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         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 283         if(aa==null)\r
 284           return;\r
 285 \r
 286 \r
 287         int height = 0;\r
 288         activeRow = -1;\r
 289 \r
 290 \r
 291         for (int i = 0; i < aa.length; i++)\r
 292         {\r
 293             if (aa[i].visible)\r
 294             {\r
 295               height += aa[i].height;\r
 296             }\r
 297 \r
 298             if (evt.getY() < height)\r
 299             {\r
 300                 if (aa[i].editable)\r
 301                 {\r
 302                     activeRow = i;\r
 303                 }\r
 304                 else if(aa[i].graph>0)\r
 305                 {\r
 306                     //Stretch Graph\r
 307                     graphStretch = i;\r
 308                     graphStretchY = evt.getY();\r
 309                 }\r
 310 \r
 311                 break;\r
 312             }\r
 313         }\r
 314 \r
 315 \r
 316         if (SwingUtilities.isRightMouseButton(evt) && activeRow!=-1)\r
 317         {\r
 318             if (av.getColumnSelection() == null)\r
 319             {\r
 320                 return;\r
 321             }\r
 322 \r
 323             JPopupMenu pop = new JPopupMenu("Structure type");\r
 324             JMenuItem item = new JMenuItem(HELIX);\r
 325             item.addActionListener(this);\r
 326             pop.add(item);\r
 327             item = new JMenuItem(SHEET);\r
 328             item.addActionListener(this);\r
 329             pop.add(item);\r
 330             item = new JMenuItem(LABEL);\r
 331             item.addActionListener(this);\r
 332             pop.add(item);\r
 333             item = new JMenuItem(COLOUR);\r
 334             item.addActionListener(this);\r
 335             pop.add(item);\r
 336             item = new JMenuItem(REMOVE);\r
 337             item.addActionListener(this);\r
 338             pop.add(item);\r
 339             pop.show(this, evt.getX(), evt.getY());\r
 340 \r
 341             return;\r
 342         }\r
 343 \r
 344         if (aa == null)\r
 345         {\r
 346             return;\r
 347         }\r
 348 \r
 349         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 350 \r
 351         if(av.hasHiddenColumns)\r
 352           res = av.getColumnSelection().adjustForHiddenColumns(res);\r
 353 \r
 354         min = res;\r
 355         max = res;\r
 356 \r
 357         if (av.getColumnSelection().contains(res))\r
 358           av.getColumnSelection().removeElement(res);\r
 359         else\r
 360         {\r
 361             av.getColumnSelection().addElement(res);\r
 362             SequenceGroup sg = new SequenceGroup();\r
 363 \r
 364             for (int i = 0; i < av.alignment.getSequences().size(); i++)\r
 365             {\r
 366                 sg.addSequence(av.alignment.getSequenceAt(i), false);\r
 367             }\r
 368 \r
 369             sg.setStartRes(res);\r
 370             sg.setEndRes(res);\r
 371             av.setSelectionGroup(sg);\r
 372         }\r
 373 \r
 374         ap.repaint();\r
 375 \r
 376     }\r
 377 \r
 378     /**\r
 379      * DOCUMENT ME!\r
 380      *\r
 381      * @param evt DOCUMENT ME!\r
 382      */\r
 383     public void mouseReleased(MouseEvent evt)\r
 384     {\r
 385       graphStretch = -1;\r
 386       graphStretchY = -1;\r
 387       mouseDragging = false;\r
 388     }\r
 389 \r
 390     /**\r
 391      * DOCUMENT ME!\r
 392      *\r
 393      * @param evt DOCUMENT ME!\r
 394      */\r
 395     public void mouseEntered(MouseEvent evt)\r
 396     {\r
 397       if(mouseDragging)\r
 398         ap.seqPanel.scrollCanvas(null);\r
 399     }\r
 400 \r
 401     /**\r
 402      * DOCUMENT ME!\r
 403      *\r
 404      * @param evt DOCUMENT ME!\r
 405      */\r
 406     public void mouseExited(MouseEvent evt)\r
 407     {\r
 408       if(mouseDragging)\r
 409         ap.seqPanel.scrollCanvas(evt);\r
 410     }\r
 411 \r
 412 \r
 413     /**\r
 414      * DOCUMENT ME!\r
 415      *\r
 416      * @param evt DOCUMENT ME!\r
 417      */\r
 418     public void mouseDragged(MouseEvent evt)\r
 419     {\r
 420       if(graphStretch>-1)\r
 421       {\r
 422         av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY();\r
 423         if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <0)\r
 424           av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;\r
 425         graphStretchY = evt.getY();\r
