 398     }\r
 399 \r
 400     /**\r
 401      * DOCUMENT ME!\r
 402      *\r
 403      * @param evt DOCUMENT ME!\r
 404      */\r
 405     public void mouseExited(MouseEvent evt)\r
 406     {\r
 407       if(mouseDragging)\r
 408         ap.seqPanel.scrollCanvas(evt);\r
 409     }\r
 410 \r
 411 \r
 412     /**\r
 413      * DOCUMENT ME!\r
 414      *\r
 415      * @param evt DOCUMENT ME!\r
 416      */\r
 417     public void mouseDragged(MouseEvent evt)\r
 418     {\r
 419       if(graphStretch>-1)\r
 420       {\r
 421         av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY();\r
 422         if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <0)\r
 423           av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;\r
 424         graphStretchY = evt.getY();\r
 425         adjustPanelHeight();\r
 426         ap.repaint();\r
 427       }\r
 428       else\r
 429       {\r
 430         mouseDragging = true;\r
 431 \r
 432         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 433 \r
 434         SequenceGroup sg = av.getSelectionGroup();\r
 435 \r
 436         if (res < min)\r
 437         {\r
 438             min = res;\r
 439         }\r
 440 \r
 441         if (res > max)\r
 442         {\r
 443             max = res;\r
 444         }\r
 445 \r
 446         if (sg != null)\r
 447         {\r
 448             if (!av.getColumnSelection().contains(res))\r
 449             {\r
 450                 av.getColumnSelection().addElement(res);\r
 451             }\r
 452 \r
 453             if (res > sg.getStartRes())\r
 454             {\r
 455                 sg.setEndRes(res);\r
 456             }\r
 457             else if (res < sg.getStartRes())\r
 458             {\r
 459                 sg.setStartRes(res);\r
 460             }\r
 461 \r
 462             for (int i = min; i <= max; i++)\r
 463             {\r
 464                 if ((i < sg.getStartRes()) || (i > sg.getEndRes()))\r
 465                 {\r
 466                     av.getColumnSelection().removeElement(i);\r
 467                 }\r
 468                 else\r
 469                 {\r
 470                     av.getColumnSelection().addElement(i);\r
 471                 }\r
 472             }\r
 473 \r
 474             ap.repaint();\r
 475         }\r
 476 \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 mouseMoved(MouseEvent evt)\r
 486     {\r
 487         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 488 \r
 489         if (aa == null)\r
 490         {\r
 491             return;\r
 492         }\r
 493 \r
 494         int row = -1;\r
 495         int height = 0;\r
 496 \r
 497         for (int i = 0; i < aa.length; i++)\r
 498         {\r
 499             if (aa[i].visible)\r
 500             {\r
 501                 height += aa[i].height;\r
 502             }\r
 503 \r
 504             if (evt.getY() < height)\r
 505             {\r
 506                 row = i;\r
 507 \r
 508                 break;\r
 509             }\r
 510         }\r
 511 \r
 512         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 513 \r
 514         if(av.hasHiddenColumns)\r
 515           res = av.getColumnSelection().adjustForHiddenColumns(res);\r
 516 \r
 517         if (row > -1 && res<aa[row].annotations.length)\r
 518         {\r
 519             if(aa[row].graphGroup>-1)\r
 520             {\r
 521               StringBuffer tip = new StringBuffer("<html>");\r
 522               for (int gg = 0; gg < aa.length; gg++)\r
 523               {\r
 524                 if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res]!=null)\r
 525                   tip.append(aa[gg].label+" "+aa[gg].annotations[res].description+"<br>" );\r
 526               }\r
 527               if(tip.length()!=6)\r
 528               {\r
 529                 tip.setLength(tip.length() - 4);\r
 530                 this.setToolTipText(tip.toString() + "</html>");\r
 531               }\r
 532             }\r
 533             else if(aa[row].annotations[res] != null)\r
 534               this.setToolTipText(aa[row].annotations[res].description);\r
 535 \r
 536             if(aa[row].annotations[res]!=null)\r
 537             {\r
 538               StringBuffer text = new StringBuffer("Sequence position " +\r
 539                                                    (res + 1) + "  " +\r
 540                                                    aa[row].annotations[res].description);\r
 541 \r
 542               ap.alignFrame.statusBar.setText(text.toString());\r
