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         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 112         int height = 0;\r
 113 \r
 114         if (aa != null)\r
 115         {\r
 116             for (int i = 0; i < aa.length; i++)\r
 117             {\r
 118                 if (!aa[i].visible)\r
 119                 {\r
 120                     continue;\r
 121                 }\r
 122 \r
 123                 aa[i].height = 0;\r
 124 \r
 125                 if (aa[i].hasText)\r
 126                 {\r
 127                     aa[i].height += av.charHeight;\r
 128                 }\r
 129 \r
 130                 if (aa[i].hasIcons)\r
 131                 {\r
 132                     aa[i].height += 16;\r
 133                 }\r
 134 \r
 135                 if (aa[i].graph>0)\r
 136                 {\r
 137                     aa[i].height += aa[i].graphHeight;\r
 138                 }\r
 139 \r
 140                 if (aa[i].height == 0)\r
 141                 {\r
 142                     aa[i].height = 20;\r
 143                 }\r
 144 \r
 145                 height += aa[i].height;\r
 146             }\r
 147         }\r
 148         else\r
 149         {\r
 150             height = 20;\r
 151         }\r
 152 \r
 153         this.setPreferredSize(new Dimension(1, height));\r
 154 \r
 155         return height;\r
 156     }\r
 157 \r
 158 \r
 159 \r
 160     /**\r
 161      * DOCUMENT ME!\r
 162      *\r
 163      * @param evt DOCUMENT ME!\r
 164      */\r
 165     public void actionPerformed(ActionEvent evt)\r
 166     {\r
 167         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 168         Annotation[] anot = aa[activeRow].annotations;\r
 169 \r
 170         if (evt.getActionCommand().equals(REMOVE))\r
 171         {\r
 172             for (int i = 0; i < av.getColumnSelection().size(); i++)\r
 173             {\r
 174                 anot[av.getColumnSelection().columnAt(i)] = null;\r
 175             }\r
 176         }\r
 177         else if (evt.getActionCommand().equals(LABEL))\r
 178         {\r
 179             String label = JOptionPane.showInputDialog(this, "Enter Label ",\r
 180                     "Enter label", JOptionPane.QUESTION_MESSAGE);\r
 181 \r
 182             if (label == null)\r
 183             {\r
 184                 return;\r
 185             }\r
 186 \r
 187             if ((label.length() > 0) && !aa[activeRow].hasText)\r
 188             {\r
 189                 aa[activeRow].hasText = true;\r
 190             }\r
 191 \r
 192             for (int i = 0; i < av.getColumnSelection().size(); i++)\r
 193             {\r
 194                 int index = av.getColumnSelection().columnAt(i);\r
 195 \r
 196                 if (anot[index] == null)\r
 197                 {\r
 198                     anot[index] = new Annotation(label, "", ' ', 0);\r
 199                 }\r
 200 \r
 201                 anot[index].displayCharacter = label;\r
 202             }\r
 203         }\r
 204         else if (evt.getActionCommand().equals(COLOUR))\r
 205         {\r
 206             Color col = JColorChooser.showDialog(this,\r
 207                     "Choose foreground colour", Color.black);\r
 208 \r
 209             for (int i = 0; i < av.getColumnSelection().size(); i++)\r
 210             {\r
 211                 int index = av.getColumnSelection().columnAt(i);\r
 212 \r
 213                 if (anot[index] == null)\r
 214                 {\r
 215                     anot[index] = new Annotation("", "", ' ', 0);\r
 216                 }\r
 217 \r
 218                 anot[index].colour = col;\r
 219             }\r
 220         }\r
 221         else // HELIX OR SHEET\r
 222         {\r
 223             char type = 0;\r
 224             String symbol = "\u03B1";\r
 225 \r
 226             if (evt.getActionCommand().equals(HELIX))\r
 227             {\r
 228                 type = 'H';\r
 229             }\r
 230             else if (evt.getActionCommand().equals(SHEET))\r
 231             {\r
 232                 type = 'E';\r
 233                 symbol = "\u03B2";\r
 234             }\r
 235 \r
 236             if (!aa[activeRow].hasIcons)\r
 237             {\r
 238                 aa[activeRow].hasIcons = true;\r
 239             }\r
 240 \r
 241             String label = JOptionPane.showInputDialog("Enter a label for the structure?",\r
 242                     symbol);\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 < av.getColumnSelection().size(); i++)\r
 255             {\r
 256                 int index = av.getColumnSelection().columnAt(i);\r
 257 \r
 258                 if (anot[index] == null)\r
 259                 {\r
 260                     anot[index] = new Annotation(label, "", type, 0);\r
 261                 }\r
 262 \r
 263                 anot[index].secondaryStructure = type;\r
 264                 anot[index].displayCharacter = label;\r
 265             }\r
 266         }\r
 267 \r
 268         adjustPanelHeight();\r
 269         repaint();\r
 270 \r
 271         return;\r
 272     }\r
 273 \r
 274     /**\r