 426         adjustPanelHeight();\r
 427         ap.repaint();\r
 428       }\r
 429       else\r
 430       {\r
 431         mouseDragging = true;\r
 432 \r
 433         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 434 \r
 435         if(av.hasHiddenColumns)\r
 436           res = av.getColumnSelection().adjustForHiddenColumns(res);\r
 437 \r
 438         SequenceGroup sg = av.getSelectionGroup();\r
 439 \r
 440         if (res < min)\r
 441         {\r
 442             min = res;\r
 443         }\r
 444 \r
 445         if (res > max)\r
 446         {\r
 447             max = res;\r
 448         }\r
 449 \r
 450         if (sg != null)\r
 451         {\r
 452             if (!av.getColumnSelection().contains(res))\r
 453             {\r
 454                 av.getColumnSelection().addElement(res);\r
 455             }\r
 456 \r
 457             if (res > sg.getStartRes())\r
 458             {\r
 459                 sg.setEndRes(res);\r
 460             }\r
 461             else if (res < sg.getStartRes())\r
 462             {\r
 463                 sg.setStartRes(res);\r
 464             }\r
 465 \r
 466             for (int i = min; i <= max; i++)\r
 467             {\r
 468                 if ((i < sg.getStartRes()) || (i > sg.getEndRes()))\r
 469                 {\r
 470                     av.getColumnSelection().removeElement(i);\r
 471                 }\r
 472                 else\r
 473                 {\r
 474                     av.getColumnSelection().addElement(i);\r
 475                 }\r
 476             }\r
 477 \r
 478             ap.repaint();\r
 479         }\r
 480 \r
 481       }\r
 482     }\r
 483 \r
 484     /**\r
 485      * DOCUMENT ME!\r
 486      *\r
 487      * @param evt DOCUMENT ME!\r
 488      */\r
 489     public void mouseMoved(MouseEvent evt)\r
 490     {\r
 491         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 492 \r
 493         if (aa == null)\r
 494         {\r
 495             return;\r
 496         }\r
 497 \r
 498         int row = -1;\r
 499         int height = 0;\r
 500 \r
 501         for (int i = 0; i < aa.length; i++)\r
 502         {\r
 503             if (aa[i].visible)\r
 504             {\r
 505                 height += aa[i].height;\r
 506             }\r
 507 \r
 508             if (evt.getY() < height)\r
 509             {\r
 510                 row = i;\r
 511 \r
 512                 break;\r
 513             }\r
 514         }\r
 515 \r
 516         if(row==-1)\r
 517           return;\r
 518 \r
 519         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 520 \r
 521         if(av.hasHiddenColumns)\r
 522           res = av.getColumnSelection().adjustForHiddenColumns(res);\r
 523 \r
 524         if ( aa[row].annotations!=null\r
 525              && row > -1\r
 526              && res < (int) aa[row].annotations.length)\r
 527         {\r
 528             if(aa[row].graphGroup>-1)\r
 529             {\r
 530               StringBuffer tip = new StringBuffer("<html>");\r
 531               for (int gg = 0; gg < aa.length; gg++)\r
 532               {\r
 533                 if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res]!=null)\r
 534                   tip.append(aa[gg].label+" "+aa[gg].annotations[res].description+"<br>" );\r
 535               }\r
 536               if(tip.length()!=6)\r
 537               {\r
 538                 tip.setLength(tip.length() - 4);\r
 539                 this.setToolTipText(tip.toString() + "</html>");\r
 540               }\r
 541             }\r
 542             else if(aa[row].annotations[res] != null\r
 543                     && aa[row].annotations[res].description!=null)\r
 544               this.setToolTipText(aa[row].annotations[res].description);\r
 545 \r
 546             if(aa[row].annotations[res]!=null)\r
 547             {\r
 548               StringBuffer text = new StringBuffer("Sequence position " +\r
 549                                                    (res + 1) + "  " +\r
 550                                                    aa[row].annotations[res].description);\r
 551 \r
 552               ap.alignFrame.statusBar.setText(text.toString());\r
 553             }\r
 554         }\r
 555     }\r
 556 \r
 557     /**\r
 558      * DOCUMENT ME!\r
 559      *\r
 560      * @param evt DOCUMENT ME!\r
 561      */\r
 562     public void mouseClicked(MouseEvent evt)\r
 563     {\r
 564     }\r
 565 \r
 566     /**\r
 567      * DOCUMENT ME!\r