 543             }\r
 544         }\r
 545     }\r
 546 \r
 547     /**\r
 548      * DOCUMENT ME!\r
 549      *\r
 550      * @param evt DOCUMENT ME!\r
 551      */\r
 552     public void mouseClicked(MouseEvent evt)\r
 553     {\r
 554     }\r
 555 \r
 556     /**\r
 557      * DOCUMENT ME!\r
 558      *\r
 559      * @param g DOCUMENT ME!\r
 560      */\r
 561     public void paintComponent(Graphics g)\r
 562     {\r
 563       g.setColor(Color.white);\r
 564       g.fillRect(0, 0, getWidth(), getHeight());\r
 565 \r
 566       if(image!=null)\r
 567       {if (fastPaint\r
 568             || (getVisibleRect().width != g.getClipBounds().width)\r
 569             || (getVisibleRect().height != g.getClipBounds().height))\r
 570         {\r
 571           g.drawImage(image, 0, 0, this);\r
 572           fastPaint = false;\r
 573           return;\r
 574         }\r
 575       }\r
 576       imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\r
 577 \r
 578       if (image == null || imgWidth != image.getWidth()\r
 579           || image.getHeight(this) != getHeight())\r
 580       {\r
 581         image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),\r
 582                                   BufferedImage.TYPE_INT_RGB);\r
 583         gg = (Graphics2D) image.getGraphics();\r
 584 \r
 585         if(av.antiAlias)\r
 586         gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
 587                             RenderingHints.VALUE_ANTIALIAS_ON);\r
 588 \r
 589         gg.setFont(av.getFont());\r
 590         fm = gg.getFontMetrics();\r
 591         gg.setColor(Color.white);\r
 592         gg.fillRect(0, 0, imgWidth, image.getHeight());\r
 593       }\r
 594 \r
 595 \r
 596       drawComponent(gg, av.startRes, av.endRes + 1);\r
 597       g.drawImage(image, 0, 0, this);\r
 598     }\r
 599 \r
 600     /**\r
 601      * DOCUMENT ME!\r
 602      *\r
 603      * @param horizontal DOCUMENT ME!\r
 604      */\r
 605     public void fastPaint(int horizontal)\r
 606     {\r
 607         if ((horizontal == 0)\r
 608             || gg==null\r
 609             || av.alignment.getAlignmentAnnotation()==null\r
 610             || av.alignment.getAlignmentAnnotation().length < 1\r
 611             || av.updatingConsensus\r
 612             || av.updatingConservation)\r
 613         {\r
 614             repaint();\r
 615             return;\r
 616         }\r
 617 \r
 618         gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);\r
 619 \r
 620         int sr = av.startRes;\r
 621         int er = av.endRes + 1;\r
 622         int transX = 0;\r
 623 \r
 624         if (horizontal > 0) // scrollbar pulled right, image to the left\r
 625         {\r
 626             transX = (er - sr - horizontal) * av.charWidth;\r
 627             sr = er - horizontal;\r
 628         }\r
 629         else if (horizontal < 0)\r
 630         {\r
 631             er = sr - horizontal;\r
 632         }\r
 633 \r
 634         gg.translate(transX, 0);\r
 635 \r
 636         drawComponent(gg, sr, er);\r
 637 \r
 638         gg.translate(-transX, 0);\r
 639 \r
 640         fastPaint = true;\r
 641 \r
 642         repaint();\r
 643 \r
 644     }\r
 645 \r
 646     /**\r
 647      * DOCUMENT ME!\r
 648      *\r
 649      * @param g DOCUMENT ME!\r
 650      * @param startRes DOCUMENT ME!\r
 651      * @param endRes DOCUMENT ME!\r
 652      */\r
 653     public void drawComponent(Graphics g, int startRes, int endRes)\r
 654     {\r
 655       if(av.updatingConsensus || av.updatingConservation)\r
 656       {\r
 657         //We'll keep a record of the old image,\r
 658         //and draw a faded image until the calculation\r
 659         //has completed\r
 660         if(fadedImage==null\r
 661            || fadedImage.getWidth()!=imgWidth\r
 662         || fadedImage.getHeight()!=image.getHeight())\r
 663         {\r
 664           fadedImage = new BufferedImage(\r
 665               imgWidth, image.getHeight(),\r
 666               BufferedImage.TYPE_INT_RGB);\r
 667 \r
 668           Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();\r
 669 \r
 670           fadedG.setColor(Color.white);\r
 671         fadedG.fillRect(0, 0, imgWidth, image.getHeight());\r
 672 \r
 673           fadedG.setComposite(\r
 674               AlphaComposite.getInstance(\r
 675                   AlphaComposite.SRC_OVER, .3f));\r
 676           fadedG.drawImage(image, 0, 0, this);\r
 677 \r
 678         }\r
 679 \r
 680       }\r
 681       else\r
 682         fadedImage = null;\r