 275      * DOCUMENT ME!\r
 276      *\r
 277      * @param evt DOCUMENT ME!\r
 278      */\r
 279     public void mousePressed(MouseEvent evt)\r
 280     {\r
 281 \r
 282 \r
 283         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 284         if(aa==null)\r
 285           return;\r
 286 \r
 287 \r
 288         int height = 0;\r
 289         activeRow = -1;\r
 290 \r
 291 \r
 292         for (int i = 0; i < aa.length; i++)\r
 293         {\r
 294             if (aa[i].visible)\r
 295             {\r
 296               height += aa[i].height;\r
 297             }\r
 298 \r
 299             if (evt.getY() < height)\r
 300             {\r
 301                 if (aa[i].editable)\r
 302                 {\r
 303                     activeRow = i;\r
 304                 }\r
 305                 else if(aa[i].graph>0)\r
 306                 {\r
 307                     //Stretch Graph\r
 308                     graphStretch = i;\r
 309                     graphStretchY = evt.getY();\r
 310                 }\r
 311 \r
 312                 break;\r
 313             }\r
 314         }\r
 315 \r
 316 \r
 317         if (SwingUtilities.isRightMouseButton(evt) && activeRow!=-1)\r
 318         {\r
 319             if (av.getColumnSelection() == null)\r
 320             {\r
 321                 return;\r
 322             }\r
 323 \r
 324             JPopupMenu pop = new JPopupMenu("Structure type");\r
 325             JMenuItem item = new JMenuItem(HELIX);\r
 326             item.addActionListener(this);\r
 327             pop.add(item);\r
 328             item = new JMenuItem(SHEET);\r
 329             item.addActionListener(this);\r
 330             pop.add(item);\r
 331             item = new JMenuItem(LABEL);\r
 332             item.addActionListener(this);\r
 333             pop.add(item);\r
 334             item = new JMenuItem(COLOUR);\r
 335             item.addActionListener(this);\r
 336             pop.add(item);\r
 337             item = new JMenuItem(REMOVE);\r
 338             item.addActionListener(this);\r
 339             pop.add(item);\r
 340             pop.show(this, evt.getX(), evt.getY());\r
 341 \r
 342             return;\r
 343         }\r
 344 \r
 345         if (aa == null)\r
 346         {\r
 347             return;\r
 348         }\r
 349 \r
 350         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 351 \r
 352         min = res;\r
 353         max = res;\r
 354 \r
 355         if (av.getColumnSelection().contains(res))\r
 356           av.getColumnSelection().removeElement(res);\r
 357         else\r
 358         {\r
 359             av.getColumnSelection().addElement(res);\r
 360             SequenceGroup sg = new SequenceGroup();\r
 361 \r
 362             for (int i = 0; i < av.alignment.getSequences().size(); i++)\r
 363             {\r
 364                 sg.addSequence(av.alignment.getSequenceAt(i), false);\r
 365             }\r
 366 \r
 367             sg.setStartRes(res);\r
 368             sg.setEndRes(res);\r
 369             av.setSelectionGroup(sg);\r
 370         }\r
 371 \r
 372         ap.repaint();\r
 373 \r
 374     }\r
 375 \r
 376     /**\r
 377      * DOCUMENT ME!\r
 378      *\r
 379      * @param evt DOCUMENT ME!\r
 380      */\r
 381     public void mouseReleased(MouseEvent evt)\r
 382     {\r
 383       graphStretch = -1;\r
 384       graphStretchY = -1;\r
 385       mouseDragging = false;\r
 386     }\r
 387 \r
 388     /**\r
 389      * DOCUMENT ME!\r
 390      *\r
 391      * @param evt DOCUMENT ME!\r
 392      */\r
 393     public void mouseEntered(MouseEvent evt)\r
 394     {\r
 395       if(mouseDragging)\r
 396         ap.seqPanel.scrollCanvas(null);\r
 397     }\r
 398 \r
 399     /**\r
 400      * DOCUMENT ME!\r
 401      *\r
 402      * @param evt DOCUMENT ME!\r
 403      */\r
 404     public void mouseExited(MouseEvent evt)\r
 405     {\r
 406       if(mouseDragging)\r
 407         ap.seqPanel.scrollCanvas(evt);\r
 408     }\r
 409 \r
 410 \r
 411     /**\r
 412      * DOCUMENT ME!\r
 413      *\r
 414      * @param evt DOCUMENT ME!\r
 415      */\r
 416     public void mouseDragged(MouseEvent evt)\r
 417     {\r
 418       if(graphStretch>-1)\r
 419       {\r
 420         av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY();\r
 421         if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <0)\r
 422           av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;\r
 423         graphStretchY = evt.getY();\r
 424         adjustPanelHeight();\r
 425         ap.repaint();\r
 426       }\r
 427       else\r
 428       {\r
 429         mouseDragging = true;\r
 430 \r
 431         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 432 \r
 433         SequenceGroup sg = av.getSelectionGroup();\r
 434 \r
 435         if (res < min)\r
 436         {\r
 437             min = res;\r
 438         }\r
 439 \r
 440         if (res > max)\r
 441         {\r
 442             max = res;\r
 443         }\r
 444 \r
 445         if (sg != null)\r
 446         {\r
 447             if (!av.getColumnSelection().contains(res))\r