 568      *\r
 569      * @param g DOCUMENT ME!\r
 570      */\r
 571     public void paintComponent(Graphics g)\r
 572     {\r
 573       g.setColor(Color.white);\r
 574       g.fillRect(0, 0, getWidth(), getHeight());\r
 575 \r
 576       if(image!=null)\r
 577       {if (fastPaint\r
 578             || (getVisibleRect().width != g.getClipBounds().width)\r
 579             || (getVisibleRect().height != g.getClipBounds().height))\r
 580         {\r
 581           g.drawImage(image, 0, 0, this);\r
 582           fastPaint = false;\r
 583           return;\r
 584         }\r
 585       }\r
 586       imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\r
 587 \r
 588       if (image == null || imgWidth != image.getWidth()\r
 589           || image.getHeight(this) != getHeight())\r
 590       {\r
 591         image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),\r
 592                                   BufferedImage.TYPE_INT_RGB);\r
 593         gg = (Graphics2D) image.getGraphics();\r
 594 \r
 595         if(av.antiAlias)\r
 596         gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
 597                             RenderingHints.VALUE_ANTIALIAS_ON);\r
 598 \r
 599         gg.setFont(av.getFont());\r
 600         fm = gg.getFontMetrics();\r
 601         gg.setColor(Color.white);\r
 602         gg.fillRect(0, 0, imgWidth, image.getHeight());\r
 603       }\r
 604 \r
 605 \r
 606       drawComponent(gg, av.startRes, av.endRes + 1);\r
 607       g.drawImage(image, 0, 0, this);\r
 608     }\r
 609 \r
 610     /**\r
 611      * DOCUMENT ME!\r
 612      *\r
 613      * @param horizontal DOCUMENT ME!\r
 614      */\r
 615     public void fastPaint(int horizontal)\r
 616     {\r
 617         if ((horizontal == 0)\r
 618             || gg==null\r
 619             || av.alignment.getAlignmentAnnotation()==null\r
 620             || av.alignment.getAlignmentAnnotation().length < 1\r
 621             || av.updatingConsensus\r
 622             || av.updatingConservation)\r
 623         {\r
 624             repaint();\r
 625             return;\r
 626         }\r
 627 \r
 628         gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);\r
 629 \r
 630         int sr = av.startRes;\r
 631         int er = av.endRes + 1;\r
 632         int transX = 0;\r
 633 \r
 634         if (horizontal > 0) // scrollbar pulled right, image to the left\r
 635         {\r
 636             transX = (er - sr - horizontal) * av.charWidth;\r
 637             sr = er - horizontal;\r
 638         }\r
 639         else if (horizontal < 0)\r
 640         {\r
 641             er = sr - horizontal;\r
 642         }\r
 643 \r
 644         gg.translate(transX, 0);\r
 645 \r
 646         drawComponent(gg, sr, er);\r
 647 \r
 648         gg.translate(-transX, 0);\r
 649 \r
 650         fastPaint = true;\r
 651 \r
 652         repaint();\r
 653 \r
 654     }\r
 655 \r
 656     /**\r
 657      * DOCUMENT ME!\r
 658      *\r
 659      * @param g DOCUMENT ME!\r
 660      * @param startRes DOCUMENT ME!\r
 661      * @param endRes DOCUMENT ME!\r
 662      */\r
 663     public void drawComponent(Graphics g, int startRes, int endRes)\r
 664     {\r
 665       if(av.updatingConsensus || av.updatingConservation)\r
 666       {\r
 667         if(image==null)\r
 668          {\r
 669            return;\r
 670          }\r
 671         //We'll keep a record of the old image,\r
 672         //and draw a faded image until the calculation\r
 673         //has completed\r
 674         if(fadedImage==null\r
 675            || fadedImage.getWidth()!=imgWidth\r
 676         || fadedImage.getHeight()!=image.getHeight())\r
 677         {\r
 678           fadedImage = new BufferedImage(\r
 679               imgWidth, image.getHeight(),\r
 680               BufferedImage.TYPE_INT_RGB);\r
 681 \r
 682           Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();\r
 683 \r
 684           fadedG.setColor(Color.white);\r
 685         fadedG.fillRect(0, 0, imgWidth, image.getHeight());\r
 686 \r
 687           fadedG.setComposite(\r
 688               AlphaComposite.getInstance(\r
 689                   AlphaComposite.SRC_OVER, .3f));\r
 690           fadedG.drawImage(image, 0, 0, this);\r
 691 \r
 692         }\r
 693 \r
 694       }\r
 695       else\r
 696         fadedImage = null;\r
 697 \r
 698 \r
 699       g.setColor(Color.white);\r
 700       g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());\r
 701 \r