 683 \r
 684 \r
 685       g.setColor(Color.white);\r
 686       g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());\r
 687 \r
 688       g.setFont(av.getFont());\r
 689       if (fm == null)\r
 690         fm = g.getFontMetrics();\r
 691 \r
 692 \r
 693 \r
 694 \r
 695         if ( (av.alignment.getAlignmentAnnotation() == null) ||\r
 696                 (av.alignment.getAlignmentAnnotation().length < 1))\r
 697         {\r
 698             g.setColor(Color.white);\r
 699             g.fillRect(0, 0, getWidth(), getHeight());\r
 700             g.setColor(Color.black);\r
 701             if(av.validCharWidth)\r
 702               g.drawString("Alignment has no annotations", 20, 15);\r
 703 \r
 704             return;\r
 705         }\r
 706 \r
 707 \r
 708         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 709 \r
 710         int x = 0, y = 0;\r
 711         int column=0;\r
 712         char lastSS;\r
 713         int lastSSX;\r
 714         int iconOffset = av.charHeight / 2;\r
 715         boolean validRes = false;\r
 716 \r
 717         boolean [] graphGroupDrawn = new boolean[aa.length];\r
 718 \r
 719 \r
 720         //\u03B2 \u03B1\r
 721         for (int i = 0; i < aa.length; i++)\r
 722         {\r
 723             AlignmentAnnotation row = aa[i];\r
 724 \r
 725             if (!row.visible)\r
 726             {\r
 727                 continue;\r
 728             }\r
 729 \r
 730 \r
 731             lastSS = ' ';\r
 732             lastSSX = 0;\r
 733 \r
 734             if (row.graph>0)\r
 735             {\r
 736                 if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )\r
 737                   continue;\r
 738 \r
 739                 // this is so that we draw the characters below the graph\r
 740                 y += row.height;\r
 741 \r
 742                 if (row.hasText)\r
 743                 {\r
 744                     y -= av.charHeight;\r
 745                 }\r
 746             }\r
 747 \r
 748             if (av.updatingConsensus && aa[i].label.equals("Consensus"))\r
 749             {\r
 750               y += av.charHeight;\r
 751 \r
 752               g.drawImage(fadedImage,\r
 753               0,y-row.height,imgWidth, y,\r
 754               0,y-row.height,imgWidth, y, this);\r
 755               g.setColor(Color.black);\r
 756              // g.drawString("Calculating Consensus....",20, y-row.height/2);\r
 757 \r
 758               continue;\r
 759             }\r
 760             else if (av.updatingConservation && aa[i].label.equals("Conservation"))\r
 761             {\r
 762 \r
 763               y += av.charHeight;\r
 764               g.drawImage(fadedImage,\r
 765                           0, y - row.height, imgWidth, y,\r
 766                           0, y - row.height, imgWidth, y, this);\r
 767 \r
 768               g.setColor(Color.black);\r
 769             //  g.drawString("Calculating Conservation.....",20, y-row.height/2);\r
 770 \r
 771               continue;\r
 772             }\r
 773             else if (av.updatingConservation && aa[i].label.equals("Quality"))\r
 774             {\r
 775 \r
 776               y += av.charHeight;\r
 777               g.drawImage(fadedImage,\r
 778                           0, y - row.height, imgWidth, y,\r
 779                           0, y - row.height, imgWidth, y, this);\r
 780               g.setColor(Color.black);\r
 781              /// g.drawString("Calculating Quality....",20, y-row.height/2);\r
 782 \r
 783               continue;\r
 784             }\r
 785 \r
 786 \r
 787             if (row.hasText)\r
 788             {\r
 789                 iconOffset = av.charHeight / 2 + 4;\r
 790             }\r
 791             else\r
 792             {\r
 793                 iconOffset = 0;\r
 794             }\r
 795 \r
 796             x = 0;\r
 797             while (x < endRes-startRes)\r
 798             {\r
 799               if (av.hasHiddenColumns)\r
 800               {\r
 801                 column = av.getColumnSelection().adjustForHiddenColumns(startRes+x);\r
 802                 if (column > row.annotations.length-1)\r
 803                 {\r
 804                   break;\r
 805                 }\r
 806               }\r
 807               else\r
 808                 column = startRes+x;\r
 809 \r
 810 \r
 811                 if ((row.annotations.length <= column) ||\r
 812                         (row.annotations[column] == null))\r
 813                 {\r
 814                     validRes = false;\r