 448             {\r
 449                 av.getColumnSelection().addElement(res);\r
 450             }\r
 451 \r
 452             if (res > sg.getStartRes())\r
 453             {\r
 454                 sg.setEndRes(res);\r
 455             }\r
 456             else if (res < sg.getStartRes())\r
 457             {\r
 458                 sg.setStartRes(res);\r
 459             }\r
 460 \r
 461             for (int i = min; i <= max; i++)\r
 462             {\r
 463                 if ((i < sg.getStartRes()) || (i > sg.getEndRes()))\r
 464                 {\r
 465                     av.getColumnSelection().removeElement(i);\r
 466                 }\r
 467                 else\r
 468                 {\r
 469                     av.getColumnSelection().addElement(i);\r
 470                 }\r
 471             }\r
 472 \r
 473             ap.repaint();\r
 474         }\r
 475 \r
 476       }\r
 477     }\r
 478 \r
 479     /**\r
 480      * DOCUMENT ME!\r
 481      *\r
 482      * @param evt DOCUMENT ME!\r
 483      */\r
 484     public void mouseMoved(MouseEvent evt)\r
 485     {\r
 486         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 487 \r
 488         if (aa == null)\r
 489         {\r
 490             return;\r
 491         }\r
 492 \r
 493         int row = -1;\r
 494         int height = 0;\r
 495 \r
 496         for (int i = 0; i < aa.length; i++)\r
 497         {\r
 498             if (aa[i].visible)\r
 499             {\r
 500                 height += aa[i].height;\r
 501             }\r
 502 \r
 503             if (evt.getY() < height)\r
 504             {\r
 505                 row = i;\r
 506 \r
 507                 break;\r
 508             }\r
 509         }\r
 510 \r
 511         if(row==-1)\r
 512           return;\r
 513 \r
 514         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 515 \r
 516         if(av.hasHiddenColumns)\r
 517           res = av.getColumnSelection().adjustForHiddenColumns(res);\r
 518 \r
 519         if ( aa[row].annotations!=null\r
 520              && row > -1\r
 521              && res < (int) aa[row].annotations.length)\r
 522         {\r
 523             if(aa[row].graphGroup>-1)\r
 524             {\r
 525               StringBuffer tip = new StringBuffer("<html>");\r
 526               for (int gg = 0; gg < aa.length; gg++)\r
 527               {\r
 528                 if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res]!=null)\r
 529                   tip.append(aa[gg].label+" "+aa[gg].annotations[res].description+"<br>" );\r
 530               }\r
 531               if(tip.length()!=6)\r
 532               {\r
 533                 tip.setLength(tip.length() - 4);\r
 534                 this.setToolTipText(tip.toString() + "</html>");\r
 535               }\r
 536             }\r
 537             else if(aa[row].annotations[res] != null)\r
 538               this.setToolTipText(aa[row].annotations[res].description);\r
 539 \r
 540             if(aa[row].annotations[res]!=null)\r
 541             {\r
 542               StringBuffer text = new StringBuffer("Sequence position " +\r
 543                                                    (res + 1) + "  " +\r
 544                                                    aa[row].annotations[res].description);\r
 545 \r
 546               ap.alignFrame.statusBar.setText(text.toString());\r
 547             }\r
 548         }\r
 549     }\r
 550 \r
 551     /**\r
 552      * DOCUMENT ME!\r
 553      *\r
 554      * @param evt DOCUMENT ME!\r
 555      */\r
 556     public void mouseClicked(MouseEvent evt)\r
 557     {\r
 558     }\r
 559 \r
 560     /**\r
 561      * DOCUMENT ME!\r
 562      *\r
 563      * @param g DOCUMENT ME!\r
 564      */\r
 565     public void paintComponent(Graphics g)\r
 566     {\r
 567       g.setColor(Color.white);\r
 568       g.fillRect(0, 0, getWidth(), getHeight());\r
 569 \r
 570       if(image!=null)\r
 571       {if (fastPaint\r
 572             || (getVisibleRect().width != g.getClipBounds().width)\r
 573             || (getVisibleRect().height != g.getClipBounds().height))\r
 574         {\r
 575           g.drawImage(image, 0, 0, this);\r
 576           fastPaint = false;\r
 577           return;\r
 578         }\r
 579       }\r
 580       imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\r
 581 \r
 582       if (image == null || imgWidth != image.getWidth()\r
 583           || image.getHeight(this) != getHeight())\r
 584       {\r
 585         image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),\r
 586                                   BufferedImage.TYPE_INT_RGB);\r
 587         gg = (Graphics2D) image.getGraphics();\r
 588 \r
 589         if(av.antiAlias)\r
 590         gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
 591                             RenderingHints.VALUE_ANTIALIAS_ON);\r
 592 \r
 593         gg.setFont(av.getFont());\r
 594         fm = gg.getFontMetrics();\r
 595         gg.setColor(Color.white);\r
 596         gg.fillRect(0, 0, imgWidth, image.getHeight());\r
 597       }\r
 598 \r
 599 \r