 702       g.setFont(av.getFont());\r
 703       if (fm == null)\r
 704         fm = g.getFontMetrics();\r
 705 \r
 706 \r
 707 \r
 708 \r
 709         if ( (av.alignment.getAlignmentAnnotation() == null) ||\r
 710                 (av.alignment.getAlignmentAnnotation().length < 1))\r
 711         {\r
 712             g.setColor(Color.white);\r
 713             g.fillRect(0, 0, getWidth(), getHeight());\r
 714             g.setColor(Color.black);\r
 715             if(av.validCharWidth)\r
 716               g.drawString("Alignment has no annotations", 20, 15);\r
 717 \r
 718             return;\r
 719         }\r
 720 \r
 721 \r
 722         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 723 \r
 724         int x = 0, y = 0;\r
 725         int column=0;\r
 726         char lastSS;\r
 727         int lastSSX;\r
 728         int iconOffset = av.charHeight / 2;\r
 729         boolean validRes = false;\r
 730 \r
 731         boolean [] graphGroupDrawn = new boolean[aa.length];\r
 732 \r
 733 \r
 734         //\u03B2 \u03B1\r
 735         for (int i = 0; i < aa.length; i++)\r
 736         {\r
 737             AlignmentAnnotation row = aa[i];\r
 738 \r
 739             if (!row.visible)\r
 740             {\r
 741                 continue;\r
 742             }\r
 743 \r
 744 \r
 745             lastSS = ' ';\r
 746             lastSSX = 0;\r
 747 \r
 748             if (row.graph>0)\r
 749             {\r
 750                 if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )\r
 751                   continue;\r
 752 \r
 753                 // this is so that we draw the characters below the graph\r
 754                 y += row.height;\r
 755 \r
 756                 if (row.hasText)\r
 757                 {\r
 758                     y -= av.charHeight;\r
 759                 }\r
 760             }\r
 761 \r
 762             if (av.updatingConsensus && aa[i]==av.consensus)\r
 763             {\r
 764               y += av.charHeight;\r
 765 \r
 766               g.drawImage(fadedImage,\r
 767               0,y-row.height,imgWidth, y,\r
 768               0,y-row.height,imgWidth, y, this);\r
 769               g.setColor(Color.black);\r
 770              // g.drawString("Calculating Consensus....",20, y-row.height/2);\r
 771 \r
 772               continue;\r
 773             }\r
 774             else if (av.updatingConservation && aa[i].label.equals("Conservation"))\r
 775             {\r
 776 \r
 777               y += av.charHeight;\r
 778               g.drawImage(fadedImage,\r
 779                           0, y - row.height, imgWidth, y,\r
 780                           0, y - row.height, imgWidth, y, this);\r
 781 \r
 782               g.setColor(Color.black);\r
 783             //  g.drawString("Calculating Conservation.....",20, y-row.height/2);\r
 784 \r
 785               continue;\r
 786             }\r
 787             else if (av.updatingConservation && aa[i].label.equals("Quality"))\r
 788             {\r
 789 \r
 790               y += av.charHeight;\r
 791               g.drawImage(fadedImage,\r
 792                           0, y - row.height, imgWidth, y,\r
 793                           0, y - row.height, imgWidth, y, this);\r
 794               g.setColor(Color.black);\r
 795              /// g.drawString("Calculating Quality....",20, y-row.height/2);\r
 796 \r
 797               continue;\r
 798             }\r
 799 \r
 800 \r
 801             if (row.hasText)\r
 802             {\r
 803                 iconOffset = av.charHeight / 2 + 4;\r
 804             }\r
 805             else\r
 806             {\r
 807                 iconOffset = 0;\r
 808             }\r
 809 \r
 810             x = 0;\r
 811             while (x < endRes-startRes)\r
 812             {\r
 813               if (av.hasHiddenColumns)\r
 814               {\r
 815                 column = av.getColumnSelection().adjustForHiddenColumns(startRes+x);\r
 816                 if (column > row.annotations.length-1)\r
 817                 {\r
 818                   break;\r
 819                 }\r
 820               }\r
 821               else\r
 822                 column = startRes+x;\r
 823 \r
 824 \r
 825                 if ((row.annotations.length <= column) ||\r
 826                         (row.annotations[column] == null))\r
 827                 {\r
 828                     validRes = false;\r
 829                 }\r
 830                 else\r
 831                 {\r
 832                     validRes = true;\r