 815                 }\r
 816                 else\r
 817                 {\r
 818                     validRes = true;\r
 819                 }\r
 820 \r
 821 \r
 822                 if (activeRow == i)\r
 823                 {\r
 824                     g.setColor(Color.red);\r
 825 \r
 826                     if (av.getColumnSelection() != null)\r
 827                     {\r
 828                         for (int n = 0; n < av.getColumnSelection().size(); n++)\r
 829                         {\r
 830                             int v = av.getColumnSelection().columnAt(n);\r
 831 \r
 832                             if (v == column)\r
 833                             {\r
 834                                 g.fillRect(x * av.charWidth, y,\r
 835                                     av.charWidth, av.charHeight);\r
 836                             }\r
 837                         }\r
 838                     }\r
 839                 }\r
 840 \r
 841                 if (av.validCharWidth && validRes &&\r
 842                         (row.annotations[column].displayCharacter.length() > 0))\r
 843                 {\r
 844 \r
 845                     int charOffset = (av.charWidth -\r
 846                         fm.charWidth(row.annotations[column].displayCharacter.charAt(\r
 847                                 0))) / 2;\r
 848                     g.setColor(row.annotations[column].colour);\r
 849 \r
 850                     if (column == 0 || row.graph>0)\r
 851                     {\r
 852                         g.drawString(row.annotations[column].displayCharacter,\r
 853                                      (x*av.charWidth)+charOffset,\r
 854                             y + iconOffset );\r
 855                     }\r
 856                     else if (\r
 857                         row.annotations[column - 1] == null\r
 858                         ||(!row.annotations[column].displayCharacter.equals(\r
 859                             row.annotations[column - 1].displayCharacter)\r
 860                         ||\r
 861                   (row.annotations[column].displayCharacter.length() <2 &&\r
 862                    row.annotations[column].secondaryStructure==' ')))\r
 863                     {\r
 864                         g.drawString(row.annotations[column].displayCharacter,\r
 865                                      x*av.charWidth+charOffset,\r
 866                                      y + iconOffset );\r
 867                     }\r
 868                 }\r
 869 \r
 870                 if (row.hasIcons)\r
 871                 {\r
 872                     if (!validRes ||\r
 873                             (row.annotations[column].secondaryStructure != lastSS))\r
 874                     {\r
 875                         switch (lastSS)\r
 876                         {\r
 877                         case 'H':\r
 878                           g.setColor(HELIX_COLOUR);\r
 879                           if (MAC)\r
 880                           {\r
 881                             //Off by 1 offset when drawing rects and ovals\r
 882                             //to offscreen image on the MAC\r
 883                             g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
 884                                             (x*av.charWidth) - lastSSX, 7, 8, 8);\r
 885                             break;\r
 886                           }\r
 887 \r
 888                           int sCol = (lastSSX / av.charWidth) + startRes;\r
 889                           int x1 = lastSSX;\r
 890                           int x2 = (x*av.charWidth);\r
 891 \r
 892                          if(sCol==0 ||\r
 893                             row.annotations[sCol-1]==null ||\r
 894                             row.annotations[sCol-1].secondaryStructure!='H')\r
 895                          {\r
 896                            g.fillArc(lastSSX, y+4+iconOffset, av.charWidth, 8, 90,180) ;\r
 897                            x1 += av.charWidth/2;\r
 898                          }\r
 899 \r
 900                           if(row.annotations[column]==null ||\r
 901                              row.annotations[column].secondaryStructure!='H')\r
 902                           {\r
 903                             g.fillArc((x*av.charWidth)-av.charWidth,\r
 904                                       y+4+iconOffset, av.charWidth, 8, 270,180);\r
 905                             x2 -= av.charWidth/2;\r
 906                           }\r
 907 \r