 600       drawComponent(gg, av.startRes, av.endRes + 1);\r
 601       g.drawImage(image, 0, 0, this);\r
 602     }\r
 603 \r
 604     /**\r
 605      * DOCUMENT ME!\r
 606      *\r
 607      * @param horizontal DOCUMENT ME!\r
 608      */\r
 609     public void fastPaint(int horizontal)\r
 610     {\r
 611         if ((horizontal == 0)\r
 612             || gg==null\r
 613             || av.alignment.getAlignmentAnnotation()==null\r
 614             || av.alignment.getAlignmentAnnotation().length < 1\r
 615             || av.updatingConsensus\r
 616             || av.updatingConservation)\r
 617         {\r
 618             repaint();\r
 619             return;\r
 620         }\r
 621 \r
 622         gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);\r
 623 \r
 624         int sr = av.startRes;\r
 625         int er = av.endRes + 1;\r
 626         int transX = 0;\r
 627 \r
 628         if (horizontal > 0) // scrollbar pulled right, image to the left\r
 629         {\r
 630             transX = (er - sr - horizontal) * av.charWidth;\r
 631             sr = er - horizontal;\r
 632         }\r
 633         else if (horizontal < 0)\r
 634         {\r
 635             er = sr - horizontal;\r
 636         }\r
 637 \r
 638         gg.translate(transX, 0);\r
 639 \r
 640         drawComponent(gg, sr, er);\r
 641 \r
 642         gg.translate(-transX, 0);\r
 643 \r
 644         fastPaint = true;\r
 645 \r
 646         repaint();\r
 647 \r
 648     }\r
 649 \r
 650     /**\r
 651      * DOCUMENT ME!\r
 652      *\r
 653      * @param g DOCUMENT ME!\r
 654      * @param startRes DOCUMENT ME!\r
 655      * @param endRes DOCUMENT ME!\r
 656      */\r
 657     public void drawComponent(Graphics g, int startRes, int endRes)\r
 658     {\r
 659       if(av.updatingConsensus || av.updatingConservation)\r
 660       {\r
 661         if(image==null)\r
 662          {\r
 663            return;\r
 664          }\r
 665         //We'll keep a record of the old image,\r
 666         //and draw a faded image until the calculation\r
 667         //has completed\r
 668         if(fadedImage==null\r
 669            || fadedImage.getWidth()!=imgWidth\r
 670         || fadedImage.getHeight()!=image.getHeight())\r
 671         {\r
 672           fadedImage = new BufferedImage(\r
 673               imgWidth, image.getHeight(),\r
 674               BufferedImage.TYPE_INT_RGB);\r
 675 \r
 676           Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();\r
 677 \r
 678           fadedG.setColor(Color.white);\r
 679         fadedG.fillRect(0, 0, imgWidth, image.getHeight());\r
 680 \r
 681           fadedG.setComposite(\r
 682               AlphaComposite.getInstance(\r
 683                   AlphaComposite.SRC_OVER, .3f));\r
 684           fadedG.drawImage(image, 0, 0, this);\r
 685 \r
 686         }\r
 687 \r
 688       }\r
 689       else\r
 690         fadedImage = null;\r
 691 \r
 692 \r
 693       g.setColor(Color.white);\r
 694       g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());\r
 695 \r
 696       g.setFont(av.getFont());\r
 697       if (fm == null)\r
 698         fm = g.getFontMetrics();\r
 699 \r
 700 \r
 701 \r
 702 \r
 703         if ( (av.alignment.getAlignmentAnnotation() == null) ||\r
 704                 (av.alignment.getAlignmentAnnotation().length < 1))\r
 705         {\r
 706             g.setColor(Color.white);\r
 707             g.fillRect(0, 0, getWidth(), getHeight());\r
 708             g.setColor(Color.black);\r
 709             if(av.validCharWidth)\r
 710               g.drawString("Alignment has no annotations", 20, 15);\r
 711 \r
 712             return;\r
 713         }\r
 714 \r
 715 \r
 716         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 717 \r
 718         int x = 0, y = 0;\r
 719         int column=0;\r
 720         char lastSS;\r
 721         int lastSSX;\r
 722         int iconOffset = av.charHeight / 2;\r
 723         boolean validRes = false;\r
 724 \r
 725         boolean [] graphGroupDrawn = new boolean[aa.length];\r
 726 \r
 727 \r
 728         //\u03B2 \u03B1\r
 729         for (int i = 0; i < aa.length; i++)\r
 730         {\r
 731             AlignmentAnnotation row = aa[i];\r
 732 \r
 733             if (!row.visible)\r
 734             {\r
 735                 continue;\r
 736             }\r
 737 \r
 738 \r
 739             lastSS = ' ';\r
 740             lastSSX = 0;\r
 741 \r
 742             if (row.graph>0)\r
 743             {\r
 744                 if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )\r
 745                   continue;\r
 746 \r
 747                 // this is so that we draw the characters below the graph\r
 748                 y += row.height;\r
 749 \r
 750                 if (row.hasText)\r
 751                 {\r
 752                     y -= av.charHeight;\r
 753                 }\r
 754             }\r
 755 \r
 756             if (av.updatingConsensus && aa[i].label.equals("Consensus"))\r
 757             {\r
 758               y += av.charHeight;\r
 759 \r
 760               g.drawImage(fadedImage,\r
 761               0,y-row.height,imgWidth, y,\r