 833                 }\r
 834 \r
 835 \r
 836                 if (activeRow == i)\r
 837                 {\r
 838                     g.setColor(Color.red);\r
 839 \r
 840                     if (av.getColumnSelection() != null)\r
 841                     {\r
 842                         for (int n = 0; n < av.getColumnSelection().size(); n++)\r
 843                         {\r
 844                             int v = av.getColumnSelection().columnAt(n);\r
 845 \r
 846                             if (v == column)\r
 847                             {\r
 848                                 g.fillRect(x * av.charWidth, y,\r
 849                                     av.charWidth, av.charHeight);\r
 850                             }\r
 851                         }\r
 852                     }\r
 853                 }\r
 854 \r
 855                 if (av.validCharWidth && validRes &&\r
 856                         (row.annotations[column].displayCharacter.length() > 0))\r
 857                 {\r
 858 \r
 859                     int charOffset = (av.charWidth -\r
 860                         fm.charWidth(row.annotations[column].displayCharacter.charAt(\r
 861                                 0))) / 2;\r
 862                     g.setColor(row.annotations[column].colour);\r
 863 \r
 864                     if (column == 0 || row.graph>0)\r
 865                     {\r
 866                         g.drawString(row.annotations[column].displayCharacter,\r
 867                                      (x*av.charWidth)+charOffset,\r
 868                             y + iconOffset );\r
 869                     }\r
 870                     else if (\r
 871                         row.annotations[column - 1] == null\r
 872                         ||(!row.annotations[column].displayCharacter.equals(\r
 873                             row.annotations[column - 1].displayCharacter)\r
 874                         ||\r
 875                   (row.annotations[column].displayCharacter.length() <2 &&\r
 876                    row.annotations[column].secondaryStructure==' ')))\r
 877                     {\r
 878                         g.drawString(row.annotations[column].displayCharacter,\r
 879                                      x*av.charWidth+charOffset,\r
 880                                      y + iconOffset );\r
 881                     }\r
 882                 }\r
 883 \r
 884                 if (row.hasIcons)\r
 885                 {\r
 886                     if (!validRes ||\r
 887                             (row.annotations[column].secondaryStructure != lastSS))\r
 888                     {\r
 889                         switch (lastSS)\r
 890                         {\r
 891                         case 'H':\r
 892                           g.setColor(HELIX_COLOUR);\r
 893                           if (MAC)\r
 894                           {\r
 895                             //Off by 1 offset when drawing rects and ovals\r
 896                             //to offscreen image on the MAC\r
 897                             g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
 898                                             (x*av.charWidth) - lastSSX, 7, 8, 8);\r
 899                             break;\r
 900                           }\r
 901 \r
 902                           int sCol = (lastSSX / av.charWidth) + startRes;\r
 903                           int x1 = lastSSX;\r
 904                           int x2 = (x*av.charWidth);\r
 905 \r
 906                          if(sCol==0 ||\r
 907                             row.annotations[sCol-1]==null ||\r
 908                             row.annotations[sCol-1].secondaryStructure!='H')\r
 909                          {\r
 910                            g.fillArc(lastSSX, y+4+iconOffset, av.charWidth, 8, 90,180) ;\r
 911                            x1 += av.charWidth/2;\r
 912                          }\r
 913 \r
 914                           if(row.annotations[column]==null ||\r
 915                              row.annotations[column].secondaryStructure!='H')\r
 916                           {\r
 917                             g.fillArc((x*av.charWidth)-av.charWidth,\r
 918                                       y+4+iconOffset, av.charWidth, 8, 270,180);\r
 919                             x2 -= av.charWidth/2;\r
 920                           }\r
 921 \r
 922                           g.fillRect(x1, y+4+iconOffset, x2-x1, 8);\r