 908                           g.fillRect(x1, y+4+iconOffset, x2-x1, 8);\r
 909                               break;\r
 910 \r
 911                         case 'E':\r
 912                             g.setColor(SHEET_COLOUR);\r
 913                             g.fillRect(lastSSX, y + 4 + iconOffset,\r
 914                                 (x*av.charWidth) - lastSSX - 4, 7);\r
 915                             g.fillPolygon(new int[] { (x*av.charWidth) - 4,\r
 916                                           (x*av.charWidth) - 4,\r
 917                                           (x*av.charWidth) },\r
 918                                 new int[]\r
 919                                 {\r
 920                                     y + iconOffset, y + 14 + iconOffset,\r
 921                                     y + 8 + iconOffset\r
 922                                 }, 3);\r
 923 \r
 924                             break;\r
 925 \r
 926 \r
 927                         default:\r
 928                             g.setColor(Color.gray);\r
 929                             g.fillRect(lastSSX, y + 6 + iconOffset,\r
 930                                 (x*av.charWidth) - lastSSX, 2);\r
 931 \r
 932                             break;\r
 933                         }\r
 934 \r
 935                         if (validRes)\r
 936                         {\r
 937                             lastSS = row.annotations[column].secondaryStructure;\r
 938                         }\r
 939                         else\r
 940                         {\r
 941                             lastSS = ' ';\r
 942                         }\r
 943 \r
 944                         lastSSX = (x*av.charWidth);\r
 945                     }\r
 946                 }\r
 947 \r
 948 \r
 949             column++;\r
 950             x++;\r
 951             }\r
 952 \r
 953             if(column>=row.annotations.length)\r
 954                 column = row.annotations.length-1;\r
 955 \r
 956           //  x ++;\r
 957 \r
 958             if (row.hasIcons)\r
 959             {\r
 960               switch (lastSS)\r
 961               {\r
 962                 case 'H':\r
 963                   g.setColor(HELIX_COLOUR);\r
 964                   if (MAC)\r
 965                   {\r
 966                     //Off by 1 offset when drawing rects and ovals\r
 967                     //to offscreen image on the MAC\r
 968                     g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
 969                                     (x*av.charWidth) - lastSSX, 7, 8, 8);\r
 970                     break;\r
 971                   }\r
 972 \r
 973                   int sCol = (lastSSX / av.charWidth) + startRes;\r
 974                   int x1 = lastSSX;\r
 975                   int x2 = (x*av.charWidth);\r
 976 \r
 977                   if (sCol == 0 ||\r
 978                       row.annotations[sCol - 1] == null ||\r
 979                       row.annotations[sCol - 1].secondaryStructure != 'H')\r
 980                   {\r
 981                     g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);\r
 982                     x1 += av.charWidth / 2;\r
 983                   }\r
 984 \r
 985                   if (row.annotations[column] == null ||\r
 986                       row.annotations[column].secondaryStructure != 'H')\r
 987                   {\r
 988                     g.fillArc((x*av.charWidth) - av.charWidth,\r
 989                               y + 4 + iconOffset, av.charWidth, 8, 270,\r
 990                               180);\r
 991                     x2 -= av.charWidth / 2;\r
 992                   }\r
 993 \r
 994                   g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);\r
 995 \r
 996                   break;\r
 997 \r
 998                 case 'E':\r
 999                   g.setColor(SHEET_COLOUR);\r
1000 \r
1001                   if (row.annotations[endRes] == null\r
1002                       || row.annotations[endRes].secondaryStructure != 'E')\r
1003                   {\r
1004                     g.fillRect(lastSSX, y + 4 + iconOffset,\r
1005                                (x*av.charWidth) - lastSSX - 4, 7);\r
1006                     g.fillPolygon(new int[]\r
1007                                   {(x*av.charWidth) - 4,\r
1008                                   (x*av.charWidth) - 4,\r
1009                                  (x*av.charWidth)},\r
1010                                   new int[]\r
1011                                   {\r