 762               0,y-row.height,imgWidth, y, this);\r
 763               g.setColor(Color.black);\r
 764              // g.drawString("Calculating Consensus....",20, y-row.height/2);\r
 765 \r
 766               continue;\r
 767             }\r
 768             else if (av.updatingConservation && aa[i].label.equals("Conservation"))\r
 769             {\r
 770 \r
 771               y += av.charHeight;\r
 772               g.drawImage(fadedImage,\r
 773                           0, y - row.height, imgWidth, y,\r
 774                           0, y - row.height, imgWidth, y, this);\r
 775 \r
 776               g.setColor(Color.black);\r
 777             //  g.drawString("Calculating Conservation.....",20, y-row.height/2);\r
 778 \r
 779               continue;\r
 780             }\r
 781             else if (av.updatingConservation && aa[i].label.equals("Quality"))\r
 782             {\r
 783 \r
 784               y += av.charHeight;\r
 785               g.drawImage(fadedImage,\r
 786                           0, y - row.height, imgWidth, y,\r
 787                           0, y - row.height, imgWidth, y, this);\r
 788               g.setColor(Color.black);\r
 789              /// g.drawString("Calculating Quality....",20, y-row.height/2);\r
 790 \r
 791               continue;\r
 792             }\r
 793 \r
 794 \r
 795             if (row.hasText)\r
 796             {\r
 797                 iconOffset = av.charHeight / 2 + 4;\r
 798             }\r
 799             else\r
 800             {\r
 801                 iconOffset = 0;\r
 802             }\r
 803 \r
 804             x = 0;\r
 805             while (x < endRes-startRes)\r
 806             {\r
 807               if (av.hasHiddenColumns)\r
 808               {\r
 809                 column = av.getColumnSelection().adjustForHiddenColumns(startRes+x);\r
 810                 if (column > row.annotations.length-1)\r
 811                 {\r
 812                   break;\r
 813                 }\r
 814               }\r
 815               else\r
 816                 column = startRes+x;\r
 817 \r
 818 \r
 819                 if ((row.annotations.length <= column) ||\r
 820                         (row.annotations[column] == null))\r
 821                 {\r
 822                     validRes = false;\r
 823                 }\r
 824                 else\r
 825                 {\r
 826                     validRes = true;\r
 827                 }\r
 828 \r
 829 \r
 830                 if (activeRow == i)\r
 831                 {\r
 832                     g.setColor(Color.red);\r
 833 \r
 834                     if (av.getColumnSelection() != null)\r
 835                     {\r
 836                         for (int n = 0; n < av.getColumnSelection().size(); n++)\r
 837                         {\r
 838                             int v = av.getColumnSelection().columnAt(n);\r
 839 \r
 840                             if (v == column)\r
 841                             {\r
 842                                 g.fillRect(x * av.charWidth, y,\r
 843                                     av.charWidth, av.charHeight);\r
 844                             }\r
 845                         }\r
 846                     }\r
 847                 }\r
 848 \r
 849                 if (av.validCharWidth && validRes &&\r
 850                         (row.annotations[column].displayCharacter.length() > 0))\r
 851                 {\r
 852 \r
 853                     int charOffset = (av.charWidth -\r
 854                         fm.charWidth(row.annotations[column].displayCharacter.charAt(\r
 855                                 0))) / 2;\r
 856                     g.setColor(row.annotations[column].colour);\r
 857 \r
 858                     if (column == 0 || row.graph>0)\r
 859                     {\r
 860                         g.drawString(row.annotations[column].displayCharacter,\r
 861                                      (x*av.charWidth)+charOffset,\r
 862                             y + iconOffset );\r
 863                     }\r
 864                     else if (\r
 865                         row.annotations[column - 1] == null\r
 866                         ||(!row.annotations[column].displayCharacter.equals(\r
 867                             row.annotations[column - 1].displayCharacter)\r
 868                         ||\r
 869                   (row.annotations[column].displayCharacter.length() <2 &&\r
 870                    row.annotations[column].secondaryStructure==' ')))\r
 871                     {\r
 872                         g.drawString(row.annotations[column].displayCharacter,\r
 873                                      x*av.charWidth+charOffset,\r
 874                                      y + iconOffset );\r
 875                     }\r
 876                 }\r
 877 \r
 878                 if (row.hasIcons)\r
 879                 {\r
 880                     if (!validRes ||\r
 881                             (row.annotations[column].secondaryStructure != lastSS))\r
 882                     {\r
 883                         switch (lastSS)\r