 923                               break;\r
 924 \r
 925                         case 'E':\r
 926                             g.setColor(SHEET_COLOUR);\r
 927                             g.fillRect(lastSSX, y + 4 + iconOffset,\r
 928                                 (x*av.charWidth) - lastSSX - 4, 7);\r
 929                             g.fillPolygon(new int[] { (x*av.charWidth) - 4,\r
 930                                           (x*av.charWidth) - 4,\r
 931                                           (x*av.charWidth) },\r
 932                                 new int[]\r
 933                                 {\r
 934                                     y + iconOffset, y + 14 + iconOffset,\r
 935                                     y + 8 + iconOffset\r
 936                                 }, 3);\r
 937 \r
 938                             break;\r
 939 \r
 940 \r
 941                         default:\r
 942                             g.setColor(Color.gray);\r
 943                             g.fillRect(lastSSX, y + 6 + iconOffset,\r
 944                                 (x*av.charWidth) - lastSSX, 2);\r
 945 \r
 946                             break;\r
 947                         }\r
 948 \r
 949                         if (validRes)\r
 950                         {\r
 951                             lastSS = row.annotations[column].secondaryStructure;\r
 952                         }\r
 953                         else\r
 954                         {\r
 955                             lastSS = ' ';\r
 956                         }\r
 957 \r
 958                         lastSSX = (x*av.charWidth);\r
 959                     }\r
 960                 }\r
 961 \r
 962 \r
 963             column++;\r
 964             x++;\r
 965             }\r
 966 \r
 967             if(column>=row.annotations.length)\r
 968                 column = row.annotations.length-1;\r
 969 \r
 970           //  x ++;\r
 971 \r
 972             if (row.hasIcons)\r
 973             {\r
 974               switch (lastSS)\r
 975               {\r
 976                 case 'H':\r
 977                   g.setColor(HELIX_COLOUR);\r
 978                   if (MAC)\r
 979                   {\r
 980                     //Off by 1 offset when drawing rects and ovals\r
 981                     //to offscreen image on the MAC\r
 982                     g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
 983                                     (x*av.charWidth) - lastSSX, 7, 8, 8);\r
 984                     break;\r
 985                   }\r
 986 \r
 987                   int sCol = (lastSSX / av.charWidth) + startRes;\r
 988                   int x1 = lastSSX;\r
 989                   int x2 = (x*av.charWidth);\r
 990 \r
 991                   if (sCol == 0 ||\r
 992                       row.annotations[sCol - 1] == null ||\r
 993                       row.annotations[sCol - 1].secondaryStructure != 'H')\r
 994                   {\r
 995                     g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);\r
 996                     x1 += av.charWidth / 2;\r
 997                   }\r
 998 \r
 999                   if (row.annotations[column] == null ||\r
1000                       row.annotations[column].secondaryStructure != 'H')\r
1001                   {\r
1002                     g.fillArc((x*av.charWidth) - av.charWidth,\r
1003                               y + 4 + iconOffset, av.charWidth, 8, 270,\r
1004                               180);\r
1005                     x2 -= av.charWidth / 2;\r
1006                   }\r
1007 \r
1008                   g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);\r
1009 \r
1010                   break;\r
1011 \r
1012                 case 'E':\r
1013                   g.setColor(SHEET_COLOUR);\r
1014 \r
1015                   if (row.annotations[endRes] == null\r
1016                       || row.annotations[endRes].secondaryStructure != 'E')\r
1017                   {\r
1018                     g.fillRect(lastSSX, y + 4 + iconOffset,\r
1019                                (x*av.charWidth) - lastSSX - 4, 7);\r
1020                     g.fillPolygon(new int[]\r
1021                                   {(x*av.charWidth) - 4,\r
1022                                   (x*av.charWidth) - 4,\r
1023                                  (x*av.charWidth)},\r
1024                                   new int[]\r
1025                                   {\r
1026                                   y + iconOffset, y + 14 + iconOffset,\r