1012                                   y + iconOffset, y + 14 + iconOffset,\r
1013                                   y + 7 + iconOffset\r
1014                     }, 3);\r
1015                   }\r
1016                   else\r
1017                    {\r
1018                      g.fillRect(lastSSX, y + 4 + iconOffset,\r
1019                                 (x+1) * av.charWidth - lastSSX, 7);\r
1020                    }\r
1021                   break;\r
1022 \r
1023                 default:\r
1024                   g.setColor(Color.gray);\r
1025                   if(!av.wrapAlignment || endRes==av.endRes)\r
1026                   g.fillRect(lastSSX, y + 6 + iconOffset,\r
1027                              (x*av.charWidth) - lastSSX, 2);\r
1028 \r
1029                   break;\r
1030               }\r
1031           }\r
1032 \r
1033             if (row.graph>0 && row.graphHeight>0)\r
1034             {\r
1035                 if(row.graph == AlignmentAnnotation.LINE_GRAPH )\r
1036                 {\r
1037                   if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])\r
1038                    {\r
1039                      float groupmax=-999999, groupmin=9999999;\r
1040                      for(int gg=0; gg<aa.length; gg++)\r
1041                      {\r
1042                        if(aa[gg].graphGroup!=row.graphGroup)\r
1043                          continue;\r
1044 \r
1045                        if(aa[gg]!=row)\r
1046                          aa[gg].visible = false;\r
1047 \r
1048                        if(aa[gg].graphMax>groupmax)\r
1049                          groupmax = aa[gg].graphMax;\r
1050                        if(aa[gg].graphMin<groupmin)\r
1051                          groupmin = aa[gg].graphMin;\r
1052                      }\r
1053 \r
1054                      for (int gg = 0; gg < aa.length; gg++)\r
1055                      {\r
1056                        if (aa[gg].graphGroup == row.graphGroup)\r
1057                        {\r
1058                          drawLineGraph(g, aa[gg], startRes, endRes, y,\r
1059                                        groupmin, groupmax,\r
1060                                        row.graphHeight);\r
1061                        }\r
1062                      }\r
1063 \r
1064                      graphGroupDrawn[ row.graphGroup ] = true;\r
1065                    }\r
1066                    else\r
1067                      drawLineGraph(g, row, startRes, endRes,\r
1068                                    y, row.graphMin, row.graphMax, row.graphHeight  );\r
1069                 }\r
1070                 else if(row.graph == AlignmentAnnotation.BAR_GRAPH )\r
1071                    drawBarGraph(g, row, startRes, endRes,\r
1072                                 row.graphMin, row.graphMax, y);\r
1073             }\r
1074 \r
1075             if (row.graph>0 && row.hasText)\r
1076             {\r
1077                 y += av.charHeight;\r
1078             }\r
1079 \r
1080             if (row.graph==0)\r
1081             {\r
1082                 y += aa[i].height;\r
1083             }\r
1084         }\r
1085     }\r
1086 \r
1087     public void drawLineGraph(Graphics g, AlignmentAnnotation aa,\r
1088                               int sRes, int eRes,\r
1089                               int y,\r
1090                               float min, float max,\r
1091                               int graphHeight)\r
1092     {\r
1093       if(sRes>aa.annotations.length)\r
1094         return;\r
1095 \r
1096 \r
1097       int x = 0;\r
1098 \r
1099       //Adjustment for fastpaint to left\r
1100       if(eRes<av.endRes)\r
1101         eRes++;\r
1102 \r
1103       eRes = Math.min(eRes, aa.annotations.length);\r
1104 \r
1105       if(sRes==0)\r
1106       {\r
1107         x++;\r
1108       }\r
1109 \r
1110       int y1=y, y2=y;\r
1111       float range = max - min;\r
1112 \r
1113       ////Draw origin\r
1114       if(min<0)\r
1115         y2 = y - (int)((0-min / range)*graphHeight);\r
1116 \r
1117       g.setColor(Color.gray);\r
1118       g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
1119 \r
1120       eRes = Math.min(eRes, aa.annotations.length);\r
1121 \r
1122       int column;\r
1123       int aaMax = aa.annotations.length-1;\r
1124 \r
1125       while( x < eRes - sRes )\r
1126       {\r
1127         column = sRes + x;\r
1128         if(av.hasHiddenColumns)\r
1129         {\r
1130           column = av.getColumnSelection().adjustForHiddenColumns(column);\r
1131         }\r
1132 \r
1133         if (column > aaMax)\r