 884                         {\r
 885                         case 'H':\r
 886                           g.setColor(HELIX_COLOUR);\r
 887                           if (MAC)\r
 888                           {\r
 889                             //Off by 1 offset when drawing rects and ovals\r
 890                             //to offscreen image on the MAC\r
 891                             g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
 892                                             (x*av.charWidth) - lastSSX, 7, 8, 8);\r
 893                             break;\r
 894                           }\r
 895 \r
 896                           int sCol = (lastSSX / av.charWidth) + startRes;\r
 897                           int x1 = lastSSX;\r
 898                           int x2 = (x*av.charWidth);\r
 899 \r
 900                          if(sCol==0 ||\r
 901                             row.annotations[sCol-1]==null ||\r
 902                             row.annotations[sCol-1].secondaryStructure!='H')\r
 903                          {\r
 904                            g.fillArc(lastSSX, y+4+iconOffset, av.charWidth, 8, 90,180) ;\r
 905                            x1 += av.charWidth/2;\r
 906                          }\r
 907 \r
 908                           if(row.annotations[column]==null ||\r
 909                              row.annotations[column].secondaryStructure!='H')\r
 910                           {\r
 911                             g.fillArc((x*av.charWidth)-av.charWidth,\r
 912                                       y+4+iconOffset, av.charWidth, 8, 270,180);\r
 913                             x2 -= av.charWidth/2;\r
 914                           }\r
 915 \r
 916                           g.fillRect(x1, y+4+iconOffset, x2-x1, 8);\r
 917                               break;\r
 918 \r
 919                         case 'E':\r
 920                             g.setColor(SHEET_COLOUR);\r
 921                             g.fillRect(lastSSX, y + 4 + iconOffset,\r
 922                                 (x*av.charWidth) - lastSSX - 4, 7);\r
 923                             g.fillPolygon(new int[] { (x*av.charWidth) - 4,\r
 924                                           (x*av.charWidth) - 4,\r
 925                                           (x*av.charWidth) },\r
 926                                 new int[]\r
 927                                 {\r
 928                                     y + iconOffset, y + 14 + iconOffset,\r
 929                                     y + 8 + iconOffset\r
 930                                 }, 3);\r
 931 \r
 932                             break;\r
 933 \r
 934 \r
 935                         default:\r
 936                             g.setColor(Color.gray);\r
 937                             g.fillRect(lastSSX, y + 6 + iconOffset,\r
 938                                 (x*av.charWidth) - lastSSX, 2);\r
 939 \r
 940                             break;\r
 941                         }\r
 942 \r
 943                         if (validRes)\r
 944                         {\r
 945                             lastSS = row.annotations[column].secondaryStructure;\r
 946                         }\r
 947                         else\r
 948                         {\r
 949                             lastSS = ' ';\r
 950                         }\r
 951 \r
 952                         lastSSX = (x*av.charWidth);\r
 953                     }\r
 954                 }\r
 955 \r
 956 \r
 957             column++;\r
 958             x++;\r
 959             }\r
 960 \r
 961             if(column>=row.annotations.length)\r
 962                 column = row.annotations.length-1;\r
 963 \r
 964           //  x ++;\r
 965 \r
 966             if (row.hasIcons)\r
 967             {\r
 968               switch (lastSS)\r
 969               {\r
 970                 case 'H':\r
 971                   g.setColor(HELIX_COLOUR);\r
 972                   if (MAC)\r
 973                   {\r
 974                     //Off by 1 offset when drawing rects and ovals\r
 975                     //to offscreen image on the MAC\r
 976                     g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
 977                                     (x*av.charWidth) - lastSSX, 7, 8, 8);\r
 978                     break;\r
 979                   }\r
 980 \r
 981                   int sCol = (lastSSX / av.charWidth) + startRes;\r
 982                   int x1 = lastSSX;\r
 983                   int x2 = (x*av.charWidth);\r
 984 \r
 985                   if (sCol == 0 ||\r
 986                       row.annotations[sCol - 1] == null ||\r
 987                       row.annotations[sCol - 1].secondaryStructure != 'H')\r
 988                   {\r
 989                     g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);\r
 990                     x1 += av.charWidth / 2;\r
 991                   }\r
 992 \r
 993                   if (row.annotations[column] == null ||\r
 994                       row.annotations[column].secondaryStructure != 'H')\r
 995                   {\r