1027                                   y + 7 + iconOffset\r
1028                     }, 3);\r
1029                   }\r
1030                   else\r
1031                    {\r
1032                      g.fillRect(lastSSX, y + 4 + iconOffset,\r
1033                                 (x+1) * av.charWidth - lastSSX, 7);\r
1034                    }\r
1035                   break;\r
1036 \r
1037                 default:\r
1038                   g.setColor(Color.gray);\r
1039                   g.fillRect(lastSSX, y + 6 + iconOffset,\r
1040                              (x*av.charWidth) - lastSSX, 2);\r
1041 \r
1042                   break;\r
1043               }\r
1044           }\r
1045 \r
1046             if (row.graph>0 && row.graphHeight>0)\r
1047             {\r
1048                 if(row.graph == AlignmentAnnotation.LINE_GRAPH )\r
1049                 {\r
1050                   if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])\r
1051                    {\r
1052                      float groupmax=-999999, groupmin=9999999;\r
1053                      for(int gg=0; gg<aa.length; gg++)\r
1054                      {\r
1055                        if(aa[gg].graphGroup!=row.graphGroup)\r
1056                          continue;\r
1057 \r
1058                        if(aa[gg]!=row)\r
1059                          aa[gg].visible = false;\r
1060 \r
1061                        if(aa[gg].graphMax>groupmax)\r
1062                          groupmax = aa[gg].graphMax;\r
1063                        if(aa[gg].graphMin<groupmin)\r
1064                          groupmin = aa[gg].graphMin;\r
1065                      }\r
1066 \r
1067                      for (int gg = 0; gg < aa.length; gg++)\r
1068                      {\r
1069                        if (aa[gg].graphGroup == row.graphGroup)\r
1070                        {\r
1071                          drawLineGraph(g, aa[gg], startRes, endRes, y,\r
1072                                        groupmin, groupmax,\r
1073                                        row.graphHeight);\r
1074                        }\r
1075                      }\r
1076 \r
1077                      graphGroupDrawn[ row.graphGroup ] = true;\r
1078                    }\r
1079                    else\r
1080                      drawLineGraph(g, row, startRes, endRes,\r
1081                                    y, row.graphMin, row.graphMax, row.graphHeight  );\r
1082                 }\r
1083                 else if(row.graph == AlignmentAnnotation.BAR_GRAPH )\r
1084                    drawBarGraph(g, row, startRes, endRes,\r
1085                                 row.graphMin, row.graphMax, y);\r
1086             }\r
1087 \r
1088             if (row.graph>0 && row.hasText)\r
1089             {\r
1090                 y += av.charHeight;\r
1091             }\r
1092 \r
1093             if (row.graph==0)\r
1094             {\r
1095                 y += aa[i].height;\r
1096             }\r
1097         }\r
1098     }\r
1099 \r
1100     public void drawLineGraph(Graphics g, AlignmentAnnotation aa,\r
1101                               int sRes, int eRes,\r
1102                               int y,\r
1103                               float min, float max,\r
1104                               int graphHeight)\r
1105     {\r
1106       if(sRes>aa.annotations.length)\r
1107         return;\r
1108 \r
1109 \r
1110       int x = 0;\r
1111 \r
1112       //Adjustment for fastpaint to left\r
1113       if(eRes<av.endRes)\r
1114         eRes++;\r
1115 \r
1116       eRes = Math.min(eRes, aa.annotations.length);\r
1117 \r
1118       if(sRes==0)\r
1119       {\r
1120         x++;\r
1121       }\r
1122 \r
1123       int y1=y, y2=y;\r
1124       float range = max - min;\r
1125 \r
1126       ////Draw origin\r
1127       if(min<0)\r
1128         y2 = y - (int)((0-min / range)*graphHeight);\r
1129 \r
1130       g.setColor(Color.gray);\r
1131       g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
1132 \r
1133       eRes = Math.min(eRes, aa.annotations.length);\r
1134 \r
1135       int column;\r
1136       int aaMax = aa.annotations.length-1;\r
1137 \r
1138       while( x < eRes - sRes )\r
1139       {\r
1140         column = sRes + x;\r
1141         if(av.hasHiddenColumns)\r
1142         {\r
1143           column = av.getColumnSelection().adjustForHiddenColumns(column);\r
1144         }\r
1145 \r
1146         if (column > aaMax)\r
1147         {\r
1148           break;\r