1134         {\r
1135           break;\r
1136         }\r
1137 \r
1138         if(aa.annotations[column]==null || aa.annotations[column-1]==null)\r
1139         {\r
1140           x++;\r
1141           continue;\r
1142         }\r
1143 \r
1144 \r
1145           g.setColor(aa.annotations[column].colour);\r
1146           y1 = y - (int) (((aa.annotations[column-1].value-min) / range) * graphHeight);\r
1147           y2 = y - (int) (((aa.annotations[column].value-min) / range) * graphHeight);\r
1148 \r
1149           g.drawLine(x*av.charWidth-av.charWidth/2, y1, x*av.charWidth+av.charWidth/2, y2);\r
1150           x ++;\r
1151        }\r
1152 \r
1153        if(aa.threshold!=null)\r
1154        {\r
1155            g.setColor(aa.threshold.colour);\r
1156            Graphics2D g2 = (Graphics2D)g;\r
1157            g2.setStroke(new BasicStroke(1,\r
1158                                          BasicStroke.CAP_SQUARE,\r
1159                                          BasicStroke.JOIN_ROUND, 3f,\r
1160                                          new float[] { 5f, 3f }, 0f));\r
1161 \r
1162            y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);\r
1163            g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
1164            g2.setStroke(new BasicStroke());\r
1165       }\r
1166     }\r
1167 \r
1168     public void drawBarGraph(Graphics g, AlignmentAnnotation aa,\r
1169                              int sRes, int eRes,\r
1170                              float min, float max,\r
1171                              int y)\r
1172     {\r
1173       if(sRes>aa.annotations.length)\r
1174         return;\r
1175 \r
1176       eRes = Math.min(eRes, aa.annotations.length);\r
1177 \r
1178       int x=0, y1=y, y2=y;\r
1179 \r
1180       float range = max - min;\r
1181 \r
1182       if(min<0)\r
1183         y2 = y - (int)((0-min / (range))*aa.graphHeight);\r
1184 \r
1185       g.setColor(Color.gray);\r
1186 \r
1187       g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);\r
1188 \r
1189       int column;\r
1190       int aaMax = aa.annotations.length-1;\r
1191 \r
1192       while( x < eRes-sRes )\r
1193       {\r
1194         column = sRes + x;\r
1195         if(av.hasHiddenColumns)\r
1196         {\r
1197           column = av.getColumnSelection().adjustForHiddenColumns(column);\r
1198         }\r
1199 \r
1200         if(column > aaMax)\r
1201         {\r
1202             break;\r
1203         }\r
1204 \r
1205         if (aa.annotations[column] == null)\r
1206         {\r
1207           x ++;\r
1208           continue;\r
1209         }\r
1210 \r
1211           g.setColor(aa.annotations[column].colour);\r
1212           y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);\r
1213 \r
1214           if(y1-y2>0)\r
1215             g.fillRect(x*av.charWidth, y2, av.charWidth, y1-y2 );\r
1216           else\r
1217             g.fillRect(x*av.charWidth, y1, av.charWidth, y2-y1 );\r
1218 \r
1219           x ++ ;\r
1220 \r
1221       }\r
1222       if(aa.threshold!=null)\r
1223       {\r
1224           g.setColor(aa.threshold.colour);\r
1225           Graphics2D g2 = (Graphics2D)g;\r
1226           g2.setStroke(new BasicStroke(1,\r
1227                                         BasicStroke.CAP_SQUARE,\r
1228                                         BasicStroke.JOIN_ROUND, 3f,\r
1229                                         new float[] { 5f, 3f }, 0f));\r
1230 \r
1231           y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);\r
1232           g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
1233           g2.setStroke(new BasicStroke());\r
1234       }\r
1235     }\r
1236 \r
1237     // used by overview window\r
1238     public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)\r
1239     {\r
1240       eRes = Math.min(eRes, aa.annotations.length);\r
1241       g.setColor(Color.white);\r
1242       g.fillRect(0, 0, width, y);\r
1243       g.setColor(new Color(0, 0, 180));\r
1244 \r
1245       int x = 0, height;\r
1246 \r
1247       for (int j = sRes; j < eRes; j++)\r
1248       {\r
1249         if (aa.annotations[j] != null)\r
1250         {\r
1251           g.setColor(aa.annotations[j].colour);\r
1252 \r
1253           height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);\r
1254           if (height > y)\r
1255             height = y;\r
1256 \r
1257           g.fillRect(x, y - height, av.charWidth, height);\r
1258         }\r
1259           x += av.charWidth;\r
1260       }\r
1261     }\r
1262 \r
1263 }\r