 996                     g.fillArc((x*av.charWidth) - av.charWidth,\r
 997                               y + 4 + iconOffset, av.charWidth, 8, 270,\r
 998                               180);\r
 999                     x2 -= av.charWidth / 2;\r
1000                   }\r
1001 \r
1002                   g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);\r
1003 \r
1004                   break;\r
1005 \r
1006                 case 'E':\r
1007                   g.setColor(SHEET_COLOUR);\r
1008 \r
1009                   if (row.annotations[endRes] == null\r
1010                       || row.annotations[endRes].secondaryStructure != 'E')\r
1011                   {\r
1012                     g.fillRect(lastSSX, y + 4 + iconOffset,\r
1013                                (x*av.charWidth) - lastSSX - 4, 7);\r
1014                     g.fillPolygon(new int[]\r
1015                                   {(x*av.charWidth) - 4,\r
1016                                   (x*av.charWidth) - 4,\r
1017                                  (x*av.charWidth)},\r
1018                                   new int[]\r
1019                                   {\r
1020                                   y + iconOffset, y + 14 + iconOffset,\r
1021                                   y + 7 + iconOffset\r
1022                     }, 3);\r
1023                   }\r
1024                   else\r
1025                    {\r
1026                      g.fillRect(lastSSX, y + 4 + iconOffset,\r
1027                                 (x+1) * av.charWidth - lastSSX, 7);\r
1028                    }\r
1029                   break;\r
1030 \r
1031                 default:\r
1032                   g.setColor(Color.gray);\r
1033                   if(!av.wrapAlignment || endRes==av.endRes)\r
1034                   g.fillRect(lastSSX, y + 6 + iconOffset,\r
1035                              (x*av.charWidth) - lastSSX, 2);\r
1036 \r
1037                   break;\r
1038               }\r
1039           }\r
1040 \r
1041             if (row.graph>0 && row.graphHeight>0)\r
1042             {\r
1043                 if(row.graph == AlignmentAnnotation.LINE_GRAPH )\r
1044                 {\r
1045                   if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])\r
1046                    {\r
1047                      float groupmax=-999999, groupmin=9999999;\r
1048                      for(int gg=0; gg<aa.length; gg++)\r
1049                      {\r
1050                        if(aa[gg].graphGroup!=row.graphGroup)\r
1051                          continue;\r
1052 \r
1053                        if(aa[gg]!=row)\r
1054                          aa[gg].visible = false;\r
1055 \r
1056                        if(aa[gg].graphMax>groupmax)\r
1057                          groupmax = aa[gg].graphMax;\r
1058                        if(aa[gg].graphMin<groupmin)\r
1059                          groupmin = aa[gg].graphMin;\r
1060                      }\r
1061 \r
1062                      for (int gg = 0; gg < aa.length; gg++)\r
1063                      {\r
1064                        if (aa[gg].graphGroup == row.graphGroup)\r
1065                        {\r
1066                          drawLineGraph(g, aa[gg], startRes, endRes, y,\r
1067                                        groupmin, groupmax,\r
1068                                        row.graphHeight);\r
1069                        }\r
1070                      }\r
1071 \r
1072                      graphGroupDrawn[ row.graphGroup ] = true;\r
1073                    }\r
1074                    else\r
1075                      drawLineGraph(g, row, startRes, endRes,\r
1076                                    y, row.graphMin, row.graphMax, row.graphHeight  );\r
1077                 }\r
1078                 else if(row.graph == AlignmentAnnotation.BAR_GRAPH )\r
1079                    drawBarGraph(g, row, startRes, endRes,\r
1080                                 row.graphMin, row.graphMax, y);\r
1081             }\r
1082 \r
1083             if (row.graph>0 && row.hasText)\r
1084             {\r
1085                 y += av.charHeight;\r
1086             }\r
1087 \r
1088             if (row.graph==0)\r
1089             {\r
1090                 y += aa[i].height;\r
1091             }\r
1092         }\r
1093     }\r
1094 \r
1095     public void drawLineGraph(Graphics g, AlignmentAnnotation aa,\r
1096                               int sRes, int eRes,\r
1097                               int y,\r
1098                               float min, float max,\r
1099                               int graphHeight)\r
1100     {\r
1101       if(sRes>aa.annotations.length)\r
1102         return;\r
1103 \r
1104 \r
1105       int x = 0;\r
1106 \r
1107       //Adjustment for fastpaint to left\r
1108       if(eRes<av.endRes)\r
1109         eRes++;\r
1110 \r
1111       eRes = Math.min(eRes, aa.annotations.length);\r
1112 \r
1113       if(sRes==0)\r
1114       {\r
1115         x++;\r
1116       }\r
1117 \r
1118       int y1=y, y2=y;\r
1119       float range = max - min;\r
1120 \r
1121       ////Draw origin\r
1122       if(min<0)\r