1149         }\r
1150 \r
1151         if(aa.annotations[column]==null || aa.annotations[column-1]==null)\r
1152         {\r
1153           x++;\r
1154           continue;\r
1155         }\r
1156 \r
1157 \r
1158           g.setColor(aa.annotations[column].colour);\r
1159           y1 = y - (int) (((aa.annotations[column-1].value-min) / range) * graphHeight);\r
1160           y2 = y - (int) (((aa.annotations[column].value-min) / range) * graphHeight);\r
1161 \r
1162           g.drawLine(x*av.charWidth-av.charWidth/2, y1, x*av.charWidth+av.charWidth/2, y2);\r
1163           x ++;\r
1164        }\r
1165 \r
1166        if(aa.threshold!=null)\r
1167        {\r
1168            g.setColor(aa.threshold.colour);\r
1169            Graphics2D g2 = (Graphics2D)g;\r
1170            g2.setStroke(new BasicStroke(1,\r
1171                                          BasicStroke.CAP_SQUARE,\r
1172                                          BasicStroke.JOIN_ROUND, 3f,\r
1173                                          new float[] { 5f, 3f }, 0f));\r
1174 \r
1175            y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);\r
1176            g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
1177            g2.setStroke(new BasicStroke());\r
1178       }\r
1179     }\r
1180 \r
1181     public void drawBarGraph(Graphics g, AlignmentAnnotation aa,\r
1182                              int sRes, int eRes,\r
1183                              float min, float max,\r
1184                              int y)\r
1185     {\r
1186       if(sRes>aa.annotations.length)\r
1187         return;\r
1188 \r
1189       eRes = Math.min(eRes, aa.annotations.length);\r
1190 \r
1191       int x=0, y1=y, y2=y;\r
1192 \r
1193       float range = max - min;\r
1194 \r
1195       if(min<0)\r
1196         y2 = y - (int)((0-min / (range))*aa.graphHeight);\r
1197 \r
1198       g.setColor(Color.gray);\r
1199 \r
1200       g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);\r
1201 \r
1202       int column;\r
1203       int aaMax = aa.annotations.length-1;\r
1204 \r
1205       while( x < eRes-sRes )\r
1206       {\r
1207         column = sRes + x;\r
1208         if(av.hasHiddenColumns)\r
1209         {\r
1210           column = av.getColumnSelection().adjustForHiddenColumns(column);\r
1211         }\r
1212 \r
1213         if(column > aaMax)\r
1214         {\r
1215             break;\r
1216         }\r
1217 \r
1218         if (aa.annotations[column] == null)\r
1219         {\r
1220           x ++;\r
1221           continue;\r
1222         }\r
1223 \r
1224           g.setColor(aa.annotations[column].colour);\r
1225           y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);\r
1226 \r
1227           if(y1-y2>0)\r
1228             g.fillRect(x*av.charWidth, y2, av.charWidth, y1-y2 );\r
1229           else\r
1230             g.fillRect(x*av.charWidth, y1, av.charWidth, y2-y1 );\r
1231 \r
1232           x ++ ;\r
1233 \r
1234       }\r
1235       if(aa.threshold!=null)\r
1236       {\r
1237           g.setColor(aa.threshold.colour);\r
1238           Graphics2D g2 = (Graphics2D)g;\r
1239           g2.setStroke(new BasicStroke(1,\r
1240                                         BasicStroke.CAP_SQUARE,\r
1241                                         BasicStroke.JOIN_ROUND, 3f,\r
1242                                         new float[] { 5f, 3f }, 0f));\r
1243 \r
1244           y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);\r
1245           g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
1246           g2.setStroke(new BasicStroke());\r
1247       }\r
1248     }\r
1249 \r
1250     // used by overview window\r
1251     public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)\r
1252     {\r
1253       eRes = Math.min(eRes, aa.annotations.length);\r
1254       g.setColor(Color.white);\r
1255       g.fillRect(0, 0, width, y);\r
1256       g.setColor(new Color(0, 0, 180));\r
1257 \r
1258       int x = 0, height;\r
1259 \r
1260       for (int j = sRes; j < eRes; j++)\r
1261       {\r
1262         if (aa.annotations[j] != null)\r
1263         {\r
1264           g.setColor(aa.annotations[j].colour);\r
1265 \r
1266           height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);\r
1267           if (height > y)\r
1268             height = y;\r
1269 \r
1270           g.fillRect(x, y - height, av.charWidth, height);\r
1271         }\r
1272           x += av.charWidth;\r
1273       }\r
1274     }\r
1275 \r
1276 }\r