1123         y2 = y - (int)((0-min / range)*graphHeight);\r
1124 \r
1125       g.setColor(Color.gray);\r
1126       g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
1127 \r
1128       eRes = Math.min(eRes, aa.annotations.length);\r
1129 \r
1130       int column;\r
1131       int aaMax = aa.annotations.length-1;\r
1132 \r
1133       while( x < eRes - sRes )\r
1134       {\r
1135         column = sRes + x;\r
1136         if(av.hasHiddenColumns)\r
1137         {\r
1138           column = av.getColumnSelection().adjustForHiddenColumns(column);\r
1139         }\r
1140 \r
1141         if (column > aaMax)\r
1142         {\r
1143           break;\r
1144         }\r
1145 \r
1146         if(aa.annotations[column]==null || aa.annotations[column-1]==null)\r
1147         {\r
1148           x++;\r
1149           continue;\r
1150         }\r
1151 \r
1152 \r
1153           g.setColor(aa.annotations[column].colour);\r
1154           y1 = y - (int) (((aa.annotations[column-1].value-min) / range) * graphHeight);\r
1155           y2 = y - (int) (((aa.annotations[column].value-min) / range) * graphHeight);\r
1156 \r
1157           g.drawLine(x*av.charWidth-av.charWidth/2, y1, x*av.charWidth+av.charWidth/2, y2);\r
1158           x ++;\r
1159        }\r
1160 \r
1161        if(aa.threshold!=null)\r
1162        {\r
1163            g.setColor(aa.threshold.colour);\r
1164            Graphics2D g2 = (Graphics2D)g;\r
1165            g2.setStroke(new BasicStroke(1,\r
1166                                          BasicStroke.CAP_SQUARE,\r
1167                                          BasicStroke.JOIN_ROUND, 3f,\r
1168                                          new float[] { 5f, 3f }, 0f));\r
1169 \r
1170            y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);\r
1171            g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
1172            g2.setStroke(new BasicStroke());\r
1173       }\r
1174     }\r
1175 \r
1176     public void drawBarGraph(Graphics g, AlignmentAnnotation aa,\r
1177                              int sRes, int eRes,\r
1178                              float min, float max,\r
1179                              int y)\r
1180     {\r
1181       if(sRes>aa.annotations.length)\r
1182         return;\r
1183 \r
1184       eRes = Math.min(eRes, aa.annotations.length);\r
1185 \r
1186       int x=0, y1=y, y2=y;\r
1187 \r
1188       float range = max - min;\r
1189 \r
1190       if(min<0)\r
1191         y2 = y - (int)((0-min / (range))*aa.graphHeight);\r
1192 \r
1193       g.setColor(Color.gray);\r
1194 \r
1195       g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);\r
1196 \r
1197       int column;\r
1198       int aaMax = aa.annotations.length-1;\r
1199 \r
1200       while( x < eRes-sRes )\r
1201       {\r
1202         column = sRes + x;\r
1203         if(av.hasHiddenColumns)\r
1204         {\r
1205           column = av.getColumnSelection().adjustForHiddenColumns(column);\r
1206         }\r
1207 \r
1208         if(column > aaMax)\r
1209         {\r
1210             break;\r
1211         }\r
1212 \r
1213         if (aa.annotations[column] == null)\r
1214         {\r
1215           x ++;\r
1216           continue;\r
1217         }\r
1218 \r
1219           g.setColor(aa.annotations[column].colour);\r
1220           y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);\r
1221 \r
1222           if(y1-y2>0)\r
1223             g.fillRect(x*av.charWidth, y2, av.charWidth, y1-y2 );\r
1224           else\r
1225             g.fillRect(x*av.charWidth, y1, av.charWidth, y2-y1 );\r
1226 \r
1227           x ++ ;\r
1228 \r
1229       }\r
1230       if(aa.threshold!=null)\r
1231       {\r
1232           g.setColor(aa.threshold.colour);\r
1233           Graphics2D g2 = (Graphics2D)g;\r
1234           g2.setStroke(new BasicStroke(1,\r
1235                                         BasicStroke.CAP_SQUARE,\r
1236                                         BasicStroke.JOIN_ROUND, 3f,\r
1237                                         new float[] { 5f, 3f }, 0f));\r
1238 \r
1239           y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);\r
1240           g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
1241           g2.setStroke(new BasicStroke());\r
1242       }\r
1243     }\r
1244 \r
1245     // used by overview window\r
1246     public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)\r
1247     {\r
1248       eRes = Math.min(eRes, aa.annotations.length);\r
1249       g.setColor(Color.white);\r
1250       g.fillRect(0, 0, width, y);\r
1251       g.setColor(new Color(0, 0, 180));\r
1252 \r
1253       int x = 0, height;\r
1254 \r
1255       for (int j = sRes; j < eRes; j++)\r
1256       {\r
1257         if (aa.annotations[j] != null)\r
1258         {\r
1259           g.setColor(aa.annotations[j].colour);\r
1260 \r
1261           height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);\r
1262           if (height > y)\r
1263             height = y;\r
1264 \r
1265           g.fillRect(x, y - height, av.charWidth, height);\r
1266         }\r
1267           x += av.charWidth;\r
1268       }\r
1269     }\r
1270 \r
1271 }\r